Home

Agilent Technologies 4000 GC/MS Version 6 Software Operation Manual

1. Mew RecalcList Open Recalcist Mew Sequencecist Open Sequence ist Print Printer Setup ow Remember Last Open Files Exit A jE Menu item Description S Activate Method Displays the Activate a System Control Method File dialog box to activate a Method and download the Instrument Control sections to the modules Upload Active Displays the Save a System Control Method File dialog box to Method from allow you to name the Method that will receive the instrument Modules control sections uploaded from all modules connected to the instrument New SampleList Displays the Create a New System Control SampleList File dialog box to name a new SampleList Open SampleList Displays the Open a System Control SampleList File dialog box to open an existing SampleList 217 Menuttem Description New RecalcList Displays the Create a New System Control RecalcList File dialog box to name a new RecalcList Open RecalcList Displays the Open a System Control RecalcList File dialog box to open an existing RecalcList New Displays the Create a New System Control Sequence File dialog SequenceList box to name a new Sequence Displays the Open a System Control Sequence File dialog box to open an existing Sequence Prints the contents of the active window in System Control Printer Setup Opens the Star Print Setup Dialog Box to select a printer and set options for it
2. 297 Click on the following EFC types for a description of the parameters that appear when the EFC type is selected Type 1 EFC for 1079 and 1177 injectors Front EFC Middle EFC Rear EFC Front EFC Type Type 1 For 1079 1177 Injectors P Rat M psi min Hold min Total min BS 1 00 1 00 Add g7 200 0 00 270 lnsert 133 o43f 853 20 00 set Delete Constant Column Flow Mode Constant Flow O C On tem Description Pressure psi 0 1 to 100 0 psi Rate psi min 0 01 to 400 00 psi min The first line is devoted to initial conditions so a rate cannot be entered Hold min 0 01 to 999 99 min Total min 0 01 to 999 99 min Calculated from the pressure program cannot be edited Constant Flow On or off Click on Constant Flow to disable the spreadsheet and allow the system to calculate a pressure program which will maintain a specified constant column flow rate See figure below Column Flow mL min Specifies the desired constant Column Flow Adds a line to the spreadsheet Insert Inserts a line above the currently selected row in the spreadsheet Deletes the currently selected row s in the spreadsheet 298 Pressure Pulse Injection Front EFC Middle EFC Rear EFC Front EFC Type Type 1 For 1079 1177 Injectors Rate psi min Constant Column Flow Mode Constant Flow C OFF On Pressure Pulse C No Yes Column Flow ralnn Pulse Pre
3. Column Oven End Time 20 00 min Ready NUM Use the tabs to select which Injector Program you wish to edit Select the type of injector 1177 or 1079 at each position or select None if no injector is installed at that position 146 1079 Injector f you indicate that a 1079 Injector is installed an Oven Power switch and a Coolant switch are displayed Front Injector Middle Injector Rear Injector Front Injector Type 1073 Injector Oven On C Off Injector Coolant On Off Enable Coolant at C z Split A atio Coolant Timeout min 20 00 E Soit Ratio Rate p Temp C c min St E Hold min Total min 20 00 20 00 Add leet Delete Column Oven End Time 20 00 min Indicate whether or not you will use the installed 1079 injector by clicking on the On or Off radio buttons buttons relate to Injector Oven and Injector Coolant If you indicate that Coolant is turned on specify the desired Enable Coolant at temperature and Coolant Timeout time Use the spreadsheet to build a temperature ramp program The first row of the spreadsheet contains the initial temperature and hold time for the 1079 injector The 1079 will equilibrate to this setting when the method is activated and will be restored to this setting when each chromatographic run is completed Rows after the first row of the spreadsheet contain the programmed
4. 3800 GC Operator s Manual This manual is included on the Varian MS Workstation CD ROM and describes in full detail the GC method instrument operation and the process of connecting your GC to a PC or to an existing network Context Sensitive Help The MS Data Review Method Builder and System Control sections of the software contain Context Sensitive Help Help can be obtained simply by positioning the mouse pointer on the item of interest right click and select What s This Workstation Toolbar Overview egg mn uit RESP S YR 500 reproducibility e Ca a ml H YA The 4000 GC MS Workstation is a suite of applications for controlling chromatographs collecting data from chromatograph detectors and analyzing those data The Workstation Toolbar provides quick and easy access to the 4000 GC MS Workstation applications When activated the Workstation Toolbar behaves like the Windows Taskbar It can be docked on any of the four sides of the display screen and other Windows programs will not cover or go behind it when they are opened in full screen mode If the Workstation Toolbar is not already opened on your 4000 GC MS Workstation open it from the Windows Start Menu windows Update fi Set Program Access and Defaults Programs A Accessories A Microsoft visual C 6 0 Favorites aif MS Workstation Biji Automation File Editor a Internet Explorer Method Builder Documents ki Outlook Express EM
5. Create a new RecalcList append to an existing RecalcList or not create nor update a RecalcList To select the RecalcList option that you want click the RecalcList button The RecalcList Generation dialog box opens RecalcList Generation x ou can automatically create or update a RecalcList with tiles generated during automated injections Specify the RecalcList generation options for this SampleList below Do not automatically create and update a RecalcList f Create and update a new RecalcList RecalcList name c Wwarianws untitled Append to an existing RecalcList RecalcLict name Browse Overnwrite the Recale List each time the SampleList Begins Cancel If you choose to create a new RecalcList this automatically generated RecalcList will not overwrite an existing RecalcList If a RecalcList with the same file name exists the newly created RecalcList will have number appended to its file name to make it unique and to prevent the older RecalcList from being overwritten Changing Default SampleList Entries When you add a new row into a SampleList default values are used for each cell To change the default values click on the Default button in the open SampleList window The following dialog box will be displayed Enter the desired default values and click on Save Set 8400 SampleList Defaults Default Name Analysis X Cancel Injection I Injectors
6. Exit Either choose a New SampleList or Open an existing SampleList from the File menu pati Automation File Editor File Edit Help Aals Els S lele lE Select a list type Select SampleList Section Type Please select a SampleList Section Type 6400 Autos ampler M Only Display Existing SampleList Types Cancel The SampleList window for the open SampleList type is displayed 178 Gai Automation File Editor New_Samples smp File Edit Help aleme S lelem New_Samples smp 8400 SampleList Injection Injection Injectors Se somni vroe o va MERET moc ves T pen Eg none none 0 1 0 Pos 1 pelete Fill Down Add Lines Hardware AU Ee Default Name ea 3 4 5 6 8 3 10 Data Files RecalcList Spreadsheet columns can be sized by dragging their border using the left mouse button Right click on the column headers for formatting options When the table is scrolled to the right the Sample Name column does not scroll so you can easily tell for which sample you are entering additional parameters Defining the Fields in the Table Along the top of the Inject Single Sample window you see fields where you can enter information about the sample Here is a quick definition of the various fields and buttons in this dialog sample Hame Enter the sample name here The final name of the file depends on settings accessed by clicking the Data Files button If
7. Post Inj Solvent Flushes Clean Solvent Source Internal Standard Use Vial More User Defined Volurne uL Drawup Speed uL zec Pause Time sec Air Gap The 8400 AutoSampler and 8410 Autolnjector operate in liquid injection mode or Solid Phase Micro Extraction SPME mode When the liquid injection mode is selected the AutoSampler window may contain up to five sections The topmost section is common to all modes of operation In addition all modes of operation also include a Default Clean section and a Clean Mode section When Viscous Volatile or User Defined modes are selected the Internal Standard section is displayed In User Defined mode the More User Defined button is displayed to provide access to the dialog box to set the User Defined parameters The Default Settings for Predefined AutoSampler Modes contains a table showing the parameters that are used by the 8400 8410 for each of the predefined modes of operation 283 tem Description S AutoSampler Type 8400 8410 or None Specifies whether or not an 8400 AutoSampler or 8410 Autolnjector is installed on the 3800 GC If an 8400 or 8410 is not installed on the GC or is turned off select None When 8400 or 8410 is selected the following items are displayed for editing Syringe Size uL 5 uL 10 uL or 100 uL Selects the size of the syringe that is installed on the 8400 8410 for use with this method Injection Mo
8. The following three steps assume you have completed steps 1 through 5 from the previous table 1 Select TCP IP from the network components list and click on the Properties button The TCP IP properties dialog box is displayed TCP IP Properties Ed ES Bindings Advanced DAS Configuration Gateway WINS Configuration IP Address An P address can be automatically assigned to this computer IF your network does not automatically assign IP addresses ask your network administrator for an address and then type it in the space below Obtain an IF address automatically IP Address 123 190 37 20F SubnetMask 1255 255 255 190 Enter the IP address to be used by this Workstation Contact your Network Administrator or whoever assigns IP addresses in your network to get the appropriate address Note that each Workstation PC must have a unique IP address Enter the appropriate Subnet Mask to be used with this IP address 81 Your Network Administrator may instruct you to obtain an IP address automatically by selecting the appropriate radio button TCP IP Properties Ea Bindings Advanced DNS Configuration Gateway WINS Configuration IF Address An F address can be automatically assigned to this computer IF pour network does not automatically assign IP addresses ask your network administrator for an address and then type it in the space below C Obtain an IF address automatically IP A
9. Time Segments program analysis conditions to get the best results for each segment in the analysis Up to 250 time segments can be created for runs up to 650 minutes in length By default there is a Filament Multiplier Delay segment at the start of the run so that the system will not be stressed during the elution of the chromatographic solvent Following this segment you could just acquire the mass spectra in full scan with a single analysis segment However you can tailor variables such as acquired mass range insert MS MS segments for individual analytes and otherwise set up the instrument to acquire the best data for each analyte Double click on the required field to edit the Segment Description Start and End times The Scan Description information is automatically entered based on the choice of Scan Type and lonization mode in the Method Segment field below Segment This describes the nature of the particular segment in question and Description usually pertains to a stage in the scan or a name of a compound perceived to be eluting during the segment Clicking the mouse in the Segment Description cell changes the lower window contents so the Method Segment details for that particular segment are displayed in the lower window area These are an lonization On checkbox Scan Type lonization Type and Scan Mode Start min This cell indicates the time at which the particular segment will begin Clicking in this cell allows you to edi
10. __ Defaults Two filaments are provided in External Internal or Hybrid configurations to reduce down time for maintenance Select the desired filament Override the Electron Multiplier voltage set from Auto Tune by entering the desired voltage Adjust the High Mass Calibration to improve the accuracy of mass assignments of samples that range from 650 to 1000 m z Increase the sensitivity of the detection of low mass ions lt 100 m z especially for EPA method 521 44 Auto Tune Tab Auto Tune is an automated process for optimizing the MS 4000 performance over the entire mass range It is necessary to perform Auto Tune when the instrument is first set up NOTE Each time the system is shut down do Auto Tune when you restart Also AutoTune after doing a bakeout Before doing Auto Tune it is advisable to check RF ramp air water and cal gas settings under the Adjustments tab in Manual Control mode Many tuning features involve using Perfluorotributylamine FC 43 ions to adjust MS4000 parameters voltages gain values etc to optimize the signal Most Auto Tune functions are performed in El mode even if the active method is Internal Cl External Cl or one of the Hybrid Cl modes For the last two cases the Cl volume is automatically retracted from the external ionization source during most Auto Tune routines When major maintenance is performed such as cleaning the ion trap or source or switching between internal and ex
11. c vananwe snp onptm meoh_cimem co hvananiwe mpoyctmemsssmp smp Add c Awarianws mpSinptm_meoh_cimsmo warianws mpS ci_msms smp2 smp Insert Delete im Browse tem Description S Shows the action chosen for each line in the Sequence Method Shows the Method chosen for each line in the Sequence Sample RecalcList Shows the SampleList or RecalcList chosen for each line in the Sequence Adds a new line to the end of the Sequence Adds a new line above the highlighted line Deletes the highlighted line in the Sequence Browse Opens the Select a Method File or Select a Sample RecalcList window to browse through directories and find a Method or Sample RecalcList file to add to the Sequence 328
12. Help on Workstation Toolbar Product Support Web Site About Workstation Toolbar uit Right click on the empty area of the bar to display the Toolbar Options A menu displays Workstation Toolbar options and operations 10 Launching Applications from the Workstation Toolbar Using the Application Icon Buttons 4000 GC MS Workstation applications appear as icon buttons on the Workstation Toolbar As you move the mouse over these buttons the name of the application is shown in a tooltip window below the cursor Click once on any icon button in the Workstation Toolbar to launch the corresponding application Using the Data File and Method Quick Link buttons RESF SYR 500 b A reronuciity gt The two buttons to the right of the application buttons are Quick Link buttons These two Quick Link buttons correspond to recently used Data Files and Methods On each Quick Link button is the name of the file associated with that button When you click on the Quick Link button a menu is displayed showing operations that can be performed on the corresponding file The Quick Link buttons in the Workstation Toolbar are always updated with the most recently used Data File and Method If the Data File or Method you wish to use is not displayed in the Quick Link button you can choose from the eight most recently used files by selecting Pick a different Data File or Method from the Quick Link button menu Workstation Toolbar Op
13. Hormel r Hormel a Fastest The default scan mode is normal Normal This Scan Mode uses a prescan in Automatic Gain Control mode to determine optimum ionization time and then ions are scanned at 5000 u sec to collect the mass spectrum Fast This Scan Mode also uses a prescan in Automatic Gain Control mode to determine optimum ionization time but ions are scanned at 10000 u sec to collect the mass spectrum Fastest This Scan Mode uses no prescan and ions are scanned at 10000 u sec to collect the mass spectrum This mode is only available in Full scan type 109 Setpoints Segment Setpoints M Calibant On E T E E Cancel Check Calibrant On to turn on the FC 43 calibration gas during an acquisition segment Overview of lonization Methods There are five sets of ionization parameters depending upon instrument configuration In this section the parameters for controlling each mode are discussed e Internal El Method Parameters on page 110 e Internal PCI Method Parameters on page 115 e External El Method Parameters on page 119 e External PCI and NCI Method Parameters on page 122 e Hybrid PCI and NCI Method Parameters on page 125 Internal El Method Parameters This section details how to set parameters for an electron ionization method in Internal configuration Internal Electron lonization on page 191 has more information about the theory of electron
14. Injection Delay 0 0 and 0 1 through 10 0 minutes Duplicate Mode or Dual l Sets the time delay between the first injection and the Mode operation only second injection in Duplicate Mode and Dual Mode operation When the value is 0 0 the injection time delay is turned off and not used For values other than zero the 8400 will prepare and load the syringe for the second injection When the syringe is loaded it will move to the inject position and wait for the injection delay to time out before injecting If the injection delay times out before the sample is injected an error message saying that the injection delay timed out before injection is placed in the message log Rapid MS Mode Setup Rapid MS Column Positions Front Indicate that a Column i installed for Rapid MS and which Injector itis connected to Only one Column can be configured this way Press OF to indicate your selection b will take a few moments for the GC to reconfigure OF Cancel RapidMS is a patented technology which allows fast separations on large bore capillary columns This list box lets you identify the injector equipped with a RapidMS column Pressing OK accepts the selection and pressing Cancel closes the dialog without making any change 268 8400 8410 Carrousel Display When an 8400 AutoSampler or 8410 Autolnjector is connected to your 3800 the Carrousel display will be visible in the 3800 GC Status and Control window 8
15. Instrument 1 Data File cl4 c1 std mix 1 2001 run created for 014 077 Std mis 1 Injection Instrument 1 3800 44 Ch Front Data Handling Nor reference peak not identified Instrument 1 Beginning Vial 1 Injection 3 on Wed Feb 18 09 58 00 1998 The chromatogram is displayed as it is acquired Saving SampleLists for Later Use When you make changes to the open SampleList the changes are automatically saved to the SampleList file and will be used for the automated runs that are in progress If you want to edit a SampleList other than the open SampleList use the offline Automation File Editor application described in the next section of this manual Using More Than One Method for Injections The Varian MS Workstation allows you to perform automated injections using more than one Method There are two ways in which this can be accomplished The first is by changing the active Method from within the SampleList The second is by using a Sequence Changing the Method in the SampleList Change the Method used during injections by activating a Method in a SampleList row gai Automation File Editor New_Samples smp File Edit Help aleme S selem New_Samples smp 8400 SampleList Injection Injection Injectors Ini Notes Patok Vial Volume Used Add Sample_1 1 0 1 0 Pos 1 _ me ss Insert Sample_2 1 none none 0 1 0 Pos 1 Sample 3 none none 0 1 0 Pos 1 Delete none Fi
16. RF Waveform Hide Keypad Monitor Window and Event Messages w Trap lon Source Multiplier 1994 Volts Emission 248 u mps Dynode 14887 Volts ions Balance 12027 Deviation 13 3 u Waveform System Filament Bias 70 6 Volts t Filament 1 OK j Filament 2 OK Dipole Supplemental Waveform 103 On Off Quadrupole Supplemental Waveform 101 Lens 2 109 Volts 120 Volts Temperatures Electron Lens 100 Volts 95 Volts Entrance Endcap 151 C Repeller Lens 170 Volts 147 Volts Exit Endcap 150 C Lens 1 22 4 Volts Manifold 52C Lens 3 20 2 Volts Transferline 172C Ring Offset 8 1 Volts Source 180C Endcap Offset 8 0 Volts The Keypad Field The upper portion of the screen is divided into three sections a Control and Status field and the Monitoring and Diagnostics Tests tab dialogs Control and Status The State field will indicate Idle when diagnostic tests are not being performed or Running if tests are in progress The Function field will indicate Monitoring Status unless a diagnostic test is being run in which case the name of the current test will be displayed The Start Diagnostic button is unavailable unless a test has been selected in the Diagnostic Test tab dialog Control and Status Idle Start Diagnostic Stabe Function Monitoring Status 53 After a diagnostic test is selected and Start Diagnostic clicked the test starts and the results are displayed in Event Messages at the bottom of the scre
17. Ready File Edit Inject Automation Recalculate Instrumen a 4000 56 Ready Display the Inject Single Sample dialog by selecting it from the Inject menu or by ai clicking on the Inject Single Sample button on the toolbar B l The Inject Single Sample dialog box is displayed The dialog will be automatically configured to match the sampling device installed in the instrument Inject Single Sample some nane somme 1e i SOS UREO maier omn ga Default Name Analysis 1 1 0 1 1 none gt Inject the Sample using the Method C VarianWw S Coltest_External mth Browse Defaults J Glear Coefficients before Calibrating Cancel Data Files RecalcList 159 Defining the Fields and Buttons The top of Sample List window has fields The following are definitions sample Hame Enter the sample name here The final name of the file depends on settings accessed by clicking the Data Files button If only s is listed in the Data Files dialog the sample name is as entered Sample T AMPE IPPS There are several choices available from the Sample Type drop down list box Sample Type Calibration Verification Baseline Cal level If you designate the Sample Type as calibration you can designate which calibration level you are injecting You can enter up to ten levels Ini Specify here the number of injections of this sample You may make up to nine replicate injections at
18. Specifies the length of time the syringe needle resides in the injector before expelling the syringe contents Post Inj Delay sec 0 to 99 9 seconds Specifies the length of time the syringe needle remains in the injector after expelling the syringe contents 289 Default Settings for Predefined AutoSampler Modes The following table lists the parameter settings used for each of the Predefined 8400 8410 modes using a 10 uL syringe If the predefined modes do not work acceptably for your samples use the User Defined mode to enter settings that will work better with your samples The values listed in this table provide a starting point for setting the various parameters Std Std On Neat Volatile Viscous Parameter Split Column Splitless Solvent Plug Solvent plug is not used with predefined modes If you wish to use Settings solvent plug injections you must use User Defined mode PreDefined Settings Fill Strokes e a a oo Sample Air Gap Air Plug after 1 uL CC uL vo uL o uL CC uL Sample Viscosity Settings Instead of fill strokes Neat mode fills the syringe with sample at 2 uL sec then expels it into the waste cup at 50 uL sec a total of six times Then it fills the syringe with sample at 2 uL sec and expels it back into the sample vial at 50 uL sec This pumping action is done three times The sample is then loaded into the syringe and injected using the parameters in the table 290 Solid Phase Micro
19. ide H E EORTC ey Ative Method Segment lon Gauge Gas Acii Hide Keypad im S petted Flestone Nunbee 1 2 AILUMUL DELAY aj a S eS E Scan Number 696 Time 0 825 min Base Peak 49 5 Base Amount 15372 RIC 1 325648 lon Range 49 5 1000 5 mlz lon 14 us Segment 1 Channel 3 Rf Voltage 1000 Acquired Range m z 42 Air Water Check Run the Set Electron Multiplier Auto Tune before doing the Air Water Check The Air Water Check routine determines the relative amount of air and water vapor in the vacuum manifold When you display the Air Water screen the following happens automatically The filament electron multiplier and RF voltage are turned on AGC is turned off and the scan range is set to display the air water spectrum m z 14 to 45 The air background is proportional to the width of the peak for m z 28 at 10 peak height The water background is proportional to the ratio of m z 19 to m z 18 For Internal Mode the ionization time is fixed at 300 usec For External Mode the intensity of the highest peak m z 18 19 and 28 is adjusted to a suitable level Width of m z 28 at Ratio 9 18 Acceptance Criteria 10 Peak Height For External and Hybrid Mode the acceptance criteria Ratio of m z 19 18 for presence of water is the same as the Internal mode However a number of External and Hybrid parameters may affect the intensity of the air peak at m z 28 for example damping gas flow
20. Actual Flow 0 1 to 100 mL min Displays the actual column flow rate calculated from the measured head pressure and column parameters carrier gas column length and internal diameter Pressure Displays in psi the measured column head pressure Linear Velocity Displays in cm sec the column linear velocity calculated from the column head pressure column temperature and column parameters carrier gas column length and internal diameter Type 4 Injector EFC Flow Pressure Status tem Description Yes or No The Type 4 Injector EFC component is Ready Yes if the setpoints have been achieved and stabilized Fault Yes or No Displays if a fault in the Type 4 EFC component has occurred Type 4 Pressure 0 1 to 100 psi Setpoint Displays the programmed column head pressure setting in the active method Actual Pressure 0 1 to 100 psi Displays the actual column head pressure at the 3800 GC Column Flow Displays in mL min the column flow rate calculated from the column head pressure column temperature and column parameters carrier gas column length and internal diameter This value is not displayed if the column length has not been set in the 3800 GC column parameters setup Total Flow 1 to 1000 mL min Displays the programmed total flow rate in the active method Linear Velocity Displays in cm sec the column linear velocity calculated from the column head pressure column temperature and column para
21. As more microscans are averaged the relative intensities of ions in the mass spectrum become more reproducible However one needs to keep in mind that collecting more data points across a chromatographic peak will improve peak area reproducibility on replicate injections Setting up to average three scans is a good recommendation to get good spectral quality along with an acceptable data rate The Mass Defect allows for a systematic correction of the difference between the nominal mass of an ion and its exact mass Its importance arises from the fact that the NIST library reports molecular weights to the nearest integer mass unit only whereas the 4000 MS stores ion intensity pairs with a mass assignment to the nearest tenth of a mass unit For library searching ion masses are rounded to the nearest integer If the m z of an ion happens to fall close to the 0 5u crossover point it may be assigned to the wrong mass This is more likely for molecules with higher molecular weights since the mass defects for several atoms may add together to produce a sizable mass defect The Multiplier Offset adjusts the EM voltage as much as 300V relative to the current multiplier setting in the Module Attributes tab dialog in Manual Control this is usually the 10 gain value from Auto Tune Sometimes better sensitivity is achieved particularly in techniques such as MS MS when the multiplier voltage is increased Note that this adjustment can be made on a
22. Click on each to see its contents Below this are the three toolbars the Main toolbar to open save and print Methods the Directory toolbar to traverse the Directory outline and the Window toolbar to position Method windows Hold the mouse cursor over each button to see a Tooltip describing its function A status bar is at the bottom of the Method Builder window The toolbars and the status bar may be hidden or shown using the View menu The Method Builder can be used to display and edit multiple Method files If the Method Builder is already displaying one method you can open another using the File Open command From the Window menu or using the Window toolbar the Methods can be selected cascaded or tiled to compare the same sections in different Method files Method Parameters The Parameters pane displays the content of the method section selected in the Directory Four types of windows can be displayed in the Parameters pane method file information method notes hardware module descriptions and editable parameters for the instrument modules data handling and reports File Information Location C VarianiwS startup _extemal mth Created Monday October 06 2003 08 28 14 Moditied Wednesday Januar 14 2004 10 44 33 SIZE 47414 butes Method File Attributes O Read only O Hidden Archive O Requires Password on Save feSpstartup1 external mth ela Method Notes Revision History E H 3800 GC Address
23. Customize The MS MS parameters are set out in tabular form Each of the three steps of MS MS isolation dissociation and scanning follow across the table 129 Isolation of the Precursor lon Isolation Precursor bo Ea Window Precursor lon Mass m z has a range is 50 to 1000 m z NOTE Integer mass values may be used if the mass isolation window next step is greater than 1 5 m z If the window size is less than 1 5 m z or if the mass defect of the precursor ion is greater than approximately 0 3 m z use the exact fractional mass The Isolation Window m z The full mass isolation window range is 1 0 to 14 0 m z the actual range is dependent on the precursor ion The default value is 3 0 m z Integral and fractional mass isolation windows are both accepted If an isolation window smaller than 1 5 m z is used then the exact mass of the precursor ion should be entered in Precursor lon Mass Maximum Isolation Window as a Function of Precursor Mass Precursor lon m z lt 80 lt 100 lt 120 lt 180 lt 280 lt 420 gt 420 Maximum Isolation 3 0 4 0 5 0 7 0 10 0 12 0 14 0 Window m z NOTE When beginning method development start with a mass isolation window of 3 m z to ensure that the ion is centered in the window For example for a precursor ion mass of 502 m z and a mass isolation window of 3 m z ions of masses 501 502 and 503 m z would be isolated If there is a need to reduce the window because of interferin
24. Customize a Non Resonant Method The parameters in the MS MS lon Prep Method Editor window are the basic ones needed to create a MS MS lon Prep Method file For the vast majority of applications no other information is required to use the MS MS technique successfully However some applications may require further customization Customize Parameters is separated into three sections lonization Isolation and Dissociation These parameters are hidden by default but can be modified by clicking the Customize button High Mass Ejection volts Precursor eE Jaia laya Level m z Customize lonization and Isolation Parameters 132 lonization Precursor lon m z The precursor ion is the desired ion m z that will be isolated in the MS MS isolation step This Precursor lon m z value is used in both Resonant and Non Resonant Methods of MS MS For more info please review the previous table titted Maximum Isolation Window as a Function of Precursor Mass lonization Storage Level The m z value at which the RF is maintained during ionization and the coarse isolation step The range is 30 to 100 m z with a default value of 35 m z Isolation Low Edge Offset The mass offset to optimize the ejection of the mass just below the precursor ion mass The Low Edge Offset range is 0 5 m z to 0 5 m z The default value is 0 Low Edge Offset affects the isolation window on the low mass side of the precursor ion Increasing
25. Data Handling 102 Delete Method Sections x Sections to Delete 3800 GC Module 44 4000 Mass Spec Module 56 4000 Standard MS Reports Module 56 1 4000 MS Data Handling Module 56 1 Select Al Cancel When the desired sections have been highlighted click the Delete button to delete them from the Method You will be prompted for confirmation before each section is deleted Printing the Method Click the Print icon on the Toolbar amp Select the desired Method sections and click Print Print Method Sections x Sections to Print 3600 GC Moadule 44 4000 Mase Spec Module 56 4000 Standard MS Reports Module 56 1 4000 MS Data Handling Module 56 1 Select Al Cancel You can print the active Method from System Control File gt Print and the Workstation Toolbar Password Protecting a Method Click Set Password l on the Method Builder Toolbar to open the Add Password dialog 103 Add Password Ro Enter new password pe concel_ Enter the password and then re enter it to confirm Once a Method is password protected it can be used in System Control for instrument control data acquisition and data handling It can be viewed in Method Builder as well However the selected password must be entered to save Method changes It is now locked and can be edited only when the password is known 4000 MS Method Section Setting Up the MS Method Editor Screen Under the Directory item 400
26. Product ion 1 Intensity coo en Product ion 2 400 1 eno HM gay Soa pe F Ne ia 0 1 2 3 3 CID Excitation Amplitude volts This figure shows a typical breakdown curve for resonant excitation using modulation The optimal excitation amplitude for maximizing product ion 1 is around 0 5 volts The optimal excitation amplitude for producing both product ions 1 and 2 is around 1 2 volts Save AMD to MS MS method MS MS with Different Precursor lons Multiple Reaction Monitoring MRM is using MS MS with different precursor ion masses and different dissociation parameters MRM is capable of doing MS MS of up to ten different precursor ions This is useful for example for a target compound and a labeled standard which have a mass difference larger than the maximum allowed isolated window and which co elude When using MRM set up the 4000MS acquisition method for 3 microscans per analytical scan Each scan function will have its own data channel When doing quantitation MS Data Review can analyze these channels separately Each of the MRM scan functions must be optimized individually using AMD The optimal AMD conditions can be saved to a MS MS method by highlighting the line and changing the scan type from AMD to MS MS You can copy a MS MS or AMD line by highlighting the line and typing lt ctrl gt c copy This line can be copied into the MRM or MS MS method by lt ctrl gt
27. The Current Set Points area displays the set points for Heated Zones the Vacuum System Pneumatics and Getter Control Heated Zones area indicates what temperature set points have been set for the Trap Manifold and Transferline in degrees C Vacuum System indicates what Pump Spin Speed has been set It is displayed as a percentage of the ideal pump spin speed 100 Pneumatics indicates if the Flow Rate is set or not ON or OFF Getter Control indicates if the temperature of the Getter Control has been set or not ON or OFF Operating Conditions The Operating Conditions area displays the actual conditions so you can compare the desired conditions current set points with the actual operating conditions Heated Zones area indicates the actual temperatures of the Trap Manifold and Transferline in degrees C Vacuum System area indicates the actual Pump Spin Speed and current of the vacuum system in mAmps Pneumatics area displays the actual Flow Rate in mL min and Inlet Pressure in psi Getter Control area displays the actual temperature of the Getter Control in degrees C Display You may choose to display either Event Messages or Module Attributes Event Messages are a log of actions and events which have occurred during the Startup or Shutdown process Module Attributes displays the current instrument configuration temperature setpoints date and results of the most recent manual adjustments date and resu
28. The two fundamental processes in mass spectrometry are ion creation and ion analysis Because the ion trap stores ions before the ion analysis step it is possible to insert ion preparation steps to manipulate the ion population before the mass spectrum is collected This manipulation can consist of simply ejecting certain ions or ranges of ions from the ion trap Selected lon Storage or SIS More involved ion preparation is required for tandem mass spectrometry MS MS In this process Precursor lons of a selected m z are first isolated by application of waveforms to the ion trap end cap electrodes Then the isolated ions are dissociated by using additional waveforms to induce energetic collisions with helium in the ion trap For some applications ion preparation methods improve both selectivity and sensitivity significantly The 4000 MS ion trap performs SIS and MS MS by means of ion preparation methods that modify the scan function Advantages associated with ion preparation methods are similar to those of other sample preparation methods e g reduction of noise increased selectivity and improved sensitivity MS MS lon Prep Method General Parameters lonization Contra Internal El Parameters MS MS Parameters MS MS Isolation Excitation Excitation Product lon Product lon seed Window Waveform Type Storage Amplitude Start Mass ane ie m z Level m z volts mzz 4 EA 3 0 Resonant x ngert Add Delete q Calculator
29. a notched waveform is applied after the ions are trapped The ions are analyzed by applying a radio frequency RF voltage to the ring electrode encircling the trap cavity As the voltage increases on the ring electrode ions are sequentially ejected from the trap according to their mass to charge ratio Supplemental waveform voltages are applied to the end cap electrodes during the analysis to improve mass resolution and mass axis stability The ions scanned out of the trap strike the conversion dynode ejecting electrons which are repelled to the electron multiplier The conversion dynode is held at 10 KV and the voltage on the multiplier is adjusted to provide an enhancement of 10 The signal is then sent through an integrator to collect an intensity reading for each m z MS data are stored as sets of ion intensity pairs for each m z over the acquired mass range A complete mass spectrum is stored for each analytical scan 193 lon Preparation Options The 4000 MS can use a combination of waveforms applied to ion trap electrodes to isolate or remove specific ions once they have been formed and are stored in the trap Options like Selected lon Storage SIS and MS MS can be performed on the ions stored in the ion trap before mass analysis takes place In MS MS a parent ion is isolated and then dissociated by energetic collisions with helium buffer gas to form product ions In SIS resonant waveforms are applied to eject unwanted ions within
30. boxes M Disable creation of new passwords in Method files 189 tem Description S Require Revision Log entry When checked the user is prompted for a description when changes to Methods of changes when a Method file is altered and saved are saved This Revision Log appears in the Notes portion of the File Open dialog box is listed in the Method Builder application window when the Method is open and is included in the Method printout Update Revision Log in When checked Data Files are updated with a time Data Files with stamp and Method name when they are recalculated Recalculation date time either from System Control or from Interactive and Method name Graphics The Data File Revision Log can be included in printed reports Enable results deletion from When checked a button appears in the Open Data Open Data File dialog File dialog box allowing results to be deleted from a boxes specified channel of a Data File Results deletion is logged in the Data File s Revision Log This option only affects standard GC results GC MS results will not be deleted Disable creation of new When checked new passwords cannot be added to passwords in Method files Methods Methods already containing passwords will still prompt you for the password before changes are saved 190 4000 MS Ionization Techniques Choices of lonization Mode Choose from the following list to go to a specific topic on the particular i
31. example of this might be to run a set of samples using Internal El and then the same set of samples using a different MS method for Internal PCI A Sequence must be open from the File menu to use this feature Begin At Starts automation at a particular sequence or SampleList line and runs until the last line is completed A SampleList or SequenceList must be currently open to use this feature Suspend Automation Stops automation at the last completed sample Resume Automation Starts automation after it has been suspended Automation starts from where it was suspended Stop Automation Ends automation immediately and resets all modules Reset Modules Brings the various modules to their ready states Enable Automated Printing Allows the printer functions to work during automation Recalculate Menu a System Control Yarian 4000 GC MS Not Ready Fie Edit Inject Automation Recalculate Instrument Windows Help alal M s081 OCLFes Begin RecalcList Begin At Selected RecalcList Line a 4000 56 Not Ready Manual Control Auto Tune T View Calibration Curves Begin RecalcList Start an automated Recalculation A Recalculation list must be prepared and opened under the File menu to do this Begin at Selected RecalcList Line Process a Recalculation list starting with a chosen line and proceeding with the rest of the list View Calibration Curves View any of the curves for the calibrated compounds
32. in the active method An example of the calibration curve screen is given below For a complete explanation of this screen go to the Quantitation section NOTE Recalculation may be performed in System Control or in MS Data Review under the menu command Quantitation Process Review Recalc List Processing a Recalc List takes more time when done from System Control than in MS Data Review but has the advantage of allowing AutoLink functions such as automated reporting with Custom MS Reports templates such as ToxProPlus or EnviroPro 22 Calibration Curve Malathion Malathion Instrument Menu The Instrument menu ef System Control sanjan ue GC MS Not Bee 23 Alt 1 Configuration Alt c Remove Module Names Restore Disabled Warnings Instrument 1 Faulks Setup Ethernet Communications Setup ADT Board IO Ports Setup COMM Ports E Demo Modules HYF 800 Interface Box ADC Board 8200 AutoSampler 3800 GC 3900 GT Mistral Column Oven ProStar Dynamax System ProStar 230 SDM ProStar 230 Inert SEM ProStar 240 SOM ProStar 240 Inert SEM ProStar 310 UV vis Detector Varian 4000 GC MS The configured instrument Configuration Add new modules to the existing instrument This is necessary if additional hardware is added such as a Combi PAL AutoSampler Remove Module Names Remove any associations between Module Names and Module Addresses This allows you to connect a Module with a dif
33. including path must not exceed 255 characters in length You may embed the special symbols listed in the window to represent sample specific information in the Data File name As you enter the specification an example file name is shown Accepts the name specification Cancels the name specification 325 RecalcList Generation Dialog Box RecalcList Generation You can automatically create or update a RecalcList with files generated during automated injections Specify the RecalcList generation options for this SanpleList below C Do not automatically create and update a RecalcList f Create and update a new RecalcList RecalcList name c Wwarianwe mp ci adjust rcl Append to an existing RecalcList RecalcList name Browse T Ovemrite the Recalc List each time the SampleList Begins ce item Toese SSS Do not automatically No RecalcList will be generated or updated when you create and update a create Data Files as a result of injections RecalcList Create and update a new Allows you to enter the name of a new RecalcList that RecalcList will be created when Data Files are generated as a result of injections If the RecalcList name that you specify already exists when the injections are performed a number will be appended to the name so that it is unique Append to an existing Allows you to browse for an existing RecalcList file RecalcList When Data Files are generated as a result o
34. see page 59 MS Method see page 65 and Operating Conditions see page 69 For fields in the keypad display go to the relevant section in System Control on page 17 Monitoring the Chromatogram For information on chromatogram display options go to Chromatogram Toolbar on page 29 and Configuring the Real Time Chromatogram Display on page 34 in the System Control section Monitoring the Mass Spectra For information on spectrum display options go to Spectrum Toolbar on page 32 and Configuring the Real Time Chromatogram Display on page 34 in the System Control section 172 Message Log Automation actions and errors are logged in the Message Log the latest line of this log is shown at the bottom of the screen When you double click on the status bar at the bottom of the instrument window the entire Message Log window is displayed Message Log MSGLOG1 MLG _ OF 094436 Instumenti AMUbOM ARI B egari r ar a a a E a E R E A Instrument 1 SampleList 1 reli smp Activated Instrument 1 Method 3800 1 mth Actyated Instrument 1 Aesults will append to new RecalcList 1 RELIOOT ACL Instrument 1 Beginning Vial 1 Injection 1 on Wed Feb 18 09 44 50 1998 Instrument 1 Data File cl4 c1 std mis 11001 run created for 014 077 Std mis 1 Injection Instrument 1 3800 44 Ch Front Data Handling Non reference peak not identified Instrument 1 Beginning Vial 1 Injection 2 on Wed Feb 18 09 51 19 1998
35. use the provided parameters as a starting point and check the relative ratios of ions in the spectrum of BFB or DFTPP as relevant If needed adjust the lon Time Factor for particular segments to increase or decrease the abundance of key ions You can use Varian s EnviroPro software to generate BFB or DFTPP Tune reports and other reports needed for environmental analysis Hybrid PCI and NCI Method Parameters This section details how parameters may be set for positive or negative chemical ionization methods in Hybrid configuration For more details on the theory of chemical ionization and how it is implemented in this instrument go to Hybrid Positive or Negative Chemical lonization on page 206 in the section 4000 MS lonization Techniques 125 General Parameters Adjust the of seconds scan SetPaints f Sean Time Maximum Scan Time Multiplier Offset Ta volts f uScans Averaged B uwocans Mass Defect Ta mma 00u Data Rate Oey Adjust the of uScans to average Centroiding Parameters Count Threshold 1 Customize SetPoints f Scan Time 1 15 Seconds scan C uScans Averaged Minimum of uS cans Averaged Data Aate 0 87 Hz Scan Time uScans Averaged and Data Rate are all linked The number of microscans averaged is updated when the scan time is adjusted and vice versa There is a trade off between how rapidly spectra are collected and the reproducibility of mass spectra or peak areas
36. v paste NOTE If you are doing linearity studies using MRM you may need to change the default prescan ionization time of 300 usec to obtain optimal linearity This value depends on the compound and the concentration range MS MS MS or MS MS uses sequential MS isolation dissociation and trapping steps to gain information about a given precursor ion In this operation a product ion from a previous CID step is isolated and becomes the precursor ion for the next CID step The additional dissociation step can be used to increase selectivity of analyte versus background or for additional structure information MS uses two precursor ions for sequential dissociation MS or MS MS MS MS MS MS MS MS MS MS is 9 isolation and dissociation steps before the final scan of product ions 141 a General Parameters lonization Control External El Parameters MS n Parameters Piccursar Isolation Excitation Excitation Product lon Product lon lon m z Window Waveform Type Storage Amplitude Start Hass End Mass m z Level m z volts m z mzz 496 0 6 0 Resonant BFT 0 35 426 0 6 0 Resonant ar O42 356 0 3 0 Resonant BrT 0 38 wn a fa Po pa papa papaya yaya AW TW WP ay 7 Ee leer Add Delete q Calculator Customize The optimization of MS is similar to MS MS First work out optimized conditions for MS MS of the first precursor ion AMD will make this process go faster Then optimize
37. when the multiplier voltage is increased Note that this adjustment can be made on a segment by segment basis The Count Threshold is normally 1 count a value of 2 3 counts will reduce the number of low level ions reported in the mass spectrum This approach may improve library searches and reduce data file size at the cost of somewhat less detailed information in the mass spectra The count threshold is shown only if the Customize is active lonization Control General Parameters lonization Control External CI Automatic Gain Control Target TIC 5000 counts The default Target TIC for positive or negative chemical ionization is 5 000 The target can be set as high as 65 000 123 General Parameters lonization Control External Automatic Gain Contral AAA Target TIC FOOO courts lonizatian Time T Fixed lonization Time lonization Time ino uzeconds Max lon Time z500 useconds When the Customize button is clicked one has the option to run fixed ion time experiments with ion times as high as 2 500 usec or to change the Maximum lon Time for Cl Auto experiments One can turn on the CI Gas and the ion trap in Manual Control and check the ion time in Cl Auto mode External CI Parameters General Parameters lonization Control External Cl Parameters Ful External Cl lonization Parameters Polarity f Positive Negative Reagent Parameters Reagent Gas AECA Save Cl Background 454
38. 0 3 0 Non Resonant w 48 0 40 00 50 420 414 0 3 0 Non Resonant w 48 0 50 00 50 420 414 0 3 0 Non Resonant w 48 0 60 00 50 420 414 0 3 0 Non Resonant w 48 0 70 00 50 420 414 0 3 0 Non Resonant w 48 0 80 00 50 420 i v GE Delete sag Calculator Customize Example of 20 V steps in AMD 138 Setting the excitation amplitude for scan segment 1 to 0 volts will verify that the precursor ion is isolated without a large loss in intensity Inject the sample and examine the spectra across the peak Set the excitation RF equal to the lowest mass product ion expected divided by 1 4 If the product ions are not yet known start with the excitation RF 48 m z Set up the AMD method to cycle through excitation voltages using increments of 10 or 20 volts If you require a more accurate value for the excitation voltage change the excitation amplitude steps to 2 or 3 volts for each group near the best values found with the 10 volt increments and re inject the sample NOTE If the RF level was raised to trap the lowest product ion and you do not have a satisfactory number of product ions either try another precursor ion or switch to resonant excitation Some ions are sufficiently stable that they are ejected from the trap before they can acquire enough energy to dissociate Also try increasing the excitation time Determine the optimum voltage by plotting the product ion intensity data as a function of CID excitation amplitud
39. 1 MS Data E Standard MS Reports ou map click Back to go back and i MS Data Handling change any configuration information Back Cancel Method Builder Window Overview 7 Fie Edit View Window Help ae ame eee Sle a le S Blo Location E Maians S startup external mth Created Monday October 06 2003 08 28 14 Aukasemaler Modittied Wednesday January 14 2004 10 44 33 Sample Delivery Size 47414 bytes Injector Method File Attributes Flow Pressure Column Oven CO Read only LI Hidden Detector Output Data Acquisition El Ey 4000 Mass Spec Address 56 Revision History AO 4000 Mass Spec Control BD MS Acquisition Method I D Channel 1 M5 Data 5 g Standard MS Reports ef Print Options g Results Format S F Chromatogram Format H5 Compound Reports E Calibration Block Report Format oo Summary Report Format a at MS Data Handling jee Calculations Setup j Compound Table Results Treatment Archive O Requires Password on Save Mo Revision History 99 The Method is displayed in two panes The Directory pane on the left is an outline of the Method Clicking on an item in the Directory changes the content of the Parameters pane on the right Click on the splitter bar separating the panes to resize them To hide the Directory click the Show Hide Method directory Cc button Ela on the Window toolbar These menus are at the top of the screen File Edit View Window and Help
40. 1041 Or 49 Ch1 Make up Set 26 Actual 28 Coolable MA AA Front FID 260 260 Ch 2 H 2 Set 30 Actual 30 Mid ECD Off 43 9 Heatable3 Mea NVA Ch 3 Air Set 300 Actual 300 Front Injector Status Middle Injector Status Front Flow Pressure Status Middle Flow Pressure Status Column Oven Statue Front Detector Status Middle Detector Status Front Detector EFC Status Middle Detector EFC Status Click a temperature entry to select the corresponding component status or select the component status from the list The component status is displayed in detail 72 Click View Setup to see the 3800 Setup dialog Column Oven Zone Temp Limit 450 C No Coolant Zone 1 Front 1079 Temp Limit 450 C No Coolant Zone 2 Mid 1041 Temp Limit 450 C No Coolant Zone 3 Not Configured Zone 4 Front FID Temp Limit 450 C Zone 5 Mid ECD Temp Limit 450 C Zone 6 Not Configured Front Injector EFC Type 1 is Configured with Outlet Atm Units psi Min Flow 20 ml min Mid Injector EFC Type 3 is Configured with Outlet Atm Units psi Rear Injector EFC not Configured Front FID Detector EFC Type 11 is Configured with Ch 1 He makeup Ch 2 H2 Ch 3 Air Mid ECD Detector EFC Type 13 is Configured with Ch 1 N2 makeup Rear Detector EFC not Configured Front Column is Configured with L 4 meters D 320 microns He Carrier Gas Mid Column is Configured with L 4 meters D 0 microns He Carrier Gas Rear Column not Config
41. 2 Select Instrument 1 for the 4000 MS and 3800 GC and click Next Select Configuration Fa Select an existing instrument configuration for the method or select a custom configuration for the method Then click Next to continue Select a Configuration Configuration Description Custom Instrument 1 coos 3 Select the channels for post run processing If there is a Combi PAL it is present as a module in the Configuration Description X For the following module 4000 at address 56 Select the channel s to Select the Post Run process processes to perform Standard MS Reports VIMS Data Handling Unselect All lt Back Cancel 4 After you select the data channels and type s of post run processing for each detector the Star Assistant creates a Method containing all the sections needed to control the hardware collect data and do the post run processing 98 specified These Method sections contain default values for all parameters which you can edit as needed for your analysis This manual has data acquisition information for GC MS methods Data handling and reports are covered in the MS Workstation Software Reference Manual Confirm configuration Ea Added configuration Tobe added to method Fl 3800 Address 44 S800 Control 4000 Address 56 Click Finish to add the module control ADOD Control andor post run processing to the i thod E Channel
42. 37 40 Mass Calibration started ad 15 16 37 40 Calibrating on mass 69 0 Mar 15 16 38 06 Centered on mass 69 0 rf dac 662 9 Mar 15 16 38 06 Calibrating on mass 131 0 There are three major sections to the Auto Tune window the Control and Status display the Spectrum and Event Message windows and the Auto Tune Method display 234 Control and Status Click Start Auto Tune to start the selected Auto Tune routines Click Stop Auto Tune to stop Auto Tune The Action field shows the tuning routine that is being performed The State field displays whether the 4000 MS is currently executing an auto tune routine or is idle Control and Status Action Mass Calibration State Calibrating Spectrum and Event Message Window Select the display for the auto tune tests by selecting from the list Hide Keypad causes the upper portion of the screen to disappear and the lower portion expand Hide Keypad Spectrum Spectrum Spectrum and Event Messages Event Messages Module Attributes Summar Report The current Module Attributes is the information stored from the last auto tune When you are finished performing the auto tune you can view this information which is stored in an auto tune log Hide Keypad Module Attributes im MAS Workstation Demo ROT Version 6 42 Module 4000 56 MODULE ATTRIBUTES as of 3 15 2005 1 31 Pil Configuration System Type GC lonization Source External Option
43. Amount Std Unid Peak MultiChannel Notes AutoLink Vial Yolume Used IS NZ only Factor Multiplier Divisor MultiStandard none none 0 1 0 Posi 1 0 1 1 none a njection Using More Than One Method for Injections The Varian MS Workstation allows you to perform automated injections using more than one Method There are two ways in which this can be accomplished The first is by changing the active Method from within the SampleList The second is by using a Sequence 182 Changing the Method in the SampleList You may change the Method used during injections by activating a Method in a SampleList row Bat Automation File Editor New_Samples smp File Edit Help aleme S ea cals New _Samples smp 8400 SampleList Injection Injection Injectors ia Sample Name Sample Type tes Nates AutoLink Vial Voluee Used Add 1 Sample_1 i 1 none none 0 1 0 Pos 1 Insert none none 0 1 0 Pos 1 1 none none 0 1 0 Pos 1 Delete none Fill Down none none 0 1 0 Add Lines Defaults Hardware ih A D o b Activate Method Bd none SS a __ Pe lalalalala Data Files RecalcList Select Activate Method from the Sample Type cell Click on the AutoLink button in the row that you are working The Activate Method dialog box is displayed Method Path ame Ic Warani SSN ewhMethod mth Browse Cancel Enter the name of the Method or
44. Ca O 4000 Mass Spec Address 56 EK 4000 Mass Spec Control Method Segment A V lonization On Scan Type Full lonization EI Scan Speed Normal Setpoints Defaults General Parameters lonization Control External El Parameters Full Scan Parameters SetPoints C Scan Time 0 63 Maximum Scan Time Multiplier Offset oJ volts uScans Averaged 3 uScans Mass Defect i romu 100u Data Rate 1 59 Hz Customize 271 Internal El and CI tiem Description Z OOOO Instrument The GC and MS will be set to the configuration of the instrument Configuration connected to the Varian MS Workstation For the 4000 MS Internal Configuration both El and CI can be performed during the same run and so there is only one internal setting For the 4000 MS External Configuration you may select either to perform External El or External CI It is not possible to do both El and CI segments in a single run unlike Internal El and CI methods Acquisition Data The Acquisition Data Type can either be Centroid or Profile Type Centroid is the preferred and default acquisition data type as data handling library searching and spectral comparison can be done from this type of data Profile data is typically used for diagnostic purposes Profile files are also approximately 10 times larger but can be converted to centroid after acquisition Chromatographic The Chromatographic Time Segments table allows you to time
45. Communications menu item from the nstrument menu to display the Star Assistant Communication Wizard Click on the Next button to advance to the Setup Ethernet Ports dialog box 90 Setup Ethernet Ports for Nabil B csb varian com 132 190 73 155 Address Module Type IP Address or Domain Name Status Actual IP J fso a fis O Available 132 190 73 182 None C No ddress None No Address 4 fe gt f No Address f Address Management BOOTP Server No IP Addresses are being assigned from this Workstation Setup M Prompt for Setup if needed lt Back OK Cancel Select Setup to display the BOOTP Server dialog box The BOOTP Server dialog is displayed ee IP addresses from this va ETI E See nee Lil o E0 J3 a0 54 0e IP Address HI Insert Delete of Check the box to enable password protection The next time you enter the BOOTP Server dialog box from the Setup Ethernet window you will be prompted for a password Password Entry fess IF Address management requires password entry Enter the password E below Cancel Change Passyyord Enter new password Re enter new password Enter a password After it is successfully entered you may change it Enter a new password twice The initial password is blank no password To set your password initially enter the desired password in the Enter new password and Re enter new password fields
46. Data Files by dragging and drop ping them on the Batch Report Window Review standard GC chromatograms interactively edit data handling parameters and recalculate results Preview standard chromatogram and results reports FS Run a sample without a Sample List Quick Start When additional 4000 GC MS Workstation options are installed such as StarFinder and Star Custom Report Writer other application buttons may be added to the Workstation Toolbar Quick Link Buttons Most Recently Used Data File Click this to display operations that can be performed on the Most Recently Used Data File A different data file can be selected from a list of most recently used files RESP S YR SO0 viewEdit M5 Chrormatograrn Frink Custom MS Report Print Standard MS Report View Custom MS Report View Standard MS Report Pick a different Data File Most Recently Used Method Click this displays a menu of operations that can be performed on the Most Recently Used Method A different method can be selected from a list of most recently used methods A reproducibility i View Edit Method Edit Compound Sets Print Method Pick a different Method F Workstation Toolbar Options Move to Windows Task Bar Show Hide Applications on Toolbar Enable Disable Instrument Modules Application Descriptions Small Buttons an Toolbar Run Application Help on Pick Data File For Quick Link Button Pick Method For Quick Link Button
47. December 30 2003 11 14 53 T MS Acquisition Method m Selected Channels and Post Run Processing Last Modified Ready NUM hi The 3800 Method section contains eight Method windows Autosampler Sample Delivery Injector Flow Pressure Column Oven Detector Output and Data Acquisition These windows contain all parameters that control the operation of the 3800 GC during a chromatographic run If the 4000 MS is the only detector and samples are injected by syringe the Sample Delivery Detector Output and Data Acquisition sections are irrelevant and will not be discussed in this manual For information on these sections of the 3800 GC method see the 3800 GC Operator s Manual Checking Method End Times All editing windows other than the Column Oven window and Detector window show the current end time of the column oven program above the Save and Cancel buttons a 50 Hold min Total min 1 00 Add 21 75 Insert Delete Column Oven End Time 20 00 min 145 If you enter program end times for components other than the column oven that exceed the column oven end time the following warning is displayed Method Editor Es 2 The following components have program end times that exceed the Column Oven r EndTime Front 1079 Injector Ramp The Column Oven EndTime determines the Method EndTime on the 3800 GC Do pou want to sawe this Method even though thi condition exists When the M
48. Detector Rear Detector Middle Detector Type TCD Detector Oven On C Off Temperature C Electronics On C Off Filament Temp Adjustments Time Constant Slow Fast EFC Type Typei4 Carrier Gas He Make up Flow ml min Filament Temp Limit C 3950 Ref Makeup Flow ml min tem Deseription Detector Oven On or off power imsmeronomnonorot O Electronics On or Off Per ites wert mainea ToC wn to uos orrot Temperature C 50 to 450 C Specifies the TCD Temperature Filament Temp C 0 to 390 C or 0 to 490 C depending on the filament temperature limit selected in the Adjustment section of this dialog Specifies the Filament Temperature For best lifetime operate the TCD at the lowest practical filament temperature initial 0 00 to 999 99 min Range mV 0 05 0 5 and 5 0 mV 304 tem Description Autozero Yes or No Yes at initial time means that Autozero is on continuously before the run starts Autozero also enables the automatic cell balance Polarity Positive or Negative Allows peaks of either polarity to be processed by Data Handling A dd Adds a line to the spreadsheet rt Insert Inserts a line above the currently selected row in the spreadsheet Delete Deletes the currently selected row s in the spreadsheet Sorts the spreadsheet rows by time Time Constant Slow or Fast Carrier Gas He or N2 Argon The automatic filament protection feature
49. Detector Detector Detector a Post Front 1177 ves tdid 1079 no Rear 1041 Indicate which Detectors are connected to each Injector that it reachable by the 6400 Syringe Tower This information i uted to manage Data Handling for Dual 5 ample Injections only those using Advance and Clean amp Adv modes for 4nd Injection cereal The 8400 AutoSampler has the ability to inject into two contiguous injectors in the same chromatographic run The 8400 Dual Mode Setup dialog allows you to define the configuration to be used when that capability is invoked The 8400 can inject into front and middle or middle and rear injectors and each of the injectors can be connected through an analytical column to any of the installed detectors When the 8400 AutoSampler or 8410 Autolnjector is used in Dual Mode this dialog box is used to assign the detector channels to the datafile for the corresponding sample In Dual Mode operation two datafiles are created one for the first sample injected the other for the second sample injected The samples that are injected are identified by their 8400 8410 Injection Position as either Position 1 or Position 2 The table in this dialog box allows the user to specify which detector information to associate with each 8400 8410 Injection Position 8400 8410 SampleList Window Extensions 8410 SampleList 8410 a smp Sample Name 2nd Sample Name jena went ies ee ae a mecos Standard Sample
50. FAMS QuickStart 1 File Screen Options Instrument Number 1 Instrument Name 4000 MS Operator Name Gunter S Sample Name Pesticid_1 Sample Description 1 Method Development Sample Description 2 Primary Method C VarianWS pest mth Folder for Data File Storage C VarianWS Data Browse 8400 Sample Type Vial fi C Baseline Injects fi Calibration Yolume fi Analysis Amount C Verification Factor ho M Clear Coefficients ee fi Divisor fi AutoLink Level fi E EE He Ext Entering Information in the QuickStart Dialog The instrument number name and operator are entered in the top three fields Enter sample name and descriptions if desired in the next three fields Click the mouse in the Primary Method field Either modify the name here or click the Browse button to select from the Windows Explorer menu 164 Select Star Method Ea E3 Look in Sy Varianws e ex Fee z C 400055 Ci sSCData j Service History SYSLOG 7 WSDataFiles f EX 26DNT NICI CI 35 mth Desktop EB 26DNT_Hybrid_N20 mth EB 26DNT_Hybrid_N20_AGC 30K mth ES 26DNT_Hybrid_N20_AGC 5000 mth ES 26DNT_Hybrid_N20_AGC mth ES 26DNT_Hybrid_N2O_MSMS mth ES 26DNT_Hybrid_N2O_MSMSNR mth My Documents File name My Network P gt Files of type Method Files mth Cancel h In a similar manner select a path for data file storage by first clicking the mouse within the
51. Folder for Data File Storage field and then either typing the path or clicking the Browse button to open the Data File Generation dialog and choose the path To tailor the file name follow the instructions in the Data File Names field 4 Data File Generation Specify the names for Data File generated by detector modules for this QuickStart screen Numbers will be appended to the file names if the file already exists Do not include the file extension in the Data File name Directory for Data Files Data File Names a EN Zizm d s 3 Yarianw S lt J Data Example C Development Sample 1 J Replicates Use the following symbols to enter the corresponding variable data to the file name New Folder s Sample ID i Injection number d Date Zm Detector Module name t Injection Time Drives erc Choose the Sample Type Analysis Calibration Baseline or Verification NOTE Selecting Baseline will actually create an Analysis file type for GC MS data Click AutoLink to add any post run processing commands you want to use optional For example you can Browse for a Custom MS Report Editor software template and insert it as an AutoLink command Then in System Control processing you can have automated printing of Custom MS Report Editor reports at the end of a run 165 of SampleList Command Method Other Parameters Pe eee Other Parameters ee hs Browse Es of SampleList Command Method O
52. Keys Cl MS MS Hybrid External EFC Module TRUE Serial Number 106 Controller Board Version Cogg FROM Software Wersion 03 01 00 03 Communication Processor Software version 01 01 00 68 Scan Processor Software version 07 07 00 68 235 Auto Tune Methods There are various checks that automatically set up tune and calibrate the mass spectrometer Each instrument configuration uses different checks Manual Control Auto Tune Temperatures Diagnostics Startup Shutdown Acquisition Control and Status Auto Tune Method Action Idle IY Auto select prerequisite tuning functions State Idle Select All Clear All H Integrator Zero Start Auto Tune Set Electron Multiplier RF Full Scale Adjust Mass Calibration Trap Frequency Calibration Auto Tune is generally performed in the order listed beginning with Integrator Zero All auto tune methods are selected if you click Select All or cleared if you click Clear All To perform Auto Tune select the desired routines and click Start Auto Tune Stop auto tune at any time by clicking the Stop Auto Tune Integrator Zero 5 a 114 E ele Scan Number 2 Time 0 002 min RIC 1741 lon Range 99 5 500 4 m z Counts 5O 2 May 20 13 15 03 Integrator zero Adjustment Set 360 May 20 13 15 04 Integrator zero Adjustment Set 356 May 20 13 15 04 Integrator zero Adjustment Set 354 May 20 13 15 04 Integrator zero Adjustment Set 354 May 20
53. Note the Hybrid HPS and LPS options in the selection menu Hybrid HPS High Pressure Source is performed with the Cl volume inserted into the ion source whereas the LPS Low Pressure Source option occurs in the El source configuration Choosing the MS Acquisition Data Type Acquisition Data Type Centroid Profile In a given method only Profile or Centroid data may be collected Centroid Data The standard data acquisition type is Centroid The apex of each mass peak is reported with as ion and intensity data this is reported to one decimal place for example m z 231 2 Centroid data are required for library searches and quantitation Profile Data Profile data may also be acquired the data files are much larger because ten data points are collected at each m z Profile data is useful for determining the charge state of multiply charged ions It is also used to diagnose difficulties with mass resolution or mass assignment 106 Spectrum 14 10 967 min Scan 95 Channel 1 lon 1385 us RIC 228526 AC BOS 143 ae Centroid Data 40 HABa 20 10 Spectrum 1B PROFILE 10 945 min Scan 1034 Channel 1 lon 1255 us RIG 374681 Profile Data Editing Chromatographic Time Segments The mass spectrometer can be programmed to acquire data in different ways by dividing the analysis into chromatographic time segments In the simplest implementation the default method always has a 3 minute filament multiplier del
54. Parameters to set the filament emission current Higher current leads to more ionization and thus higher sensitivity but may also lead to shorter filament lifetime 231 Method Active Seament Checks and Adjustments Module Attributes Method Segment V lonization On Scan Type Full X lonization l Scan Mode Normal Defaults General Parameters lonization Control Intemal El Parameters Full Scan Parameters Internal El Parameters Emission Current in uAmps Full Scan El Full Scan Parameters Use Full Scan Parameters to select the mass range for this segment You can customize the mass range RF storage level and ion time factor for each segments to optimize the sensitivity for selected compounds or match the desired spectral characteristics required for tuning with BFB or DF TPP Method Active Segment Checks and Adjustments Module Attributes Method Segment I lonization On Scan Type Full v lonization El v Scan Mode Normal Setpoints Defaults General Parameters Ionization Control Internal El Parameters Full Scan Parameters Mass Range q r Tune Low Mass ai m z Type Auto l Save Low Mass High Mass RF Storage lon Time FIP St _ ii m22 m z Level m z Factor D E 5 105 100 249 35 100 250 399 35 100 400 1000 35 100 Customize Insert Add Delete 232 Checks and Adjustments The Checks and Adjustments tab allo
55. Reaction Time usec Cl Storage Level m z Background Mass m z Ejection Amplitude v Target TIC Prescan lon Time usec 196 PCI with CH 0H Properly Adjusted Methanol Reagent Spectrum Prescan lon Time usec 100 Internal PCI Scan Function El space charge control uses the integrated ion current from a prescan to calculate the analytical scan ionization time By contrast Internal Cl space charge control does not use a prescan to measure the charge formed Internal Cl uses a portion of the ions detected during the previous analytical scan to calculate the ionization and reaction times for the next analytical scan The following figure shows the scan function for internal chemical ionization 197 ta Oo eae onization eaction canning Internal Cl Scan Function A Reagent ionization time determined by the previous scan B Ejection of unwanted ions i e non reagent ions using waveform C Reaction of reagent ions with sample molecules time determined from previous scan D Ejection of ions with masses lower than the start mass of scan range E Acquisition of Cl mass spectrum Chemical ionization occurs by forming reagent ions by electron impact These reagent ions then react with the sample to form product ions by ion molecule reactions The ionization and reaction storage RF can be set at the same level or different levels Unwanted sample ions formed by electron ionization during the formation o
56. Ready Eile Edit Inject Automation Recalculate Instrument Windows Help Ps i i i i ISIE Wiew E dit Method SHP SEQ rn gt m Print Method Re Achvate Method Click Re Active Method for additional options The 3800 GC Status and Control Window The 3800 Module Window is like the following The left side of the window shows the 3800 Operation parameters RunTime End Time Method State and Fault State The Start Reset and Method buttons control the 3800 GC 71 Se THLE Bely S Doers FlunTine DOO rin Stat Manae Endlese Hilen Aer i iCooksble Hofa oa A Enable Cote Oven Cogis ot S0C Wale 1 2 4547 s Timesut 2000 min Timed Qut Mo Hide Ka i Caki Dvn Statai pa vense roci i If a detector other than the MS is used for data acquisition the detector signal can be viewed in the real time chromatogram display xg 3600 44 Equilibrating 3900 Operation Temp Zones Set Actual Runtime 0 00 min Start gt EndTime 4 00 min Reset i ore Equilibrating Method s Mih Fault 260 i Ot Valves 1 2 3 4 5 6 7 BAA View Front Only View Middle Only iew F amp Ml Horz View F M Vert Output from multiple detectors can be viewed horizontally or vertically The component status display can be changed to view detailed status of each component in the GC Temp Zones Set Actual Front Detector EFC Status Col Over 90 90 Type 1 Ready No Fault No B Mid
57. Shutdown allows the user to start or shut down the vacuum system and heated zones in an orderly manner Acquisition Run samples and acquire data files often in conjunction with the Inject and Automation menus of the System Control window Hide Show Keypad The Control and Status window can be hidden by clicking the Hide Keypad This becomes a Show Keypad button to restore the Control and Status display While the keypad is hidden the On Off controls for the trap Cal Gas and Cl gas are still accessible as well as the method segment selector and the Profile Centroid control 228 Manual Control Manual Control is very closely linked with the Method Builder function of the software A method may be built in Method Builder activated in System Control then manipulated segment by segment in Manual Control Conversely a method may be modified and fine tuned in Manual Control then uploaded and saved under the same name or as a new named method The important distinction is that the effect of changes made in Manual Control can be seen immediately in the real time spectrum display using Cal Gas or background ions as a surrogate sample or using a device such as a Chromatoprobe to provide a continuous supply of a sample Control and Status Control and Status displays a graphic of the ion trap system and status of the vacuum system and temperatures Clicking the trap in the graphic display to turn on off the ion source RF system and the
58. Stabilization Time The first row of the spreadsheet contains the Initial temperature and hold time for the Column Oven The Column Oven will equilibrate to this setting and stabilize for the specified Stabilization Time when the method is activated and will be restored to this setting when each chromatographic run is completed Rows after the first row of the spreadsheet contain the programmed settings for each of the ramp segments Each segment will ramp to the specified temperature at the specified rate assuming the rate is achievable and then hold the temperature for the specified time NOTE The Rate in the first row is always blank and cannot be edited Also note that the entire Total column cannot be edited 153 Autosampler Window The Autosampler window contains sampling parameters for the 8400 8410 Autosampler when attached to the 3800 GC The parameters include selection of the sampling syringe size the penetration depth for sample and solvent wash vials the default clean and clean modes and the injection modes E Method Builder Method1 iof x E File Edit View Window Help l x Helas B Aee 2 Ee 5 14 4 gt gt Method1 Method Notes E E 3800 GC Address 45 Autosampler 8400 z mp aner oa Syringe Size uL fio uL Sample Depth Injection Mode Std Split Splitl Solvent Depth jo m Default Clean Clean Mode Vial i ff Pre Inj Solvent Flushes V
59. Subsequent entry into the BOOTP Server will require this password NOTE See Recovering a Lost Password for BOOTP Server Access in the Diagnostics Troubleshooting section for instructions on resetting the password 91 Adding a GC and MS to the Instrument Once you have configured your Workstation computer and 3800 GC for network communication you may select one GC to be controlled from each Varian MS Workstation If it is not already running start System Control The Star Assistant Communication Configuration Wizard will be displayed if you have not yet configured your GC Ethernet connections Click on the Next button to advance to the Setup Ethernet Ports dialog box Setup Ethernet Ports for Nabil B csb varian com 132 190 73 155 Address Module Type IP Address or Domain Name Status Actual IP 4 e Ap No Address 4 Noe A No Address 46 e A No Address a Poe A No Address IP Address Management BOOTP Server No IP ddresses are being assigned from this Workstation Setup M Prompt for Setup if needed lt Back Cancel Click on the Address button to attach to a 3800 GC on the Ethernet network When the Address button is selected the Module Selection dialog box is displayed Select an Available Module from these found on the Network x MP1 4 makaha In Use By inthab 132 190 73 760 3000 mpd 5 Available 132 190 735 750 4000 mp Available 132 1790 79 184 3000 pilot 0 In Use By md
60. These buttons become active only after a change has been made in the Temperatures dialog Pressing Save will execute any changes to setpoints made since the last Save or the opening of the dialog Pressing Restore will discard any changes made since the last Save or the opening of the dialog and will restore setpoints to the status quo ante If changes are pending when you leave the Temperature dialog you will be prompted to save or discard the changes Bakeout The Bakeout tab allows you to set temperatures and a timer to control the instrument in Bakeout mode These parameters may be changed only while Bakeout is not active or stopped Bakeout Trap Temperature A temperature between 50 and 250 C may be entered The default is 150 C and a typical setpoint for Bakeout is 220 C Bakeout Manifold Temperature A temperature between 0 and 120 C may be entered The default setpoint is oo GC 240 Diagnostics 4000 56 Not Ready Transfer Line Temperature A temperature between 0 and 350 C may be entered The default setpoint is 170 C The transfer line should not be heated above the maximum operating temperature of the capillary column installed in the GC Hold Time The Hold Time establishes the duration of the Bakeout starting when the system components reach their Bakeout temperature setpoints Values from 0 to 72 hours may be entered The default is 8 hours Start Stop Bakeout The Start Bakeout button activa
61. Time ions are allowed to react with sample molecules to form ions The typical reaction time is 100 milliseconds Depending on the Cl reagent and the target compound of the analysis sensitivity may be affected significantly by varying this parameter Range 1 2000 milliseconds lt Scan Type gt This tab will appear differently depending on the Scan Type that is Parameters selected For example if AMD is the Scan Type selected then the tab will read AMD Parameters If Full is the selected Scan Type then the tab reads Full Scan Parameters Full Scan You can change the values of the Full Scan Parameters Low Mass Parameters m z and High Mass m z If you click the Customize button then you can edit the Tune Type Auto BFB DF TPP or Single Segment as well as enter Low Mass High Mass RF Storage Level and lon Time Factor for each segment Low Mass m z Unless the Customize button is active the lower and upper limits of the mass range to be acquired are entered here If in Customize High M Meee mode then the Low Mass and High Mass will be entered into the table by clicking on each cell to edit Range 10 1000 m z full range RF Storage Level This is the m z value at which the RF is maintained during ionization and the coarse isolation step The typical range is 35 to 100 m z anion Pr onizauon with a default value of 35 m z Storage Level Range 8 150 m z full range lon Time Factor When a scan is perfo
62. Windows Taskbar You can display the Workstation Toolbar as a Windows Taskbar icon Taskbar icons appear in the lower right or bottom of the Windows Taskbar the bar on which the Start button appears When displayed as a Taskbar icon the toolbar no longer takes up space on the screen When you click on the Workstation Toolbar icon the options menu is displayed Show Hide Applications on Toolbar Selecting this option displays the Show and Hide Applications on the Toolbar dialog box 12 Show and Hide Applications on Toolbar Applications shown on Toolbar Applications not shown on the Toolbar Select applications you wish to remove fron the Select applications you wish to add to the Toolbar Toolbar and click on the Remove button and click on the Add button Aurora Batch Reporting Compound Set Editor Custom MS Reports e Edit Automation Files Folien Z000 Quick Start Review Process MS Data Security Administration SMSVMS File Conversion Standard Chrom Reports Standard MS Reports System Control Automation Yew Edit Chromatograms View Edit Methods geddi Cancel Use this dialog box to select which 4000 GC MS Workstation applications are represented by icons on the Workstation Toolbar The box on the right shows all applications that are currently displayed in the toolbar The box on the left shows all applications that are installed but not displayed in the toolbar To remove an icon from th
63. a E se eccexpuecatawncs 187 OVO a arm nen eR fd A T oe 187 PACS 10 0 oan eee eee eer ee RCO NE TR a ee er ee ee eee ees 187 PRE OUI AIO MEO SLING oair a a ee aretiaa ean ceed aetna ea ys ese eie a eee ee a 188 FM RSS OLN AS het toe aeectyen belts gata aca nee estuntee a a 189 A000 MS lo oniza tion TECNMIGQUES issii aaa a aa E Raa EREE 191 CAGIGES OF 1ORMIZ ATOM ModE iion E E R E E E A 191 Nermal Electron IONIZAUON senis E a E TE tal mare ead E E alana 191 internal Positive Chemical l nzatlo Nsa ninr n a a a a a Gees ese eee 194 External Elec tTomloNnZal ON minenin a a a a edeeea eee 199 External Positive or Negative Chemical lOniZation cccccccseeeeeeseeeeeeeeeeeeesseeeeeaeeeeeeseeseeeseeeeeesaeeeeeeseeeeesaeeeeeeas 202 Hybrid Positive or Negative Chemical lOniZation ccccceccccceeeeeeeeeeeeeeeeeeeeeseeeesseeeeeeseeeeesaeeeeesseeeeeeseeeeeesaeeeeeas 206 Ion Preparation TECHNIQUES narii 209 MS MS Tandem Mass Spectrrome ny 22sec rnishso se nanna e a nani ataeaeh ota A A E E 209 Selected ION Storage verenin a e aaa e vananhadon e aE A a alam T 214 System Control Command Reference cccsssccceseecceneeeeeseecenseeeenseesenneesenseesensessensesses 217 Syster COMMON MENUS rios o e E A E N E 217 4000 MS System Control Command Reference ccccseseecssseccenseeeesseeeeseeeeenessensesseaes 227 DISPIS ae cee cance eat a reece macaw ncaa ume aye anc ea noeamla 22 System Contool Tabs irosun rc eR
64. automation in progress Suspends execution of automation after the current run has been completed Resumes execution of automation after it has been suspended Stops the current run resets all modules simultaneously and suspends automation Stops the current run resets all modules simultaneously Automation proceeds to the next injection after all the modules go to the Ready state Turns on or off the printing of reports automatically generated during any automation action This is useful when you wish to disable printing if the printer is out of paper for example without having to modify the Print Options portion of the Report Method 220 Recalculate Menu a System Control Ferguson_1 Not Ready Fie Edit Inject Automation Recalculate Instrument Windows Help i a A hy Begin RecalcList igi El SPME mth Hja SPME Begin At Selected RecalcList Line l L 4000 01 Read TETA Manual Control Ao Tune Temperatures Description Begin RecalcList Begins recalculation of the open RecalcList using the active Method Begin at Selected Begins the open RecalcList at the selected RecalcList line This RecalcList Line item is enabled when a RecalcList is open Upon selecting this menu item a prompt for the line in the RecalcList appears This is useful when recovering from a power failure that interrupted automation in progress View Calibration Opens the Open a Method File to Vi
65. background that would normally arise from a high emission current emission currents of 50 100 yA can proportionately increase sensitivity over that of the default 10 pA current Full Scan Parameters General Parameters lonization Control Internal El Parameters Full Scan Parameters Mass Range Low Mass 504 miz High Mass 100 mez The lower and upper limits of the mass range to be acquired are entered in this tab dialog General Parameters lonization Control Full Scan Parameters Tune Type Auto Save lon Time Factor Mass Range Low Mass ma mz High Mass 300 mz Customize With Customize active it is possible to program up to six different segments of the acquisition mass range You can use the Insert Add and Delete buttons to adjust the number of segments Notice that the RF Storage Level can be programmed for each segment as well as the lon Time Factor When a scan is performed in Auto mode the prescan is followed by an ionization time and scan of each segment needed to cover the Mass Range designated to the left of the segment table The actual lon Time for each segment is the AGC lon Time multiplied by the percentage in the lon Time Factor field Setting Up the Method for DF TPP or BFB Tuning Tune Type Auta Avuto ee Single Segment Segment Use the menu in the Tune Type field to designate BFB Tune or DFTPP Tune This displays a segment table in whi
66. be deposited as internal energy by increasing the number of collisions Increasing 1 The dipole field is simply an electric field oriented along the axis of the trap 211 the excitation time increases the number of collisions Thus it is possible to fragment precursor ions that require the breakage of multiple chemical bonds or that undergo significant rearrangements Periodic modulation through ion resonance results in an averaging of the energy coupled into the ion motion and provides a reproducible product ion spectrum even with changes in concentration An additional parameter is available with resonant excitation Increasing the number of CID frequencies permits simultaneous excitation of ions within a range of masses This may be useful when trying to excite an entire isotopic cluster at once As the number of CID frequencies increases the range of excited masses also increases At a given number of CID frequencies the range of excited masses increases with increasing ion mass and decreases with increasing excitation RF storage level Mass Range Excited 60 Excitation RF Storage Level m z 48 C 7 7 SS Oo Gos oO 5 SS eee E te S a l l l I I 4 I l l 4 l l l l l A 7 a ee eee ae efoto 4 i a a es a co 4 MEN 29 Number of CID Frequencies oO oO Mass range excited vs number of CID frequencies for an excitation RF stora
67. been achieved and stabilized Fault Yes or No Displays if a fault in the Type 1 EFC component has occurred Type 1 0 1 to 100 psi Pressure Displays the programmed column head pressure setting in the active Setpoint SE pigg j i mee method Actual 0 1 to 100 psi Pressure Displays the actual column head pressure at the 3800 GC Column Flow Displays in mL min the column flow rate calculated from the column head pressure column temperature and column parameters carrier gas column length and internal diameter Linear Displays in cm sec the column linear velocity calculated from the Velocity column head pressure column temperature and column parameters carrier gas column length and internal diameter Total Flow Displays in mL min the total flow rate through the system Split State On or Off Displays the current split state of the 1079 1177 injector method Split Ratio 1 to 10000 Displays the current split ratio of the 1079 1177 injector method The split ratio is defined as the Column Flow the Split Flow the Column Flow 257 Type 3 Injector EFC Flow Pressure Status tem Description Yes or No The Type 3 Injector EFC component is Ready Yes if the setpoints have been achieved and stabilized Fault Yes or No Displays if a fault in the Type 3 EFC component has occurred Type 3 Flow 0 1 to 100 mL min Setpoint Displays the programmed column flow rate setting in the active method
68. can change the end time of the acquisition from the Status and Control window Status 4nd Control Run Time 0 32 minutes Shop Acquisition 10 00 minutes Eeli olai Running gt No Fault Wait For Readln Click End Time Endtime Please enter a new endtime g J Cancel Enter the new end time and click OK 69 Effects of Hardware Configuration Changes After changing the configuration for example from External to Internal configuration System Control restarts When the 4000 MS module connects it compares the current configuration stored in the current Module Attributes with the configuration reported by the hardware If these do not match the Module Attributes are updated preset to the appropriate configuration A similar process occurs for the default method Default mth After making the hardware configuration change any new method has the appropriate instrument configuration by default NOTE The presetting of Module Attributes requires that the user run all Auto Tune routines as the prior Auto Tune results will be invalid 3800 GC System Control Window The Instrument Window After you have configured your 3800 GC in an instrument you may view the Instrument Window The instrument window allows you to monitor the status of all modules assigned to the instrument perform injections of one or more samples and perform batch Recalculations my System Control Configuration Eile Edit Inject Auto
69. clicking the Customize button You may also edit the parameters to accommodate another Cl reagent e g d3 acetonitrile and then Save these parameters under a user selected name Reagent Low Mass is the lowest mass stored in the trap during ionization The combination of Reagent Low and Reagent High Mass and Reaction Storage Level allows for the selection of a specific reagent ion in the Cl process For example only mass 29 of methane could be used as the reagent ion by ejecting mass 41 during ionization and by reacting at a mass greater than 19 in the reaction step Range 15 149 m z Reagent High Mass is the highest mass stored in the trap during ionization All masses above this mass are ejected during the ionization step This reduces the number of El generated ions that are in the trap The combination of Reagent Low and Reagent High Mass and Reaction Storage Level allows for the selection of a specific reagent ion in the Cl process For example only mass 29 of methane could be used as the reagent ion by ejecting mass 41 during ionization and by reacting at a mass greater than 19 in the reaction step Range 16 150 m z When in Cl the Customize button is visible Clicking on the Customize button displays additional components pertinent to the time segment method being edited There are options to edit the Reaction Storage Level Ejection Amplitude and Max Reaction Time There are no Custom features when in El Reaction
70. ee oo E ee Module Keypad Dialog Hide Mevpad Chromatograrn Default Wiem Click Hide Keypad to display a larger chromatogram and spectrum windows during data acquisition Click Show Keypad to restore the 4000 MS Keypad 28 Chromatogram Toolbar The Chromatogram display can be viewed only when the 4000 MS module is in Acquisition mode The Chromatogram Toolbar appears in the upper left corner of the display The functions of buttons on this toolbar are as follows 5 10 AJ Be r A Click the Arrow to hide the toolbar Click in the upper left of the display to restore the toolbar fa Click Full Scale to normalize the chromatogram vertically and horizontally Double clicking in the lower left corner of the display has the same effect Click Previous Scale to return the chromatogram display to the last scaling before the current one If you have zoomed the chromatogram twice to view smaller time intensity ranges this button steps you back through the previous scales m Click Scale to choose between Auto Scale and Fixed Mode Intensity w Auto Scale Fixed Mode Stacked Overlaid wf Normalized cy Click Chro Display to display this menu A Click Spectrum Select to display the spectra The chromatogram display stops updating ii a Click Chromatogram Viewer to load the acquiring data file into MS Data Review where you can compare this data with other data and do analysis i Mh C
71. explain how to use these features Navigating the 4000 MS Instrument Window 4000 01 Not Ready ale Manual Control Auto Tune Temperatures Diagnostics Startup Shutdown Acquisition p Control and Status Method Active Segment Checks and Adjustments Module Attributes Edit Method Upload MS Method Instrument Configuration Acquisition Data Type intemal El and CI Centroid Profile gt Source Internal Method Internal Vacuum System OK Temperatures OK Source OK Chromatographic Time Seaments lon Gauge Pressure 0 0 uTorr Fil 1 Valid Add Trap Segment Description Insert 3 00 _lonization Off Sami p2 a 8 00 90 00 EN Ato Fl Dete lt p multiplier I Trap Soms E 1o usin aop Haho aeie erod Seo a Sn r Gh on Hauge as Activate EPR ar Number 1 FIL MUL DELAY i Cycle ES 1 Hide Keypad Spectrum gt Changes Restore Number Snne pen N CEEP Peers 1 Acquired TA miz System Control features include System Control Menu bar System Control Toolbar 4000 MS Keypad Dialog Chromatogram Spectrum Toolbar and Chromatogram Spectrum Displays 17 File Menu Activate Method Upload Active Method From Modules New SampleList Open Samplecist Mew RecalcLlist Open RecalcList New SequenceList Open SequenceLisl Print Printer Setup w Remember Last Open Files Exit Activate Method Choose
72. for the range of sample ions Scanning lons to Collect Mass Spectra The SIS scanning process is very similar to that for full scan electron ionization After ionization trapping and ion preparation steps ions are scanned out to the conversion dynode and electron multiplier Mass scanning is implemented by increasing the RF voltage on the ring electrode the mass spectrum is collected in order from low to high mass over the user designated scan range In positive mode electrons are ejected from the conversion dynode held at 10000V and repelled to the electron multiplier In negative mode positive ions are ejected from the 10000V dynode and repelled toward the multiplier The signal is enhanced by 10 by the multiplier and sent through an integrator to collect an intensity for each m z MS data are stored as sets of ion intensity pairs for each m z over the acquired mass range A complete mass spectrum is stored for each analytical scan 215 216 System Control Command Reference System Control Menus File Menu a System Control Ferguson_i Not Ready File Edit Inject Automation Recalculate Instrument Windows Help Activate Method a dis enen gt 8 Upload Active Method From Modules a pil SHP SEn J New SampleList Open SampleList Diagnostics Startup Shutdown Acquisition MS Method Segment Number 1 of 2 Segment Description FILAMUL DELAY Scan Description Filament Off Scan Range 20 25
73. from the Chromatographic Time Segment table However there must always be one segment in the method To delete multiple segments the entire row for each segment must be selected Defaults This button sets the selected segment to default values for the selected instrument configuration Every field of the segment is set to default values Restore This button is used to restore a chromatographic time segment to its values from the original method file or from the last time the file was saved within the current editing session Restore is only valid for saved or existing method files For a new method file the Defaults button is used to set the segment values to default values Method Segment The 4000 MS Method Segments control what MS scan function is performed The different scan functions in the Internal configuration are El and CI Full scan AMD MS MS MRM MS n SIS and uSIS For each Scan Segment selected in the upper Chromatographic Time Segments table you will see a plethora of drop down menus and tabs which provide you with the options to create the exact method required for each Chromatographic Time Segment Only if the lonization On radio button is chosen will you be able to view all the available options lonization On If the lonization On radio button is not checked the filament and radio button multiplier will be OFF during the segment This is the default setting for Segment 1 when a new method is created to protect
74. gt fj N gt fi n 191 Internal El Scan Function In electron ionization mode electrons emitted by a filament interact with sample molecules to form ions For internal ionization mode the ion formation occurs within the trap For external ionization mode electron amp chemical the ion formation occurs within the source with subsequent transfer of ions to the trap by a set of lenses For both internal and external ionization the ions are stored and stabilized in the ion trap cavity by an RF field applied to the ring electrode of the ion trap The ion trap has a maximum storage capacity for ions beyond which mass resolution and spectral quality deteriorate The number of ions created is proportional to the ionization time with more ions being produced the longer the ionization time Automatic Gain Control AGC controls the ionization time in order to maintain the number of ions in the trap at the optimum level Four modes of operation Internal El External El External Cl and Hybrid Cl use a similar scanning sequence involving Automatic Gain Control AGC to scan ions out of the trap The AGC scan function consists of a prescan and up to six scan segments The prescan uses a fast scan rate and the number of ions detected in the prescan is used to calculate the ionization time for the succeeding scan segments The figure below illustrates the AGC prescan and four scan segments corresponding to the following four portions of the
75. hardware and software used for communications with pour Instrument modules If pou prefer to wait you can use the Setup commands in the Instrument Menu at any time Click the Mest button to continue Y Show this introduction nest time 4 Back i Cancel Read the description presented in each window and click Next 86 Configuring Communications Ready to Setup Ethernet Communications Click the Next button to continue Configuring Communications You have installed a driver for the S800 GC that uses Ethernet to communicate with the GC The communications software needs to be configured so that the Star Workstation can locate and identify the Instruments on Your network Click the Next Button to continue Cancel From the Setup Ethernet Ports dialog box select Setup to display the BOOTP Server dialog box Setup Ethernet Ports for nabilB csb yarian com 132 190 73 155 Address Module Type IP Address or Domain Name Status Actual IP Ea Ne A p No Address 6 f hoe Ff No Address D fhe A No Address Ea Ne Ff No Address IP Address Management BOOTP Serve No IP ddresses are being assigned from this Workstation f LS MV Prompt for Setup if needed lt Back OK Cancel Select Setup to display the BOOTP Server Dialog Box 87 The BOOTP Server dialog contains a table listing all 3800 and 3900 GCs to which IP addresses may be assigned NOTE If more than
76. heat the getter to its operating temperature of 400 C This does not appear when the instrument is in Internal configuration 60 Operating Conditions Operating Conditions Heated ones Trap Temperature 100 C Manifold Temperature 540 Transterdine Temperature 257 C Source Temperature 22a Vacuum System Pump Spin Speed 100 Current S06 manips Preumatics Flow Aate 4 0 mL run Inlet Pressure a4 PSI Getter Control De 402 C Heated Zones The current temperatures of all heated zones are displayed You can compare these readings with the set points to the left in the Current Set Points field Vacuum System The speed of the turbomolecular pump is100 2 during normal operation Monitor the speed during Startup Shutdown here The rate at which the turbomolecular pump is started up is proportional to how long it has been shut down After short shutdowns for instrument maintenance the time to reach 100 speed should be less than 2 minutes After extended shutdowns the pump speed is increased in stages related to power consumption This slower startup improves pump lifetime NOTE Failure to reach 100 pump speed in a reasonable time indicates a vacuum leak and corrective action should be taken Go to the Troubleshooting section in the 4000 GC MS Hardware Operation Manual Pneumatics If the instrument is in External or Hybrid configuration the damping gas flow rate and Inlet Pressure are displayed Compa
77. if the corresponding instrument is connected and turned on you can create a Method section for it and format reports The list on the left shows all instrument modules that are currently installed and enabled in the 4000 GC MS Workstation The list on the right shows all instrument modules that are installed but not enabled To disable an instrument module select it from the top list and click Disable To enable an instrument module select it from the bottom list and click Enable Application Descriptions Ferform automated injections and r ecalculatians and monitor instrument status When this menu item is checked application descriptions are displayed when you move the mouse over application buttons in the Workstation Toolbar Small Buttons on Toolbar ie ES FY ed a Es ad SS l oad ES BY 2 zi rese svr s002 2 gt fa reproducibiity_oc P Click this to display small buttons on the Workstation Toolbar 14 Run Application This hierarchical menu item lists all applications showing on the Workstation Toolbar When you select an item from this list the corresponding application is launched Help on This hierarchical menu item lists all applications showing on the Workstation Toolbar When you select an item from this list the online help corresponding to the application is displayed Pick Data File for Quick Link Button This hierarchical menu item lists the eight most recently used Data Files in orde
78. ionization and how it is implemented in this instrument General Parameters Select Scan Time to adjust the seconds scan General Parameters The minimum of uScans to average and data rate will be automatically computed SetPoints C Scan Time Maxinnum Scan Time Multiplier Offset T volts f wScans Averaged b ucang Mass Defect Ta mmut 0y Data Rate 0 87 Hz 7 Select uScans Averaged to adjust the of Centroiding Parameters uScans to average The Maximum Scan Count Threshold 1 Time and data rate will be automatically computed Customize 110 SetPoints Scan Time 1 15 Seconds scan f uScans Averaged Minimum of uS cans Averaged Data Rate 0 87 Hz Scan Time uScans Averaged and Data Rate are linked The number of microscans averaged is updated when the scan time is adjusted and vice versa There is a trade off between how rapidly spectra are collected and the reproducibility of mass spectra or peak areas As more microscans are averaged the relative intensities of ions in the mass spectrum become more reproducible However one needs to keep in mind that collecting more data points across a chromatographic peak will improve peak area reproducibility on replicate injections Setting up to average three scans is a good recommendation to get good spectral quality along with an acceptable data rate The Mass Defect allows for a systematic correction of the difference between t
79. is disabled when N2 Argon is selected Filament Temp Limit C 390 or 490 C Automatic Filament Protection will limit filament temperature to this value during solvent peaks etc EFC Type None Type 13 Type 14 Type 16 Specifies the installed type Type 13 is a single channel EFC used with packed columns Type 14 is a dual channel EFC used with capillary columns and helium or nitrogen carrier Type 16 is a dual channel EFC used with capillary columns and hydrogen carrier Make up Flow mL min O to 50 mL min Ref Make up Flow O to 100 mL min mL min 305 TSD Detector Front Detector Middle Detector Rear Detector Middle Detector Type Tso Detector Oven On C Off Temperature C Bead Current jA 13 017 Add Heert Pelete Sant Make up Flow ml min H2 Flow mimin Air Flow ml min Adjustments Time Constant Slow Fast EFC Type Type 12 Item Description Detector Oven On or off Turns the detector oven on or off Temperature C 50 to 450 C Specifies the TSD temperature Bead Current 2 4 to 3 8 A Initial 0 00 to 999 99 min Autozero Yes or No Yes at initial time means that the TSD Autozero is on continuously before the run starts in EFC Type None or Type 12 for the TSD detector Make up Flow 0 to 50 mL min mL min H2 Flow mL min 0 to 6 0 mL min Air Flow mL min 0 to 200 mL min 306 ECD Detector Front Detecto
80. it can connect to any Workstation This Workstation will assign these settings to each 3800 GC Subnet Mask 255 0 0 0 Balewa 0 0 0 0 Domain unnamed Click on the Manage IP addresses from this Workstation checkbox to manage your GC s IP address from this Workstation As the GC is turned on its Ethernet address is added to the list The IP address is automatically generated Enter a host name for each GC This name is used to identify the GC in the Workstation You cannot connect to a GC until you provide it a name Click on OK when host names for each GC have been entered NOTE Proceed to Using a Password to Protect BOOTP Settings on page 90 Configuring the GC for a Company Network Use the following instructions if both a 3800 GC and Varian MS Workstation PC are being connected to a company network that is a multi purpose network used for services in addition to instrument control In this case a Network Administrator will be involved in assigning IP addresses If the GC and the Varian MS Workstation computer are the only devices being connected see Configuring the 3800 GC Communication No Company Network on page 83 85 You may connect virtually any number of 3800 and 3900 GCs and any number of Varian MS Workstation computers to a company Ethernet network Depending upon your network configuration all Varian MS Workstations will be able to control all 3800 and 3900 GCs on the network After you ha
81. lonization mode None can be used for other time segments as well NOTE For all data acquisition segments the lonization On box must be checked 108 Scan Type Group The scan type is either full scan or an ion preparation techniques The default is Full Full Full scan data for the selected mass range AMD Automated Method Development of MS MS conditions Up to ten voltages for collision assisted dissociation of the MS MS precursor ion can be tested on a single chromatographic peak using this feature Once the best dissociation condition has been identified it can be selected for MS MS MRM or MS MS MS MS MS or tandem mass spectrometry is the isolation of a precursor ion formed during ionization dissociation of the precursor ion by applying energy trapping and scanning the resulting product ions You can select multiple precursor ions MS This is multistage MS MS in which a product ion from one tandem MS experiment becomes the precursor ion for the next stage MS MS up to MS The practical analytical range of MS has not yet been evaluated at introduction of the 4000 MS system SIS Selected lon Storage allows selection of up to 6 ion ranges for monitoring lonization lorizatiars E The available ionization modes depend on instrument configuration Internal El and Cl offers either option External and Hybrid offer but one ionization mode for a given configuration choice Scan Mode Scan Mode
82. m Pneumatics m Pneumatics Pneumatics Damping Gas On Turn Off Flow Rate 4 0 mL min Flow Rate 4 0 mL min Inlet Pressure 84 PSI rm Getter Control Getter Control Getter Control Heater On Turn Off Temperature 400 C Temperature 441C Hide Keypad Event Messages 58 Status and Control Status and Control Conditions Analysis State Ready Vacuum System Statu Ready Preumatics Damping Gas On Turn Off l Getter Control Heater On Tum Off Conditions displays either Analysis or Shut Down State field is either Ready Shutting Down or Starting Up Conditions Shut Down State Shutting D omr Status and Control Conditions Start Up State Starting Up Vacuum System The vacuum system is either Not Ready or Ready The turbomolecular pump speed must be 100 for the Ready state to be reached Pneumatics If the instrument is in External or Hybrid configuration this field shows if auxiliary Helium damping gas is flowing to the ion trap Damping gas flow is required for adequate mass spectral resolution and sensitivity in External mode Although sensitivity is compound dependent a flow of 3 mL min is a suggested starting point and the flow rate is listed in the Current Set Points area This field does not appear when the instrument is in Internal configuration Getter Control When the instrument is in External or Hybrid configuration the getter re
83. mass spectrum This approach may improve library searches and reduce data file size at the cost of somewhat less detailed information in the mass spectra The count threshold is shown only if the Customize button is active lonization Control General Parameters lonization Control Internal CI F Automatic Gain Control Target TIC somo counts The default Target TIC for positive chemical ionization is 5000 The target can be set as high as 65 000 General Parameters lonization Control Internal EI F Automatic Gain Control Target TIC som counts lonization Time Fixed lonization Time lontzation Time oof Wseconds Max lon Time 25004 uiseconds When you click Customize you can run fixed ion time experiments with ion times as high as 65 000 usec or to change the Maximum lon Time for Cl Auto experiments You can turn on the Cl Gas and the ion trap in Manual Control and check the ion time in Cl Auto mode If this time is less than 1 000 usec lowering the Max lon Time may improve performance The closer the actual ionization time is to the Max lon time the closer the actual reaction time will be to the Max Reaction Time 116 Internal CI Parameters General Parameters lonization Control Intemal Cl Parameters Full Internal Cl Parameters Emission Current 0wa ump Reagent Parameters Reagent Methanol Save Reagent Low Mass z5 m z Reagent High Mass 50 mrz Set the emission cu
84. microscan Prescan Analytical Scan a Segments 1 4 High mass 7 RF End of Low Segment mass Variable lonization Time The AGC Scan Function Scan Segment Setup Period The prescan is followed by the first of the scan segments Each segment is divided into two parts a setup period and a scanning period Each setup period is subdivided into the following four stages First stage The RF voltage is set to near OV for 2 milliseconds This setting allows the RF voltage generator circuit to stabilize while clearing the trap cavity of all ions Second stage The RF voltage is set to and stabilizes at the storage voltage selected to store or trap all ions of interest in the ion trap cavity Third stage Energetic electrons from the heated filament are accelerated into the ion source to ionize sample molecules with subsequent transfer of these ions to the trap by a set of lenses The newly formed sample ions are then permitted to stabilize in their orbits at the storage voltage This stabilization period is referred to as the cool time The length of this period is fixed 201 Fourth stage The dynode and electron multiplier is made ready and the RF voltage is ramped quickly from the storage voltage to a value appropriate to begin the mass scanning of the segment Scan Segment Scanning Period During the scanning period the RF voltage is steadily increased causing ions of increasing m z to be ejected from the trap to be
85. miz Although there is a menu to allow you to choose from several CI reagents initial evaluation indicates that methane is the reagent of choice for chemical ionization when the instrument is in External configuration Reagent Parameters Reagent Gas Methane bd Acetonitrile Cl Background eee lzobutane Full Scan Parameters General Parameters lonization Control External Cl Parameters Full Scan Parameters Maze Range Low Mass sA miz High Mass 1000 4 mez Only the start and end mass for the acquisition range are entered in this tab dialog Do not use a start mass below 50 for External PCI with methane This causes reagent ions to be counted in the prescan and leads to ion times that are too short 124 Setting up the Method for DFTPP and BFB Tuning Tune Type Auto Y Sa abe 100 249 25 100 ea 250 450 35 100 4 45 1000 35 100 From the list select BFDB Tune or DFTPP Tune Doing this displays a segment table in which mass ranges and lon Time Factors have been suggested to meet US EPA tune requirements for determination of environmental contaminants BFB tune is used for volatiles analysis and DF TPP tune for semi volatiles analysis Here is the set of factors for BFB tune in External El mode Full Scan Parameters lon Time Factor 4 Low Mass High Mass RF Storage m z m z Level m z of 39 S0 39 100 39 100 35 100 To meet tune requirements
86. mode even if the active method is Internal Cl External Cl or one of the Hybrid Cl modes For the last two cases the Cl volume is automatically retracted from the external ionization source during most Auto Tune routines After doing major maintenance such as cleaning the ion trap or source or switching between internal and external ionization modes run all Auto Tune routines Some routines should be run after changing operating conditions such as trap temperature or helium buffer gas flow rate Specific routines may be run periodically as part of a system check a 4000 56 Not Ready Manual Control Auto Tune Temperatures Diagnostics Startup Shutdown Acquisition Control and Status Auto Tune Method Action Mass Calibration V Auto select prerequisite tuning functions Er O Integrator Zero J Electron Lens Tuning O Set Electron Multiplier CJ lon Lens Tuning IAF Full Scale Adjust Mass Calibration O Trap Frequency Calibration CO Trap DC Offset Voltage State Calibrating NORMAL Spectrum and Event Messages B i TEJE Scan Number 3 Time 0 032 min RIC 4378 lon Range 80 6 181 5 m z E Base Peak 129 8 Base Amount 986 lon 333 us Segment 1 Channel 1 kCounts 0 75 0 50 0 25 0 00 100 125 150 125 aoua Hands m z ited 15 16 37 39 QuickVerify Started Mar 15 16 37 39 QuickVerify Completed Mar 15 16 37 40 Mar 15 16 37 40 ear 15 16
87. needs to keep in mind that collecting more data points across a chromatographic peak will improve peak area reproducibility on replicate injections Set up to average three scans to get good spectral quality along with an acceptable data rate The Mass Defect allows for a systematic correction of the difference between the nominal mass of an ion and its exact mass Its importance arises from the fact that the NIST library reports molecular weights to the nearest integer mass unit only whereas the 4000 MS stores ion intensity pairs with a mass assignment to the nearest tenth of a mass unit For library searching ion masses are rounded to the nearest integer If the m z of an ion happens to fall close to the 0 5u crossover point it may be assigned to the wrong mass This is more likely for molecules with higher molecular weights since the mass defects for several atoms may add together to produce a sizable mass defect 115 The Multiplier Offset adjusts the EM voltage as much as 300V relative to the current multiplier setting in the Module Attributes tab dialog in Manual Control this is usually the 10 gain value from Auto Tune Sometimes better sensitivity is achieved particularly in techniques such as MS MS when the multiplier voltage is increased Note that this adjustment can be made on a segment by segment basis The Count Threshold is normally 1 count a value of 2 3 counts will reduce the number of low level ions reported in the
88. none 1 0 Standard Sample Same Sample Vial First Sample Vial Second Sample Vial Same Sample Vial en 1 Clean amp Dup w First Sample Vial Second Sample Vial i en 2 Clean amp Adv 10 0 i Add Lines Oo bu i Defaults 1 2 3 4 5 6 7 8 9 aib Begin Suspen When a 3800 GC controls an 8400 AutoSampler or 8410 Autolnjector the SampleList for that instrument contains the following device dependent fields Many of these SampleList fields are only shown and available for editing when the 8400 AutoSampler or 8410 Autolnjector is used in Duplicate Mode or Dual Mode Refer to the help on the generic SampleList Window for a description of the fields not listed below 266 2nd Sample Name Up to 19 characters Dual Mode operation i Sets the name of the second sample injected This column only is only displayed when the 2 Injection is Advance or Clean amp Adv 2nd Inject Notes Dual Up to 180 characters Mode operation only Opens the Notes window for the selected second sample to edit or create a note about the sample This column is only displayed when the 2 Injection is Advance or Clean amp Adv O through 99 for 8400 AutoSampler 1 through 21 for 8410 Autolnjector Sets the AutoSampler vial number of each sample in the SampleList When the 2nd Injection is Advance or Clean amp Adv two sequentially numbered vials will be shown The fir
89. on the channel s row then click on the Edit Standard Peak s push button If the peak table does not contain multiple internal standards these fields will be disabled Amount Standard 2 8 0 000001 to 1 000 000 Sets the amounts of the second through eighth internal standards Used to calibrate results for Internal Standard and Normalized Percent calculations involving multiple internal standards If the peak table does not contain multiple internal standards these fields will be disabled Add Adds a line to the end of the list Inset Adds a new row before the highlighted line Deletes the highlighted row in the list Edit Calibration Setup Opens the Calibration Setup Dialog Box to permit inspection and editing of the calibration parameters in the method for the indicated detector channel Edit Standard Peak s Opens the Peak Table Dialog Box to permit inspection and editing of the Standard Peak names in the method for the indicated detector channel Open the Peak Table and press OK to transfer the standard peak names and amounts from the Peak Table to the indicated detector channel row 320 Open Data File Dialog Box Open Data File Ei E4 O E Look ir E c_MsMs eE H i pg OFN 1 42 38 PM 1 12 2004 5M5 Fa WPTMOO2 SMS iH pg OFN 11 15 47 4M 1 12 2004 5M5 H 8 NPTMOO3 5M5 B Z pg OFN 1 22 59 PM 1 12 2004 5M5 B NPTMOD4 5M5 m 2 pg OFN 11 43 29 AM 1 12 2004 5M5 B NPTM SMS 1B N
90. only s is listed in the Data Files dialog the sample name will be as you entered it here Sample T ANPE TYPE There are several choices available from the Sample Type drop down list box Use the scroll bar to see all the options Sample Type Analysis Sample Type Baseline Print Calib New Calib Block Autolink Activate Method Print Summar by r 4 lJ 5 Calibration Vertication Baseline Print Calib New Calib Block Cal level if you designate the sample type as calibration you can designate which calibration level you are injecting You can enter up to ten levels In Specify here the number of injections of this sample You may make up to nine replicate injections at each calibration level 179 Injection Notes Enter notes about the sample Notes Revert Cancel AutoLink See the Specifying Data Handling Parameters section in this manual the sample The fields beginning with Amt Std are only used for data files acquired with standard GC detectors Inject the Sample using the Method Ic Walarn S Coltest External mth Browse Select the Method to use for the run Click the Browse key to select a file using Windows Explorer What the Buttons Do Add Adds a new line to the end of the list o net Inserts a new line before the currently active line _ Delete Deletes the currently active line ae ell When sections of columns or entire lines are highlighted the in
91. repeats e Once the m z value of the product ion is determined make the following calculation Product ion m z divided by 1 4 the highest CID RF excitation level For example if the product ion is m z 140 then the excitation storage level should be no higher than 100 to ensure good trapping efficiency of the product ion e Once the excitation storage level is set the only variable to optimize is the CID voltage This can be done with two injections using AMD The first injection can use voltage increments of 10 volts Non resonant or 0 2 volts Resonant The second injection uses smaller increments of the excitation amplitude near the optimal level The optimal excitation amplitude and excitation storage level are dependent on the compound and the analysis Optimal excitation amplitude may be such that the precursor ion has been completely dissociated and only the product ions are scanned or a small fraction of the precursor is still present and both precursor and product ions are scanned Determine the Voltage for Non Resonant Excitation AMD Follow these steps to determine the optimum voltage for non resonant excitation by using AMD while injecting the precursor compound len tans ppa Waveform Type pre pep Pe ia enp ea Ees sadi m z Level m z volts m z m 3 0 Non Resonant w 48 0 10 00 414 0 3 0 Non Resonant w 48 0 20 00 50 M 414 0 3 0 Non Resonant w 48 0 30 00 50 420 414
92. save changes to Methods Click on the button below to select the Method Select Method 187 tem Description Password for this application Allows you to specify a password required to enter the Security Administration application Note that there is no way to recover this password if it is lost so it is recommended that you document the password in a secure location Change Method Passwords Method passwords can be added changed and removed from the Security Administration application Click on the Select Method button to browse for and select the desired Method After the Method has been selected you are either prompted for a new password if no previous password exists for the Method or are prompted for the old and new password if the Method already contains a password Note that if creation of new passwords is disabled in the File Revision tab you will not be able to add a new password to a Method that does not already contain one Method passwords can also be added and changed in the Method Builder and Interactive Graphics applications Remove Method Passwords Method passwords can be removed by the Security Administration application without entering the existing password This is useful if the password for a Method has been lost Click on the Select Method button select the desired Method and the password is removed Application Locking MS Workstation k X Passwords pplication Locking F
93. settings for each of the ramp segments Each segment will ramp to the specified temperature at the specified rate assuming the rate is achievable and then hold the temperature for the specified time NOTE The Rate in the first row is always blank and cannot be edited The Total column cannot be edited either 1079 Split Ratio Front Injector Middle Injector Rear Injector Front Injector Type jiovg Injector Over f On C Off Injector Coolant C On Off Enable Coolant at C Split Ratio Coolant Timeout min 20 00 HA Pit matig Emp Emin O Add 20 00 147 If the 1079 Injector is connected to a Type 1 EFC press the Split Ratio button to build the Split Ratio Time Program NOTE You must have already configured the Type 1 EFC in the corresponding position in the Flow Pressure Section before you can program the Split Ratio Specifically to build a 1079 Split Ratio Program a Front 1079 must have a corresponding Front Type 1 EFC a Middle 1079 must have a corresponding Middle Type 1 EFC and a Rear 1079 must have a corresponding Rear Type 1 EFC Use the Split Ratio spreadsheet to build a Split Ratio Time Program to control the 1079 injector Type 1 EFC combination Split Ratio for Front 1079 Front Type 1 EFC Fa Initial On 0 01 Off Sort Column Oven End Time 20 00 min ce This is a typical program for a splitless injection A low split ratio conserves carrier g
94. system After each module connects to System Control configure it in an Instrument by moving its icon from the bottom of the Configuration Window into the Instrument Areas System Control will remember where to put the icon the next time that the system connects Place the 3800 GC icon in the AutoStart Module window if either a CP 8400 or CP 8410 AutoSampler will be used with the GC If a Combi PAL will be used for automation place the Combi PAL icon inside the AutoStart Module window If the 3800 will be operated without an AutoSampler controlled from the Varian MS Workstation leave the AutoStart Module box empty If you are using a sampling device with the 3800 the device must be connected to the synchronization port of the GC 94 a System Control Configuration File Edit Inject Subomation Recalculate Instrument Windows Help Majs nore a n gt Instrument 1 Varian 4000 GOMS Operator Jean Louis Ready Auto Start Module 3600 Fr 4000 m 44 bobs_mg 56 Available Modules Once the modules are in place you are ready to proceed Setting Instrument Parameters Some parameters used by the Instrument are set in the Instrument Parameters dialog box accessed from the Configuration window Instrument 1 Parameters Instrument MEERE Operator Heady File Max Errors 0 Prompt on Automation Start Cancel The instrument name appears in the instrument window Also note that the instrument and op
95. tee ee me eee 228 Manual Qo a io erreseina artes rer re ete en men ee eee eee 229 AUO TUNG sie sah as ai ae she a eh aa i cir aon a A eld Ci cat ea Lic ene a 234 Temperature S aminn a dans seats een ed aaese nace E E E wacbenem Baer eaeathce mae 239 DIAGMOSIICS eanissicsmstecntachneb idee sia ahoce eauaesecty as coee Ad nase ie bicamen a A RTA 241 ney fe 40 8 01 a 6 16 0 1 9 eee neler east te nee mene a eee erat eee ee ee a a ee eee ee 244 7016 18 51 06 a ener eee mance eo eh ee AE ee eee ee eee en eee 246 3800 GC System Control Command Reference cccceeseeceeseeeeeneeeeeseeeeeneeeeeneeeeaneeneanenees 249 Status and Control WWINGOW sscsstsescste st eet scare aoe eee eee ee ee 249 8400 8410 SampleList Window Extensions cccccccceeccceeceeceeeeeceeeeeaeeeecaeeeecaeeeeseeeeeseeeesseceesecesseueeeeseeeeseneessaees 266 4000 MS Method Builder Command Reference cccsssceceseeeceneeeeenseeeeneeseeseesenseesoaes 271 Wig C r Mt Eland Cl ecsorrscrann re ene E ere eee ee eee eee 272 3800 GC Method Command Reference ccssseccesseeessescesseeceseeeeeseesenseesenseesensessenseeses 283 51018 8 Say 2 W C ners a ier eaten erie nent cer ty Me tet ect EL Sen eae a eee er eee ee 283 3000 GC Sample DEVEN se a ee tee i eee en ee eer eee eee ee a eee 294 SOOO SS IMC CON asset vas tiian Seiwa etn E tania levee uated aaa a act al eam A AEAEE 294 8000 GC Fow Pressure iriran e nis aves ke ee ee 29
96. the filament and multiplier from damage by the solvent front during GC MS runs This disabling of the lonization can be used for other time segments as well NOTE For all data acquisition segments the lonization On box must be checked Scan Type This drop down menu has the seven Scan Types to choose from Full AMD MS MS MRM MS4n SIS and uSIS Selecting a scan type loads the default values for that Scan Type into the Parameters and Control tabs in the lower section lonization The available ionization options El and Cl depend on the Instrument Configuration Internal El and Cl offers either option on a segment by segment basis External and Hybrid require that all segments of the method be acquired by a selected ionization mode Scan Mode This drop down menu may have 1 or more options depending on which Scan Type and lonization type has been selected The available Scan Modes are Normal Fast and Fastest Setpoints The Setpoints button when clicked opens a Segment Setpoints dialog box with an option to turn the Calibrant On Choose this option to turn on the FC 43 calibration gas during an acquisition segment 2 3 item Description S General The General Parameters tab has editable fields which indicate the Parameters Tab Set Points you want to establish for that particular time segment The Set Point option default values vary depending on which Scan Type and lonization type you have selected There are fiv
97. the MS MS technique derives from the following e Optimally filling the ion trap with the selected precursor ion e Obtaining qualitative structural information about the sample by forming the product ion spectrum and e Increasing the signal to noise ratio by eliminating interfering matrix ions in the product ion spectrum through isolation and dissociation the only ions in the product ion mass spectrum originate from ions that fall into the isolation window The MS MS Scan Function Eject lt m Eject gt m Oe RF Voltage lt _ lt SOO lonization Isolation Dissociation Scanning MS MS Scan Function Analytical scan only 209 This section describes the four basic operations in 4000 MS lon Trap Tandem Mass Spectrometry MS MS e lon formation and matrix ion ejection e Precursor ion isolation e Product ion formation through collision induced dissociation e Product ion mass scanning lon Formation and Matrix lon Ejection lonization of the sample and any co eluting matrix occurs by electron or chemical ionization A notched waveform is applied to the end caps of the ion trap as described above to resonantly eject ions above and below the specified precursor ion mass Removal of most of the space charge from the trap improves mass resolution in subsequent MS MS steps The ions remaining in the trap include the optimum number of precursor ions along with any ions which fall into the coarse isolation window Precursor lon
98. the lowest mass product ion If for example a precursor ion of m z 403 dissociated to product ions with m z values of 350 200 and 131 you would not want to use a storage level value above 94 m z 131 1 4 94 Storage RF values are often reported in terms of the Mathieu q parameter in the scientific literature The value of the q parameter determines the stability of the precursor ion trajectory More stable trajectories allow higher excitation voltages to be applied before ions are ejected from the trap It has been empirically observed that a q value of 0 4 provides an optimum yield of product ions This calculator utility determines the corresponding CID storage RF value m z following user entry of the desired q value Excitation Amplitude in volts The amplitude range for non resonant excitation is O to 120 volts For resonant excitation the range is O to 60 volts The default values are 20 volts for the non resonant excitation method and 0 2 volts for the resonant excitation method NOTE If the excitation amplitude used is too large the precursor ion and product ion spectra will be absent because both ions will be ejected from the trap If the value is too small the precursor ion spectrum will be dominant and the product ion spectrum will be weak or missing Scanning the Product lons Product lon Start Mass m z Set the Product lon Start and End Masses to cover the mass range required
99. the mass offset increasing the default from 0 to 0 1 m z makes the isolation window on the low mass side of the precursor ion larger Decreasing the offset decreasing from the default O to 0 5 m z decreases the window on the low mass side The offset should be adjusted to minimize the amplitude of the adjacent masses below the precursor ion Initially adjust in 0 2 m z increments High Edge Offset The mass offset to optimize the ejection of the mass just above the precursor ion mass The High Edge Offset range is 0 5 m z to 0 5 m z The default value is 0 High Edge Offset affects the isolation window on the high mass side of the precursor ion Increasing the mass offset increasing the default from 0 to 0 1 m z makes the isolation window on the high mass side of the precursor ion larger Decreasing the offset decreasing from the default O to 0 1 m z decreases the window on the high mass side The offset should be adjusted to minimize the amplitude of the adjacent masses below the precursor ion Initially adjust in 0 2 m z increments If the Low or High Edge Offset range is not sufficient to completely isolate the desired ions either increase in the case of desired ions not being present or decrease in the case of unwanted ions being isolated the isolation window High Edge Amplitude Amplitude of broadband waveform used to eject masses above the isolated precursor ion Default value is 35 volts If loss of precursor ions due t
100. the pump current in mAmps and pump power in Watts The lon Gauge 242 area indicates the ion gauge pressure in uTorr and the status of the Filaments OK open broken The Foreline Pressure is indicated in mTorr Trap The Trap area in the Monitor Window is active only if the Multiplier Dynode checkbox has been selected in the Monitoring Tab top level The Trap Area if active indicates the Multiplier voltage and Dynode voltage in Volts Waveform System The Waveform System area is active when the user has chosen RF Control in the Monitoring Tab top area The percentages of the Entrance End Cap Trapping Field Dipole and Exit End Cap Trapping Field Dipole are indicated when the RF radio button is chosen underneath the RF Control checkbox The percentages of the Dipole Supplemental Waveform and Quadrupole Supplemental Waveform are indicated when the Waveform radio button is chosen underneath the RF Control checkbox Temperatures The Temperatures area indicates the temperatures of the Entrance End Cap Exit End Cap Manifold and Transferline in degrees C lon Source The lon Source Area indicates the values and status for the following components Emission current in Amps indicates the lon Source emission current Balance of the ion source in uAmps per second This is a proprietary diagnostic used by Varian to determine the quality of the ion source and for instrument tuning and troubleshooting Deviation of t
101. the sample ions The ionization and reaction storage RF can be set at the same level or different levels The View Reagent lons function can be used to tune the isolation of individual reagent ions Scanning lons to Collect Mass Spectra The scanning process for hybrid chemical ionization is similar to that for electron ionization After ionization trapping and ion preparation steps ions are scanned out to the conversion dynode and electron multiplier Mass scanning is implemented by increasing the RF voltage on the ring electrode the mass spectrum is collected in order from low to high mass over the user designated scan range In positive mode electrons are ejected from the conversion dynode held at 10000V and repelled to the electron multiplier In negative mode positive ions are ejected from the 10000V dynode and repelled toward the multiplier The signal is enhanced by 10 by the multiplier and sent through an integrator to collect an intensity for each m z MS data are stored as sets of ion intensity pairs for each m z over the acquired mass range A complete mass spectrum is stored for each analytical scan 207 208 lon Preparation Techniques MS MS Tandem Mass Spectrometry Overview MS MS is the isolation of a precursor ion formed by either El or Cl ionization dissociation of the precursor ion by energetic collisions with helium atoms and trapping and scanning of the resulting product ions The utility of
102. the stored mass range and fill the trap only with ions in the mass range s of interest The Internal configuration can have SIS MS MS MS and MRM as ion preparation options SIS is included with all instruments while MS MS MS and MRM are available when the MS MS option is installed Internal Positive Chemical lonization Chemical ionization Cl provides mass spectral data that complement electron ionization El data for the analysis of complex compounds The generation of ions in chemical ionization is a two step process A Cl reagent gas is introduced into the ion trap analyzer The reagent gas is ionized by El Then the sample molecules are ionized by ion molecule reactions with the reagent gas ions Cl is a softer ionization technique than El That is Cl imparts less energy to the sample molecules than does El Thus the ionized sample molecule undergoes less fragmentation and an ion indicative of the molecular weight is more likely to be observed In addition to molecular weight confirmation Cl mass spectra often provide other significant structural information that may not be available from El mass spectra Adjusting Cl Pressure 1 Connect a reservoir containing the chosen reagent liquid or gas to the Cl Gas inlet block using the correct restrictor Use the 50 mL min Cl restrictor for liquid CI reagents when you are in Internal configuration Open the Cl needle valve 6 7 turns counterclockwise Open the Cl gas valve s
103. to open the Import Method File dialog 3 Method Builder startup1_external mth C Fie Edit view window Help ea New Ctrl M SEN Thrl 0 L g Close Save Chrl 5 Save Os Import Method File Ei Look in E Varianiws e c EB Set Password Prompt For Action ak Startup Print Ctrl P ae 7 i Service E 26DNT_Hybrid_N20_AGT SOL i Print Preview 7 ieee SYSLOG EB Z6DNT _Hybrid_N20_AGC mtl i WSDataFiles EB 26DNT _Hybrid_N20_MSMS rr add Module Control TS ZEDNT MICI CI 35 mth FB 26DNT_Hybrid_N2O_MSMSNF Add Post run Processing FS 26DNT_Hybrid_N2c mth 25 _Ext_Cl mthi Fl Delete Section ES 26DNT_Hybrid_N2O_AGC 30K mth M 525_Ext_ELmth Import Section y 1 starktup1_external mth Coltest_External mth File name 525 E wt CI mth 3 startup 1 mth l 4 9081_OCLPests_ExtEI 1a mth Files of type Methods mth Cancel Recent Files gt Exit Select the source Method from which you will import Select the sections that you wish to import by clicking on them If you click on one section and the hold down the shift key while clicking on another section all of the sections in between will be selected Holding down the control key while clicking on a section adds that selection to those files already selected Clicking on a highlighted section while 101 holding down the control key will remove that section from the list of selected files Import Method S
104. to reach its peak for an RF storage level of about 45 50u If this were the only consideration in the process the default value in the Method Builder would be set at this value However in looking at the NIST library search results for a wide variety of compounds it is found that using a lower RF storage level of 35u as the default gives better search results Upon closer examination we found that fragile ions in the spectra of some compounds particularly ions at low mass can decompose due to energetic collisions with Helium buffer gas as they enter the ion trap from the external source Whereas the RF storage level of 35u has been chosen as default and reduces or eliminates decomposition during ion transport for most ions sometimes it is useful to use RF storage values as low as 20 30u in the lower mass segments to reduce these effects even further Link to NIST Database The NIST Chemistry Web Book contains a wealth of information on organic thermochemistry including the mass spectra found in the NIST 2002 Library e http webbook nist gov chemistry The subsection on Gas Phase lon Thermochemistry by Lias ands Bartmess gives a detailed explanation of the gas phase energetics relevant to mass spectrometry e http webbook nist gov chemistry ion External El Scan Function with Automatic Gain Control AGC In External El mode electrons emitted by a filament interact with sample molecules to form ions in the ion source where unimolec
105. voltage drops etc Fault Yes or No Cesta ttn FI sor comport ed FID Electronics On or Off Peer moy me AO etones engin toato metod Range 9 10 11 or 12 Displays the FID Range initial condition setting or the time programmed setting in the active method Time Const Fast 50 usec or Slow 200 usec Displays the electrometer time constant setting from the FID Adjustments in the active method 259 Displays in mV the actual FID detector signal at the 3800 GC Displays the data acquisition bunch size Displays the data acquisition bunch rate in Hz ECD Status tem Description S Fault Yes or No Displays if a fault in the ECD detector component has occurred ECD On or Off Range 1 or 10 facets Eco margesotna OO Time Const Fast 50 usec or Slow 200 usec Displays the electrometer time constant setting from the ECD Adjustments in the active method Signal Displays the data acquisition bunch size Displays the data acquisition bunch rate in Hz TSD Status Description Yes or No Fault Yes or No fe Gapan ataut n me Tsotsi me TSD Bead On or Off Range 9 10 11 or 12 S upan neces TSD Rano sota OO Time Const Fast 50 usec or Slow 200 usec Displays the electrometer time constant setting from the TSD Adjustments in the active method Bead Current 2 4 to 3 8 A or Off Displays the TSD Bead Current setting in the active method or Off if the Bead Power is off Displays in mV the actual T
106. waste cup before flushing with next cleaning solvent if more than one cleaning solvent source is specified LU WL T amp T T amp T TP amp TH ord amp UW amp Til Selects which solvent vial or sequence of solvent vials will be used to flush the syringe before and or after injection 285 Internal Standard Section nternal Standard Use Vial Volume uL Drawup Speed uLsec Pause Time sec Aur Gap Yes or No If Yes an internal standard addition will be used When internal standard addition is used the internal standard solution will be drawn up into the syringe from the specified solvent vial before the sample is drawn up Vial I Ul or Il Selects which solvent vial contains the internal standard Volume uL O to 99 uL with 100 uL syringe O to 9 0 uL with 10 uL syringe O to 4 9 uL with 5 uL syringe Specifies the amount of internal standard to be drawn into the syringe before it draws the sample Drawup Speed 1 to 100 uL sec with 100 uL syringe uL sec 0 1 to 50 0 uL sec with 10 uL syringe 0 1 to 25 0 uL sec with 5 uL syringe Specifies the speed at which the internal standard will be drawn up into the syringe Pause Time sec 0 to 9 9 seconds Specifies how long the syringe is to remain in the internal standard vial after drawing up the internal standard Yes or No If Yes a 1 uL of room air will be drawn into the syringe to create an air gap between the internal standard an
107. 0 This parameter is found in the main control section of the window Use the solvent depth parameter to determine whether the fiber is immersed in the Derivatization reagent solution or is exposed to reagent vapors in the headspace above the reagent 292 Prep ahead tem Description S Use Prep ahead Prep ahead Delay Sampling Yes No If prep ahead is used the AutoSampler will begin the sampling process after the prep ahead timer has expired This allows you to sample for extended lengths of time while the previous sample chromatogram is running without adversely affecting the throughput of your system The prep ahead timer starts after the Auto Sampler has finished all injection actions for the previous injection 0 to 999 99 minutes Adjust this time such that sample adsorption is complete just as the GC becomes Ready following the previous sample run tem Description Sample Depth Agitation Strokes Adsorb Time 0 to 100 Sample depth determines whether the sample is adsorbed from the liquid sample or from the headspace above the sample For liquid sampling carefully adjust the sample depth so that the fiber holder does not contact the sample liquid to prevent potential sample carryover 0 to 500000 If Headspace sampling is used no agitation is required so a value of 0 should be entered For liquid sampling agitation is generally desirable to speed adsorption of the sample Assume a
108. 0 1000 msec This parameter appears when you click on the Customize button This parameter checked true specifies whether the RF storage field is modulated during resonant CID This modulation greatly reduces any effect of changing secular frequency with concentration This parameter appears when you click on the Customize button This is the number of frequencies at which the CID excitation waveform is applied The default value is 1 frequency applied at the end caps A value of 3 generates three frequencies the resonance frequency and frequencies 500 Hz above and below that frequency Range 1 119 frequencies odd numbers only This parameter appears when you click on the Customize button For certain applications it may be desirable to offset the dissociation frequency The CID frequency can be adjusted between 10 kHz CID frequency offset can only be applied to a single frequency If the number of frequencies is greater than 1 this field is hidden Range 10 to 10 kHz The Defaults button is used to set the parameters of a method segment to their default values Generally any user modified mass values are preserved This parameter only appears in SIS Scan Type while in Customize mode The Target factor is also known as lon Time Factor When a scan is performed in Auto mode the prescan is followed by a scan of each segment needed to cover the Mass range designated to the left of the segment table The actual loniza
109. 0 to 450 C MARR Specifies the temperature at which to enable the coolant Coolant Timeout min 0 01 to 999 99 min Provides a safety measure to save coolant after the specified time if either the column fails to reach its set temperature or the GC does not go into run Stabilization Time min O to10 0 min Specifies the column Stabilization Time Adequate stabilization time will improve retention time precision in temperature programmed analyses Temp C 99 to 450 C Rate C min 0 01 to 100 0 C min The Rate in the first row is always blank and cannot be edited Hold min 0 01 to 999 99 min Total program time cannot exceed 999 99 minutes Total min 0 01 to 999 99 min Cannot be edited Column Oven End Time Total is displayed in all time programmed windows of the Method Add a line to the spreadsheet Insert Inserts a line above the currently selected row in the spreadsheet Deletes the currently selected row s in the spreadsheet 301 3800 GC Detector Front Detector Middle Detector Rear Detector Front Detector Type Fio Detector Oven On C Off Temperature C Electronics On C Off Add Heert Welete Sort Adjustments Time Constant Slow amp Fast EFC Type Type li Make up Flow rlin He lav miini Air Flaw ml min 300 0 Front Detector The 3800 GC can have up to three detectors installed front Middle Detector middle and rear
110. 0 Mass Spec Control click MS Method Editor The Parameters pane will now show the MS acquisition method iS Method Builder 4000 MS Ext Coltest mth File Edit view Window Help asums A B exel Sle 14 41 gt gt i ke SEn E3 4000 MS Ext Coltest mth Method Notes m Instrument Configuration Acquisition Data Type version Info External El 7 Centroid Profile 3800 GC Address 44 fi 3800 GC Control Chromatographic Time Segments a Autosampler aoa Sa Add a Sample Delivery Segment Description Scan Description feast T kea FIL MUL DELAY M 4 00 onization Of Delet Be a 4 00 18 00 El Auto Ful e i Column Oven Defaults al Detector Es Siar a Output Ea __Festore ai Data Acquisition Ea z 4000 Mass Spec Address 56 F 4000 Mass Spec Control Fa BMS Acquisition Method Method Segment IV Ionization On Scan Type Full 7 lonization eI 7 Scan Mode Normal 7 Setpoints Defaults General Parameters lonization Control External El Parameters Full Scan Parameters Mass Range r Tune Low Mass 50 m z Type Auto Save High Mass 350 m z Low Mass High Mass RF Storage lon Time m z m z Level m z Factor Customize Insert Add Delete 104 Setting a Full Screen Display Ela If you are going to do a thorough editing operation to click Hide Directory on the toolbar so that you can see the MS Method Editor full scr
111. 00 000 0 Standard GC Files Sets the amount of the first internal standard Used to calibrate results for Internal Standard and Normalized Percent calculations Not used by calibration samples MS files Sets an ISFactor which is used by Analysis and Verification samples It will be multiplied by the appropriate Compound Calibration Level Amount that is in the DH Method being used Note that internal standards in Analysis and Verification samples always use the amount that is specified in Calibration Level 1 317 Item Description MultiChannel None multiple specific channel MultiStandard G C files Opens the Data Handling Channels dialog box to specify the calibration parameters for up to four different Detector Channels MS files Not used by MS data handling These are GC detector channels which are different from the scan function channels that may be specified in the MS method d Add JAdds a line to the end of the RecalcList Insert Adds a new line before the highlighted line Deletes the highlighted line in the RecalcList d Fill Down Causes the contents of the top cell in a series of highlighted cells to be copied to the cells below it Used to edit all the cells in a column quickly Browse Opens the Open Data File dialog box to select a Data File to add to the RecalcList Shows the results report for the selected Data File Defaults Displays the Set Defaults dialog box allowing you to specify d
112. 00 56 Trap Frequency Tuning required Map 24151530 Module 4000 56 Some Auto Tunes not up to date 3800 44 Click to display the 3800 GC control screen a System Control Yarian 4000 GC MS Not Ready File Edit Inject Automation Recalculate Instrument Windows Help alala E 8081 _0CLPests_ExtEl mth gt ca SJEN pael sl So gt m Not Ready ap 3800 44 Ready Pals m 3800 Operation TempZones Set Actual Column Oven Status ils Mc SESE ae Ee A alg 7 ron ven Power On Coolant Bratis etuna p ls N res N A N A Setpoint 80C Actual 80 C Ready Method Rear 1079 Off 66 Stabilization Time 0 05 min Sain No Fault Heatable NZA N A Heatable2 N A N44 Enable Column Oven Coolant at 50 C Valves 1 2 3 4 5 6 7 Heatable3 N A N24 Timeout 20 00 min Timed Out No Hide Keypad View Setup Resu x Column Oven Status or m Intensity Normalization By lonization Time None Segment 2 Channel 1 104 4 Base Amount 1 _ 500 Acquired Range miz 7 25 4000 56 Click to display the 4000 MS control screen a Sysicm Control VarianWS 1 Not Ready Phe Coe met woms Recskulce Insrmart wid Iep Biss rez ah gt js alal Si pel late fro jl not Ready s 4000 01 Nol Heady Marusl Comal Aube Ture Tevesranass Disgrossce Sampl Smddema Scquisiocn Coevanl ved Stabe d
113. 00 usec May 21 16 07 34 EM voltage 1675 Y ion time 65000 usec May 21 16 07 34 Electron Multiplier gain is 3 71 May 21 16 07 34 Electron Multiplier voltage setting is 1675 May 21 16 07 34 Electron Multiplier Gain Adj completed May 21 16 07 34 9 rc May 21 16 07 34 Auto Tune Passed May 21 16 07 34 Electron Multiplier Voltage 1675 Pass May 21 16 07 34 Auto Tune Passed Before starting the EM gain algorithm the RF Full Scale is adjusted so that the cal gas ion at m z 502 is calibrated The Set Electron Multiplier method adjusts the multiplier voltage and ion time to look at low mass fragments from the unstable m z 502 ion The objective is to set the multiplier voltage such that each electron emitted by the dynode will create a known signal from the multiplier The gain in this example is 3 71 x 10 When the 10 gain voltage of your electron multiplier reaches 2000V you should order a new multiplier to have on hand When the10 gain voltage exceeds 2500V you should install a new multiplier Electron Lens Tuning In typical external ion sources electrons are continuously directed into an ion volume containing the sample to be ionized Eventually the interior surface of the ion volume becomes contaminated by material that can charge up and disturb the extraction of ions from the ion source To minimize ion volume contamination the 4000 MS pulses electrons into the ion volume only when needed for ionization Two p
114. 061 injectors are isothermal injectors Setpoint 50 to 450 C Displays the 1041 1061 injector oven programmed temperature setting in the active method Actual 50 to 450 C Displays the actual temperature of the 1041 1061 injector oven at the 3800 GC SPT Injector Status tem Description Ready Yes or No The SPT injector oven is Ready Yes if the setpoints have been achieved and stabilized Fault Yes or No Displays if a fault in the SPT injector component has occurred SPT Oven On or Off Displays if the SPT injector oven component is turned off or on at the 3800 GC Coolant On or Off Displays if the SPT injector oven coolant is enabled in the active method 256 tem Description Setpoint 99 to 450 C Displays the SPT injector oven programmed temperature setting in the active method Actual 99 to 450 C Displays the actual temperature of the SPT injector oven at the 3800 GC Enable SPT 30 C to 450 C Coolant at Displays the programmed injector oven temperature at which the SPT injector oven coolant is enabled Timeout 0 01 min to 999 99 min Displays the programmed coolant time out value in the active method for the SPT injector oven Timed Out Yes or No Displays Yes if the coolant time out period has elapsed for the SPT injector oven Type 1 Injector EFC Flow Pressure Status Item o Description Yes or No The Type 1 Injector EFC component is Ready Yes if the setpoints have
115. 079 Oven On or Off inal Displays if the 1079 injector oven component is turned off or on at the 3800 GC Coolant On or Off Displays if the 1079 injector oven coolant is enabled in the active method Setpoint 99 to 450 C Displays the 1079 injector oven programmed temperature setting in the active method Actual 99 to 450 C aan Displays the actual temperature of the 1079 injector oven at the 3800 GC Split State On or Off ee ety bce psc 107o metot 255 tem Description Split Ratio 1 to 10000 or Off Displays the current split ratio of the 1079 injector method The split ratio is defined as the Column Flow the Split Flow the Column Flow Enable 1079 30 C to 450 C Injector Cool Displays the programmed injector oven temperature at which the 1079 oolant at injector oven coolant is enabled Timeout 0 01 min to 999 99 min Displays the programmed coolant time out value in the active method for the 1079 injector oven Timed Out Yes or No Displays Yes if the coolant time out period has elapsed for the 1079 injector oven 1041 1061 Injector Status item o Description Ready Yes or No The 1041 1061 injector oven is Ready Yes if the setpoints have been achieved and stabilized Fault Yes or No Displays if a fault in the 1041 1061 injector component has occurred 1041 1061 On or Off Oven Displays if the 1041 1061 injector oven component is turned off or on at the 3800 GC The 1041 and 1
116. 13 15 04 Av intensity 0 433 Acceptable limits 0 300 to 0 500 May 20 13 15 05 Integrator zero Adjustment Completed May 20 13 15 05 j 4 933333 38 3 5 5 5 8 8 5 5 8 5 May 20 15 15 05 Auto Tune Passed May 20 13 15 05 Integrator zero Dac 354 FASS May 20 13 15 05 Auto Tune Passed The Integrator Zero Adjustment routine sets the signal level coming from the Integrator Circuitry with the filament off When the filament is off the major source of signal coming from this circuitry is electronic noise The Integrator zero is adjusted such that the average value of electronic noise is slightly greater than zero The acceptance range is between 0 3 and 0 5 counts The integrator 236 should then record signals only when ions actually strike the dynode and electrons emitted from the dynode strike the electron multiplier Set Electron Multiplier Hide Keypad Spectrum and Event Messages Al lAl l TT e om l lE l May 21 16 07 25 EM voltage 1400 ion time 65000 usec May 21 16 07 25 EM voltage 1500 ion time 10000 usec May 21 16 07 27 EM voltage 1500 ion time 65000 usec May 21 16 07 28 EM voltage 1525 VY ion time 65000 usec May 2l 16 07 29 EM voltage 1550 ion time 65000 usec May 21 16 07 30 EM voltage 1575 VY ion time 65000 usec May 21 16 07 31 EM voltage 1600 VY ion time 65000 usec May 21 16 07 32 EM voltage 1625 VY ion time 65000 usec May 21 16 07 33 EM voltage 1650 Y ion time 650
117. 400 AutoSampler Carrousel 8410 Autolnjector Carrousel tem Description Red fill Indicates vials listed in the active SampleList that have not yet been sampled or are missing Green fill Indicates the vial vials in Dual Mode currently being sampled Blue fill Indicates the vials in the active SampleList that have been sampled Action Description Displays the vial number for that position for 5 seconds Double click ona Opens the Inject Single Sample dialog box to inject a single sample vial position Displays the active SampleList if one is selected Double click Displays the active RecalcList if one is selected outside carrousel 269 270 4000 MS Method Builder Command Reference The Method Builder commands available to you depend on which Instrument Configuration you have selected In the following graphic the Instrument Configuration is External El E Method Builder 4000 MS Ext Coltest mth File Edit view Window Help Heusy ARB sexa S 2 fal 41 gt gt E 5 Sel 4000 MS Ext Coltest mth E3 Method Notes Instrument Configuration Acquisition Data Type AF 3800 GC Address 44 extemal El Centroid Profile 3800 GC Control sera a Autosampler Chromatographic Time Segments Sample Delivery E lt i a Injector Segment Description Scan Description Mi Flow Pressure 1 FIL MUL DELAY 4 00 lonization Off p o atiii 4 00 18 00 ___El Auto Full i Detector i Output EA i HF j Data Acquisition
118. 44 T wf No Revision History Fn S800 GC Control ee dl Selecting the file name at the top of the Directory displays method related information including name and directory path creation and modification dates file size file attributes and the revision history 100 Method Notes fg Method Builder startup i_external mth Bel jal gt pil ee El BSc The m ry default startup method oe E tema Configuration The micio and column are both net to 150C and Bre spit ic S51 to beep the GC clean Selecting Method Notes displays a blank Parameters pane Enter notes about the method as text You can enter any information you like about the method sample preparation laboratory practices etc It is possible to copy text from a Microsoft Word or Excel document and paste into the Method Notes however graphics images cannot be copied and pasted in this way Method Notes are printed when the Method is printed Instrument Modules Highlighting low level outline branches for the 3800 GC 4000 MS or Combi PAL those that cannot be expanded displays Parameter panes with editable parameters for controlling the instrument for data acquisition and for post run data processing and reporting Importing Method Sections You may wish to copy sections from one Method to another Open the target Method file This is the Method to which you want to Import one or more sections Use File Import Section
119. 6 7 Heatable3 N A NZA Ch 3 Air Set 300 4 Front FID 0 044 m Click on the module window to give it the focus Select Edit Module Info to display the Module Information Editor dialog B Module Information Editor C 5TAR MODULE45 HDF File Help Add Edit Delete Description 3800 GC in Evaluation Lab Serial Number 198 _P2 Date Installed January SO 1987 Injections 1234 Servise Last Service Date February 24 1987 Service Contract AB 123456 Add or edit sections and items in sections The injections value is updated for each injection Select Help for details on creating and editing module information Click Done to close the window Module information is copied into Data Files generated after injections and can be included in the Run Log portion of the results report 19 Configuring the GC MS System Starting System Control the First Time Before you enter System Control for the first time confirm that the proper instrument modules have been enabled and that any instrument modules that are not part of the system have been disabled To enable or disable instrument modules see the Workstation Toolbar section Enable Disable Instrument Modules on page 13 Configuring the Instrument Before beginning the configuration process you should know whether you will be attaching your Workstation and 3800 GC to a company network or to an isolated network only used for instrument control If you
120. 7 3800 GE GCOMIMM OVEN ties eee ede ates ela eer Salata deans sd Slaten eh as oes E ce vee 301 38000 GG Detector rrenen ere en rt ne een ee eee eee Te 302 SO00 NSC OUD UM tascam en E op acehiietacend eases a aahiat ara hanes 309 BO00 ASC Data ACQUISIHON ota wtccti eho ieee a a E E foes eel sccens ea emus 310 Automation File Editor Command Reference c cscsccceseseeeseesseeeeenseeeeenseeseenseeseeseeesons 311 VTLS ia hen ete ate es ae Nir ae cea Ec ts eA a er ein a i ee las 311 M n il oo f gegen terete rere E ee ee ee ee eae 312 Open Automaton File Dialog BOX sigasictas tis cect hs atin dances ad oe ncaa eek een raion ce eee eae 313 Save Automation File AS Dialog BON sisi ctiies ce ccpec atthe dS avian ctcs a T id detest vale cao Saeco ei gatacseade 314 Pint Setup Dialog BOX secman iy eater intr tei tee a emcee Tce ee eee eee ere ae 315 Edit Notes Dialog BOX etsia aimee een en hance tian mts eam eee 315 PROCAIGEISE VVINGOW cst stab cetera hola ales E heim cence bet asl y Wonk uel areal td chee im a eee ace eid Manel 316 SampleList Window SequenceList Window Getting Started This manual shows you how to acquire data build methods and operate the Varian 4000 GC MS using the Varian MS Workstation The manual also describes the configuration of the 3800 GC for standard Ethernet communication with the 4000 MS and MS Workstation s System Control application Use this manual with the other manuals supplied with your MS Workstat
121. Auto Tune Temperatures Diagnostics Status And Control Ei Run Time 0 00 minutes Start Acquisition See ee ine SampleList 1200cat smp End Time 10 00 minutes E dit Method SE RecalcList CL MSM rel Ready SC Instrument 1 Status 2 No Fault Wait For Readyln Message Log w 4000 01 Ready Hide Keypad Spectrum and Chromatogram 3800 44 Equilibrating Show Module Opens the Status and Control windows for all the modules in Windows the Instrument It is disabled when all the windows are open even if some are hidden under others Iconize Module Iconizes the Status and Control windows for all the modules in Windows the Instrument It is disabled when all the windows are iconized Show Automation Displays the windows for all the automation files open in the Windows Instrument It is disabled when all the automation windows are open even if some are hidden under others Iconize Automation Iconizes the windows for all the automation files in the Windows Instrument It is disabled when all the windows are iconized Arrange Icons Arranges the icons if any in a row at the bottom of the System Control window SequenceList Opens the window for the selected file or moves it to the front Used to display the open SequenceList SampleList or RecalcList SampleList RecalcList Instrument Status Displays the corresponding window for the instrument or moves it to the front Used to see the instrument status Messa
122. C and a Rear 1177 must have a corresponding Rear Type 1 EFC Use the Split Ratio spreadsheet to build a Split Ratio time program to control the 1177 injector Type 1 EFC combination Split Ratio for Front 1177 Front Type 1 EFC Fa Initial On 0 01 Off Column Oven End Time 20 00 min ce This is a typical program for a splitless injection A low Split Ratio conserves carrier gas while keeping contaminants from building up in the injector The injector is kept splitless for about 1 minute so that all analytes injected can focus on the column A Split Ratio of 100 after injection flushes residual solvent from the injector 149 The first row of the spreadsheet contains the Initial Split State and Split Ratio for the 1177 injector The 1177 will equilibrate to this setting when the method is activated and will be restored to this setting when each chromatographic run is completed Rows after the first row contain the time programmed settings for the 1177 Split Ratio The Split Valve switches to the ratio at the indicated time Flow Pressure Window The Flow Pressure window contains up to three Electronic Flow Control EFC Programs Front Middle Rear Only Type 1 and Type 5 EFC modules can be configured on the 4000 GC MS system Type 5 EFC is used for applications like purge and trap or static headspace sample introduction gS Method Builder Method1 OF x J Eile Edit View Window Help 1 x alealea ek
123. Chro Anes Spectra Reports Spectra Plots Spectra Colors Report Header IY Show Spectra Header Report Features IM Show Spectrum lon Intensity Pairs IY Show Spectra Comparison IY Show Difference Spectrum IM Show Difference lon Intensity Pairs Thick Line General Preferences Miscellaneous Scientific Notation Information List Fonts Decimal Digits for File Data Display fh Number of lon Decimal Digits Greek Characters in NIST Names 7 Use Greek Characters Otherwise they are spelled alpha Plots in Chromatogram Window V Auto Select Channels Rounding Mass to Integer Shift foo daltons 0 to 0 4 Help Reset to Defaults Reset All to Defaults Cancel 31 Spectrum Toolbar The Spectrum display can be viewed when the 4000 MS module is in Manual Control Auto Tune or Acquisition modes The Spectrum Toolbar appears in the upper left The toolbar functions are as follows 4 lo a ad we ai A Click the Arrow to hide the toolbar Click in the upper left of the display to restore the toolbar pct Click Full Scale to normalize the chromatogram vertically and horizontally Double clicking in the lower left corner of the display has the same effect Click Previous Scale to return the chromatogram display to the last scaling before the current one If you have zoomed the chromatogram twice to view smaller time intensity ranges this button steps you back through the previous scales 5 Click Spec
124. Create a New Automation File dialog box to name a new file of the selected type A sub menu displays RecalcList SampleList and Sequence Selecting one of them displays the Open an Automation File dialog box to open an existing automation file of the selected type Save Saves the currently displayed automation file with the existing name Save As Displays the Save Automation File As dialog box allowing you to save the currently displayed automation file with a new name Prints the currently displayed automation file Printer Setup Opens the Printer Setup Select a printer and set options You can open the Print Setup dialog box from the Printer Setup dialog box Exit Quits the Automation File Editor If any file is open and changes have not been saved you will be prompted to do so Edit Menu Menu ttem Description S Cut Deletes a selection and copies it to the Clipboard Used to remove or move a selected part of a spreadsheet Copy Copies a selection to the Clipboard Used to duplicate a selection and place the duplicate in a new place using Paste Paste Inserts previously cut or copied information that was stored in the Clipboard into a spreadsheet Deletes a selection but leaves the Clipboard unchanged 311 Main Toolbar Menu Item Description o Fill Down Causes the contents of the top cell in a series of added or existing highlighted cells to be copied to the cells below it Used to edit all the cells in a column
125. Description Temp C 50 to 450 C Split Ratio If the appropriate EFC type has been configured displays the Split Ratio dialog box Split Ratio Dialog Box This dialog is displayed from the 3800 GC Injector window when a 1079 or 1177 injector is configured with type 1 EFC 296 Split Ratio for Middle 1079 Middle Type 1 EFC Initial On 0 00 OFF Column Oven End Time 20 00 min car Time 0 00 to 999 99 minutes Split State On Off If the split state is ON then the sample is split according to the split ratio specified If the split state is OFF then all the sample enters the column Split Ratio Off 1 to 10 000 Use a split ratio of 100 after injection to vent the injector Use a very low split ratio after flushing to conserve carrier gas Adds a line to the spreadsheet Inserts a line above the currently selected row in the spreadsheet Deletes the currently selected row s in the spreadsheet Sorts the spreadsheet rows by time tem Description S 3800 GC Flow Pressure Electronic Flow Control EFC Front EFC Middle EFC Rear EFC Front EFC Tye tem Description Front EFC The 3800 GC can have up to three injector EFC modules installed Middle EEC front middle and rear The tabs at the top of the window select the EFC position Rear EFC EFC Type None Type 1 for 1079 1177 injectors Type 4 for valved systems Specifies the type of EFC installed in the selected position
126. Extraction SPME Sampling Mode Adsorb Time min Autosampler s400 Desorb Time min Agitation Strokes sample Depth 2 Injection Mode SPME made solvent Depth 22 Clean Mode Fre Inj Solvent Strokes Post In solvent Strokes Clean solvent source fi H Adsorb Time mint Desorb Time mint Dernyvatization Positiar II Adzorb Time min Use Prep Shead peg Prep Ahead Delay min Column Oven End Time 19 75 min SPME mode is designed to use the special Solid Phase Micro Extraction fibers and fiber holder Note that you cannot select the SPME Sampling mode from the CP 3800 keypad In order to configure the system to use SPME you must set a switch on the syringe sled to the correct position and install the special SPME fiber holder block This process of setting up the system to use SPME was adopted to avoid unintentional damage to either SPME hardware or syringes SPME mode actions are summarized below Clean Mode caution Do not use the clean mode actions unless you have experience with SPME or have very dirty samples with insoluble materials that need to be removed Indiscriminate use of cleaning can introduce contaminants into your analytical run and degrade your results 291 tem Deseription Pre Injection 0 to 99 Solvent Strokes The number of pre injection solvent clean flushes specified in the method will be performed by dipping the fiber into the solvent and waiting
127. FILMUL DELAY FA Ep Splitter Bar deng C Tip I Catiann Gasp Method Scan Function Channel I lintase l ta Actas aunn Mumbec T FILAMLIL DELAY F Cycle bra 1 9 R Haje Kevon Spectrum z Ceros The 4000 MS Icon The ion trap icon is displayed on the left side of the 4000 MS Keypad If the icon text is red the ion trap is disabled This is because the current Active Method segment is a filament multiplier delay segment one with an ionization mode of None The ion trap is also disabled if there is an instrument Fault Changing the Active Method Segment to 2 changes the trap status to enabled and the color of the icon text changes to black If the icon is not currently disabled clicking in the center of the ion trap turns on the trap The icon text will turn green to denote that the ion trap is on 36 MULTIPLIER 7 You can independently turn On or Off the RF Multiplier and lon Source Filament by clicking the appropriate icon Quick Control Toolbar Below the trap icon are selections for turning on the Trap the lon Gauge and the flow of either Calibration Gas or Cl Gas lv Trap Calibration Gas lon Gauge Cl Gas Hide Keypad Spectrum When the trap is turned on the active method segment must have an ionization method other than None a mass spectrum appears in the spectrum display Scanning g5 5 3 126 463 183 225 253 25 23 16 32 42 42 28 If the Calibration Gas is turned on i
128. Fault No Fault No Fault green light or Fault red light indicator When a hazardous or disabling fault occurs any run in progress will halt and the affected component will shut down If the fault is recoverable then the run is not terminated Valves Displays the 3800 GC valve status A plus sign precedes the valve number if its state is energized A minus sign precedes the valve number if the valve is in the default state or if the valve is unused Start If the system is Ready starts the GC Method and sends a start signal to the GC Equivalent to pressing Start on the front panel of the GC The Start button is disabled unless the 3800 GC is in the Ready state Reset Resets the GC advancing it to the next state If it is RUNNING the GC aborts the current run goes to the READY state and continues with the next injection in the Sequence Equivalent to pressing Stop on the front panel of the GC Method Opens the Method Builder application for editing the active 3800 GC method 250 Temperature Zones Status Display Temp ones Set Actual D Col Over Ay OF D Front 1079 mO 50 D Mid 1079 AU 50 D Rear 1079 FO 50 D Front TCD AU A D Mid FID KO 50 D Rear ECD AO 50 The temperature zones status display is in the middle portion of the 3800 Status and Control window The display includes the setpoints and actual temperatures of the column oven the three coolable zones and the three heatable only z
129. Front Split On split 260 260 Valve 5 Front Split On split Off 61 Valve 6 Front Split On split NA NA Valve 7 Front Split On split Start Reset Runtime 0 00 min EndTime 4 00 min ajaj 156 When you click on this button Method Builder is opened with the active Method loaded and the corresponding Instrument Module selected You can then edit that section or any other section of the Method as described previously Once you have edited the Method and closed the Method Builder window you are prompted to reactivate the Method Reactivating the Method downloads the changes to the Module System Control Fa 3 Module 3800 44 Method has changed Reacthyate it 157 158 Acquiring GC MS Data Injecting a Single Sample Overview If you are doing method development or are just looking at one sample you may prefer to acquire data one sample at a time If you want to run multiple samples automation using a SampleList is the most efficient route If the 3800 GC and 4000 MS are configured and a GC MS Method has been built for data acquisition you are ready to acquire data with either of these approaches If this has not been done please see the previous sections for instructions Using the Inject Single Sample Dialog Box You can inject a single sample from System Control by using the Inject Single Sample dialog box a System Control Yarian 4000 GC MS5
130. GC Files Sets the amount of the first internal standard Used to calibrate results for Internal Standard and Normalized Percent calculations Not used by calibration samples MS files Sets an ISFactor which is used by Analysis and Verification samples It will be multiplied by the appropriate Compound Calibration Level Amount that is in the DH Method being used Note that internal standards in Analysis and Verification samples always use the amount that is specified in Calibration Level 1 none multiple specific channel GC files Opens the Data Handling Channels dialog box to specify the calibration parameters for up to four different Detector Channels MS files Not used by MS data handling These are GC detector channels which are different from the scan function channels that may be specified in the MS method Adds a line to the end of the SampleList Adds a new line before the highlighted line Deletes the highlighted line in the SampleList Fill Down Add Lines Causes the contents of the top cell in a series of highlighted cells to be copied to the cells below it Used to edit all the cells in a column quickly Displays the Add Lines dialog box allowing you to specify the number of lines to either insert or append to the spreadsheet along with the values to use for each applicable field Certain fields such as Sample ID and vial number can be automatically incremented Defaults Displays the Set Defaults dialog
131. Isolation The precursor ions are then isolated from any remaining matrix ions in a two step process The first step ejects the ions with masses below the precursor ion mass by ramping the RF amplitude while applying the supplemental waveforms to the end cap electrodes This step resonantly ejects all ions having masses up to and including the mass just below the precursor ion mass The supplemental waveforms are then turned off In the second step a broadband waveform WEF 2 is applied to the trap to simultaneously eject all masses above the precursor ion mass Isolation occurs at elevated RF levels where mass resolution is optimal Thus it is possible to achieve unit mass isolation over the entire mass range of the ion trap which may be useful in isolating a single mass in an isotopic cluster or in separating the precursor ion from interfering matrix ions Product lon Formation Product ions are formed from the precursor ions by collision induced dissociation CID The precursor ions constantly undergo collisions with helium gas in the ion trap Normally these collisions involve relatively small energies but if the translational energy of the precursor ion is increased the collisions may convert the translational kinetic energy into internal vibrational energy If the precursor ion acquires enough vibrational energy one or more chemical bonds in the ion may be broken forming ions of lower m z than the original precursor ion The i
132. MS Data Review Seine LSS winzip t Quick Start y Rg Security F h Search Standard M5 Reports Help System Control ug Workstation Toolbar Run Custom MS Reports Elements of the Workstation Toolbar Application Buttons give immediate access to the selected application You can display them as large buttons Z A a Fal i resp svesooa A react 0 EJEJE om P oe plil ce a 7 Ey ai nes eae or as small buttons ie ES ed ad Es ad SS l od ES BE 2 si resp svr s002 2 gt fa repraducibilty_o Tooltips show the application name when the cursor rests on the Application Button Quick Link Buttons provide menu selections of operations to be performed on the listed file Application Descriptions give brief descriptions of the application that will be opened when the cursor rests on the Application Button Application Buttons System Control IFSA Monitor instrument status and perform automated injections and batch Automation recalculations View and edit instrument operation data acquisition and data handling methods ae Do off line editing of SampleLists RecalcLists and SequenceLists Review Process MS Data mmr Review chromatograms and spectra perform library searches and review a and process quantitation results a Create edit and view standard MS reports SMS MS File Conversion Convert data files between DOS and Windows formats Generate standard reports for a group of
133. NOTICE Varian Inc was acquired by Agilent Technologies in May 2010 This document Is provided as a courtesy but is no longer kept current and thus will contain historical references to Varian For more information go to www agilent com chem Varian Inc 2 00 Mitchell Drive Walnut Creek CA 94598 1675 USA ie Agilent Technologies 4000 GC MS Version 6 software Operation Manual Printed in U S A 03 914999 00 Rev 8 Varian Inc 2004 2009 Trademark Acknowledgments Microsoft Windows Windows 98 Second Edition Windows NT 4 0 Windows 2000 Professional and Windows XP Professional are registered trademarks of Microsoft Corporation DemoShield and InstallShield are registered trademarks of InstallShield Corporation Acrobat Reader Copyright 1984 2009 Adobe Systems Incorporated All rights reserved Adobe and Acrobat are trademarks of Adobe Systems Incorporated which may be registered in certain jurisdictions Other brand and product names are trademarks or registered trademarks of their respective owners Contents Getting vol i La s Bearer eer enene rena aera en EE EEEE Ea ire neater ert ian tne ry EE enn art nner a haere sate merece eae ne eer iene a 5 Additional MantalS GIO xihsesse its tonne a a ton d detest a a 5 WOrk Station POO ID Al sitece tere teteesn tei a E eet 7 OVEM 2 aan oa aoe rt Se Ee A dO Rn MR A S 7 Elements of the Workstation Toolbar ccccccccseccccesceccesceceececees
134. Network Neighborhood icon should appear on your Windows desktop 76 NOTE For the following procedure the use of disks other than the ones that were used for the original Windows installation may result in an Ethernet driver version mismatch that keeps Windows from starting Should this occur it may be necessary to remove the Ethernet Board from the computer to remove the incorrect Ethernet drivers To Configure your computer s network settings to communicate with the 3800 GC do the following 1 Run the Control Panel by selecting it from the Start menu under Control Panel or Settings 2 Double click the Network icon J Control Panel OF x File Edit View Help a Control Panel amp Bjel xal safi zala 6 Accessibility Options SS Add New Hardware RG Date Time E Display ll Fonts QB Internet y Mail and Fax GA Microsoft Mail Postoffice 2 Multimedia T Passwords 3 Regional Settings 4 Sounds W Varian Star Configures network hardware and software YW 3 If TCP IP is already listed in the list of network components skip to the Note after step 6 otherwise click Add Hetwork 7 Configuration Identification Access Contral The following network components are installed m Client for Microsoft Networks m Client for Netware Networks Som EtherLink ISA 30509 3C509b in 154 mode IPH SP compatible Frotocol NetBEUI Add Remove Properties Primary Netw
135. PTMO01 SMs gt Filename i pg OFN 11 18 47 AM 1 12 2004 SMS Files of type Data Files run sme m3 Cancel Result Information hannel A Recalc D ate 1 12 2004 11 33 AM Peak Measurement Aea Calculation Type Percent O0 Detected Peaks 0 Compounds OK Rejected Peaks 0 Missing 0 Failed Identified Peaks D TICs 34 Unknowns Run Information Fila S a Sample TpoOFN Inject D ate pazzo 1118 AM OOOO Run Time 0 000 14 685 min Workstations fo a Instrument Maian MSI Module 4000 56 4 4 2 Aun Mode Analysis tem Description Look in Lists the available folders and files To see how the current folder fits in the hierarchy on your computer click the down arrow To see what is inside a folder click it The box above shows the folders and files in the selected location You can also double click a folder or file in that box to open it To open the folder one level higher click the up arrow button on the toolbar File list Lists the folders and files in the selected location To see what s inside a folder double click it You can also use the Look In box to see the hierarchy of folders To open the folder one level higher click the up arrow button on the toolbar Shows the currently selected file Files of type Restricts the list of files to only those matching the selected type Run Information Shows information about the currently selected file Result Shows in
136. Properties The TCP IP properties dialog box is displayed TCPAIP Properties 19 2 Enter an IP address in the range 10 2 128 1 through 10 255 255 254 Note that if you are adding more than one Workstation to this network each Workstation PC must have a unique IP address within this range The Subnet Mask is automatically set to 255 0 0 0 Do not change this value TCP IP Properties Px Bindings Advanced DHS Configuration Gateway WINS Configuration IP Address An F address can be automatically assigned to this computer IF your network does not automatically assign IP addresses ask your network administrator for an address and then type it in the space below Obtain an IP address automatically is Specify an IF address IP Address 1 2 126 1 SubmetMask 1255 0 0 0 Cancel Ensure that no entries have been made in your Gateway and that Domain Name Server DNS and WINS Configuration have been disabled These entries are not used in an isolated network They may cause problems if they are present Delete any settings that may have been entered from a previous configuration 3 Click OK in the Network dialog box You will need to reboot Windows for the changes to take effect NOTE See Communication Problems in the Diagnostic and Troubleshooting section for information about diagnostic tools to verify that your network installation is correct 80 Configuring TCP IP Parameters for a Company Network
137. QUENCE ewe ee Erit Printer Setup Exit Either choose a New RecalcList or Open an existing RecalcList from the File menu i Automation File Editor File Edt Help Ale S 4 e eB The RecalcList window for the open RecalcList is displayed It contains most of the same fields contained in the SampleList Where the SampleList may contain AutoSampler and sample specific data handling information the RecalcList contains the Data File name and data file specific data handling information The fields that are common to both the RecalcList and the SampleList are described in the sections following the creation of the SampleList ey ES m ay Nd 9 Jz 4000 580315 gt Fcottest_external mt gt 333 Automation File Editor Pesticide rcl File Edit Help Q s Mls S selem Pesticide rcl RecalcList Xx SE SE Eee New Calib Block Insert Ea c varianws data version_631 pesticide_linearity flow_5ml pest_2nq_5ml_1 sm Pest_2nq_5ml Calibration 21 none Es c varianws data version_631 pesticide_linearity flow_5ml pest_1nq_5ml_1 sm Pest_1ng_5ml Calibration none EA c warianws data version_631 pesticide_linearity flow_5ml pest_500pgq_5ml_1 Pest_500pg_5ml ibrati none 5 c varianws data version_631 pesticide_linearity flow_Sml pest_200pq_5ml_1 Pest_200pq_5ml ibrati none 6l c varianws data version_631 pesticide_linearity flow_5Sml pest_100pq_5ml_1 Pest_100pg_5ml ibrati none c warianws dat
138. RecalcLists rcl Cancel Recent Files gt NOTE You may process a RecalcList either in System Control or in MS Data Review In MS Data Review use the menu command Quantitation Process Review RecalcList to access this feature Also note that processing of a RecalcList takes more time when done from System Control but has the advantage of allowing AutoLink functions including automated reporting with templates such as EnviroPro ToxProPlus and Multicompound Reports New SequenceList Open the dialog box to create a Sequence list Open SequenceList Select and activate an existing Sequence list The SequenceList dialog box is shown below Open a System Control Sequence File Look in Varianws e ce EE Co 500 M5 Methods 3 40005ys Examples 9 Service io SOOMSMethods Autotune logs Manuals 5 SL0G CO 12005ervice 3 ChromExamples methods System 2 1200sys data 3 MSGLoG 3 UserPML 4000 data xyz M5 Tutorials C UserPMLSave 4000S5ervice debug satsys 3 WSDataFiles lt ii Edit Menu Click Edit and select Edit Module Info ic System Control Varian 4000 Gt Inject Automation Recalculat Cue Chris J shift Del Copy Cr f Chrl Ins Paste Cr f Shift Ins Clear Del Add Insert Ins Select All Chrl 4 Ctrl Enter Fill Down Edit Motes Edit Module Info Each module 3800 GC 4000 MS or Combi PAL AutoSampler has a message log and documentation screen Use Mod
139. S can provide library searchable El spectra However because the isolation waveform is applied at a low q value unit mass isolation is not possible across the mass range Space charge control in the SIS mode is achieved by using the results from an AGC prescan to calculate the ionization time for each analytical scan Each SIS segment uses its own prescan collecting ions only from the range specified in that segment The stored spectrum is the sum of the individual spectra from each individual scan segment NOTE Because each SIS segment has its own prescan and analytical ionization time the reported ion time for each analytical scan can only reflect a subset of the ion time data The reported ion time is the shortest ion time among the set of SIS segment ion times This allows users to identify situations where overloading may distort mass spectra Distortion is likely when the ion time becomes very short approaching the minimum ion time of 10 usec Segment 1 Segment 2 cc SE S a TT Prescan 1 Analytical Scan 1 Prescan 2 Analytical Scan 2 End of RF Low Segment Variable Mass lonization Time SIS Scan Function 214 During the SIS scan the following steps occur e The prescan measures the number of ions within the specified scan segment and calculates an ionization time for the associated analytical scan segment e The selected range of ions is stored in the ion trap e The SIS mass spectrum is acquired
140. SD detector signal at the 3800 GC Signal Displays the data acquisition bunch size Displays the data acquisition bunch rate in Hz 260 PFPD Status Yes or No Displays if a fault in the PFPD detector component has occurred PFPD Electronics On or Off rene nant PEPD ecto saing mt ac mehed Range 8 9 or 10 a APDRae soe Square Root Mode On or Off Displays the PFPD Square Root Mode setting in the active method Type 11 Detector EFC Status tem Description S Type 11 Displays the Detector EFC type Detector EFC Type 11 has 3 channels and is used for FID detector gas control Fault Yes or No Displays if a fault in the Detector EFC component has occurred Ch 1 Make up Set Displays in mL min the programmed and actual channel 1 Actual flow rate Ch 2 H2 Set Actual Displays in mL min the programmed and actual channel 2 flow rate Ch 3 Air Set Actual Displays in mL min the programmed and actual channel 3 flow rate Type 12 Detector EFC Status tem Description Type 12 Displays the Detector EFC type Detector EFC Type 12 has 3 channels and is used for TSD detector gas control Ch 1 Make up Set Displays in mL min the programmed and actual channel 1 Actual flow rate Ch 2 H2 Set Actual Displays in mL min the programmed and actual channel 2 flow rate Ch 3 Air Set Actual Displays in mL min the programmed and actual channel 3 flow rate 261 Type 13 Detec
141. Storage Level is the value of the smallest mass stored in the ion trap during the reaction period The Reaction Storage Level is typically set to a value that is lower than the mass of the reagent ion of interest The optimum Reaction Storage Level will depend on the molecular ion of the analyte Generally you should use higher Reaction Storage levels for higher molecular ions without raising the storage level to cause ejection of Cl reagent ions For example the molecular ion of the analyte is 352 m z Using acetonitrile raising the RF storage level to 25 m z may give better sensitivity than the default of 19 m z If the Cl storage level is raised the Ejection amplitude will have to be increased Range 10 150 m z full range 2 6 tem Description S Ejection Amplitude Ejection Amplitude V is a voltage that corresponds to a low mass ejection cutoff that is slightly higher than the Reagent High Mass This voltage actively ejects unwanted ions i e not reagent ions that are produced during ionization Generally higher CI storage values require higher ejection voltages The voltage should not be set so high as to cause the ejection of CI reagent ions The Ejection amplitude is applied at the end of the ionization time to eject unwanted high mass EIl artifact ions The default value for each reagent usually does not need adjustment Range 0 59 volts Max Reaction Maximum Reaction Time is the maximum time that reagent gas
142. Temperatues OK Source OK Defaults lon Gouge Pressure O 0uTor F11 Valid T General Parameters Ionization Control Irtemal E Parameters Full Scan Parameters rap Mass Range Tune Low hlass E Epes mz Type Auto zi Save m Low Mass High Mass RF Storage lon Time High Mass 10002 m m 2 m z Level m z Factor 2 a S S mulipker y Customize Insert Add Delete 5 pe ie Method Segment Active Method Segment Scan Function Channels 9 FM fon Gauge TT Activate 7 Number TS FILMUL DELAY f Chern Hide Keypad Spectrum x _Changes nases z a N Access most of the 4000 MS functions through Control and Status The various functions are organized into six tabs Manual Control Interactive adjustment of all the method parameters of the currently active method The Checks and Adjustments tab allows adjustment of Cl gas and Cal gas flow RF ramp and a check of air water levels The Module Attributes tab permits the selection of filament 1 or 2 and the setting of electron multiplier voltage and Trap Damping Gas Flow External mode Auto Tune Run the built in tuning routines of the 4000 MS Temperatures Set trap manifold and transfer line temperatures for normal operation and for Bakeout and set the timer for the Bakeout period Diagnostics allows the user to run built in diagnostic routines to assess the state of the vacuum system and electronics Startup
143. The precursor ion is the desired ion m z that will be isolated in the MS MS isolation step This Precursor lon m z value is used in both Resonant and Non Resonant Methods of MS MS For more info please review the previous table titled Maximum Isolation Window as a Function of Precursor Mass 134 lonization Storage Level The m z value at which the RF is maintained during ionization and the coarse isolation step The range is 30 to 160 m z with a default value of 35 m z Isolation Isolation Window m z The full mass isolation window range is 1 0 to 14 0 m z The actual range is dependent on the precursor ion The default value is 3 0 m z Integral and fractional mass isolation window values are both accepted If an isolation window smaller than 1 5 m z is used then the exact mass of the precursor ion should be entered in the Precursor lon Mass field If the Low or High Edge Offset range is not sufficient to completely isolate the desired ions either increase in the case of desired ions not being present or decrease in the case of unwanted ions being isolated the Isolation Window value Low Edge Offset The mass offset to optimize the ejection of the mass just below the precursor ion mass The Low Edge Offset range is 0 5 m z to 0 5 m z The default value is 0 Low Edge Offset affects the isolation window on the low mass side of the precursor ion Increasing the mass offset increasing the default from 0 to 0 1 m z makes the i
144. The tabs at the top of the window select the detector position None FID TCD TSD ECD PFPD Specifies the type of detector installed in the selected position On or off Rear Detector Turns the detector oven in the selected position on or off On or off Temperature C 50 to 450 C Displays the Methanizer dialog box for the selected position Click on the following detector types for a description of the parameters that appear when the detector is selected 302 FID Detector Front Detector Middle Detector Rear Detector Front Detector Type Fio Detector Oven On C Off Temperature C Electronics On C of Adjustments Time Constant Slow Fast EFC Type Type1 1 Make up Flow rml mirn H2 Flow ml min Air Flows ml min On or off Turns the detector oven on or off On or Off Indicates whether the installed FID will be used or not Electronics must be ON to enable the ignitor Initial 0 0 to 999 99 min Range 9 10 11 12 Autozero Yes or No Yes at initial time means that the FID Autozero is ON continuously before the run starts Adds a line to the spreadsheet Inserts a line above the currently selected row in the spreadsheet 0 to 50 mL min mL min H2 Flow mL min 0 to 50 mL min 303 tem Description Air Flow mL min O to 500 mL min Methanizer Oven On or Off Temperature C 50 to 450 C TCD Detector Front Detector Middle
145. You can open the Print Setup dialog box from the Star Printer Setup dialog box The Varian MS Workstation only uses the printer for instrument 1 Remember Last When checked upon startup System Control will restore the Open Files active Method and any automation files that were open when System Control was last closed Closes System Control If System Control is in the process of performing a critical operation you may be prompted before the application is closed Edit Menu File Inject Automation sil Dii Siiner BIS Eopy En Aline Paste Shitty re Hear me Lt Co leer le Fit Select ll fet Ferber Er a Fall ayer fd co Edit Hotes Edit Module Info These commands are for use with SequenceLists SampleLists and RecalcLists Menuttem Description S Deletes a selection and copies it to the Clipboard Used to remove or move a selected part of a spreadsheet or entered text Copies a selection to the Clipboard Used to duplicate a selection and place the duplicate in a new place using Paste Inserts previously cut or copied information that was stored in the Clipboard into a spreadsheet Deletes a selection but leaves the Clipboard unchanged 218 Menuttem Description S o Add Adds a new line in a SequenceList SampleList or RecalcList Inserts a new line in a SequenceList SampleList or RecalcList Select All Selects all lines ina SequenceList SampleList or RecalcList Fill Down Causes the conten
146. Zero tune Then perform the Electron Multiplier tune Now go back to the Cal Gas adjustment to set the pressure Repeat this until the Cal Gas and Electron Multiplier settings stabilize 40 Method Segment Checks and Adjustments Module Attributes Cal Gas Adjustment He alae Last Set Date 1 5 2004 9 39 AM iF Ramp Adjustment Result OK Ionization Time 474 Total Ion Count 6370 Cancel Acton Adjusting Adjustment Results The calibration gas pressure i OF Allow time for the gas to flow and the emission curent to equilibrate Active Method Segment Scan Function Channels Mass Data Type r Intensity Horm Activate 5 F Cud j C Centroid C By lonizatio Ehanges Restore Number M Cycle Channel Profile 0 None Base Peak 69 Base lon 465 us Segment 1 z gpz 131 421 a 119 105 49 T 100 125 2 CI Gas Adjustment Assure that the appropriate CI reagent is plumbed into the CI gas inlet in the rear of the 4000 MS or contained in the Liquid CI reagent vial Choose the CI Reagent to adjust from the Parameters Reagent menu Then adjust the flow using the CI Gas valve inside the front door labeled with numeral 3 Turn the valve clockwise to increase the flow or counterclockwise to decrease the flow The readback in the Adjustment Results field identify when the flow is OK Method Active Segment Checks and Adjustments Module Attributes J Gas Ariustme CI Gas Adustment La
147. a method from those already prepared This will set the conditions for the GC MS AutoSampler and data handling Other sections will also be activated if they are part of the method Upload Active Method from Modules Get the conditions from the existing modules to be saved in a new or existing method This method becomes the active method with the conditions of the active modules New SampleList Open the dialog box to create a sample list Open SampleList Select and activate an existing sample list The sample list dialog box is shown below Open a System Control SampleList File x Look ir Varianws c Eg B 500 M5 Methods 9 40005ys Examples D SOOMSMethads 9 Autotune Logs 3 Manuals O 12005ervice Cd ChromExamples methods 2 1200sys data S Ms6Log 4000 data xyz M5 Tutorials 40005ervice debug 3 satsys New RecalcList Open the dialog box to create a Recalculation list Open RecalcList Select and activate an existing Recalculation list Open a System Control RecalcList File oot Vainws SY eR oo 500 M5 Methods 40005ys Examples 3 Service io SoOMSMethods Autotune logs Manuals 3 5 5L0G i 12005ervice ChromExamples methods System ian 1200sys data 3 MSGLoG 3 UserPML iy 4000 data xyz 3 M5Tutorials C UserPMLSave co 40005ervice 3 debug 2 satsys 3 WSDataFiles lt i 2 File name Fire Files of type
148. a version_631 pesticide_linearity flow_5ml pest_50pq_5ml_1 sr Pest_50pq_5ml ibrati none 8 c varianws data version_631 pesticide_linearity flow_5ml pest_20pq_5ml_1 sr Pest_20pq_5ml ibrati none 9 c varianws data version_631 pesticide_linearity flow_5Sml pest_10pq_5ml_1 st Pest_10pq_5ml Calibration none Delete Fill Down Defaults Browse Report Actions _ 176 Recalc Notes Enter notes about the Recalculation of the Data File AutoLink Enter post calculation operations to be performed Fiepott Press the Report button to generate a report for the currently selected data file Note that if a data file is not highlighted in the Data File column no report will be generated MS Report Sample Report for pest_20pg_5ml_1i sms Page 1 of 9 Fife ES File View Preferences Options Window Help oo 4D 2 e 8 i E pest 200_ gt ocene K Sample Report for pest_20pg_5ml_1 sms Page 1 of 9 For Help press F1 NUM Wy Actions lf a report was generated with the Report button clicking on the Actions button shows a selection of actions that may be done BENE View Edit MS Chromatogram Frink Custom MS Report Print Standard MS Report View Custom MS Report View Standard MS Report 177 Creating or Editing a SampleList sa Automation File Editor em Edit Help Recast Open d SampleList jave SEQUENCE ewe ee Erit Printer Setup
149. addresses which are unique to each communication card installed in each 3800 and 3900 GC along with the IP addresses that are to be assigned to the corresponding device You may obtain the Ethernet address for each GC from the GC s front panel or the label on the Ethernet card within the 3800 GC Turn on the 3800 GC and press any key to allow it to start in local mode The Ethernet address will be automatically loaded into the BOOTP Server list for 3800 and 3900 GCs PAGE CURSOR START STOP NOT READY READY RUN TABLE EDIT NEW DELETE CLEAR LINE LINE TABLE METHOD ACTIVATE EDIT MENU ENTRY HELP UNDO AUTOMATION SINGLE METHOD SELECT METHOD SEQUENCE EDIT GC CONTROL INSTRUMENT SAMPLE FLOW PRIORY SAMPLE DELIVERY INJECTOR PRESSURE STATUS SETUP COLUMN SUSPEND RESUME OVEN DETECTOR OUTPUT MENU INCR DECR ENTER When the GC has completed its initialization process press the menu button 89 The Instrument menu is displayed Press 1 to select the Remote Local Control screen The Ethernet address IP address and Alias which may not yet be assigned are displayed ACTIVE EDIT METHOD METHOD Method 1 Method 1 REMOTE LOCAL CONTROL Ethernet Address XX XX XX XX XX XX IP Address XXX XXX XX XXX Alias 3800A Use the Ethernet address shown here when setting up the BOOTP Server The IP Address and Alias host name are assigned by the BOOTP Server If the BOOTP Server that you are using automatically updates its table w
150. age voltage This stabilization period is referred to as the cool time The length of this period is fixed Fourth stage The dynode and electron multiplier are made ready and the RF voltage is ramped quickly from the storage voltage to a value appropriate to begin the mass scanning of the segment Scan Segment Scanning Period During the scanning period the RF voltage is steadily increased causing ions of increasing m z to be ejected from the trap to be detected by the dynode and electron multiplier The AGC software automatically selects an ionization time from 10 usec to 65 usec for each of the scan segments of the microscan depending on the amount of analyte in the ion trap and the tuning parameters An estimate of the number of ions formed in the ion trap is provided by a prescan with a varying ionization period 10 to 2500 usec For low levels e g for baseline or small GC peaks the maximum ionization time of 65 milliseconds is selected which offers maximum sensitivity As the amount of analyte increases the ionization time is decreased automatically in order to prevent overloading of the ion trap with ions The ion signals in each microscan are scaled automatically to compensate for the variation in ionization time Microscans may be averaged to improve the spectral quality To optimize trapping of the ions of interest a notched waveform is applied during ionization for internal El mode For external El amp external Cl mode
151. akeout Trap Temperature 150 C Trap Temperature OL Ne edie Manifold Temperature B C Manifold Temperature OC cal Wires CL es Transfer Line Temperature 170 aa C Transterline Temperature OC Save Restore 239 Analysis Temperature setpoints entered in the Analysis dialog will be executed at all times when the instrument is not in Bakeout mode It is recommended that temperatures be allowed to stabilize for 2 to 3 hours in Analysis mode before tuning or acquiring data Trap Temperature A temperature between 50 and 250 C may be entered The default is 150 C It is recommended that the trap be operated at the lowest temperature consistent with proper chromatographic performance typically about 50 C less than the maximum column temperature employed Manifold Temperature A temperature between 0 and 120 C may be entered However a setpoint near or below the ambient temperature will not be achieved as there is no cooling available for the manifold The default setpoint is 35 C Manifold heating is used primarily for Bakeout Transfer Line Temperature A temperature between 0 and 350 C may be entered However a setpoint near or below the ambient temperature will not be achieved as there is no cooling available for the transfer line The default setpoint is 170 C The transfer line should not be heated above the maximum operating temperature of the capillary column installed in the GC Save Restore
152. alel Demonstration b gt e NEN PB ftl fl seal gt or by clicking on the New or Open Automation File button on the toolbar a The Sequence window for the open Sequence is displayed SequenceList Pilot_9 seq Iof Xx Action Method Sample RecalcList Inject c star 3800 1 mth c star pilotS_507 smp c star c1 4 cl 78 3800 44 1 8 98001 I c star 2reli smp Click Add to add lines to Sequence List You may enter any number of Sequence lines Choose the action to be done in that step of the Sequence from the drop down box Browse for a Method and SampleList file in the active cells Press Begin to start the automation Automation File Editor Overview The Automation File Editor is used for creating and editing SampleLists RecalcLists and SequenceLists outside of the Varian MS Workstation System Control application The off line Automation File Editor allows access to these files without disrupting automated runs that may be occurring in System Control NOTE SampleLists and Sequences that are active and running in System Control cannot be accessed simultaneously in the off line Automation File Editor Accessing the Automation File Editor Sh ny 1 Click on the Automation File Editor icon on the Workstation Toolbar ee The Automation File Editor is displayed 175 Creating or Editing a RecalcList sai Automation File Editor Edt Help d RecalcList SampleList SE
153. andard addition volume and air gaps volume specified in the active method on the 3800 exceed the syringe volume a 3800 hardware fault will occur This will cause the Star Workstation to halt automation and reset the 3800 After changing the method settings and or the injection volume to reduce the total below the installed syringe volume shown in the 3800 setup screen you should begin the SampleList at the selected line to bypass the samples that have already been run Injectors Used Pos 1 Pos 2 1 then 2 or 2 then 1 Selects the 8400 Injection position to be used for the sample If the 8400 is not configured for both injection positions entering the wrong position will cause the sample 267 line to be skipped and a Bad Injector message entered into the message log To run samples in Duplicate Mode or Dual Mode you must select either 1 then 2 or 2 then 1 2nd Injection Duplicate Advance Clean amp Dup or Clean amp Adv Duplicate Mode or Dual Specifies the action that the 8400 will take before making Mode operation only the second injection during a run If you choose Duplicate or Clean amp Dup the same sample will be used for both injections This is called Duplicate Mode If you choose Advance or Clean amp Adv the 8400 will advance to the next vial location and will sample the vial if any that is there for the second sample injection This is called Dual Mode
154. anges cccccsssccccsesecceesececceusceecseseeecseseecseaseeeesageeecseueesssusseeessegeseesenseeesas 70 3800 GC System Control WiINKOW ccccecccccseeeeeceeeeeeecseeeeeeaeeeeeeeeeeeeseeeeesseaeeeeseaeeeessaeeesseeseesseaseeeeseeeeesaeeeeesaneees 70 Configuring the GC MS System cccccssscccceseeeccesseecceeseeecseeeecseuseeeseaeeessageeeceseeeseseeessageeessuaseeessgseesssugeesssageees 76 Building GC MS MethodS sannnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn nnmnnn nnmnnn nnne 97 Using Star Assistant to Create a New Method cccccccsescecceeseeeceeseeeceeneeeceeaseeeseuseeessageeseeaseessssseeeesegeeessegeeeeees 97 Method Bulder VV ING OW 26 toe feces ni vesditercnt seid in n Ta a a aa aa eerste eee 99 4000 MSHS TAOS SCHON ie octetaan nd tusee Syeacase a bana eae a a a a 104 38000 GC MEMO SCHON sce misses cect coeacetcshctsces code a S A emia teakcs 145 Acquiring GC MS Data aa ae saa wc eh eatcs sere em news eas en aoe cancer meneame cc nawemeianeuennmataneneies 159 IN ECUNG asinge Sample iiae a a a a r 159 jecting Multiple Sample Sisiane a ar cede ase oreaehd sultan Gabateebe auleabageumewakdeuleveeacenban 167 AULOMALNON RING EONON ristenn salecedinlasecatiacassusaal teddies a nbhotads selec a a a a EEA 175 Automated MS Report Generation sis s2e bsiccs aus bcceielsnti aise agetences odes ahadceles be cauedeen deus neces wheeedehneeevhdewlteaseuaehd 185 Securty CLAMS Uc ON oie
155. any existing segment of the active method for review or modification under Manual Control Existing segments cannot be deleted nor can additional segments be added through Manual Control 229 Scan Function Channels Some of the 4000 MS methods are broken up into multiple channels The channels can be thought of as a subset of a segment where the scan conditions can be different than in other channels These are most frequently used in the case of MS n MRM etc In Manual Control there is the ability to continuously scan a single channel or to rotate through all of them sequentially as happens in the acquisition mode Mass Data Type Centroid data is the default acquisition type as data handling library searching and spectral comparison can be done from this type of data Profile data is typically used mainly for diagnostic purposes Profile files are also approximately 10 times larger but can be converted to centroid format after acquisition Intensity Normalization Click UNI to turn normalization on or off When it is on the intensities are normalized by the ionization time The normalization is different for El and Cl Intensities collected under CI conditions are multiplied by the square of the ion time ratio Intensities collected under El conditions are multiplied by the ion time ratio The ion time ratio is the maximum ion time specified divided by the actual ionization time for that scan segment Method The M
156. are electron lens ON and OFF voltages and Repeller lens ON and OFF voltages ON and OFF refer to ionization ON and OFF The electron lens ON voltage is set to optimize electron transmission to the ion volume electron lens OFF voltage is set to thoroughly exclude electrons from the ion volume The Repeller Lens ON and OFF voltages balance the emission current Electron Repeller Lens Adjustment Electron lens tuning involves measuring the transient behavior of the emission current immediately after the lenses have been switched on or off If the lenses are unbalanced the emission current will change in time and be proportional to the imbalance If the balance is outside the range of 200 to 300 pA the algorithm will search the optimal values by changing values of four variables one at a time If it fails to find the best voltage setting for lens tuning auto tune will generate an error message and restore the last values in the instrument 48 When the Electron Lens Tuning Box is clicked an additional Turn on Cl gas flow during tune option appears For Cl methods in External or Hybrid mode the Electron Repeller lens must be tuned with the Cl plunger CI volume in place and the Cl gas turned on The user should adjust the Cl gas flow in Manual Control before this tune function is done lon Lens Tuning The lon Lens system consists of three lenses Lens 1 2 amp 3 These lenses are tuned using Cal Gas ions at m z 131 and 414 Optimum v
157. as while keeping contaminants from building up in the injector The injector is kept splitless for about 1 minute so that all analytes injected can focus on the column A split ratio of 100 after injection flushes residual solvent from the injector The first row of the spreadsheet contains the Initial Split State and Split Ratio for the 1079 injector The 1079 will equilibrate to this setting when the method is activated and will be restored to this setting when each chromatographic run is completed Rows after the first row of the spreadsheet contain the time programmed settings for the 1079 Split Ratio The Split Valve will be switched to the ratio in each row at the indicated time 148 1177 Injector If you indicate that an 1177 Injector is installed an Injector Oven Power switch a Temperature setting and a Split Ratio button are displayed Click On or Off to use the oven Front Injector Middle Injector Rear Injector Front Injector Type 1177 Injector Over On C Off Temperature C Set the desired Temperature If Type 1 EFC is used press Split Ratio to build a Split Ratio Time Program NOTE The Type 1 EFC in the corresponding position in the Flow Pressure Section must be configured before you can program the Split Ratio Specifically to build an 1177 Split Ratio Program a Front 1177 must have a corresponding Front Type 1 EFC a Middle 1177 must have a corresponding Middle Type 1 EF
158. aseline of the chromatogram is not reduced below the maximum ion time the ion trap is not being filled with ions to the level designated by the Target TIC One can do three things in Internal El mode to increase the ion signal 1 raise the emission current 2 raise the multiplier voltage 3 increase the Maximum lon Time If the third approach is used and you are collecting data for quantitation make sure that enough data points are collected across the chromatographic peaks for reliable quantitation At least five but preferably seven or more data points are needed for good quantitative data Remember that using Fast Data Rate may allow the use of higher Maximum lon Times without compromising quantitative data quality Internal El Parameters jeneral Parameters lonization Control Internal El Parameters Internal El Parameters E mission Current amps The emission current is the current of electrons produced by the filament and it controls the number of electrons that enter the trap It is a good rule for full scan data acquisition to adjust the emission current so that the AGC ion time of the baseline is approximately the maximum ion time By doing this the system will have its maximum dynamic range The number of ions stored in baseline scans will require the Maximum lon Time and the AGC lon Time will be cut back for any chromatographic peaks In El MS MS where the MS MS isolation step eliminates 112 the higher chemical
159. atio Add lnsert Delete Column Oven End Time 20 00 min tem Description S Injector Coolant On or Off Turns the coolant valve on when the injector is cooling down The Coolant valve will not be used if the Off position is selected Enable Coolant at C 30 to 450 C Specifies the temperature at which the coolant valve turns on Coolant Timeout min 0 01 to 999 99 min Disables coolant flow to save coolant after the specified time if either the injector fails to reach its set temperature or the GC does not go into run Split Ratio If the appropriate EFC type has been configured displays the Split Ratio dialog box 295 mem pesen oOo Temp C 99 to 450 C Rate C min 1 to 200 C min The Rate in the first row is always blank and cannot be edited Hold min 0 01 to 999 99 min Total program time cannot exceed 999 99 minutes Total min 0 01 to 999 99 min Calculated from the injector temperature program Cannot be edited Add Adds a line to the spreadsheet Insert Inserts a line above the currently selected row in the spreadsheet Deletes the currently selected row s in the spreadsheet 1177 Injector Front Injector Middle Injector Rear Injector Middle Injector Type 177 Injector Oven On C Off Temperature C Split Ratio for Middle 1177 Middle Type 1 EFC 0 00 Off 1 00 On Column Oven End Time 20 00 min cca tem
160. ation times entered Range Internal El 10 65 000 microseconds Range Internal PCI 10 2 500 microseconds Changing the Max lonization time can improve the sensitivity of techniques such as MS MS or SIS This parameter can be increased to 65 milliseconds for Internal El If the ion time in the baseline of the chromatogram is not reduced below the maximum ion time the ion trap is not being filled with ions to the level designated by the Target TIC You can do three things in Internal El mode to increase the ion signal 1 raise the emission current 2 raise the multiplier voltage and 3 increase the Maximum lonization Time If the third approach is used and you are collecting data for quantitation make sure that enough data points are collected across the chromatographic peaks for reliable quantitation At least five bur preferably seven or more data points are needed for good quantitative data Remember that using Fast Data Rate may allow the use of higher Maximum lonization Times without compromising quantitative data quality When the Customize button is clicked in Cl ionization mode you will have the option to run fixed ion time experiments with ion times as high as 2500microseconds or to change the Maximum lon Time for Cl Auto experiments You can turn on the Cl Gas and the ion trap in Manual Control and check the ion time in Cl Auto mode If this time is less than 1 000 microseconds lowering the Max lon Time may improve perf
161. aveform is applied is called the excitation time The first method involves non resonant excitation In this approach a low frequency supplemental dipole field is applied to the end caps of the trap resulting in an instantaneous change in the potential energy of the ion in the trapping field The restoring force of the trapping field converts the newly increased potential energy of the ion into increased translational kinetic energy A portion of this kinetic energy is then converted into internal vibrational energy upon subsequent collisions This process is repeated during each oscillation cycle of the low frequency dipole field An advantage of using non resonant excitation is that it is not critical to match the applied dipole frequency to that of the ion Consequently electronic drift space charge effects and sample concentration do not affect the method This results in reproducible product ion spectra This method is often useful with precursor ions that fragment by the breakage of a single weak chemical bond to form highly stable ions containing functional groups that do not undergo significant rearrangements A disadvantage of the method is that it is not selective with respect to excitation of ions in the trap Therefore the method cannot be selectively tuned to excite only ions having a particular m z The method is also less useful with precursor ions in which multiple chemical bonds are broken and with precursor ions that undergo c
162. ay in Time Segment 1 before the instrument is turned on to collect data in Segment 2 This protects the system during the elution of the sample solvent front However for more complicated analyses such as GC MS MS on multiple analytes you can define up to 250 time segments for a single analysis The maximum run time is 650 minutes Chromatographic Time Segments Segment Description iE Add Scan Description r a a ES Insert 0 00 3 00 lonizatian Off Delete 3 00 10 00 El Auto Full 1 FILMUL DELAY Ea i Highlight rows by clicking on the row numbers on the left side of the segment table e Add adds a new segment with the same MS parameters of the last segment in the table except for the segment description e Insert inserts a new row before the currently selected row with the same parameter values e Delete delete the currently selected row e Default button inserts system default parameters to the current segment e Restore restores current segment parameters that were present when the method was first opened or last saved 107 You can enter a segment description of up to 60 characters into the Segment Description field for each segment Enter the desired time in minutes in the Start and End Times fields The Scan Description field is entered automatically based on the choice of Scan Type and Ionization mode in t
163. box allowing you to specify default values for each applicable field in the SampleList 323 Item Description S Data Files Opens the Data File Generation dialog box to specify the naming scheme being used for Data Files generated from injections Note that if the method contains both MS and standard GC DH method sections then both sms and run files will be generated RecalcList Opens the RecalcList Generation dialog box to specify the options for generating or updating RecalcLists after injections Note that if the method used contains both MS and standard GC DH sections then the generated Recalc List will contain both sms and run files Select SampleList Section Type Dialog Box Please select a SampleList Section Type 6200 Autos ampler 8200 Stand lone Autos ampler 8400 45 on 3900 S400 Autos ampler 8410 45 on 3900 6470 Autos ampler Combi FAL Autos ampler Cancel A SampleList File may contain multiple SampleList Sections Each installed AutoSampler can contribute its own unique type of section having special features that correspond to its special hardware Generally each installed AutoSampler has its own unique SampleList with special columns for its features A SampleList File can contain a section for each type of AutoSampler similar to the way that a Method file can contain a section for each type of Instrument Module This dialog box lets you pick the specific section that you want to edi
164. ch mass ranges and lon Time Factors have been suggested to meet the US EPA tune requirements for determination of environmental contaminants BFB tune is used for volatiles analysis and DFTPP tune for semi volatile analyses Following is the set of factors for DFTPP Tune 113 Method Segment I lonization On Scan Type Full v lonization Scan Mode Normal General Parameters lonization Control Internal El Parameters Full Scan Parameters Mass Range Tune Low Mass 50 m z Type elma Save m Low Mass High Mass RF Storage lon Time High Mass 1000 2 mz Wai Level mte Factoria Customize Insert Add Delete DF TPP Tune Parameters To meet DF TPP tune requirements use these parameters as a starting point and check the relative ratios of ions in the spectrum of DF TPP compared to the requirements of the particular semi volatile method If needed adjust the lon Time Factor for particular segments to increase or decrease the abundance of key ions You can use Varian s EnviroPro software to generate DF TPP Tune and other reports needed for environmental analyses Similarly one can designate BFB Tune to display a table of parameters that is a good starting point toward meeting US EPA tuning requirements for volatiles analyses General Parameters lonization Control Internal El Parameters Full Scan Parameters Mass Range Low Mass s4 miz High Mass 300 mz Low Mass Hi
165. ct the Samples using the Method Browse Data Files will be saved in c warianwsidata Cancel Enter the method name directly or Browse for the Method file Click OK the Method downloads to the 3800 GC and the run begins If using a manual injector or a sampling device not controlled by the Varian MS Workstation start the device manually Specifying the Data File Name and Path Data File names can be up to 255 characters long Sample ID injection date module name and injection number can be embedded in the file name making the Data File name correlate with each sample injection When you click on the Data File button the Data Files Generation dialog box is displayed Select the path and the file name specification for the data file The left side of the Data File Generation dialog box has the drive letter and subdirectory path where the data files stored Use the right side to create a file name specification Combine text entry with the Variable symbols to specify file names that contain sample injection specific information An example of the file name is dynamically updated as the file name specification is typed This feature makes it easy to see how a Data File created with this file name specification will appear 170 Data File Generation xi Specify the names for Data Files generated by detector modules using this SampleList Numbers will be appended to file names if the file already exists Do not i
166. ctivating that filament in Manual Control mode and then returning to Diagnostics mode For analysis of positive ions Lens 2 is pulsed negative during ionization and positive otherwise so that ions enter the trap only when they are needed For negative Cl Lens 2 is pulsed positive during ionization All lens voltages are set by the Lens Tuning method in Auto Tune The ring and end cap offsets are set by the Trap DC Offset Voltage method in Auto Tune Event Messages Display This area displays messages when diagnostic tests are performed Startup Shutdown Tab EY a a a Nd le Je e 4000 s6029 sms gt FSs081_octPests_E gt a System Control Yarian 4000 GC MS Not Ready File Edit Inject Automation Recalculate Instrument Windows Help alala 3 startup1 mth r E E pB fl Sel Eol uj gt jmj Not Ready 4000 56 Not Ready X Manual Control Auto Tune Temperatures Diagnostics Startup Shutdown Acquistion Status and Control Current Set Points Operating Conditions m Heated Zones Heated Zones Conditions Analysis Trap Temperature 100C Trap Temperature 100C State Ready Manifold Temperature 50C Manifold Temperature 52C Transferline Temperature 250 C Transferline Temperature 252 C Source Temperature 220C Source Temperature eel Vacuum System Vacuum System Vacuum System Status Ready Pump Spin Speed 100 Pump Spin Speed 100 Current 292 m mps
167. ctor modules using this SampleList Numbers will be appended to file names if the file already exists Dio not include the file extension in the Data File name Data File names Test_ s E ample Directory for Data Files gt vananwe E gt data C 1200 El and NCI Pest 8081 C BC Cl test C BFE C B4P_PCI Eo DFTFP Test 5Sample 11 Use the following symbols to enter the comesponding variable data to the file name New Folder Sample ID Injection number Date Detector Module name Injection Time Cancel The Data File names field allows you to create a file name specification Follow the directions in the text shown below this field to specify file names that contain sample injection specific information In the Example field you will see a dynamic update of an example file name as you type in the specification This makes it easy to see how a Data File created with this file name specification will appear 161 Specifying Per Sample Data Handling Parameters NOTE Data Handling Parameters in the Sample List are applied only to data collected with standard GC detectors Most Data Handling parameters are specified in the Method used during the injection Some parameters may vary on a per sample basis and are therefore specified when you perform the injection The following Data Handling parameters can be specified on a per sample basis e Unidentified Peak Factor e Mu
168. cts As with Internal and Hybrid modes it is advisable to bake the system out after maintenance AGC Target TIC Value In El mode with AGC on the target TIC value determines how many ions AGC allows into the ion trap during the calculated ionization time While increasing the target TIC value will increase peak heights increasing it too far will result in a loss of mass resolution This would be observed as mass miss assignments and or incorrect isotope abundance ratios For full scan El operation a target TIC of 20 000 is a good starting point Under special circumstances e g MS MS a much lower target TIC such as 5 000 is required As the m z distribution of the stored ions becomes smaller fewer ions can be trapped without a loss of resolution Using 4000 MS Methods in System Control The Startup Methods When you open System Control and display the 4000 MS System Control Window the Startup1 mth first time or the last active Method for the 4000 GC MS is activated The Startup method is a copy of the Default method You can use it to build new 4000 MS control methods The Default method is placed in the file directory to ensure the existence of a valid method for the operator to build on Do not alter this method when developing new methods Change the Startup method if you are going to use a customized set of base parameters to build methods NOTE In building new methods clicking Defaults places instrument valid defaul
169. d by an icon at the bottom of the Configuration Window The icon will have a label reading 3800 44 and will include the Host Name of the GC appended to the label The number 44 is a System Control communication addresses that correspond to the Ethernet port connected to the device Modules and Instruments Defined The Varian 4000 GC MS system consists of two modules the 3800 GC and 4000 MS A third module is present if you have the Combi PAL AutoSampler Note that the CP 8400 and CP 8410 AutoSamplers will not have a separate icon but will be included on the 3800 Status and Control Window These modules also have addresses and the message logs frequently refer to the module and address The modules and allowed addresses are listed below Elements of the Configuration Screen After the 3800 connects to System Control configure it in an Instrument by moving its icon from the Available Modules of the Configuration Window into the Instrument Area System Control will remember where to put the icon the next time that the 3800 connects to System Control 93 a System Control Configuration File Edit Inject Automation Recalculate Instrument Windows Help Mja Onore sf euler pelle mlm Instrument 1 Yarian 4000 GCIMS Operator Jean Louis Mo Module Configured for this Instrument Auto Start Moadule The 4000 GC MS is usually configured into 2 modules the 4000 MS and the 3800 GC A Combi PAL AutoSampler can also be part of the
170. d the sample 286 More User Defined Settings Dialog Box Solvent Plug Fill Speed uL sec 7 4 Inject Speed uL sec so Pre Inj Delay zec oio Post Inj Delay sec wu User Defined Fill Wolurrie uL 7 Fill Strokes Sample Air Gap _Caree Air Plug after Sample Solvent Plug Settings Solvent Plug Vial Volurne uL Drawup Speed uL sec se Pause Time sec i Ar Gap yes Vial l II or Il Selects which solvent vial to use for the solvent plug Volume uL O to 100 uL with 100 uL syringe O to 10 0 uL with 10 uL syringe 0 to 5 0 uL with 5 uL syringe Specifies the amount of solvent to be drawn into the syringe before the sample or internal standard Drawup Speed 1 to 100 uL sec with 100 uL syringe UL sec 0 1 to 50 0 uL sec with 10 uL syringe 0 1 to 25 0 uL sec with 5 uL syringe Specifies the speed at which the solvent will be drawn up into the syringe Pause Time sec 0 to 9 9 seconds Specifies how long the syringe is to remain in the solvent vial after drawing up the solvent Yes or No If Yes a 1 uL of room air will be drawn into the syringe to create an air gap before the solvent plug 287 User Defined Settings User Defined Fill Volurne uL a Fill Strokes 0 H Sample Air Gap Air Plug after Sample 1 0 tem Description Fill Volume uL O to 100 uL with 100 uL syringe O to 10 0 uL with 10 uL syrin
171. ddress 132 190 73 207 Contact your Network Administrator or whoever assigns IP addresses for your network to see what the appropriate settings are for your Gateway and whether Domain Name Server DNS and WINS Configuration are needed 1 Your Network Administrator may also instruct you to specify parameters in the Bindings and Advanced tabs 2 Click on OK in the Network dialog box You will need to reboot Windows for the changes to take effect NOTE See Communication Problems in the Diagnostic and Troubleshooting section for information about diagnostic tools to verify that your network installation is correct Connecting the 3800 GC to a PC or Network See the nstallation Instructions for the 3800 GC Communications Board packaged with the 3800 GC Communications Kit for details on adding the communications board to your 3800 GC if it has not been previously installed and the Communications section of the 3800 GC Operator s Manual for instructions on connecting your GC to the PC or a company network Before proceeding your GC should be connected to your PC or network 82 Configuring the 3800 GC Communication No Company Network Use the following instructions if both a 3800 GC and Varian MS Workstation PC are being connected to an isolated network that is a network dedicated to Varian MS Workstations and the instruments they control In this case a Network Administrator will not be involved in assigni
172. de Std Split Splitless Std On Column Neat Viscous Volatile or User Defined Sets the 8400 8410 parameters for the predefined modes of operation Note that changing the injection mode will change the parameters displayed for editing It is not advisable to use the User Defined mode unless you are developing a special injection program Sample Depth 0 to 100 Specifies how far the syringe needle is to go down into the sample vial 100 is the bottom of the vial 0 is the bottom of the vial septum Solvent Depth 0 to 100 Specifies how far the syringe needle is to go down into the solvent vial 100 is the bottom of the vial 0 is the bottom of the vial septum Default Clean Section Default Clean Vial Volume uL Strokes Speed uL zec Default Cleaning occurs when the Stop button on the front panel of the 3800 GC the Reset button on the 3800 Status Window in System Control or the Stop Automation menu item in the System Control Automation menu is pressed after the 8400 8410 has started its run and before it has finished its sampling and post injection washing operations Default Cleaning also occurs when the 3800 GC has a fatal automation fault after the 8400 8410 has started its run and before it has finished its sampling and post injection washing operations 284 tem Description Volume uL Speed uL sec I II or Tl Specifies which of the three solvent vials will be used by the De
173. detected by the dynode and electron multiplier The AGC software automatically selects an ionization time from 10 usec to 65 usec for each of the six scan segments of the microscan depending on the amount of analyte in the ion trap and the tuning parameters An estimate of the number of ions formed in the ion trap is provided by a prescan with a varying ionization period 10 to 2500 usec For low levels e g for baseline or small GC peaks the maximum ionization time of 65 milliseconds is selected which offers maximum sensitivity As the amount of analyte increases the ionization time is decreased automatically in order to prevent overloading of the ion trap with ions The ion signals in each microscan are scaled automatically to compensate for the variation in ionization time Microscans are averaged to improve the spectral quality To optimize trapping of the ions of interest for external El amp external Cl mode a notched waveform is applied after the ions are trapped The ions are analyzed by applying a radio frequency RF voltage to the ring electrode encircling the trap cavity As the voltage increases on the ring electrode ions are sequentially ejected from the trap according to their mass to charge ratio Supplemental waveform voltages are applied to the end cap electrodes during the analysis to improve mass resolution and mass axis stability The ions scanned out of the trap strike the conversion dynode ejecting electrons which a
174. djustment is completed Method Segment Checks and Adjustments Module Attributes Cal Gas Adjustment Cl Gas Adjustment Last Set Date 1 5 2004 9 39 AM RF Ramp Adjustment A E r T Result Alin vy ater LAeck Ionization Time Total Ion Count Cancel Action Adjusting Method Segment Checks and Adjustments Module Attributes Cal Gas Adjustment Cal Gas Adjustment Cl Gas Adjustment Last Set Date 1 5 2004 9 39 AM AF Ramp Adjustment Ain ater Check Result OF Ionization Time 474 Total Ion Count 6370 Eancel Acton Idle Calibration Gas Adjustment Make this adjustment using the Calibration Gas valve inside the front door of the 4000 MS This valve has a black knob with the number O labeled on it Turn the valve counterclockwise to increase Cal Gas flow and clockwise to decrease the flow Adjust the flow so that the readback in the Adjustment Results field indicates that the flow is OK as seen in the following picture NOTE If you are doing an initial tune for example When first starting up a system the integrator zero may be far enough off that even with the cal gas closed all the way down the cal gas adjustment will indicate success There are interrelationships between the Cal Gas the Integrator Zero and the Electron Multiplier Therefore stabilize the settings by performing a Cal Gas adjustment more than once Initially set the Cal Gas to the midpoint 8 turns and then perform the Integrator
175. e excitation energy output drifts NOTE The maximum yield of product ions shifts to higher CID excitation amplitudes as the RF level is increased Save AMD conditions to MS MS How to Determine the Optimum Voltage for Resonant Excitation Using Automated Method Development AMD Follow these steps to determine the optimum voltage for resonant excitation using AMD while injecting the precursor compound AM Pie uoi Isolation Excitation Excitation Product lon Product lon lon m z Window Waveform Type Storage Amplitude Start Mass m z Level m z volts 3 0 Resonant 3 0 Resonant 3 0 Resonant 3 0 Resonant 3 0 Resonant 3 0 Resonant 3 0 Resonant 3 0 Resonant Set the excitation storage level equal to the lowest mass product ion expected divided by 1 4 If the product ions are not yet known start with the excitation RF 48 m z and an excitation time of 20 ms Set up the AMD method to cycle through excitation voltages using increments of 0 2 or 0 5 volts Determine the optimum voltage by plotting the product ion intensity data as a function of CID excitation amplitude as shown below 140 Resonant Excitation of a Typical lon 1200 7 as B a Parent ion roduct ff od o
176. e the ion formation and matrix ion ejection steps described above are modified Insertion of the three subsequent MS MS operations i e precursor ion isolation product ion formation and product ion mass scanning into the basic Cl scan function following the ionization and reaction steps creates the CI MS MS scan function EIl MS MS and CI MS MS Automatic Space Charge Control Space charge control for El MS MS and Cl MS MS uses a prescan to measure the number of precursor ions obtained using the same scan function as the analytical scan up through the fine isolation step Based on the signal intensity of the precursor ions in the prescan an ionization time is calculated for the analytical scan which will maintain the optimum number of ions in the trap even as the sample and matrix levels change resulting in consistent reproducible product ion spectra When using MS MS lower target values may be required to prevent adverse space charging effects Based on the isolated precursor ion the following target values are recommended Precursor lon Target 60 lt m z lt 150 10000 150 lt m z lt 500 5000 500 lt m z lt 1000 2000 213 Selected lon Storage Selected lon Storage Scan Function Selected lon Storage SIS may be used with external El or internal El to store and scan narrow and or discontinuous mass ranges Using waveforms unwanted parts of the mass range are ejected When used for target compound analysis SI
177. e the software will automatically shift the MS module into Acquisition mode omy Fe Fd e a Sed arose Pye covert a baban Cindia Warden Gets H A hety Pie Cot hiet Jette ieks beeen ri Ha e er Pd Ld Hoa eade a ADEM Mealy Haus Cortes uta Tura Tampakan Diapente Siphon Aerin mip Greg Li E Piae U par Lorra Po Tas DOD eri Hgin iepa Hais ot Dais Fide Gad Tiree 10 O rrai Ebute Tepai hepi em Hoa D i Aard Tee Danti Mierari 0 kaire Tira D Herne WatPoaReadde StanHange i i tort Hek Feed iea easa ECOPERERTEEN After starting Acquisition the yellow Not Ready light turns green Ready The 4000 module is ready for analysis If the GC is not ready a Not Ready message is displayed After the GC and AutoSampler become ready the Not Ready message changes to Ready To determine the individual ready states of the components go to the menu under Windows and see the states for the 4000 63 3800 and Combi PAL modules After all components are ready an analysis can be started Run an analysis as a single sample or using an automated sequence To run a single sample go to the topic Injecting a Single Sample on page 159 To run an automation go to the topic Injecting Multiple Samples on page 167 Status and Control Status 4nd Control Aun Time 0 00 minutes Start Acquisition End Time 10 00 minutes Edit Method oO Ready gt No Fault Wait For Readyln Befor
178. e 0 2 volts for the resonant excitation method and 20 volts for the non resonant excitation method If the excitation amplitude used is too large the precursor ion and product ion spectra will be absent because both ions will be ejected from the trap If the value is too small the precursor ion spectrum will be dominant and the product ion spectrum will be weak or missing Excitation Time The excitation time is the time required for collision induced dissociation CID by ion excitation The excitation time range is 0 to 650 msec The default excitation time is 20 msec for both resonant and non resonant excitation Modulate RF Whether the RF storage field is modulated during resonant CID This modulation greatly reduces any effect of changing secular frequency with concentration Number of Frequencies The number of frequencies at which the CID excitation waveform is applied The range is 1 to 119 frequencies odd numbers only The default value is 1 frequency applied at the end caps A value of 3 generates three frequencies the resonance frequency and frequencies 500 Hz above and below that frequency CID Frequency Offset For certain applications it maybe desirable to offset the dissociation frequency The CID frequency can be adjusted between 10 kHz CID frequency offset can only be applied to a single frequency If the number of frequencies is greater than 1 this field is hidden Customize Precursor lon Isolation If you wish to
179. e Analysis Analysis Calibration Verhication Baseline Do the same for injection notes Any notes that you enter are saved with the data file The AutoLink button works in the same way AutoLink Parameters Command Other parameters Inject the Sample using Browse Cancel Enter a command to execute a program after the data file acquisition is completed For example you can activate a custom MS Report to print the sample reports To run a Custom MS Report in automation enter the directory path and the name of the Custom MS Report template for example C VarianWS EPA525 swt Note that Custom MS Reports templates should always be stored in the VarianWS directory You can use the browse command can to select the command executable file Select OK after you make your selection Automation Menu The following shows the Automation menu and describes the functions System Control Varian 4000 GC MS Not Read File Edit Inject Wean yy Begin SampleList Begin Sequence Begin 4t Selected Sarnplecist Line Begin At Selected Sequence Line Recalculate Instrument Suspend Automation Resume Automation Stop Automation Reset Modules w Enable Automated Printing 21 Begin SampleList Automation starts at line 1 and ends at the last line A SampleList must be open from the File menu to use this feature Begin Sequence Change methods and sample lists during automation An
180. e Sle fee E Blo a gt i ES Methodi Front EFC Middle EFC Rear EFC 8 Method Notes 8200 AutoS ampler Control Address 26 Front EFC Type Ty pe 1 for 1079 Injectors a T Configuration fF 3800 GC Address 44 5 Hold min Total min F 3800 GC Control 100 TT Add ar Sample Delivery 14 00 20 00 Insert Delete Constant Column Flow Mode s Constant Flow Off C On E Calibration Setup Verification Setup LS Time Events Table 2 Ee a Reports Print Options Results Format Column Oven End Time 20 00 min NUM y Use the tabs to select which EFC Program you wish to edit Select the type of EFC Type 1 Type 3 or Type 4 at each position or select None if no EFC is installed at that position 150 Type 1 EFC for 1079 1177 Injectors If you indicate that a Type 1 EFC is installed a pressure ramp spreadsheet will appear Front EFC Middle EFC Rear EFC Front EFC Type Type 1 for 1079 Injectors Add 20 00 Insert Delete Constant Column Flow Mode Constant Flow Off C On Column Oven End Time 20 00 min Use the spreadsheet to build a pressure ramp program to control the Type 1 EFC The first row of the spreadsheet contains the Initial pressure and hold time for the Type 1 EFC The EFC will equilibrate to this setting when the method is activated and will be restored to t
181. e an acquisition starts the Status and Control field looks like the preceding The Run Time is 0 00 minutes The End Time is the run length specified for the 4000 MS module in the active method The Ready and No Fault lights are green Use Acquisition to override automation and start a run automatically before the system is Ready However the file name of the run is 4000 x sms not the file name specified for automation runs Click Edit Method to open the Method Builder and modify the method You are prompted to re activate the method after you save changes and return to System Control Wait For Readyln This feature is used with external devices that are not networked in to the system such as Purge and Trap systems If Wait For Readyln is selected the system waits for a signal before starting an acquisition Status And Control Aun Time 10 96 minutes Stop Acquisition 15 00 minutes Edit Method OO Running gt No Fault Wait For Readylin After an acquisition starts the run time increases in 0 01 minute increments Stop Acquisition terminates the MS run but does not terminate the GC run Terminate the GC from the GC module window accessed from the Windows menu To increase the end time click End Time and select the desired time NOTE Changing the End Time for the MS module does not change the GC End Time Extend the GC run time from the GC keypad Please enter a new endtime 20 00 cca 64 MS Method MS Met
182. e analyte A e lt 1eV A A Recommended External CI Reagents Methane is the most frequently used CI reagent for both positive and negative chemical ionization Ammonia can also be used for External PCI Liquid CI reagents are not recommended for External CI Liquid reagents have insufficient vapor pressure to be used the pressure of reagents in the ion source is not adequate for the high pressure reactions required External CI Scan Function For external chemical ionization mode ion formation occurs within the source with subsequent transfer of ions to the ion trap by a set of lenses The ions are stored and stabilized in the ion trap cavity by an RF field applied to the ring electrode The ion trap has a maximum storage capacity beyond which mass resolution and spectral quality deteriorate The number of ions created is proportional to the ionization time with more ions being produced the longer the ionization time Automatic Gain Control AGC controls the ionization time in order to maintain the number of ions in the trap at the optimum level 204 Four modes of operation Internal El External El External Cl and Hybrid Cl use a similar scanning sequence involving Automatic Gain Control AGC to scan ions out of the trap The AGC scan function consists of a prescan and up to six scan segments The prescan uses a fast scan rate and the number of ions detected in the prescan is used to calculate the ionization time for the s
183. e as shown below Nonresonant Excitation of a Typical lon 1200 7 1000 Parent ion Product 800 A OA Product ion 1 lon is Res rN Intensity 600 2 a Product ion 2 m z w Noh X 400 FA a 200 Ps 0 E E E m E O O l 0 10 20 30 40 50 60 70 80 90 100 CID Excitation Amplitude volts In the case above the optimal excitation amplitude would be about 40V This is because there is still some precursor ion present the primary product ion intensity is at the maximum and the secondary product ion has just started to form Determine the optimum storage level by plotting the product ion intensity data as a function of CID excitation amplitude for different RF levels as shown below 139 Product lon Formation vs Excitation RF for a Typical lon Using Nonresonant Excitation 1000 RF 48 m z RF 63 m z RF 95 m z 0 10 20 30 40 50 60 70 80 90 100 Excitation amplitude volts In the case shown above the storage level of 48 m z has a very narrow optimal excitation range This may result in a change in dissociation over time as th
184. e electron with the target molecule may deposit enough internal energy to the molecular ion to cause fragmentation If there are several chemical bonds in the molecule different fragment ions and neutrals will be produced A e gt A 2e lonization 10 eV He A gt ft n Fragmentation gt f n gt f n 199 The minimum energy required to create a fragment ion is called the appearance energy or the appearance potential for the fragment ion The fragmentation of molecular ions is on a very fast time scale compared to other processes in the mass spectrometer In fact it happens so fast that the molecular ion fragments before there is time to collide with other atoms molecules or surfaces in the external ion source Energetics of the Trapping Processes lons are transferred to the ion trap by applying voltages of the opposite polarity to the three lenses between the ion source and the ion trap Lens voltages are negative for PCI and positive for NCI The voltages on the lenses are tuned in Auto Tune to optimize focusing of the ions toward the ion trap The Trap DC offset voltage applied to the ion trap creates a potential well to trap all ions above a mass determined by the RF Storage Level The default RF storage level is 35u so only ions above this m z are stored in the ion trap Several performance issues are related to the setting for the RF storage level First the efficiency for storing high mass ions gt 300u seems
185. e set points Scan Time Scans Averaged Data Rate Mass Defect and Multiplier Offset An additional parameter Count Threshold becomes available when the Customize button is selected Scan Time Scans Scan Time Scans Averaged and Data Rate are all linked The Averaged Data number of scans averaged is updated when the scan time is Rate adjusted and vice versa The best way to set the scan time is to set the mass range from the Scan Parameters tab and then change the scans averaged to three 3 Three 3 scans averaged gives the best compromise between a high chromatographic data rate and good spectral averaging There is a trade off between how rapidly spectra are collected and the reproducibility of mass spectra or peak areas As more microscans are averaged the relative intensities of ions in the mass spectrum become more reproducible However one needs to keep in mind that collecting more data points across a chromatographic peak will improve peak area reproducibility on replicate injections San Time Range 0 02 30 seconds full range Scans Averaged Range 1 to 99 Mass Defect The Mass Defect allows for a systematic correction of the difference between the nominal mass of an atom or ion and its exact mass The importance of the Mass Defect arises from the fact that the NIST library reports molecular weights to the nearest integer mass unit only whereas the 4000 MS stores ion intensity pairs with a mass assignment to the
186. e toolbar select it from the top list and click on the Remove button To add an icon to the toolbar select it from the bottom list and click on the Add button Enable Disable Instrument Modules Select this option to display the Enable Disable Instrument Modules dialog box 13 Enable Disable Instrument Modules Instrument Modules curently enabled Instrument Modules curently disabled Select instrument modules you wich to disable Select instrument modules you wish to enable 2000 Mase Spec 2002 Micro GC 12 LE Solvent Delivery Systern 2003 Micro G0 3600 GC 3400 GC 3900 GC _2 gt Disable gt gt 3600 GC 4000 Mase Spec 348L GC SUO MS Mass Spec 4900 Micra GC a00 Interface Box 9001 Solvent Deliver System 8200 Autos ampler 9002 Solvent Deliver System ADC Board 9010 Solvent Deliver System CombiRAL Autos ampler 9012 Solvent Deliver System Mistral Column Over 9060 UV vis Detector ProStar 220 SOM S100 Autos ampler ProStar 230 Inert SOM 9200 Prospekt ProStar 230 SOM 9300 Autos ampler ProStar 240 Inert SOM Al 200 Autos ampler ProStar 240 SOM ProStar 520 Column Oven ProStar 310 UV Vis Detector lt Enable lt lt ProStar 325 UV Vis Detector ProStar 330 POA Detector ProStar 335 PDA Detector ProStar 363 Fluorescence Detector ProStar 400 Autos ampler OF Cancel Use this to select which 4000 GC MS Workstation instrument modules are available When an instrument module is available it appears in System Control
187. each calibration level Injection Notes Enter notes about the sample In the Vial Injection Volume and Injectors Used fields enter information about the sample The fields beginning with Amt Std are used only for data files acquired with standard GC detectors 160 Inject the Sample using the Method Ic Waray S Coltest External mth Browse Select the Method to use for the run Click the Browse key to select a file using Windows Explorer Defaults _Defauts Click here to change the default entries in the table above such as Injection Volume Injector Used etc After defining new defaults click the Save button to activate the new defaults Data Files Change the location and name of the Data Files here RecalcList a Click to generate automatically a Recalc list associated with single sample acquisitions Click Inject to start the run Specifying the Data File Name and Path Data File names can be up to 255 characters long Sample ID injection date module name and injection number can be embedded in the file name making the Data File name correlate with each sample injection When you click on the Data Files button the Data File Generation dialog box is displayed The left side of the Data File Generation dialog box allows you to select the drive letter and subdirectory path where the data files are to be stored Data File Generation Specify the names for Data Files generated by dete
188. ections Sections to Import 3000 GC Module 44 4000 Mass Spec Module 56 Select all Cancel Click Import to import selected sections to the target Method If the Method already has sections with the same module address and channel ID you will be prompted to assign a new module address and channel number to the imported section or overwrite the existing section in the current method Deleting Method Sections Open the Method containing the sections to remove Click the Delete Section button on the Method Builder Toolbar or use the File Delete Section E Method Builder Method 7 p d Eile Edit View Window Help pisus ae g ajexie a2 fe E Semn ts Method File Not Saved Created ae 1a Configuration B 5 3800 GC Address 44 Modified Size 9401 bytes Et rD 3800 GC Control E Sample Deliver Injector Flow Pressure Column Oven Method File Attributes O Read only DT Hidden DO Archive TC Requires Password on Save Revision History Ne Revision History A dialog box of the sections in the Method opens Highlight the sections to delete by clicking on them Click one section and hold down the shift key while clicking on another section to select a range Hold down the control key while clicking on a section to add that selection to the list Click a selected section while holding down the control key to remove that it from the list F Data Acquisition Channel Front
189. ector EFC Type 11 ts Configured with Ch 1 He makeup Ch 2 H2 Ch Air Mid FI Detector EFC Type 11 ts Configured with Ch 1 He makeup Ch 2 H2 Ch 3 Air Rear ECD Detector EFC Type 13 is Configured with Ch 1 H2 makeup Front Column is Configured with L 1 500 cm 0 250 microns H2 Carrier Gas Mid Column it Configured with L 1500 cm D 250 microns H2 Carrier Gas Rear Column i Configured with L 1 500 cm O 250 microns H2 Carrier Gas Valve 1 i Unused Default is Off Energized is On Valve 2 is Unused Default is Off Energized is On Valve 3 is Unused Default is Off Energized is On Valve 4 is Unused Default is Off Energized is On Valve 5 is Unused Default is Off Energized is On Valve 6 is Unused Default is Off Energized is On Valve is Unused Default is Off Energized is On Nothing connected to SID 1 S400 Autosampler connected to SID 2 is Configured for SPME Inj Ports in Both Positions S400 Dual Mode Setup Frint OF The 3800 Setup dialog displays all the hardware configuration information input through the GC keyboard and currently saved in the GC memory The Print button allows you to make a printed copy of this information for your records The OK button closes the dialog The remaining two buttons allow you to input additional configuration information detailed below 265 8400 Dual Mode Setup 8400 Dual Mode Setup Ea S400 Mounting Position Front 6400 Injection Front FID Hid FID Rear ECD Position
190. ed from the ion trap The Cl Background Mass is the lowest m z counted during the Cl prescan It can be higher than the low mass of the acquisition range but is usually set to be at or below the Start Mass value The Polarity is selected here to perform either positive or negative hybrid Cl Set the Start and End Mass ions to View in this dialog Click the View box when the method is opened in Manual Control to observe the effects of Reagent Start Mass and Reagent End Mass isolation adjustments Remember you must manually turn on the ion trap and Cl gas icons to observe the Cl reagent ions in this way Full Scan Parameters General Parameters lonization Control Hybrid Parameters Full Scan Par Mase Range Low Mass High Mass m z m z EE zi Insert Add Delete It is typical to use only a single mass range segment in Cl in which case one simply enters the desired values for Low Mass and High Mass of the acquisition range However as shown below one can enter up to six non contiguous mass ranges separated by at least 10u This feature can also be time programmed on a chromatographic segment basis It is then possible to tailor the Cl acquisition ranges for Cl to different target analytes depending on the mass spectrum of each compound An example of a three range acquisition is shown here 128 Mase Range lneert Add Delete Overview of lon Preparation Methods lon Preparation Methods
191. ed from the relative amounts of the m z 18 and 19 peaks The more water in the system the larger the m z 19 18 ratio Module Attributes The Module Attributes tab has three sections In the first section select a filament and set the voltage for the electron multiplier In the second section adjust the high mass calibration for either the normal or fast scan mode In the third section enable low mass enhancement which requires a new mass calibration Method Active Segment Checks and Adjustments Module Attributes Filament High Mass Calibration Low Mass Enhancement ei C32 Adjust high mass calibration Enable CAUTION Enablng Disabling Low Mass Electron Multiplier Enhancement requires new Mass Calibration Last Set Not Applicable Result Default Values Voltage 1200 a volts u Defaults 233 Auto Tune Auto Tune is an automated process for optimizing the MS 4000 performance over the entire mass range It is necessary to perform Auto Tune when the instrument is first set up Each time the system is shut down Auto Tune should be performed when it is restarted and after running a bakeout Before doing Auto Tune it is advisable to check RF ramp air water and cal gas settings under the Adjustments tab in Manual Control mode Many tuning features involve using Perfluorotributylamine FC 43 ions to adjust MS4000 parameters voltages gain values etc to optimize the signal Most Auto Tune functions are performed in El
192. ed to 250 C Click the Bakeout tab to set Bakeout temperatures The default bakeout temperatures are in the table above The bakeout t can be between 0 and 100 hours The default time is 8 hours 51 Analysis Bakeout Trap Temperature 150 E Manifold Temperature 120 L Transfer Line Temperature eal E i Hold Time Save Restore Generally do a Bakeout after the system has been restarted following shutdown and venting to the atmosphere Hours i The manifold is heated during bakeout to remove water and other volatile contaminants such as residual light hydrocarbons The 50 C default manifold temperature is usually used when acquiring MS data The transfer line temperature should be no lower than 30 C below the highest temperature of the GC column oven program in the active method NOTE The transfer line should NOT be heated above the maximum isothermal temperature specified for the capillary column Adjustments After Temperature Changes Whenever the ion trap temperature is changed 2 hours should be allowed for equilibration after the trap temperature has reached its set point Once equilibrium is reached the RF tuning should be checked and adjusted if necessary under Adjustments in Manual Control and Mass Calibration and Trap Frequency Calibration should be run in Auto Tune Bakeout Click Start Bakeout The State becomes Equilibrating until bakeout temperatures are reached then Holding until t
193. een Instrument Configuration Acquisition Data Type Extemal El 7 Centroid Profile Chromatographic Time Segments 1 FIL MUL DELAY Ms 4 00 _lonization Off 4 00 18 00 El Auto Full Defaults a __ Restore Restore EM EA Method Segment IV lonization On Scan Type Full v lonization eI Scan Mode Normal Setpoints Defaults General Parameters lonization Control Extemal El Parameters Full Scan Parameters m Mass Range r Tune Low Mass 10 m z Type Auto l Save Low Mass High Mass RF Storage lon Time m z m z Level m z Factor 150 8 100 151 300 25 100 399 100 High Mass 350 4 m z Customize _invet_ Add oe l Setting the MS Instrument Configuration Instrument Configuration External El Internal El and CI External CI Hybrid HPS Hybrid LFS Configuration Menu There are three hardware configurations Internal External and Hybrid The configuration defines what ionization modes can be used for data acquisition The choices are Electron lonization El or Chemical lonization Cl The instrument Configuration is set in the upper left corner of the MS Method Editor by selecting from the drop down list box When you change from one ionization configuration to another for example from Internal ionization to External ionization you must either activate an existing method
194. eeseeeeeseaeeeseucesseeeseusessaeeessaseesaeaeessaueesseeessaeeeseeesss 8 Launching Applications from the Workstation TOOID P ccccccccccceececeeeceeaeececeeeeceeeceseeseeseeeessecesseeceesaeeeseneessgeees 11 VVOKKSI ation TOO Da O PHOMS a a a dell cn ctiaanc toda cnataa tinea enuadenysiontpenaeanals 11 SVS COM CONO lcis aU a aa ccna seqeuenesonsetcusoneeceaseaseeecooe 17 Oa an a cies ade E E A cuecsamateone teresa 17 Navigating the 4000 MS Instrument WINGOW cccecccecseeeeeeeeeeeeeeeeeeeeaeeeeeeaeeeeeeseeeeeeseeeeeeseeeeeeseaeeeesaaeeeeaeaeeeesaess 17 Mandak eoni or TaD arerranese Meee omni tes re ERC on feet On TaN ree Pn OTE E ren RC SPR Pe eT 36 AO TUNE WA oto eae a a he ot soe cman eee cael ose ee de tee tian sce tetra os erena ooteeeee eieaeetes 45 PST FAM SNA A AE EE tac co EE E EEE ots ge eet me EE ces cole utes cess EE eee eee 50 EVI ACINO SUC SU aD as egatn sicher ctacenstot scant fas tasensaaed sane braceaatabet nurtestoentamd teteentanetetos sein ental datent oslo a naditseten aati ennuceanenam ley eantateltiele 53 Stanu SING OW iA T aD sania a a a a a as 58 ACQUISIHON LaNena a a a en ee Sere ee ST crS ae eer 63 Parameters That Affect MS Operation see icc ices cs gsbaceahddocesenciwecswteies i eedetaeehdiatecvend eta steed ended ee 66 Using 4000 MS Methods in System Control cccccccesccccseseeeceesseecceeeeeeceeseeeceeeeeseaeceecsaaeeeesaeeessegeeessgeeessegseeseas 67 Effects of Hardware Configuration Ch
195. efault View Select Chromatogram to see the chromatogram as it is acquired 34 ima a e ry Ber Pee 8 ewes DE anr dateen j Eea rusk al 1D bela I whale Plame CANA Le Cote Fo ne pe is E Click Hide Keypad to expand the display In the following picture that the text information at the top is hidden and the chromatogram is expanded RC ANE Lin Caa paa To display the Keypad click Show Keypad Select Spectrum and Chromatogram to display them side by side You can dock the Spectrum window for example above the Chromatogram Aj lej 4 Ed 4 e rend 3 Ei kaires 1 Jul 1 eS Mele 00D 7 OD l 35 Manual Control Tab In Manual Control the status of the MS module is displayed in real time This window is divided into two panes the 4000 MS Keypad above and the Spectrum Module Attributes display below There are many features in this mode and depending upon the screen resolution set in the Display section of Microsoft Windows Control Panel all of the 4000 MS Keypad features may not be displayed Configuring the Display Slide the Scroll Bar on the right to view the lower section of the keypad Also you can click the Splitter Bar to expand the keypad viewing area and the Scroll Bars to scroll the view System Control Varian 500 MS Mol Ready Instrument Configuration Bequiition Dats Tepe frat a G Cenimi V Prole ret S i Chromatesraphes Tine Segment 4
196. efault values for each applicable field in the RecalcList Actions Displays a list of applications which can be opened with the selected data file e g Print Standard Report Begin Opens the Begin RecalcList Dialog Box to specify a method to be used while recalculating or printing all RUN files in this RecalcList and to then begin recalculating or printing the files Only available in the System Control version of the RecalcList Suspend Suspends execution of this RecalcList after the current file has been completed Only available in the System Control version of the RecalcList Resume Resumes execution of this RecalcList after it has been suspended Only available in the System Control version of the RecalcList Data Handling Channels Dialog Box NOTE This dialog box is only used to specify standard GC data handling MS data handling uses only one detector channel You can specify the Multiplier Divisor and Unidentified Peak Factor on a channel by channel basis for up to four different detector channels And you can specify up to eight internal standards for each of the four channels for a total of 32 internal standards If you only want to specify a single Multiplier Divisor Unidentified Peak Factor and Amount Standard to be used for all channels of all detectors you may do so directly in the SampleList RecalcList or Inject Single Sample dialog box and do not need to use this dialog box If you plan to specify paramet
197. either check or uncheck all the boxes for diagnostic testing Test results are displayed in the event messages window If a test fails go to the relevant section of the Troubleshooting Guide in the 4000 GC MS Hardware Operation Manual Configuring the Monitor and Event Messages Display Create a larger area for displaying the Monitor window and Event Messages by clicking Hide Keypad or recover the Keypad by clicking Show Keypad You can display the Monitor Window or Event Messages displays alone or in combination by selecting from the drop down menu Hide Keypad Monitor Window and Event Messages Monitor Window Only Event Messages Onl F Turbo Pump Aaea ana a r Messages Tbe S she Vacuum System Vacuum System Turbo Purp Status Normal Speed 100 Curent 242 m Amps Power 11 Watts Temp 29C lon Gauge Pressure 18 2 uTorr Filament 1 OK Filament 2 Untested Foreline Pressure 24 mT orr Trap Camping Gas Flow 1 0 mL rnor The turbomolecular pump current and power readings displayed are typical during routine operation In this example the instrument is in External configuration with an auxiliary Helium flow of 1 mL min The values for current and power are lower in Internal configuration 95 The ion gauge reading depends on if there is auxiliary Helium flow in this case the system is in External configuration and the reading of 29 uTorr is reasonable for an auxiliary flow of 4 mL min The reading drops to 6 uTor
198. either raise the multiplier voltage or increase the Maximum lon Time If using Maximum lon Time at least five but preferably seven or more data points are needed for reliable quantitative data Using Fast Data Rate may allow the use of higher Maximum lon Times without compromising quantitative data quality Full Scan Parameters General Parameters lonization Control Full Scan Parameters Mass Range Low Mass mE mz High Mass 300 m z The lower and upper limits of the mass range to be acquired are entered in this tab dialog 121 Method Active Segment Checks and Adjustments Module Attributes Method Segment I Ionization On Sean Type Full v lonization ely Scan Mode Norma x Defaults General Parameters Ionization Control Intemal El Parameters Full Scan Parameters Mass Range Tune LowMass 50 2 m z Type Save High Mass 1000 m z Low Mass High Mass RF Storage lon Time m z m z Level m z Factor Customize When Customize is enabled it is possible to program up to six different segments of the acquisition mass range You can use the Insert Add and Delete buttons to adjust the number of segments Notice that the RF Storage Level can be programmed for each segment as well as the lon Time Factor If excessive fragmentation is observed in the mass spectrum it may be useful to lower the RF storage level below 35u for a given segment of the acquisition range Note that low
199. el 1E0212 Instrument 1 Sune Sample Aoma BeOS a smmmnmmmmneensemnseneeeieeene 16 02 13 Instrument 1 Activating Single Sample C14 017 TEATS Instrument 1 Method 3800 1 mth Activated 16 02 13 Instrument 1 Results will append to new RecalcList SINGLET018 ACL 16 02 25 Instrument 1 Beginning Yial 1 Injection 7 on Fri Feb 1316 02 25 1998 J amp 0r 27 Instrument 1 Data File c14 c171 3800 44 2 13 98007 un created for 014 077 Injection 1 16 07 54 Instrument 1 StarFinder c staryc14 c171 3800 44 2 13 98001 run added to database 16 09 05 Instrument 1 Completed 1 Inject Actions for 014 077 with D Errors 16 09 05 Instrument 1 Completed 0 AutoLink Actions for 014 017 16 09 05 Instrument 1 Completed 0 New Calibration Block Actions for 014 017 16 09 05 Instrument 1 Completed 0 Calibration Block Report Actions for 014 017 16 09 05 Instrument 1 End of Automation reached All Message Log entries are stamped with the time they occurred 163 Using QuickStart to Acquire a Single Sample QuickStart is a fast way to inject a single sample without using System Control directly QuickStart can be customized and is ideal when setting up instruments for routine use See the on line help in QuickStart for further details Ce aa i was i a Oe cal 4000 56043 SM gt bottoncimth gt ie i 5 QuickStart starts System Control and waits for the modules to log in When the instrument is ready the QuickStart dialog is displayed
200. el mie Eni HE E me Cl Background Mass eo miz Polarity The Reagent Low Mass and Reagent High Mass values are set to bracket the Cl reagent ion mass range of interest The Reagent Low Mass must be set to at 127 least 10u below the mass of the lowest reagent ion of interest without a loss of intensity for that reagent ion It is helpful to make adjustments of these parameters in Manual Control with the View box checked in the field to the right of this dialog The Reagent Low Mass parameter sets the RF storage level to exclude ions below the selected m z This is not a precise way to perform isolation By contrast the Reagent High Mass isolation step occurs after the ionization time when resonant waveforms are applied to the ion trap end caps to eliminate ions with m z above the selected Reagent High Mass Ejection Amplitude is the voltage of the waveforms for high mass isolation of Cl reagent ions The default value is 15V Max Reaction Time is the maximum time in usec allowed for Cl reaction If the ion time is reduced below the maximum based on the results of the prescan the ion time will be scaled back proportionately The allowed range for this parameter is 1 2000 usec The Reaction Storage Level is the RF storage level in the ion trap during Cl reaction following the ionization period It should not be set above the m z of the Cl reagent ion with which you wish to perform the Cl reaction else these ions will be eject
201. eld Clicking the Base Peak icon does not affect the display of the extracted ion chromatogram 248 3800 GC System Control Command Reference Status and Control Window Sq 3800 44 Equilibrating m 3800 Operation TempZones Set Actual gt Component Status 0 00 min Start Col Oven 80 127 Valve 1 Unused Off Front 1079 220 220 Valve 2 Unused Off Mid 1041 Off 100 Valve 3 Unused Off Runt ime EndTime 9 00 min Reset Equiibrating Coolable3 N A N A Valve 4 Unused Off No Fault Front TSD 290 290 Valve 5 Unused Off beatable2 N A NZA Valve 6 Unused Off Valves 1 2 3 4 5 6 7 Rear PFPD Off 36 Valve 7 Unused Off Hide Keypad Resume Plot View Front Only x x Kik H Fik baits REHE REE BEE RK tH EHET i baths x XXX 3 Xx XKX RERI x XK MRMERMENH The 3800 Status and Control window is divided into five display areas These are the 3800 Operation display the Temp Zones Status display the Component Status display the 8400 8410 Carrousel display and the Chromatogram display The left most display area is the 3800 Operation display which contains information about the current run and the overall state of the GC The next display area to the right is the Temperature Zones Status display which shows the setpoint and current actual temperature of each heated zone in the GC Next is the Component Status display You select the component for which you wish to see more de
202. en Manual Control Auto Ture Temperatures Diagnostics Control and Status Stabe Function System Yerfication Test Running Stop Diagnostic Monitoring Tab Dialog Monitoring Diagnostic Tests Trap On Off lon Gauge W lon Source lon Gauge f Filament 1 f Filament 1 Filament 2 C Filament 2 W Multiplier Dynode W RF Control RF Waveform Select the desired ion trap features to monitor in the Trap On Off area Select lon Source and the filament emission current is displayed in the lon Source Select Multiplier Dynode and the voltages of the electron multiplier and conversion dynode are displayed in the Trap Select RF Control with the RF radio button the Entrance and Exit Trapping Field Dipole values are displayed Select Waveform with RF Control and the Dipole and Quadrupole Supplemental Waveform Voltages are monitored Select lon Gauge option and the ion gauge pressure in utorr is displayed in the lon Gauge area NOTE If System Control is started in Diagnostics Mode no method was activated and the Dynode readback is a default value of about positive 9 000V Once a method has been activated in Manual Control or Acquisition the correct Dynode voltage associated with the method is displayed in Diagnostics 54 Diagnostic Tests Monitoring Diagnostic Tests Select ll Clear ll C System Verification J waveform Generator Scan and Acquisition Test Click Select All or Clear All to
203. en you start System Control and display an Instrument Window the last active Method for that instrument is activated When System Control is started it will return to the initial settings in the Method that was last used on the instrument To change Methods simply click on the Activate a Method button on the system Control Toolbar or choose Activate Method from the File menu o System Control Yarian Star 1 Suspended File Edit Inject Automation Recalculate Instrument Windows Help 3800 Operation TempZones Set Actual RunTime 0 00 min Start Col Oven 90 690 Yalve 1 Front Split On split ee Front 1073 100 100 Valve 2 Front Split On split EA ee eee a eos Off 41 Valve 3 Front Split On split Ready Coolable3 N A N A Valve 4 Front Split On split No Fault Front FID 260 260 Valve 5 Front Split On split Mid TSD Off 61 Valve 6 Front Split On split Valves 1 2 3 4 5 6 7 Heatable3 N A NZA Valve 7 Front Split On split Ajaj Editing Methods from the 3800 Status and Control Window The 3800 GC Status and Control Window contains a Method button that allows you to directly edit the active Method corresponding to that GC sa 3800 44 Ready Miel Es 3800 Operation Set Actual r Sample Delivery Status Col Oven 90 390 Valve 1 Front Split On split Front 1079 100 100 Valve 2 Front Split On split Mid 1073 Off 41 Valve 3 Front Split On split NAA NZA Valve 4
204. erator names entered here will appear on any automated reports generated by the MS Workstation The Ready File is not used with 4000 GC MS systems When the maximum number of non fatal errors Max Errors is exceeded during automation the automation sequence halts Setting this value to zero disables this feature You are optionally prompted for this information when you start an automated sequence of injections or Recalculations If the Prompt on Automation Start box is checked this dialog will appear when an Automation is started This feature can be particularly useful if different operators use the GC MS instrument 95 NOTE Do not enter any characters in the Ready File field or the MS will not come to Ready for injections For example if the characters aa were entered in the Ready File field the System Control title bar would contain the Waiting for aa Ready warning as shown here Even an invisible space character in this field can cause the problem Blea leh er 9 8081 _Lin_10pg 5 gt a System Control Yarian MS 1 Waiting for aa Ready File Edit Inject Automation Recalculate Instrument Windows Running an MS Method without a GC Method To run an MS method without the GC module or GC method open System Control Under the menu Instrument select Configuration Using the mouse click and drag the GC icon and AutoSampler icon if present from the middle field to below the bar labeled Available M
205. ering the RF storage level below 35u will decrease the storage efficiency for high mass ions particularly above m z 250 When a scan is performed in Auto mode the prescan is followed by an ionization time and scan of each segment needed to cover the Mass Range designated to the left of the segment table The actual lon Time for each segment is the AGC lon Time multiplied by the percentage in the lon Time Factor field External PCI and NCI Method Parameters This section details how parameters may be set for positive or negative chemical ionization methods in External configuration For more details on the theory of chemical ionization and how it is implemented in this instrument go to External Positive or Negative Chemical lonization on page 202 in the section 4000 MS lonization Techniques General Parameters Adjust the seconds scan to average General Paramete SetPyatrits f Scan Time Maximum Scan Time Multiplier Offset Ta volts fe_uScans Averaged za ucang Mase Defect Ta mmu Ou Data Aate 0 87 H Adjust the of uScans to average Centroiding Parameters Count Threshold 1 Customize 122 SetPoints f Scan Time 1 15 Seconds scan C uScans Averaged a Minimum of uocans Averaged Data Rate 0 87 Hz Scan Time uScans Averaged and Data Rate are all linked The number of microscans averaged is updated when the scan time is adjusted and vice versa There is a trade off between
206. erline Temperature 250 C Transferline Temperature 71 C Source Temperature 220 C Source Temperature 63C Vacuum System Vacuum System Vacuum System Status Not Ready Pump Spin Speed 100 Pump Spin Speed 74 Current 849 m mps r Pneumatics Pneumatics gt Pneumatics Damping Gas Off On Flow Rate 4 0 mL min Flow Rate 0 0 mL min Inlet Pressure 85 PSI m Getter Control Getter Control m Getter Control Heater Off Gn Temperature OFF Temperature SAC Hide Keypad Event Messages Jan 09 16 08 27 Startup Pump Heated Zones are starting up Jan 09 16 06 27 Startup Damping Gas or Getter not turned ON Observe the increase in Pump Spin Speed during system startup in Operating Conditions The software is locked in the Startup Shutdown mode until the speed reaches 100 You will also see the temperature readings for heated zones begin to increase in the Operating Conditions field If the system is in External or Hybrid configuration turn on the Damping Gas flow and the Getter Heater in the Status Control field after the Pump Spin Speed reaches 100 NOTE Failure of the system to reach 100 pump speed in about five minutes indicates a vacuum leak See Troubleshooting section in the 4000 GC MS Hardware Operation Manual About Running Analyses Selecting the Acquisition button activates the 4000 module for analysis If you start an analysis while the instrument is in another mod
207. ers on a channel by channel basis before opening this dialog box make sure that the active method contains the data handling sections for each channel and that their peak tables contain the standard peaks if any properly named and checked The dialog box uses information from the active method to help you make the proper specifications for the type of calibration method that you will be using If you later change the standard peak names in the peak table you will need 318 to revisit this dialog for each sample to update the names and amounts Data Handling Channels For Method Another mth Sample First analysis Calculation Unid Peak Factor Amount Standard 1 Multiplier Divisor Standard Detector Channel Peak 1 ADCB 16 Channel amp Internal Std 0 1 Peak 1 000 Cancel Edit Calibration Setup Edit Standard Peak s tem Description S Detector Channel Indicates the detector channel that is specified by the remaining fields in the row Channels are indicated by the detector module name bus address and channel identifier The combo box contains entries for all channels having data handling sections in the active method If the desired channel is not visible in the combo box make sure that the correct method is active and that it contains data handling sections for the desired channel Calculation Type Internal Std External Std Normalized No Calibration Indicates t
208. essure program to hold the Column Flow at the specified value as the Column Temperature is ramped during each run 152 Column Oven Window The Column Oven window contains the Column Oven Program Use the Column Oven Program to specify the Coolant Parameters and Stabilization Time of the Column Oven and to specify its programmable temperature ramp E Method Builder Method1 Oy x B File Edit View Window Help 18 x lelas Method1 Method Notes 8200 AutoSampler Control Address 26 T Configuration E E 3800 GC Address 44 eal eax s Column Oven Coolant On Enable Coolant at C Coolant Timeout min 20 00 ke E SE Off ld 4 P E E 3800 GC Control sry Sample Delivery Injector ory Flow Pressure gat olumn Oven sr Detector S Output sry Data Acquisition E a Channel Front a Data Handling Stabilization Time min Temp C Calibration Setup Verification Setup LE Time Events Table E RA Standard Reports Print Options EA Results Format Chromatogram Format Calibration Block Report Format Ready NMN 2 Indicate whether or not you will use the Coolant by clicking on the On or Off radio buttons Use the spreadsheet to build a temperature ramp program to heat and or cool the Column Oven Specify the desired temperatures at which to Enable Coolant and then set the times for Coolant Timeout and
209. etect Actes Seed Dacke aneltubiedieieds Reddi atitin Suas ean p Retaed Segment Hehodirjemal Lakad HS Method Uskead HE Method IF enzation On Coan Tope Fa Si baska FE Sceakteds Hora Yacuun Syston US Tovesracace UC Sou JK Dals niania ODuTm Fi eed Gerersl Parsereters onzen Convo Inteva2Psvaneters Ful Scan Paismeters LOE Han Hance une ion Ma m we Tye aur ikh nt Low Wor High M AF Stes high Mass f ICO 2 uy a Laval Z Fancher 2 Scamirg l Tw F Cates n Herod Seared cive detod Seavert Sonn Funcion Omaras M lon Gauge F 1 e a e a AE a E Save Fear 68 2 Save Ariunl 6 lor 1231 us Sagmant 1 Chsrnal 1093 Acoured Rance vz Help Menu The Help menu is as follows Yarian 4000 GC MS Not Ready Jtomation Recalculate Instrument Windows Help Help Topics _OCLPests_ExtEl mith lca E Product Support Web Site ady About System Control Tune Temperatures Diagnostics Startup Sh Select Help Topics from the Help menu to display the following Click an item in the Contents box to go to the online help In the Help dialog box from the Index tab you can select a particular area in which you need help Click on the selection you want and go to the bottom of the screen and click on Display Help T opic 5 pstem Control Contents Indes Fina 1 Type the first few letters of the word you re looking For Fh 2 Click the inde
210. ethod Editor xj This 3800 Method iz not compatible with the Hardware Setup for the 3800 that is Online at Bus Address 44 Do you want to automatically change the Method to make it compatible with the Hardware Click on Yes to change the Method to match the GC Click on No to accept the Method as is If you choose to auto configure the Method the following dialog is displayed Method Editor G The Method has been automatically updated to make it compatible with the Hardware Uploading the Method from the 3800 GC You can get the Method from the GC and save it in the Varian MS Workstation This allows you to do local Method editing on the 3800 GC front panel and then save this Method for later use on the Workstation a System Control Yarian Star 1 Heady Edit Inject Automation Recalculate Instrument Windows Help Activate Method Upload Active Method from Modules 5 Fo SHF SEO New SampleList Open SampleList New RecalcList Open RecalcList New SequenceList Open SequencecList Print Printer Setup w Remember Last Open Files E mit To upload the Method from the 3800 GC to System Control select Upload Active Method from Modules from the File menu You are then prompted for the name of the file under which to save the Method The active Method in System Control is updated to reflect the parameters obtained from the 3800 GC 155 The Startup Method Wh
211. ethod functions are illustrated here using the internal El mode of operation Details of other ionization modes and ion preparation options are in the Method Builder section of the manual While the contents of the segments can be modified the begin and end times of the segments cannot be changed from the Method Segments window You can add insert or delete segments using the buttons to the left of the segments Method Active Segment Checks and Adjustments Module Attributes Instrument Configuration Acquisition Data Type intemal El and CI Centroid Profile Chromatographic Time Segments T emt ajeje IL MUL DELAY 0 00 3 00 lonization Off 3 00 10 00 El Auto Full Full Scan El General Parameters The Scan Time and Scans Averaged fields are linked with each other and with the Scan Type lonization and Scan Mode fields If you adjust the Scans Averaged value the Scan Time and Data Rate values will also change the values obtained depending upon the Scan Type lonization mode and Scan Mode selected Changing the Scan Time changes the values for Scans Averaged and Data Rate Defaults returns all values to defaults for the selected Scan Type lonization mode and Scan Mode If the lonization On box is not checked all other controls become inactive indicating that the segment is a Filament Multiplier Delay segment 230 Method Active Segment Checks and Adjustments Module Attributes Method Segment lv
212. ethod is downloaded to the 3800 GC component program end times that exceed the column oven end time will be truncated Injector Window The Injector window contains up to three Injector Programs Front Middle Rear Only the isothermal 1177 and temperature programmable 1079 injectors are available on the 4000 GC MS system Use the Injector Programs to specify the temperature set point and split ratio of the isothermal 1177 Injectors and to specify the temperature ramp and split ratio of the programmable 1079 Injector LE Builder Method1 OF x E File Edit View Window Help z laj x asale ala leeke eal lee El Selmo aa gt pil Methodi Front Injector Middle Injector Rear Injector Method Notes 5 9200 AutoS ampler Control Address 26 Front Injector Type 1079 Injector Oven On C Off T Configuration Injector Coolant C On Off Ery 3800 GC Address 44 3800 GC Control Enable Coolant at C Sample Deliver Split Ratio ae A Coolant Timeout min 20 00 ee cry Flow Pressure ery Column Oven ery Detector 20 00 Add ery Output sr Data Acquisition Insert E Channel Front Data Handling E Integration Parameters E Peak Table E Calibration Setup Verification Setup E Time Events Table SA Standard Reports Print Options Results Format A Chromatogram Format E Calibration Block Report Format
213. ew Curves dialog box to Curves view calibration curves that are stored in a Method file Instrument Menu a System Control Ferguson_1 Not Ready Fie Edit Inject Automation Recalculate Instrument Windows Help alele F SPME mth wo Ferguson _1 Alt 1 Configuration ner ss Remove Module Names Manual Control Auto Tune Temperatures Instrument 1 Faulks status And Contra Setup Ethernet Communications Run Time 0 00 minutes Start Acq Setup ADC Board 1 0 Ports End Time 10 00 minutes M Editke Setup COMM Ports The Instrument Menu commands are used to switch the display between the configuration screen and the instrument Menultem Description instrument name Displays the Instrument Status window and Status and Control windows for the named Instrument e g 4000 GC MS 1 Configuration Displays the System Control Configuration window Remove Module Brings up a dialog listing any associations you have set up You Names may select items from this list to remove individual associations in preparation for renaming LC modules Instrument Faults Displays the Instrument Faults dialog box showing recent and self test messages and faults The list of faults may be printed from this dialog box 221 Menu tem Description Setup Ethernet Available if an optional module driver is installed that uses Communications Ethernet to communicate with the device See the Operation Manual for your modu
214. excitation storage level allows more energy to be imparted to the precursor ions by allowing a higher excitation amplitude The storage efficiency for product ions will be reduced if the storage level is greater than about 70 of the m z of the ion For some analyses a compromise may be needed to observe any product ions An excitation storage level may need to be chosen which will result in reduced trapping efficiency of the product ions As a rule of thumb the highest recommended excitation storage level will be the product ion m z divided by 1 4 For example if the product ion m z is 140 then the excitation storage level should be no higher than m z 100 for optimum trapping efficiency of the product in The MS q Calculator GG 3 For convenience The MS q Calculator is available in all lon Preparation Options g Calculator x q Calculator Specify a desired q value and click Calculate to determine the Excitation Storage Level comesponding to the q value Click Update and Close to copy the calculated Excitation Storage Level value back into the table Click Cancel to discard any calculation and return to the table Precursor lan Mass Desired g Value Excitation Storage Level 198 2 mz Update and Clase f Cancel a 131 The q value can be changed and a new excitation storage level calculated for a given precursor ion NOTE Set the excitation storage level to avoid ejection of
215. f injections their information will be appended to this file Accepts the RecalcList specification Cancels the RecalcList specification 326 AutoLink Parameters Dialog Box With AutoLink you can specify a program to be executed after all injections of a sample have been performed or two programs to be executed after each injection of that sample When AutoLink appears as a sample type in a SampleList or RecalcList the associated program is executed at that point in the SampleList RecalcList after the previous SampleList RecalcList line has completely finished The AutoLink can also be specified as part of a SampleList line that has a Baseline Analysis Calibration or Verification sample type In such cases the two AutoLink programs are executed after each injection of the sample AutoLink Parameters Command Other parameters Browse Cancel tem Description S Command DOS command lines to open DDE applications Sets the command line that will be used when AutoLink is invoked Other Commands understood by the remote application Parameters Provides information to the remote application when it is invoked Browse Opens the Select an AutoLink Program dialog box to select the name of an AutoLink program and enter it into the Command field 327 SequenceList Window a Automation File Editor CI Adjust seq File Edit Help Als Bls al ese ei CI Adjust seq SequenceList JO Ed
216. f the reagent ions are ejected by a broadband waveform prior to the chemical ionization step The ion trap operates in a pulsed mode The supply of reagent ions is created during the ionization pulse and consumed during the reaction period to form analyte ions The number of analyte ions depends on the concentration of the analyte the initial reagent ion intensity and the reaction time Because the spectral intensity is proportional to sample concentration and reaction time linear calibration curves can be obtained During the internal Cl scan the following steps occur e The reagent gas is ionized for the length of time determined by the previous scan A e All ions with a mass greater than the reagent ions are ejected i e all El ions from the sample B e Reagent ions react with sample molecules to form sample ions The reaction time was determined by the previous scan C e Reagent ions are ejected D e The Cl mass spectrum is acquired for the sample ions E 198 Ejection of all El artifact ions above Reagent High Mass is accomplished by applying a broadband waveform between the ionization and reaction periods It should be noted that fragmentation can still be observed in Cl spectra due to energy imparted when the proton is transferred from the reagent ion to the sample molecule Scanning lons to Collect Mass Spectra The scanning process for chemical ionization is similar to that for electron ionization Afte
217. fault Cleaning O to 100 microliters with 100 uL syringe O to 10 0 microliters with 10 uL syringe 0 to 5 0 microliters with 5 uL syringe Specifies the amount of cleaning solvent that will be drawn up with each syringe cleaning stroke O to 10 Specifies the number of times the cleaning solvent will be drawn up into the syringe and expelled into the waste cup 1 to 100 uL per sec with 100 uL syringe 0 1 to 50 0 uL per sec with 10 uL syringe 0 1 to 25 0 uL per sec with 5 uL syringe Specifies the speed at which the cleaning solvent will be drawn up into the syringe and the speed at which it is expelled into the waste cup Clean Mode Section Clean Mode Pre Inj Solvent Flushes Pre Iny Sample Flushes Post Inj Solvent Flushes Clean Solvent Source tem Description S Pre Inj Solvent Flushes Pre Inj Sample Flushes Post Inj Solvent Flushes Clean Solvent Source 0 to 99 Specifies the number of times each selected cleaning solvent will be drawn up into the syringe and expelled into the waste cup before flushing with the sample or the next cleaning solvent if more than one cleaning solvent source is specified 0 to 99 Specifies the number of times the sample will be drawn up into the syringe and expelled into the waste cup before the syringe is loaded for injection 0 to 99 Specifies the number of times each selected cleaning solvent will be drawn up into the syringe and expelled into the
218. fault option for the 4000 MS in Internal PCI its reagent ion is at m z 18 The final adjustable parameter in the Customize screen area is the Maximum Cl Reaction Time The operating range is from 1 2000 usec Depending on the Cl reagent and the target compound of the analysis sensitivity may be affected significantly by varying this parameter Full Scan Parameters General Parameters lonization Control Internal Cl Parameters Full Scan Parameters Low Mazz mfz EE 50 Insert Add Delete 118 It is typical to use only a single mass range segment in PCI in which case one simply enters the desired values for Low Mass and High Mass of the acquisition range However as shown below one can enter up to six non contiguous mass ranges separated by at least 10u This feature can also be time programmed on a chromatographic segment basis It is then possible to tailor the Cl acquisition ranges for Cl to different target analytes depending on the mass spectrum of each compound An example a three range acquisition is shown here Mass Range Low Mass High Mass m z Insert Add Delete External El Method Parameters This section details how parameters may be set for an electron ionization method in External configuration For more details on the theory of electron ionization and how it is implemented in this instrument go to External Electron lonization on page 199 in the section 4000 MS lonization Tec
219. ferent Module Name at that address The next time the associated Module connects at that address you will be prompted to select the correct name for the Module Instrument 1 Faults See if there are any faults in any of the modules contained in Instrument 1 An example of this screen is shown Use the update key to periodically check for new faults without opening and closing the dialog box 4000 MS faults are not reported in this window Module Address Faults Module 3800 44 0 Fauli Module 4000 56 0 Fault s Recent Messages and Faults Update C Selflest Messages and Faults Close Setup Ethernet Communication Set up the communication between the 3800 GC and System Control Depending on your network status go to one of the following sections for more details on this operation at the end of the System Control section Configuring the 3800 GC Communication No Company Network on page 83 or Configuring the GC for a Company Network on page 85 Windows Menu Use the Windows menu to view other System Control windows a System Control Yarian 4000 GC MS Not Ready File Edit Inject Automation Recalculate Instrument Windows Help alele 0081 _OcLPests_Ext l mth crio Module Windows C OE Module Winds a 4000 56 Not Ready Show Automation Windows Manual Control Auto Tune Temperatures Diagnostics Iconize Automation Windows lt SequenceList EI_CI SEQ nirera Lene E wf Seque
220. for each clean stroke the time specified in the Adsorb Time for Cleaning Once the cleaning strokes are completed the tower will rotate over the waste station the fiber holder will descend and the fiber will be exposed for drying desorbing desorbing requires a heated gas stream to be gently blown over the fiber Post injection 0 to 99 solvent strokes Executed the same as pre inject strokes following the end of the sample desorb time Clean Solvent I Hl or Il Source The solvent vial location in which the solvent clean will be done Adsorb Time 0 to 999 99 minutes The time the fiber will be exposed to the solvent during each clean stroke Desorb Time 0 to 999 99 minutes The time the fiber will be exposed in the waste cup area following each clean stroke Derivatization Use Yes No If Derivatization is specified after pre injection cleaning if any the fiber will be introduced into the Derivatizing Agent vial specified in the Derivatization page The fiber will penetrate into the Derivatizing agent vial the depth set for the Solvent penetration depth on the main SPME parameters page The fiber will be exposed for the specified Adsorb time and then be withdrawn Position I Il or IIl The position in the solvent vial rack of the Derivatization vial to be used The default is position Ill Adsorb Time O to 999 99 minutes The time period during which the fiber is exposed to the Derivatizing reagent Solvent Depth O to 10
221. formation about the results if any calculated from the Information current data file Channel Specifies the detector channel to show Result Information for Note that this applies only to standard GC results 321 tem Description S Delete Results Allows you to delete results from the currently select channel of the currently selected data file This button does not appear if it has been disabled from the Varian MS Workstation Security Administration application Note that this only affects standard GC results MS results are not deleted Opens the selected data file using the selected channel Cancels file selection SampleList Window The SampleList window contains injection parameters that are specific to the sample introduction device you are using on your instrument This section describes the generic SampleList fields Refer to the appropriate Instrument Control help topic in the System Control Reference Help for a description of the device specific extensions to the SampleList Generic SampleList untitled smp Sample Type Gu mi es autotik Default Sample Analysis 1 none Fill Down Add Lines Defaults Oops oom wy h 4f 4j 4fj 4 4 4 4 4 4 5 i Data Files RecalcList Item Description S Sample Name Up to 19 characters Sets the name of each sample in the SampleList Sample Type Baseline Analysis Calibration Verification Print Calib New Calib B
222. formation in the top highlighted row is repeated to the lowest selected row Add Lines If you need to add several similar lines to the Sample list click on the Add Lines button You can then enter the common information in the dialog box Add Lines to 8400 SampleList sae tane sonne 1m S wa efault Name Analysis X 1 Injection Injectors Amount Std Unid Peak ee s MultiChannel Volume Used IS NZ only Factor Mutiplier Divisor a usictandard 1 0 1 1 none Injection A toLink Notes none none 0 1 0 Posi Number of Lines to Add fi 0 IV Number Sample Names from fi I Number Vials from fo Insert Cancel For sequentially numbered Sample names check the box and enter the starting 180 number and the number of entries to add to the SampleList The Sample Names will have these numbers appended to them Defaults _Defauts Click here to change the default entries in the table above such as Injection Volume Injectors Used etc After defining new defaults click the Save button to activate the new defaults Data Files RecalcList l l l Click here to select whether to generate automatically a RecalcList associated with single sample acquisitions Change the location and name of the Data Files Specifying the Data File Name and Path Data File names can be up to 255 characters long Sample ID injection date module name and inject
223. further optimize precursor ion isolation by reducing the isolation window first build a method with a mass isolation window of 3 m z an excitation time of 0 usec and a CID excitation amplitude of O volts This permits you to observe only the isolation of the precursor ion without the influence of CID The exact fractional mass of the ion should be used for the precursor ion mass For practice use a fixed sample source such as perfluorotributylamine PF TBA calibration gas or the column bleed obtained by raising the gas chromatograph oven temperature Adjust the isolation parameters to isolate a single ion 136 Select an Excitation Technique The compound and matrix you are using determine which excitation technique you should use Resonant excitation works well with most compounds but non resonant excitation has been found to work better with some You are advised to begin your analysis with resonant excitation because it gives better results If the results desired cannot be obtained using resonant excitation switch to non resonant excitation Optimize the Non Resonant or Resonant CID Parameters Follow these steps to optimize the non resonant or resonant excitation CID parameters Determine whether the CID excitation amplitude used was too large or too small NOTE If the CID excitation amplitude used was too large the precursor ion and product ion spectra will be absent because both ions will have been ejected from the
224. g ions this should be done in a later step because the customized parameters may require optimization NOTE Some ions are more easily dissociated during the isolation step Therefore increasing the window may reduce the ion loss by dissociation at the expense of selectivity Dissociation of the Precursor lon Select the Waveform Type by selecting Non Resonant or Resonant excitation in the drop down list box Excitation Excitation Waveform Type Storage Amplitude Level m z volts Resonant Brr 0 20 Resonant 130 Excitation Storage Level Resonant or Non Resonant excitation Definition the RF storage level in m z when the dissociation waveform is applied following isolation The excitation storage level range depends on the precursor mass but the lowest product ion must be more than several mass units above the excitation storage level A starting excitation storage level for a precursor ion can be calculated using the q calculator The q calculator is accessed by right clicking on any of the fields in the MSMS parameters table Excitation Product Amplitude Start Me volts m z nn g Calculator What s This The optimum excitation storage level is a tradeoff between a storage level high enough to allow fragmentation of the precursor ion and a storage level low enough to allow efficient trapping of the lowest m z product ion Excitation Storage Level m z A higher
225. ge 0 to 5 0 uL with 5 uL syringe Specifies the sample volume that will be used for each fill stroke Fill Strokes 0 to 99 Specifies the number of the times the sample will be pumped in and out of the syringe before loading the sample volume into the syringe Sample Air Gap Yes or No If Yes a 1 uL of room air will be drawn into the syringe to create an air gap before the sample plug Air Plug after O to 100 uL with 100 uL syringe Sample O to 10 0 uL with 10 uL syringe 0 to 5 0 uL with 5 uL syringe Specifies the volume of room air that will be drawn into the syringe after it is loaded with sample 288 Viscosity Settings Wiecosiky Viscosity Delay sec OO Fill Speed uL sech 5 0 Inject Speed uL secl 0 Fre lInj Delay sec oo Fost Inj Delay zec wu tem Description S Viscosity Delay sec 0 to 9 9 seconds Specifies how long the syringe is to remain in the sample vial after drawing up the sample Fill Speed uL sec 1 to 100 uL sec with 100 uL syringe 0 1 to 50 0 uL sec with 10 uL syringe 0 1 to 25 0 uL sec with 5 uL syringe Specifies the speed at which the sample will be drawn up into the syringe Inject Speed uL sec 1 to 100 uL sec with 100 uL syringe 0 1 to 50 0 uL sec with 10 uL syringe 0 1 to 25 0 uL sec with 5 uL syringe Specifies the speed at which the contents of the syringe will be expelled into the injector Pre Inj Delay sec 0 to 99 9 seconds
226. ge Log M L essage Log or Configuration Log Configuration Log only if Configuration window is open Module Window Displays the Status and Control window for the chosen module name varies or brings it to the front depending on module 224 Help Menu a System Control Ferguson_i Not Ready File Edit Inject Automation Recalculate Instrument Windows Help Help Topics SEE EA SPME mth rl les es Esme a Product Support Web Site a 4000 01 Ready Manual Control Auto Tune Temperatures Diagnostics Startup Shutdown About System Control Menu ltem Description Help Topics Displays the Help Topics window for System Control Product Support If you have Internet access and a web browser installed on your Web Site computer this option will automatically open the Varian MS Workstation Product Support Web Site Here you will find the latest software and documentation updates for the Varian MS Workstation suite of products along with additional notes tips and answers to frequently asked questions You may wish to visit this site periodically to see if new information is available that may be pertinent to you About System Displays the About Box for the System Control application The Control About Box contains information about the software version installation information and a list of the instrument control modules that you have installed You can also validate the ins
227. ge level of 48 m z Mass Range Excited 30 Excitation RF Storage Level m z 143 a N O i l I a 1 J L l l l l l l l l wl a l eet See oe Se ee a N o1 i l l l rp 4 3 N Ii Q __ So o1 i l l l l l l l l l H I I I 10 ff L i I L l J l l l l 4 4 eae eee E co oS 25 Number of CID Frequencies N lt e oO 09 oO N i s e _ m z 500 m z 400 m z 300 m z 200 Mass range excited vs number of CID frequencies for an excitation RF storage level of 143 m z 212 Note that at a storage level of 48 m z and with 9 CID frequencies the mass range increases from 3 to 40 m z when the precursor ion mass increases from 100 to 400 m z Given a precursor ion mass of 400 m z and 9 CID frequencies the mass range decreases from 40 m z for a storage level of 48 m z to a range of 12 m z for a storage level of 143 m z Product lon Mass Scanning Following formation of the product ions by collision induced dissociation an RF ramp is used along with the supplemental waveforms to resonantly scan ions from the trap to the conversion dynode and electron multiplier This process generates the product ion mass spectrum Chemical lonization MS MS Chemical ionization Cl may also be used to selectively fill the ion trap In this cas
228. ger Level mV tem Description S Use Auto Gain Factor Yes No Yes enables the built in compensation for gate width No allows the user to fine tune gain to optimize dynamic range of the amplifier 2 63 Used when Use Auto Gain Factor NO 3800 GC Output Fort 4 Fort B Fort C Fort Alnstalled Yes C Mo Attenuation Add fd neern z Pelete Sort 4 4 Use these fields to control the analog outputs from the GC These parameters have no effect on the digital signal transmitted to the Varian Workstation tem Description S The 3800 GC can have up to three output ports installed A B and C The tabs at the top of the window select the output port position Port Installed Yes or No Indicates whether or not the Port at each position is installed For the installed Port the Output time program is used to program the detector signal source and attenuation d Sorts the spreadsheet rows by time 309 3800 GC Data Acquisition Detector Bunch Rate points 10 0 Hz Noize Monitor Lenath c bunched points 6 4 sec The following settings will be ignored for all detectors other than the FID and TSD Front Middle Rear FID TSO Detector Full Scale 1Y tem Description S Detector Bunch Rate Noise Monitor Length FID TSD Detector Full Scale Font Middle Rear Powers of 2 from 1 to 128 points Sets the detector bunch rate in numbers of points sh
229. gh Mass AF Storage lon Time m z Level m z Factor 4 Customize Insert Add Delete DF TPP Tune Parameters NOTE The recommended starting parameters for DFTPP and BFB are somewhat different for Internal and External El modes 114 Internal PCI Method Parameters This section details how parameters may be set for a positive chemical ionization method in Internal configuration For more details on the theory of positive chemical ionization and how it is implemented in this instrument see the 4000 MS lonization Techniques section Internal Positive Chemical lonization on page 194 General Parameters Adjust the seconds scan General Parameter SetP ot C Sean Time klasimum Scan Time Multiplier Offset Ta volts f uScans Averaged B Wwocans Mass Defect Ta mmu OO Data Rate OGY Hz Adjust the of uScans to average Centroiding Parameters Count Threshold 1 Customize SetPoints f Scan Time 1 15 Seconds scan l uScans Averaged Minimum of uS cans Averaged Data Aate 0 87 Hz Scan Time uScans Averaged and Data Rate are all linked The number of microscans averaged is updated when the scan time is adjusted and vice versa There is a trade off between how rapidly spectra are collected and the reproducibility of mass spectra or peak areas As more microscans are averaged the relative intensities of ions in the mass spectrum become more reproducible However one
230. hat the CID frequency applied to the end caps is properly resonant and that the trap function has been correctly calibrated To excite multiple ions at once increase the CID bandwidth by increasing the Number of Frequencies from 1 to 3 frequencies This increases the mass range around the precursor ion that is excited Several frequencies may be used with or without modulation and may be useful when exciting isotopic clusters 137 Automated Method Development Automated Method Development AMD is used to optimize CID conditions for product ion formation in a MS MS method AMD uses up to 10 different sets of conditions for the same precursor ion When using Automated Method Development AMD option set the ion time for 1 microscan per analytical scan by adjusting Scans Averaged General Parameters This will ensure that the maximum number of cycles through the different voltages scan segments across each peak is performed Below is a strategy for using AMD to determine the optimum excitation storage level and excitation voltage e Determine the precursor ion and retention time for each compound from an injection using normal El mode Build a multi segment acquisition method with one segment per compound e Use the default conditions with Automatic Method Development to determine the mass of the product ion s AMD allows the CID voltage to be incremented on a scan by scan basis 20v 40v 60v for up to 10 scans and then the cycle
231. have a Network Administrator on site you may wish to ask which configuration is recommended Use this table to determine the order in which you should read the following sections 1 If an Ethernet card has not been installed and configured on your PC read Installing and Configuring the Ethernet Card on page 76 and one of the following e No Company Network See Configuring the 3800 GC Communication No Company Network on page 83 e Company Network See Configuring the GC for a Company Network on page 85 Read Connecting the 3800 GC to a PC or Network on page 82 If you have not already installed the Varian MS Workstation do so before proceeding e No Company Network See Configuring the 3800 GC Communication No Company Network on page 83 e Company Network Read Configuring the GC for a Company Network on page 85 4 Continue reading the rest of the sections starting with Adding a GC and MS to the Instrument on page 92 Installing and Configuring the Ethernet Card NOTE The following section describes a procedure that is relatively generic consult your Windows documentation and that of the Ethernet card manufacturer for more detailed explanations See the installation instructions packaged with your Ethernet card for information on installing the Ethernet card in your computer Before proceeding your Ethernet card should be recognized by your Windows version When done the
232. he arrow in the top of each Valve column and select from the choices displayed in the combo box The second row contains the initial setting for each Valve when the Method is activated The following rows contain the time programmed settings for each of the seven Valves Adds a line to the spreadsheet Inserts a line above the currently selected row in the spreadsheet Deletes the currently selected row s in the spreadsheet Sorts the spreadsheet rows by time 3800 GC Injector Front Injector Middle Injector Rear Injector Front Injector Type Injector Oven On C Off Temperature C 294 tem Description Front Injector The 3800 GC can have up to three injectors installed front middle and rear The tabs at the top of the window select the injector Middle Injector a position Rear Injector Injector Type 1079 1177 Specifies the type of injector installed in the selected position Select None if no injector is installed at that position Injector Oven On or off Turns the injector oven in the selected position on or off See individual injector Click on the following injector types for a description of the parameters that appear when the injector is selected 1079 Injector Front Injector Middle Injector Rear Injector Middle Injector Type i073 Injector Oven On C Off Injector Coolant On C Off Enable Coolant at C Split Ratio Coolant Timeout mir 20 00 pit F
233. he nominal mass of an ion and its exact mass Its importance arises from the fact that the NIST library reports molecular weights to the nearest integer mass unit only whereas the 4000 MS stores ion intensity pairs with a mass assignment to the nearest tenth of a mass unit For library searching ion masses are rounded to the nearest integer If the m z of an ion happens to fall close to the 0 5u crossover point it may be assigned to the wrong mass This is more likely for molecules with higher molecular weights since the mass defects for several atoms may add together to produce a sizable mass defect The Multiplier Offset adjusts the EM voltage as much as 300V relative to the current multiplier setting in the Module Attributes tab dialog in Manual Control this is usually the 10 gain value from Auto Tune Sometimes better sensitivity is achieved particularly in techniques such as MS MS when the multiplier voltage is increased Note that this adjustment can be made on a segment by segment basis The Count Threshold is normally 1 count a value of 2 3 counts will reduce the number of low level ions reported in the mass spectrum This approach may improve library searches and reduce data file size at the cost of somewhat less detailed information in the mass spectra The count threshold is shown only if the Customize button is active lonization Control General Parameters lonization Control Internal El F Automatic Gain Control Targe
234. he Hold Time counts down to zero NOTE Hold Time does not start counting down until bakeout temperatures have been reached or until 20 minutes have elapsed Control and Status Conditions Bakeout Stop Bak eout State Holding Hold Time 0 99 hours At the end of the bakeout the trap manifold transfer line and source temperatures will return to the Analysis set points If you want to change bakeout duration or temperatures during a bakeout click Stop Bakeout make changes and Save them and then restart the bakeout 52 Diagnostics Tab Diagnostics mode is used to monitor the status of the vacuum system applied voltages and temperatures in real time It is also where diagnostic tests are performed The Manual Control Window is divided into two panes the Keypad on top and the Module Window and Event Messages display below a 4000 57 Not Ready Manual Control Auto Tune Temperatures Diagnostics Startup Shutdown Acquisition Control and Status State Idle Function Monitoring Status Yacuum System Turbo Pump Status Normal Speed 100 Current 242 m mps Power 11 Watts Temp 29C lon Gauge Pressure 18 2 uTorr Filament 1 OK Filament 2 Untested Foreline Pressure 24 mTorr Trap Damping Gas Flow 1 0 mL min Monitoring Diagnostic Tests poanie Trap On Off lon Gauge i oI cous Filament 1 Filament 1 C Filament 2 C Filament 2 WV Multiplier Dynode V RF Control
235. he Method Segment field below Chromatogram Time Gaps in Multi Segment Methods Depending upon the instrument configuration data can be acquired in different lon Modes EI CI Auto Fixed and or using different lon Preparation techniques When multiple segments have been acquired MS Data Review displays each segment independently in the Chromatogram display There will be no connection between the last point in one segment and the first point of the next segment There is a small time gap between segments This gap will be less than one second Programming Individual Time Segments Method Active Segment Checks and Adjustments Module Attributes Method Segment I lonization On Scan Type Full v lonization El v Scan Mode Norma Setpoints Defaults General Parameters lonization Control Intemal El Parameters Full Scan Parameters Mass Range Tune Low Mass 50 m z Type Auto Save Low Mass High Mass RF Storage lon Time m z Level m z Factor 4 High Mass 1000 m z Customize Add Features selected in the top of the Method Segment dialog determine which tab dialogs will be displayed in the remainder of the screen lonization On Selection If lonization On is not checked the filament and multiplier will be OFF during the segment This is the default setting for Segment 1 when new methods are created to protect the filament and multiplier from damage by the solvent front during GC MS runs
236. he Monitoring tab dialog The values should be near 100 Temperatures Temperatures Entrance Endcap 99C Exit Endcap 99 0 MM aritold a E Transterline 2na E SOUrCE lle 56 The current temperatures of all heated zones are shown here Note that the temperatures of both Entrance and Exit End Caps are reported When the trap temperature has been changed this information helps to monitor the equilibration process lon Source Internal lon Source Ernssiory 12 wimps Balance usec Deviation 0 0 us Filament Bias 11 7 Volts Filament 1 OF Filament 2 Untested On Off Gate 127 Volts 121 Volts When the system is in Internal configuration you can set the emission current between 10 and 100 uAmps The emission reading may vary by 1 uAmps from the value set in the MS method Balance is a measure of how well balanced the emission current is between ionization on and off Deviation is a measure of the total deviation of emission current as ionization turns on and off Deviation is an indication of the lens ability to provide a symmetrical pulse of electrons into the source If Deviation gt 5 Amps the electron lens needs to be tuned The filament bias is its voltage relative to ground The bias is 11 9V for El mode and 9 8V for Cl mode The status of both filaments is indicated as OK Open or Untested If the Filament is untested you can determine its status by activating that filament in Manual Control mode and then retur
237. he calibration method specified for the detector channel in the active method To change the calibration method for a specific channel first click on the channel s row then click on the Edit Calibration Setup push button If the Calculation Type is not Internal Std or Normalized the Edit Standard Peak s push button will be disabled Unid Peak Factor O to 1 000 000 Sets a calibration factor for unidentified peaks 0 000001 to 1 000 000 Sets a value for the multiplier Results for the sample are multiplied by this value 0 000001 to 1 000 000 Sets a value for the divisor Results for the sample are divided by this value Standard Peak 1 40 character standard peak name from peak table Indicates the name of the first Internal Standard Peak The Amount Standard 1 will be applied to the Internal Standard Peak having the same name To change the standard peak name for a specific channel first click on the channel s row then click on the Edit Standard Peak s push button 319 tem Description S Amount Standard 1 0 000001 to 1 000 000 Sets the amount of the first internal standard Used to calibrate results for Internal Standard and Normalized Percent calculations Standard Peak 2 8 40 character standard peak name from peak table Indicates names of the multiple internal standard peaks present in the specific channel s peak table To change the standard peak names for a specific channel first click
238. he end of the list o inset Inserts a new line before the currently active line _ Deet Deletes the currently active line ees When sections of columns or entire lines are highlighted the information in the top highlighted row is repeated to the lowest selected row Add Lines Add several similar lines to the Sample list You can then enter the common information in the dialog box Add Lines to 8400 SampleList sme ane sometre wi Default Name Analysis X 1 en Aol ak Injection eee Amount Std Unid Peak Multiplier Divisor MultiChannel Volume se IS N only Factor MultiStandard Pos 1 1 0 1 1 none none none 0 1 0 Number of Lines to Add fi 0 Iv Number Sample Names from fi J Number Vials from jo Insert Cancel To sequentially number the Sample names check the box and enter the starting number and the number of entries to add The Sample Names will have these numbers appended to them 169 Defaults _Deiaute Change the default entries in the table above such as Injection Volume Injector Used etc After defining new defaults click the Save button to activate the new defaults Data Files Change the location and name of the Data Files RecalcList i f Select to automatically generate a Recalc list for with single sample acquisitions __Beain Click and a prompt for the Method opens Begin Sample List OOOO O System Control will inje
239. he lon Source Balance in uAmps relates to the proprietary diagnostic used to determine the quality of the ion source and for instrument tuning and troubleshooting Filament Bias of the ion source in Volts Filament 1 Filament 2 status will indicate either OK or open broken or faulty filament lon Source Gate status and voltage indicates the voltage for the gate when it is On and Off Emission Balance and Deviation will only be active if the lon Source checkbox has been selected in the Trap area of the Monitoring Tab 243 Startup Shutdown The Startup Shutdown tab provides status and control for the vacuum system the heated zones and the damping gas pneumatics a 4000 56 Not Ready Manual Control Auto Tune Temperatures Diagnostics Startup Shutdown Acquisition Operating Conditions Heated ones Current Set Points Heated ones Status and Contral Conditions Analysis State Ready Vacuum System Status Ready Trap Temperature 150 C Trap Temperature 150 C Manifold Temperature 35C Manifold Temperature 34C Transferline Temperature 170 C Transterline Temperature 170 C Vacuum System Pump Spin Speed 100 Current 220 mAmps Preumatics Flow Rate 0 0 mL min Inlet Pressure 101 Pl Getter Control Temperature 420 Vacuum System Pump Spin Speed 100 Preumatics Flow Aate OFF Getter Control Temperature OFF Preurmatics Damping Gas Off Tur O
240. hemical ionization Symbolizing the sample analyte by A with mass M and the neutral reagent by R these are Proton Transfer The reagent ion donates a proton to the sample molecule to produce a protonated analyte sometimes called a pseudomolecular ion with mass M 1 RH A gt AH R This is the most commonly recognized PCI reaction Note that the AH ion may fragment to lower mass ions because of excess energy deposited during the PCI reaction Charge Transfer The Cl reagent may transfer only charge to the analyte molecule by electron transfer to the reagent RH A gt A RH Adduct lon Formation The Cl reagent ion may bond in its entirety to the sample molecule to create an adduct ion RH A ARH Hydride Abstraction Some reagent ions have a tendency to remove a hydrogen atom to create an analyte product ion that is still positively charged but having a weight of M 1 Rt A gt A H RH 195 Recommended Internal PCI Parameters PCI with CH4 The pressure of methane is adjusted so the ratio of the peak heights at mass 17 CH to mass 16 CH is about 10 1 the ratio of the peak heights at mass 17 to 29 C2H5 is about 1 1 and mass 41 C3H5 is visible Maximum lonization Time usec 2000 Maximum Reaction Time usec Cl Storage Level m z Cl Background Mass m z Ejection Amplitude v 90 PCI with CH3CN Properly Adjusted Acetonitrile Reagent Spectrum Reagent Liquid Maximum
241. his setting when each chromatographic run is completed The Rows after the first row of the spreadsheet contain the programmed settings for each of the ramp segments Each segment will ramp to the specified pressure at the specified rate assuming the rate is achievable and then hold the pressure for the specified time Note that the Rate in the first row is always blank and cannot be edited Also note that the entire Total column cannot be edited Constant Column Flow mode for Type 1 EFC is enabled in the Flow Pressure window 151 Front EFC Middle EFC Rear EFC Front EFC Type Type 1 for 1079 Injectors areal Rate ae a pst pzi min aen 1 Ada i Bett a Delete O5 6 Constant Column Flow Mode Constant Flow Off On Column Flow ml min x Column Oven End Time 20 00 min Click on the Radio Button to turn on the Constant Column Flow Mode This mode disables the spreadsheet and reveals the Constant Flow rate value Enter the desired Column Flow When the method is activated in System Control the Varian MS Workstation will generate and download the appropriate pressure program corresponding to the Column Temperature program the Column Setup Length and Diameter the Carrier Gas and the ambient Barometric Pressure These parameters are specified at the 3800 GC front panel and the Barometric Pressure is measured by the 3800 at the time the Method is downloaded The 3800 will run the pr
242. hniques General Parameters General Paramet eneral Parameters Adjust the seconds scan SetPopet f Scan Time Maximum Scan Time Multiplier Offset Ta t volts f uScans Averaged b wocang Mass Defect Ta mimarT OO Data Aate Oey Hz Adjust the of uScans to average Centroiding Parameters Count Threshold 1 Customize SetPoints f Scan Time 1 15 Seconds scan C uwScans Averaged Minimum of uS cans Averaged Data Rate 0 87 Hz Scan Time scans Averaged and Data Rate are all linked The number of microscans averaged is updated when the scan time is adjusted and vice versa 119 There is a trade off between how rapidly spectra are collected and the reproducibility of mass spectra or peak areas AS more microscans are averaged the relative intensities of ions in the mass spectrum become more reproducible However one needs to keep in mind that collecting more data points across a chromatographic peak will improve peak area reproducibility on replicate injections Setting up to average three scans is a good recommendation to get good spectral quality along with an acceptable data rate The Mass Defect allows for a systematic correction of the difference between the nominal mass of an ion and its exact mass Its importance arises from the fact that the NIST library reports molecular weights to the nearest integer mass unit only whereas the 4000 MS stores ion intensity pairs with a mass assign
243. hod Segment Number 1 of 2 Segment Descriptions Scan Description Filament Off Scan Range 200 205 Before an acquisition starts the active method is in Segment 1 which is normally a Filament Multiplier Delay segment The length of the segment keeps the MS off until after the GC solvent elutes MS Method Segment Number 2 of 2 Segment Descriptions Scan Description El Auto FULL Scan Range 40 300 After a run starts the Segment Number increments as each segment of the method runs The Segment Description is the user entered description in the Segment Description field of the MS Acquisition Method in the active method The Scan Description indicates the ionization and ion preparation methods used for acquiring data these methods are chosen in the Scan Type Group and lonization fields of the Method Segment field of the method Scan Range is the acquisition mass range Operating Conditions Data File shows the name of the file being acquired The Scan Number lonization Time and lon Count for the current scan are displayed in their respective fields This display is updated on a scan by scan basis throughout the GC MS run Operating Conditions Data File 8061 _Lin_ Column Test g94 lonization Time 2683 115117 Scan Humber lon Court 65 Parameters That Affect MS Operation Electron Multiplier Gain Normal 4000 GC MS operation assumes that the electron multiplier gain is set up to produce appr
244. how rapidly spectra are collected and the reproducibility of mass spectra or peak areas As more microscans are averaged the relative intensities of ions in the mass spectrum become more reproducible However one needs to keep in mind that collecting more data points across a chromatographic peak will improve peak area reproducibility on replicate injections Setting up to average three scans is a good recommendation to get good spectral quality along with an acceptable data rate The Mass Defect allows for a systematic correction of the difference between the nominal mass of an ion and its exact mass Its importance arises from the fact that the NIST library reports molecular weights to the nearest integer mass unit only whereas the 4000 MS stores ion intensity pairs with a mass assignment to the nearest tenth of a mass unit For library searching ion masses are rounded to the nearest integer If the m z of an ion happens to fall close to the 0 5u crossover point it may be assigned to the wrong mass This is more likely for molecules with higher molecular weights since the mass defects for several atoms may add together to produce a sizable mass defect The Multiplier Offset adjusts the EM voltage as much as 300V relative to the current multiplier setting in the Module Attributes tab dialog in Manual Control this is usually the 10 gain value from Auto Tune Sometimes better sensitivity is achieved particularly in techniques such as MS MS
245. hy on your computer click the down arrow To see what is inside a folder click it The box below shows the folders and files in the selected location You can also double click a folder or file in that box to open it To open the folder one level higher click the up arrow button on the toolbar File list Lists the folders and files in the selected location To see what s inside a folder double click it You can also use the Look In box to see the hierarchy of folders To open the folder one level higher click the up arrow button on the toolbar Shows the currently selected file Files of type Restricts the list of files to only those matching the selected type 313 tem Description S Recent Files Click on this button to display a list of recently selected files When you select a file from this list its name is displayed in the File name box Notes When checked displays any notes and or revision log associated with the currently selected file Opens the selected file Cancels file selection Save Automation File As Dialog Box This dialog box is used to name an automation file The Save Automation File As dialog box appears with several different titles depending upon how you access it In all cases it contains the fields listed below in forms appropriate for the type of file you are about to save Save Automation File As Saye ihi E Examples File name Juntitled rc Save as type RecalcLists
246. icking Start Auto Tune to start the selected routines Click Stop Auto Tune to stop them The Action field shows the tuning routine that is being performed The State field shows if the 4000 MS is executing an auto tune routine or idle Control and Status Actor Mass Calibration State Calibrating Spectrum and Event Message Window You can select the information displayed during the auto tune tests by selecting from the list Click Hide Keypad button to hide the upper portion of the screen and expand the lower portion Hide Keypad Spectrum Pectin Spectrum and Event Messages Event Messages Module Attibutes Summary Report Module Attributes is the information stored from the last auto tune After you do an AutoTune you can view this log Hide keypad Module Attributes MS Workstation Demo RC1 version 0 42 Module 4000 56 MODULE ATTRIBUTES as of 3 15 2005 1 31 PM Configuration system Type GE lonization Source External Option keys Cl MS MS Hybrid External EFC Module TRUE Serial Number 106 Controller Board wersion Cong FROM Software Version 03 01 00 03 Communication Processor Software Version 01 01 00 55 Scan Processor Software Version 01 01 00 58 46 Auto Tune Methods The auto tune checks that you can automatically set up tune and calibrate the mass spectrometer with depend on the instrument configuration The following show the checks availab
247. ile Revision Settings Unlocked Applications Select applications you wish to lock and click on the Lock Button Carian S Program Manager Star Toolbar Pack System Control Varian GC MS 1 Not A Locked Applications Select applications you wish to unlock and click on the Unlock Button Unlock 188 tem Description Unlocked Applications This list box shows all top level windows currently running that are not locked You may select any number of them and click on the Lock button When you do they are moved to the Locked Applications list box and their windows are disabled they will not respond to mouse or keyboard input Note that applications that are locked by the Security Administration application remain locked even after the Security Administration application is closed Locked Applications This list box shows all top level windows that are currently running and are locked You may select any number of them and click on the Unlock button When you do they are moved to the Unlocked Applications list box and their windows are enabled they respond to mouse or keyboard input File Revision Settings MS Workstation Eo X Passwords Application Locking File Revision Settings T Require Revision Log entry when changes to Methods are saved M Update Revision Log in Data Files with recalculation date time and Method name Enable results deletion from Open Data File dialog
248. in SampleList Begin Sequence Begin At Selected SampleList Line Hegnet Selected Sequence ine Suepend EUtonnaton Resume ubonretord Stop Automaton Reset Modules w Enable Automated Printing When this item is not checked report printing is disabled ASCII file generation is still performed if specified in the Report Method section Disabling automated printing is analogous to disconnecting the printer automation continues but no reports are printed This is useful if you are about to run out of printer paper but do not wish to suspend automation 185 186 Security Administration Overview The Security Administration window contains three window tabs that can be used to select the categories of security parameters that can be specified for Varian MS Workstation applications Click on the category names below for more information on each e Passwords e Application Locking e File Revision Settings Passwords MS Workstation Demo Monday 05 17 04 Secur ity x Passwords Application Locking File Revision Settings Paseword for this application Tou may set change or remove the password required to enter this application Change Method Passwords Tou may set or change passwords required to save changes to Methods Click on the button below to select the Method and then modify the password Select Method Remove Method Passwords Tou may remove passwords required to
249. initiated after the trap has reached its equilibrium point approximately 2 hours after the set point temperature has been established For External and Hybrid modes changing the trap damping gas flow may require both Mass Calibration Trap Frequency Calibration There could also be subtle effects on mass assignments after ion source temperature changes Trap Frequency Calibration When the mass calibration has been completed the trap frequency calibration must be performed This routine determines resonant frequencies required for the generation of notched waveforms used in most modes of operation In particular the resonant frequencies for FC 43 ions at m z 69 and 414 are determined The method takes several minutes to complete NOTE Do Trap Frequency Calibration each time you do a mass calibration 49 Upon completion of Trap Frequency Calibration the Event Message Window displays the secular frequency values for the two trap function calibration points Nominal values are 249 kHz and 248 kHz respectively These values can vary up to 4 kHz between instruments Trap DC Offset Voltage The trap offset is a DC voltage applied to the ion trap electrodes end caps and ring electrode to facilitate the injection of the externally generated ions into the trap The intensity of the m z 414 ion from FC 43 is used to maximize the signal thus optimizing for the midpoint of the mass range The trap offset has a range from 3 to 15 volts Lower v
250. ion and your 3800 GC All of the information included in this manual is also available in the On Line Help section of the software Additional Manuals Help Other sources of information are available to help you get the most from this product 4000 GC MS Users Guides These Users Guides are tailored to help the user get started with the 4000 GC MS system in any of its three ionization modes There is advice on configuring and starting up the GC MS Then there is advice on tuning building methods and acquiring data There are also discussions of the ionization and ion preparation MS MS methods that can be used in the configuration e 4000 MS Internal lonization Users Guide e 4000 MS External lonization Users Guide e 4000 MS Hybrid lonization Users Guide 4000 GC MS Hardware Operation Manual The Hardware Operation Manual provides the necessary information for installing maintaining using and repairing your 4000 GC MS System All of the information included in this manual is also available in the On Line Help section of the software MS Workstation Software Reference Manual This Manual provides a practical way to quickly learn how to perform basic tasks using the MS Workstation Software These operations include displaying and reviewing chromatographic and mass spectral data library searching and quantitative analysis Although these tutorials use Saturn 2000 ion trap files they illustrate the principles of the Varian WS software
251. ion number can be embedded in the file name making the Data File name correlate with each sample injection When you click on the Data File button the Data Files Generation dialog box is displayed This dialog box allows you to select the path and the file name specification for the data file The left side of the Data File Generation dialog box allows you to select the drive letter and subdirectory path where the data files are to be stored Data File Generation Specity the names for Data Files generated by detector modules using this SarmpleList Numbers will be appended to file names if the file already exists Do not include the file extension in the Data File name Data File names sd s Example b 26 2004 S ample 1 1 Directory for Data Files foo oc gt Varianws E gt AN00M odule Use the following symbols to enter the comesponding variable data to the file fe 41 Injection number 40 Date 2m Detector Module name nection Time The right side of this dialog box allows you to create a file name specification You can combine text entry with the variable symbols shown to specify file names that contain sample injection specific information An example of the file name is dynamically updated as you type in the file name specification This feature makes it easy to see how a Data File created with this file name specification will appear 181 Specifying a RecalcList
252. ion step eliminates the higher background that would normally arise from a high emission current lon Trap and lon Source Temperatures Internal or Hybrid Configuration It is important that the ion trap temperature be high enough so that analytes eluting from the column do not condense on trap surfaces If condensation happens the chromatographic peaks tail Trap temperatures can be 50 75 C below the highest temperature for the GC column temperature ramp without compromising chromatographic performance Certain compounds such as straight chain hydrocarbons fragment more at higher ion trap temperatures Using a low column flow rate in combination with a trap temperature below 150 C will improve the mass spectra when fragile ions are present After the system is shut down and the ion trap vented to the atmosphere do an initial bakeout period at elevated temperatures to rapidly removal water vapor After this reduce the trap temperature to 150 175 C Use the manifold bakeout functions to do this overnight and reset the temperatures to operating conditions 66 automatically Some applications may require higher temperatures and this is acceptable In general use the lowest temperature that provides good chromatography External Configuration A low ion trap temperature does not cause tailing of chromatographic peaks when the instrument is in External configuration although a Source temperature set too low may cause similar effe
253. ion to these scaling controls you can scale vertically using the Attenuation Control to the right of the chromatogram display window This adjusts the amplitude range on a logarithmic scale When using the attenuation control the lowest point of the active trace is fixed and the amplitude range is adjusted to a smaller range as you slide the position indicator up and to a larger range as you slide it down If the detector signal exceeds the range of the display a vertical offset control is added to the right border of the display This control allows you to move the chromatogram up or down in the display window 263 x 1120874 Minutes 6 81 moks Cursor Display turns the cursor on or off The cursor follows the chromatogram trace and displays the time and amplitude of its current position in an info panel Hold the control key down to allow the cursor to move anywhere on the screen without following the active trace Basic colors gi eae Et ERE ae Ei BREE Bee nee Eee BT Custom colors I Display Faded Background Define Custom Colors gt gt Cancel Background Color Allows you to select any of the standard colors or a custom color as the background for the chromatogram display The Display Faded Background checkbox allows you to use either a uniform color or an artistic faded color effect as the background Interactive Scaling The following mouse actions are possible for the chromat
254. ith Ethernet addresses broadcast by devices on the network then the Ethernet addresses from 3800 and 3900 GCs connected to your network and powered on will automatically appear Note that the frequency with which these addresses are broadcast by the GC decreases over time to a minimum rate of once per minute This means that the BOOTP Server may not receive an Ethernet address for up to a minute from any given GC Once you have entered the Ethernet address for each networked GC into the BOOTP Server power each GC off then on again Check that the IP address shown on the front panel of each GC in the Remote Local Control screen matches the intended address entered into the BOOTP Server If they do not match verify the Ethernet address updating the BOOTP Server if necessary Powering the GC off and on will update the IP address NOTE When IP addresses are managed from central location by a Network Administrator the BOOTP Server on your workstation must be disabled Verify that the Manage IP addresses from this Workstation is unchecked in the Setup Ethernet Ports dialog box Setup BOOTP Server at 132 190 73 155 Using a Password to Protect BOOTP Settings You may wish to restrict access to the BOOTP Server dialog box to avoid inadvertent or unauthorized changes to IP address assignments To do so enable password protection in the BOOTP Server dialog box If the Setup Ethernet Ports dialog box is not displayed select the Setup Ethernet
255. ith sample molecules as they enter the ion trap forming Cl product ions by ion molecule reactions Hybrid Cl may be used with either positively charged or negatively charged reagent ions The ion trap operates in a pulsed mode Reagent ions are created only during the ionization pulse and are consumed during the reaction period to form analyte ions The number of analyte ions depends on the concentration of the analyte the initial reagent ion intensity and the reaction time 206 Space charge control in the Hybrid Cl mode is achieved by using the results from an AGC prescan to calculate the ionization time and reaction time for the analytical scan Because the spectral intensity is proportional to sample concentration and reaction time linear calibration curves can be obtained End Mass RF Start Mass lonization Reaction Scanning Hybrid CI Scan Function Analytical scan only During the Hybrid Cl analytical scan the following steps occur A The reagent gas is ionized for the length of time determined by the prescan B The selected reagent ions are stored in the ion trap Ejection of ions above the Selected Reagent High Mass is accomplished by applying a broadband waveform between the ionization and reaction periods C Reagent gas ions react with sample molecules to form sample ions The reaction time is determined by the prescan D Reagent ions are ejected E The Hybrid Cl mass spectrum is acquired for
256. ix scan segments The figure below illustrates the AGC prescan and four scan segments corresponding to the following four portions of the mass range default values 10 to 99 m z 100 to 249 m z 250 to 399 m z and 400 to 1000 m z One scan involves one complete ramping of the RF voltage over the mass range selected by the user The RF voltage is ramped at a constant rate of approximately 5000 daltons sec for normal scan and 10000 daltons sec for fast scan One complete scan at this fixed rate produces a microscan Prescan Analytical Scan U_ i E Segments 1 4 High mass cae RF End of Low segment mass Variable lonization Time The AGC Scan Function Scan Segment Setup Period The prescan is followed by the first of the scan segments Each segment is divided into two parts a setup period and a scanning period Each setup period is subdivided into the following four stages First stage The RF voltage is set to near OV for 2 milliseconds This setting allows the RF voltage generator circuit to stabilize while clearing the trap cavity of all ions Second stage The RF voltage is set to and stabilizes at the storage voltage selected to store or trap all ions of interest in the ion trap cavity Third stage Energetic electrons from the heated filament are accelerated into the ion trap where they interact with sample molecules to form sample ions For external ionization mode the ion formation occurs within the source with subse
257. lates bracket the filament to control electron pulsing The plate closest to the ion volume is the electron lens and the plate away from the ion volume is the repeller lens The electron lens is set positive and the repeller lens negative to admit electrons to the ion volume only during the ionization period Otherwise the voltages are reversed to exclude electrons from the ion volume Tuning of electron repeller lens voltages is important for linear signal response and filament lifetime The four variables to deal with are electron lens ON and OFF voltages and repeller lens ON and OFF voltages ON and OFF refer to ionization ON and OFF The electron lens ON voltage is set to optimize electron transmission to the ion volume electron lens OFF voltage is set to thoroughly exclude electrons from the 237 ion volume The Repeller Lens ON and OFF voltages balance the emission current Electron Repeller Lens Adjustment Electron lens tuning involves measuring the transient behavior of the emission current immediately after the lenses have been switched on or off If the lenses are unbalanced the emission current will change in time and be proportional to the imbalance If the balance is outside the range of 200 to 300 pA the algorithm will search the optimal values by changing values of four variables one at a time If it fails to find the best voltage setting for lens tuning auto tune will generate an error message and restore the last values in
258. lay additional options to configure Fixed lonization time Max lonization Time as well as the Prescan lon Time if applicable 274 tem Description S Automatic Gain Control Target TIC Fixed lonization Time Max lonization Time Internal El Cl Parameters Tab The AGC Target TIC Total lon Current is specified here The Automatic Gain Control AGC algorithm uses the ion count from a prescan at a fixed ion time along with this target value to calculate an ion time necessary to fill the ion trap with the target number of ions during the analytical scan The objective is to fill the trap with an optimal number of ions during each analytical scan The Target TIC is usually not set below 10000 for full scan acquisitions but it should also not be set too high or spectral distortions due to space charge loss of MS resolution and or shift in mass assignments for strong chromatographic peaks may result Typically a Target TIC between 20000 and 40000 gives the best results This component is disabled if you choose the Fixed lon Time checkbox in the Customize area If Fixed lonization Time is checked it becomes possible to run fixed ion time experiments Fixed ion time experiments are generally limited to diagnostic tests and are not advised for qualitative or quantitative analysis in the ion trap Choosing this check box disables both the Automatic Gain Control AND the Prescan lon Time functions and uses your Fixed and Max loniz
259. le Set the amplitude axis to full scale Set the time axis to full scale Return to previous stored scaling Go to next stored scaling Enable disable the Auto Scale feature Enable disable the cursor display Select the background color for the display Drag an area of the display to view a more detailed section of the plot or zoom in both axes by pressing and holding the left mouse button on the spot you wish to enlarge Holding the Shift key down will allow you to zoom out Front FID 0 051 m w Adjust amplitude scale Adjust zero offset Hide unhide vertical amplitude scale slider Adjust time scale 74 Documenting Module Information You may wish to document the configuration of your modules their installation and most recent service dates and other information pertinent to your instrument To do so use the Module Information Editor accessed from the Edit menu in the instrument window ut Shite Copy EHS Haste Shittans GEST Del 3800 Operation Set Actual r Front Detector EFC Add Stat Col Oven 90 90 Type11 Ready N Insent ins Front 1079 90 90 Select All GhitEnter Mid 1041 Of 48 Coolable3 N A N A Fill Down FrontFID 260 260 Edit Notes Mid ECD Off 42 Edit Module Info RunTime 0 00 min EndTime 4 00 min Reset Ready Method No Fault Ch 1 Make up Set Ch 2 H2 Set 30 Ar Valves 1 2 3 4 5
260. le driver for a detailed description if applicable Allows set up of the communication between the 3800 GC and System Control Setup ADC Board Opens the Setup ADC Board I O Ports Dialog Box to configure I O Ports the ADC Board base address and determine the Switch S1 settings for each ADC Board Applicable only if the ADC Board module driver is installed Setup COMM Ports Available if an optional module driver is installed that uses Serial I O to communicate with the device See the Operation Manual for your module driver such as the 3400 GC for a detailed description if applicable Configuration Window ital System Control Configuration File Edit Inject Automation Recalculate Instrument Windows Help els Queries een peel gt Instrument 1 Ferguson_1 Operator xavier Onassis Mot Ready Auto Start Module B ADO 44 mpi Available 300 Modules 2 The Configuration screen is divided into two parts the Instrument window and the Available Modules window Initially modules are displayed in the Available Modules window as they log in and can then be added to the Instrument by clicking and dragging the module icon into the Instrument window The configuration of modules is remembered when System Control closes and modules will be restored automatically to their proper locations when System Control is opened 222 The AutoStart Module area is used to designate which module will start the syste
261. le for an internal source Auto Tune Method W Auto select prerequisite tuning functions Select All Clear All Integrator era Set Electron Multiplier AF Full Scale Adjust Mase Calibration Trap Frequency Calibration Other functions are only needed when the instrument is in Hybrid or External ionization configuration Auto Tune is generally performed in the order listed All of the auto tune methods are selected if you click Select All or cleared if you click Clear All To perform Auto Tune click the desired check boxes and click Start Auto Tune You can stop the auto tune at any time by clicking Stop Auto Tune Integrator Zero Scan Number 2 Time 0 002 min RIC 1747 lon Range 99 5 500 4 m z Counts Integrator Zero Adjustment Set 360 May 20 13 15 04 Integrator Zero Adjustment Set 356 May 20 13 15 04 Integrator Zero Adjustment Set 354 May 20 13 15 04 Integrator Zero Adjustment Set 354 May 20 13 15 04 Av intensity 0 433 Acceptable limite 0 300 to 0 500 May 20 13 15 05 Integrator Zero Adjustment Completed Hay 20 13 15 05 qceneeeeceeeseeceesecessoesceeseesceeesescoessoosssossses May 20 13 15 05 Auto Tune Passed May 20 13 15 05 Integrator Zero Dac 354 PASS May 20 13 15 05 kuto Tune Passed The Integrator Zero Adjustment routine sets the signal level from the Integrator Circuitry with the filament off When the filament is off the major source of signal coming from this circuitry i
262. lick to display a plot of the Base Peak ion To display the trace and the Base Peak plot click the icon and enter BPI in the Ions field Clicking the Base Peak icon does not affect the display of the extracted ion chromatogram 29 Chromatogram Preferences Hide Kerpad Spectrum and Chromatogram Default Wier Al Sle A Eji e w Stacked Plots Overlaid Plots Normalized Plots Chromatogram Plot Preferences Report Preferences General Preferences Right click the chromatogram window to display a menu that offers these selections Chromatogram Plot Preferences Report Preferences or General Preferences Use Chromatogram Plot Preferences to modify the appearance of the plot This is used by chromatogram plot displays and reports in all MS applications including Standard MS Reports and Custom MS Reports Chromatogram Plot Preferences Colors Labels Axes Font E Background E Te E Foi E Pict 2 Plot 3 E Fi E Pict 5 E Plot E E Pict N FE E Pict 3 E Plot 10 Plot 11 PG Plat 12 PS Piet 13 E Fiii Plot 15 Pict 16 E Plet 17 E Fie E Fi 19 E Plet 20 D Background Correction Faded Background IY Color To White Help Reset to Defaults Save All as Defaults Reset All to Defaults 30 Use Report Preferences to select chromatogram and spectrum report options Report Preferences Spectra Anes Cal Curves Fonts Spooler Chro Reports Chro Markers Chro Colors
263. licking Upload MS Method However if you wish to also edit other sections such as data handling reports or 3800 GC sections click Edit Method in either the Manual Control or Acquisition Window to open the method in Method Builder Control and Status Source Internal Edit Method Method Internal Upload MS Methad Vacuum System OF Temperatures UF S Ounce OF Method Builder opens with the active Method loaded You can edit that section or other sections of the Method After editing and closing the Method Builder window you are prompted to reactivate the Method Reactivating the Method downloads the changes System Control h pa Method VarianwS Methse 1 mth has changed Reactivate ik 68 yNOTE If you access the active method from Method Builder via the Workstation Toolbar and then close the method editor or save a file the method must be reactivated in System Control To reactivate the current method click the button for the method in this example startup1 mth in the System Control toolbar and then select Re Activate Method a System Control Yarian 4000 GC MS Not Ready Fie Edit Inject Automation Recalculate Instrument indor eer F startup mith i viewlEdit Method pO Sui Nok Ready Edit Compound Sets Manual Control Auto Tune Tempe Print Method Re Activate Method gt Control and Status Changing Method End Time from the 4000 MS Status and Control Window You
264. lier voltage is set so that each electron emitted by the dynode creates a known signal from the multiplier The gain in this example is 3 71 x 10 Occasionally systems with an external or hybrid source fail this adjustment Increasing the flow of FC 43 usually allows the multiplier gain to be set An Event Window message Is displayed When the 10 gain voltage of your electron multiplier reaches 2000V order a new multiplier to have on hand When the 10 gain voltage exceeds 2500V should install a new multiplier Electron Lens Tuning In typical external ion sources electrons are continuously directed into an ion volume containing the sample to be ionized Eventually the interior surface of the ion volume becomes contaminated by material that can charge up and disturb the extraction of ions from the ion source To minimize ion volume contamination the 4000 MS pulses electrons into the ion volume only when needed for ionization Two plates bracket the filament to control electron pulsing The plate closest to the ion volume is the electron lens and the plate away from the ion volume is the Repeller lens The electron lens is set positive and the Repeller lens negative to admit electrons to the ion volume only during the ionization period Otherwise the voltages are reversed to exclude electrons from the ion volume Tuning the Electron Repeller lens voltages is important for linear signal response and filament lifetime The four variables
265. ll Down Sample_4 none none 0 1 0 Pos 1 Add Lines Activate Method ad Hardware LE 173 1 Select Activate Method from the Sample Type cell 2 Click on the AutoLink button in the row that you are working The Activate Method dialog box is displayed Method Path ame E WarianiwS Aewhethod mth Browse Cancel 3 Enter the name of the Method or use Browse to pick from a list of files 323 Automation File Editor New_Samples smp File Edit Help als Mls S lelem New_Samples smp 8400 SampleList Injection Autalink Injection Injectors Notes Volume Used Add Pos 1 Insert Delete Fill Down Add Lines Defaults 1 TU ic ee H alalala ms o ak lalalalala Data Files RecalcList When this line is encountered during automated injections the specified Method is activated You may specify any number of Methods to be used in the SampleList Using the Sequence Window The Sequence window allows you to specify multiple Methods and SampleLists to be processed during automation Edit Inject Automation Recalculate Activate Method Upload Active Method from Modules Hew SampleList Open Samplecist New RecalcList Open RecalcList New SequenceList Open SequenceList Pririt Printer Setup Exit Choose to open either a New SequenceList or an existing SequenceList from the File menu 174
266. llable if the notes exceed the available space The notes can be edited here either by typing text directly or by pasting text from the Clipboard by pressing the keys CTRL V simultaneously RecalcList Window Data Files can be added to a RecalcList by clicking on a cell in the Data File column and typing the file name or by pressing the Browse button and selecting the file name Another way to quickly add one or more Data Files to a RecalcList is to select the files of interest in the Explorer and drag them over the RecalcList Window When you release the mouse button the Data Files are automatically appended to the RecalcList Note that a Recalc List may contain standard GC data files run extension as well as MS data files sms extension Some of the Recalc List items described below are handled differently for the two data file types When the list is processed the appropriate data handling will be used automatically for each data file aii Automation File Editor SEPTA RCL File Edit Help Ales Bls S 4 lee SEPTA2 RCL RecalcList Iof Data File Add ce cl aranwe mpd septum cau sms CE ccWarlanwes mpd septum ce sms 316 Item Description Data File Shows the name and path of the Data File for each sample Sample Name Cannot be edited Shows the name of each sample in the RecalcList Sample Type Baseline Analysis Calibration Verification Print Calib New Calib Block Au
267. lock AutoLink Activate Method Sets the sample type or automation action of each line in the SampleList Cal Level 1to10 Sets the calibration level of each calibration or verification sample in the SampleList Inj 1to9 Sets the number of injections to be made of the sample Injection Notes Up to 180 characters Opens the Notes window for the selected sample to edit or create a note about the sample 322 Item Description S O AutoLink Unid Peak Factor Multiplier Amount Standard MultiChannel MultiStandard Add Two AutoLink commands when Sample Type is Baseline Analysis Calibration or Verification One AutoLink command when Sample Type is AutoLink One Activate Method Command when Sample Type is Activate Method Opens the AutoLink Parameters dialog box to set the options for linking to a remote application during automation through System Control Opens the Activate Method dialog box to set the path name for activating a new method during automation of a SampleList through System Control O to 1 000 000 0 Sets a calibration factor for unidentified peaks Not used by calibration samples 0 000001 to 1 000 000 0 Sets a value for the multiplier Results for the sample are multiplied by this value Not used by calibration samples 0 000001 to 1 000 000 0 Sets a value for the divisor Results for the sample are divided by this value Not used by calibration samples 0 000001 to 1 000 000 0
268. lonization r Scan Type Full v lonization El v Scan Mode Normal v Setpoints Defaults General Parameters lonization Control Internal El Parameters Full Scan Parameters SetPoints C Scan Time Maximum Scan Time Multiplier Offset 0 volts uScans Averaged 3 uScans Mass Defect 0 mmu 100u Data Rate 0 87 Hz Customize Full Scan El lonization Control Use lonization Control to set the Automatic Gain Control AGC target the total number of ions the system will attempt to generate within the trap using up to the Maximum ionization time selected A lower target reduces space charge effects on resolution while a higher target may improve quantitation Click Customize to display lonization Time If the Fixed lonization Time box is checked the AGC adjustment of ionization time is replaced by the fixed ionization time selected Click Defaults to restore the default times for the segment Scan Type lonization mode and Scan Mode Method Active Segment Checks and Adjustments Module Attributes Method Segment I lonization On Scan Type Full lonization El hd Scan Mode Normal hd Defaults General Parameters Ionization Control intemal El Parameters Full Scan Parameters Automatic Gain Contral Target TIC ad counts lonization Time Fixed lonization Time Max lon Time 25000 useconds Customize Full Scan El Internal El Parameters Use Internal El
269. ltiplier e Divisor e Amount Standard when one Internal Standard is being used See the GC Data Handling and Reports Manual for a brief description of these parameters See the Star Workstation Regulatory Compliance Manual for a complete description of how these parameters are used to calculate results Specifying a RecalcList You can choose to create a new RecalcList append to an existing RecalcList or neither create nor update a RecalcList To select an option that you want click on the RecalcList button and the related dialog box will be displayed RecalcList Generation a x ou can automatically create or update a AecalcList with files generated during automated injections Specify the RecalcList generation options for this SampleList below Do not automatically create and update a RecalcList Create and update a new RecalcList RecalcList name evara untitled rel Append to an existing RecalcList RecalcList name BTOWSE Overmrite the Recalc List each time the SampleList Begins Cancel If you choose to create a new RecalcList this automatically generated RecalcList will not overwrite an existing RecalcList If a RecalcList with the same file name exists the newly created RecalcList will have number appended to its file name to make it unique and to prevent the older RecalcList from being overwritten Alternatively you may select the checkbox to overwrite the RecalcList each time the Sam
270. lts of the most recent Autotune procedures and a log of any tuning errors encountered 245 Acquisition Selecting the Acquisition button activates the 4000 module for analysis The module loads the information for the active method so that it is ready to collect data according to the conditions prescribed in the method You will see a screen similar to the following Manual Contral Auto Tune Temperatures Diagnostics Startup Shutdown Acquisition a 4000 01 Ready Status nd Control Run Time End Time Ready No Fault 10 00 minutes Edit Weise Segment Description FILMUL DE L n MS Method Start Acquisition Segment Number 1 of 2 Operating Conditions Data File Scan Number Scan Description Filament Off lonization Time 0 T Wait For Readyln Scan A ange 20 25 lon Court T The red lights turn to green to indicate that the 4000 module is ready for analysis If the GC and or AutoSampler are not ready you will see a Not Ready message at the top of the screen Once the GC and AutoSampler come to a ready state the Not Ready message will change to Ready To determine the individual ready states of the components you can go to the top pull down menu under Windows and see the states for the 4000 3800 and AutoSampler modules Once all components are ready you are ready to start an analysis Start Acquisition Click Start Acquisition to immediately start the 4000 MS collecting data
271. m in Automation e Ifyou are not using an AutoSampler or other automated injection device do not place any module in this area e Ifyou are using a CP 3800 GC with an 8400 AutoSampler place the GC icon in the Autostart area e Ifyou are using an 8200 or a Combi PAL AutoSampler place the AutoSampler icon in the AutoStart area e If you are using any other device which will start the system through the Sync signal inputs of the GC leave the AutoStart area empty Instrument 1 Parameters Instrument Ferguson_1 Operator Sealers Heady File Mas Errors fO Prompt on Automation Start Cancel The Instrument 1 Parameters dialog allows you to enter an instrument name and operator name The Ready File is used only by earlier versions of the Saturn GC MS and should be left blank for operation with 4000 MS The Max Errors number sets the allowable number of non fatal errors during Automation When the limit is reached Automation halts An entry of 0 defeats this feature The Prompt on Automation Start checkbox allows you to view and edit information in this dialog each time Automation is started 223 Windows Menu a System Control Ferguson_1 Not Ready File Edit Inject Automation Recalculate Instrument Windows Help o lezlez Eysememn ls E Show Module Windows Iconize Module Windows 4000 01 Ready Show Automation Windows Iconize Automation Windows Arrange Icons Manual Control
272. mass range default values 10u to 99u 100u to 249u 250u to 399u and 400u to 1000u One scan involves one complete ramping of the RF voltage over the mass range selected by the user The RF voltage is ramped at a constant rate of approximately 5000 daltons sec for normal scan and 10000 daltons sec for fast scan One complete scan at this fixed rate produces a microscan Prescan Analytical Scan a ea Segments 1 4 High mass 7 RF End of Low segment mass Variable lonization Time The AGC Scan Function 192 Scan Segment Setup Period The prescan is followed by the first of the scan segments Each segment is divided into two parts a setup period and a scanning period Each setup period is subdivided into the following four stages First stage The RF voltage is set to near OV for 2 milliseconds This setting allows the RF voltage generator circuit to stabilize while clearing the trap cavity of all ions Second stage The RF voltage is set to and stabilizes at the storage voltage selected to store or trap all ions of interest in the ion trap cavity Third stage Energetic electrons from the heated filament are accelerated into the ion trap where they interact with sample molecules to form sample ions For external ionization mode the ion formation occurs within the source with subsequent transfer of ions to the trap by a set of lenses The newly formed sample ions are then permitted to stabilize in their orbits at the stor
273. mation Recalculate Instrument Windows Help meses Qos mn eel nfl Instrument 1 Varian 4000 GOMES Operator Jean Louis Ready Auto Start Module 3800 4000 i mi 44 bobs mp 56 Available Modules 70 Double click in the instrument area or select the instrument from the Instrument menu to view the 3800 GC Status and Control window If the 4000 MS window is displayed use the Windows menu to select the 3800 GC module arian AMi 0S Waiting lar Ready Fie Edt Inet Automation Recalculate Instrument windews Helo alal aeeoe Etim a 4000 5 Hol Branly Maru Cortal Auto Tune Temgerahaes Disgnoches ri Son Function Channels y Mocs Data Type Leberitity Noe ation a Contecid By lonization Time m Cy Charred tf 1 C Polis E Hons If the Status and Control Windows for the modules configured in the instrument are not currently displayed you can select Show Module Windows from the Windows menu and select a module for display at the bottom of the menu Elements of the System Control Toolbar The System Control Toolbar provides you with buttons to do the most common tasks performed in System Control Most Toolbar buttons correspond to a menu command You can learn what each button does by resting the pointer on the button Note that the buttons controlling the SampleList Sequence and RecalcList become available after you activate a corresponding automation file a System Control Star 2
274. me necessary to fill the ion trap with the target number of ions during the analytical scan The objective is to fill the trap with an optimal number of ions during each analytical scan The Target TIC is usually not set below 10 000 for full scan acquisitions but it should also not be set too high or spectral distortions due to space charge loss of MS resolution and or shift in mass assignments for strong chromatographic peaks may result Typically a Target TIC between 20 000 and 40 000 counts gives the best results 120 General Parameters lonization Control Full Scan Parameters Automatic Gain Control Target TIC 200004 counts lonization Time Fixed lonization Time lonteation Time 100 Useconds ES cs L rT Max lon Time 2500 useconds If one activates the Customize features it becomes possible to run fixed ion time experiments and or to change the Maximum lon Time for Automatic Gain Control Fixed ion time experiments are generally limited to diagnostic tests and are not advised for qualitative or quantitative analysis in the ion trap Changing the Maximum lon Time can improve the sensitivity of techniques such as MS MS or SIS This parameter can be increased to 65 000 usec If the ion time in the baseline of the chromatogram is not reduced below the maximum ion time the ion trap is not being filled with ions to the level designated by the Target TIC To increase the ion signal in External El mode
275. ment to the nearest tenth of a mass unit For library searching ion masses are rounded to the nearest integer If the m z of an ion happens to fall close to the 0 5u crossover point it may be assigned to the wrong mass This is more likely for molecules with higher molecular weights since the mass defects for several atoms may add together to produce a sizable mass defect The Multiplier Offset adjusts the EM voltage as much as 300V relative to the current multiplier setting in the Module Attributes tab dialog in Manual Control this is usually the10 gain value from Auto Tune Sometimes better sensitivity is achieved particularly in techniques such as MS MS when the multiplier voltage is increased Note that this adjustment can be made on a segment by segment basis The Count Threshold is normally 1 count a value of 2 3 counts will reduce the number of low level ions reported in the mass spectrum This approach may improve library searches and reduce data file size at the cost of somewhat less detailed information in the mass spectra The count threshold is shown only if the Customize button is active lonization Control General Parameters lonization Control Full Scan Parameters Automatic Gain Control Target TIC 20000 counts The Target Total lon Current or TIC is specified here The Automatic Gain Control AGC algorithm uses the ion count from a prescan at fixed ion time along with this target value to calculate an ion ti
276. mes that the syringe plunger has been stroked up and down This can be used to help monitor syringe wear and plan for syringe replacements Injection Mode Shows the injection mode specified in the active 3800 GC method Injection number where x and y are any number between 1 and 9 x of y Shows the number of the injection that is currently being run and the total number of injections scheduled for that sample Injectors used Pos 1 Pos 2 Pos 1 then 2 Pos 2 then 1 Shows the injector positions that the 8400 8410 will use for current run 2nd Injection Duplicate or Advance This field is only displayed when the 8400 8410 is in Dual Mode or Duplicate Mode Tray Orientation Vials 1 through 10 8410 Autolnjector Vials 11 through 16 or Only Vials 17 through 21 Shows the range of vials accessible from the current 8410 carrousel location 253 Sample Delivery Status tem Description S Valve 1 through If the valves are configured in the 3800 GC displays the assigned Valve 7 valve name and current state at the 3800 GC The possible valve names default state of the valve and the energized state of the valve are listed below Off On Unused Front Split On split Off splitless Middle Split On split Off splitless Rear Split On split Off splitless Gas Sampling Fill Inject Liquid Sampling Fill Inject Sample Off On Internal Std Off On Surrogate Std Off On Series Bypass Series Bypass Backflush
277. meters carrier gas column length and internal diameter 258 TCD Status Fault Yes or No A eee TCD Electronics On or Off re Bonet TOD Eee wigs ae netet Range 0 05 0 5 or 5 0 aye tare Too Raneseing Time Const Fast 50 usec or Slow 200 usec Displays the electrometer time constant setting from the TCD Adjustments in the active method Filament Temp O to 490 C Displays the TCD Filament Temperature setting in the active method Displays in mA the actual TCD current Balance Pct Displays in the TCD bridge balance On the 3800 GC the bridge is balanced automatically each time an Autozero is performed and should normally set around 0 A large offset in bridge balance or could indicate a potential problem Polarity Positive or negative Displays the current TCD Polarity setting Detector Signal Displays in mV the actual TCD detector signal at the 3800 GC Displays the data acquisition bunch size Displays the data acquisition bunch rate in Hz FID Status tem Description o Yes or No The FID detector is Ready Yes if the setpoints have been achieved and stabilized The FID detector is Not Ready No if readiness to start a run has not been achieved or if during a run the FID detector becomes not ready or goes out of tolerance Some reasons the GC may go Not Ready during a run are the temperature program is too aggressive the oven door is opened the coolant runs out the power line
278. mn oven is Ready Yes if the setpoints have been achieved and stabilized Fault Yes or No Displays if a fault in the column oven component has occurred Oven Power On or Off Displays if the column oven component is turned off or on at the 3800 GC Coolant On or Off Displays if the column oven coolant is enabled in the active method Setpoint 99 to 450 C Displays the column oven programmed temperature setting in the active method Actual 99 to 450 C Displays the actual temperature of the column oven at the 3800 GC Stabilization 0 00 to 10 00 min Time Shows the 3800 GC column oven stabilization time in minutes The stabilization time counts down from the programmed method value and then displays 0 00 minutes when the stabilization period is over Enable Column 30 C to 450 C Oven Coolant at Displays the programmed column oven temperature at which the column oven coolant is enabled Timeout 0 01 min to 999 99 min Displays the programmed coolant time out value in the active method for the column oven Timed Out Yes or No Displays Yes if the coolant time out period has elapsed for the column oven 252 AutoSampler Status This option is only shown on 3800 GCs that have an 8400 AutoSampler or 8410 Autolnjector connected to them tem Description 8400 8410 State Ready or Running Current Vial O through 99 for 8400 AutoSampler 1 through 21 for 8410 Autolnjector Plunger Strokes Displays the number of ti
279. moves water and other contaminants from the helium damping gas flow Turn on the getter heater after turning on the damping gas flow This does not appear when the instrument is in Internal configuration 59 Current Set Points Current Set Points Heated ones Trap Temperature 100 C Manifold Temperature KOC Transterline Temperature 250 C Source Temperature el C Vacuum System Pump Spin Speed 100 2 Pneumatics Flow Aate 4 0 mL rmir Geter Control Temperature 400 C Heated Zones The current set points of all heated zones are displayed The source temperature is not shown when the instrument is in Internal configuration Vacuum System The pump speed is indicated in the vacuum system field It should be 100 2 during normal operation Pneumatics The auxiliary Helium flow rate is shown for instruments in External or Hybrid configuration The flow is set in the Module Attributes tab dialog of Manual Control Turn the flow on by clicking Turn On under Damping Gas in the Control and Status field This does not appear when the instrument is in Internal configuration Getter Control The getter removes water oxygen and other contaminants from the Helium auxiliary damping gas flow This field is shown only when the instrument is in External or Hybrid configuration After starting the system and turning on the Damping Gas flow click Turn On button in the Getter Control field to
280. multiplier Clicking on the ion sources RF and multiplier will turn these parameters on off individually Edit Method Edit Method opens Method Builder with the current method in System Control Upload MS Method Upload MS Method opens a Save Method dialog to allow the MS method parameters currently active in System Control to be copied to an existing method or to a new method name Changes made in Manual Control must be Activated using the Activate Changes before they can be uploaded Checkboxes Clicking the Trap checkbox to turn on the entire ion trap system Click the lon Gauge checkbox to monitor the pressure inside the trap Clicking Calibration Gas and Cl Gas to open the valves to allow those gasses into the trap Method Segment Activate Changes Restore These become active only after one or more changes have been made through Manual Control Any changes made through Manual Control may be made a part of the active method by clicking Activate Changes Before this changes may be reversed and the method segment restored to its previous condition by pressing the Restore button To make changes a permanent part of the active method click Activate Changes then click Upload MS Method select a folder and file name and save the method You will be prompted to save any unactivated changes when you leave the Manual Control tab or change Segment number Active Method Segment Number The active method segment control allows you to select
281. n El mode you can see the characteristic spectrum with prominent ions at m z 69 131 264 414 and 502 The mass assignments of these ions and of m z 464 and 614 are checked during the Mass Calibration procedure in the Auto Tune mode Scan Number 13944 Time 183 787 min RIC 15582 lon Range 50 1000 mf KC oun 59 400 4474 oF 134 0 50 oy Oe ij 219 298 414 502 0 2 144 4 116 100 0 00 i i 250 S00 37 When the ion gauge is turned on a pressure reading is displayed in the area above the trap icon in the 4000 MS Keypad In this image the ion trap is in External El mode so the Damping Gas check is displayed Control and Status Source External Edit Method Method External El Upload MS Method Vacuum System OF Damping Gas UF Temperatures OK SOUE OF lon Gauge Pressure 11 6 uTorr Fil Walid Manual Control Tabs The 4000 MS Keypad has the following tabs Method Active Segment Checks and Adjustments Module Attributes Method Segment Method Active Segment Checks and Adjustments Module Attributes Method Segment 7 Ionization On Scan Type Ful Ionization E1 Scan Mode Normal z Defaults General Parameters Ionization Control Internal El Parameters Full Scan Parameters SetPoints C Sean Time Maximum Scan Time Multiplier Offset 0 4 volts uScans Averaged 3 44 uScans Mass Defect 4 mmu 100u Data Rate 0 87 Hz Customize ant Active Method Segment Scan Func
282. n all addresses and names have been entered When the Assign IP addresses starting from radio button is selected the bottom portion of the dialog changes 88 This Workstation will assign IP Addresses from a reserved black of addresses as 3800 GCs are powered on Use this feature when IP Addresses have been reserved for use by a pool of 3800 GCs but IF Address management is not performed by a Network Administrator ou must enter a Host Name for each 3800 GC after its IP Address ts assigned before it can connect to any Workstation C Assign IP addresses manually f Assign j IF addresses starting from i 32 190 73 208 This Workstation will assign these settings to each 3800 GC Subnet Mask 265 255 255 192 ateway 132 1790 73 1729 Domain cb vanan com Cancel Consecutively assign IP addresses beginning from a particular address Enter the number of IP addresses you want to assign automatically Enter the starting address here As 3800s are powered on IP addresses are automatically assigned starting with this address NOTE Proceed to Using a Password to Protect BOOTP Settings on page 90 Specifying IP Addresses from a Central BOOTP Server If IP addresses are managed by a Network Administrator from a central source the 3800 and or 3900 GCs must be added to the list of devices requiring IP addresses IP addresses must be assigned to GCs using a BOOTP Server A BOOTP Server lists Ethernet
283. n file of the selected type a Save Automation File Saves the currently displayed automation file with the existing name 5 Save Automation File As Displays the Save Automation File As dialog box allowing you to save the currently displayed automation file with a new name amp Print Automation File Prints the currently displayed automation file 312 Al Cut Deletes a selection and copies it to the Clipboard Used to remove or move a selected part of a spreadsheet Ep Copy Copies a selection to the Clipboard Used to duplicate a selection and place the duplicate in a new place using Paste B Paste Inserts previously cut or copied information that was stored in the Clipboard into a spreadsheet il Fill Down Causes the contents of the top cell in a series of highlighted cells to be copied to the cells below it Used to edit all the cells in a column quickly Open Automation File Dialog Box This dialog box is used to specify or open an automation file The Open Automation File dialog box appears with several different titles depending upon how you access it In all cases it contains the fields listed below in forms appropriate for the type of file you are about to open Open a RecalcList File Look ir Ej Examples paradc rel parais rel Files of type RecalcLists rcl Cancel E o Recent Files gt Look in Lists the available folders and files To see how the current folder fits in the hierarc
284. n l Getter Control Heater Olt Tum Wn Hide Keypad Event Messages Jan 13 15 45 43 Turning Damping Gas OM Jan 13 15 46 00 Turning Getter OM Start Up Shutdown When the system is shut down the Startup button is displayed Pressing the Startup button starts the pumping system and the zone heaters The status display shows the heated zone setpoints and current temperatures along with information on the turbo pump spinup and current draw After the system has been started the ShutDown button is displayed Pressing this button begins an orderly shutdown of the vacuum system and the heated zones The progress of the shutdown can be monitored on the status displays Vacuum System status indicating whether the Vacuum system is Ready To adjust damping gas see the Manual Control Tab instructions See Startup Shutdown Tab instructions to turn on the damping gas Pneumatics Damping Gas Turn On Turn Off If you have the Damping gas option installed the Turn On Turn Off button on this dialog will allow you to control the damping gas flow The flow rate is set in the Manual Control section under the Module Attributes tab 244 Getter Control Heater Turn On Turn Off If you have the Damping Gas option installed the Heater Turn On Turn Off button allows you to control the heater The heater cannot be turned on until the Damping Gas is turned on The getter temperature setpoint is fixed at 400 C Current Set Points
285. nce List EICI SEQ h SampleList New Samples smp RecalcList Pesticide rcl Instrument 1 Status Message Log 3800 44 Ready 4000 56 Not Ready Show Module Windows See all module windows configured in the instrument In this example the modules available are the 3800 GC and the 4000 MS 24 Iconize Module Windows The individual module windows become icons at the bottom of the screen Show Automation Windows Click to view the automation screens that are open These are the SampleList RecalcList and SequenceList Iconize Automation Windows Transform open automation screen windows into icons so you can access windows that were behind the automation windows Arrange Icons Arranges the icons if any in a row at the bottom of the System Control window SequenceList Click to display the active SequenceList SampleList Click to display the active SampleList RecalcList Click to display the active Recalculation list Instrument 1 Status Click to view the status of the modules connected to the system Message Log Click to view the event log for the MS module The log display is shown below The error messages for the 4000 MS Module are displayed Message Log MSGLOGI 5 24 2004 _13 54 47 MLG May 2415144 Module 4000 56 Some Auto Tunes not up to date VMay 24 151529 Ins 1 WorkStation DOWNLOADING May 24 1515 29 Method DEFAULT MTH Activated hap 24151529 Ins 1 Work Station IDLE i May 24151530 Module 40
286. nclude the file extension in the Data File name Directory for Data Files Data File names gt VARIANWS xs E gt data C 1200 El and NCI Pest 8081 Example E3 BC CI test BFE Sample 11 aii Use the following symbols to enter the O corresponding variable data to the file name New Folder il s Sample ID Injection number 4d Date m Drives 4 Detector Module name c gt t Injection Time Cancel Specifying a RecalcList You can choose to create a new RecalcList append to an existing RecalcList or not create nor update a RecalcList To select the RecalcList option that you want click on the RecalcList button The RecalcList Generation dialog box is displayed RecalcList Generation e X fou can automatically create or update a RecalcList with files generated during automated injections Specify the RecalcList generation options for this SarnpleList below Do not automatically create and update a RecalcList Create and update a new RecalcList RecalcList name Jc warianws untitled rel Append to an existing RecalcList RecalcList name Browse Overvarite the Recale List each time the SampleList Begins Cancel If you choose to create a new RecalcList this automatically generated RecalcList will not overwrite an existing RecalcList If a RecalcList with the same file name exists the newly created RecalcList will have number appe
287. nded to its file name to make it unique and to prevent the older RecalcList from being overwritten Alternatively you may select the checkbox to overwrite the RecalcList each time the SampleList begins Changing Default SampleList Entries When you add a new row into a SampleList default values are used for each cell To change the default values click on the Default button in the open SampleList window The following dialog box will be displayed Enter the desired default values and click on Save 171 Set 8400 SampleList Defaults xi MultiChannel MultiStandard 1 0 Pas 1 7 Cancel Monitoring the Status of Runs Monitor the status of a run in the instrument window AATRE Eaa maton aas e Ecosu erare ITH a Seuiem Casiral Yarian 4000 GEO HR Aurii Pia Eat Inject Mimmin Ficatodste Inetrurant Window Hie alla Caie Ennala r ej Hald Fiti E Run ing Tihi Arid Corin ME beth Dasig Dornia Segre hurts jat Dra Fa BIH Lis Caira Tet Dap Dhaai Stan Piada Sid Sean Deep El duno FULL lcii Tare SEA zenia Sean Panga 2 200 lon Cou 17117 E inl B H H Ela E Bilib Fige ir lined a Hi E Ea kom hian iers ka ig a eer a ele Elm al Bel kmis ME ABO Un coun Tes Ses F j a dl l J 2a 5 E5 1 124 The module status is shown in the status and control windows and on the Toolbar Keypad Display For information on Status and Control
288. nearest tenth of a mass unit For library searching ion masses are rounded to the nearest integer If the m z of an ion happens to fall close to the 0 5 u crossover point it may be assigned to the wrong mass This is more likely for molecules with higher molecular weights since the mass defects for several atoms may add together to produce a sizable mass defect Range 500 to 5000 milli mass units per 100 mass units mmu 100u Multiplier Offset The Multiplier Offset adjusts the EM voltage as much as 300V relative to the current multiplier setting in the Module Attributes tab dialog in Manual Control this is usually the 10 gain value from Auto Tune Sometimes better sensitivity is achieved particularly in techniques such as MS MS when the multiplier voltage is increased Note that this adjustment can be made on a segment by segment basis The same multiplier gain must be used for determining the calibration curve and analyzing unknown samples Range 300 to 300 volts lonization Control The lonization Control Tab has either 1 or 2 editable fields Tab depending on the Scan Type selected The Automatic Gain Control Target TIC Total lonization Count always appears albeit with differing default values depending on the Scan Type When either AMD or MRM has been selected you will see a field to set the Prescan lon Time in microseconds for that particular time segment Also you may click the Customize button which will disp
289. ng IP addresses NOTE If you are connecting your 3800 GC and Varian MS Workstation PC to a multi purpose company network managed by a Network Administrator see Configuring the 3800 GC Communication for a Company Network You can connect one 3800 GC directly to one Workstation S MS Ethernet S800 GC Workstation Cable After you have configured your computer s network settings start System Control ejeje a G fem AS o HANE EAA ir HIRA iR Click on the System Control Automation button PAINE RE RAT INE IAN Poi _ waee A Hin Ai i AY itr oi pi s af A x Ya i t 3 Rt RLN F 67 B a s fun P KY Default mth AES ie ie y th x _ D u M A S i x Tr MOAT EMT E LLACMA Ci LAAT AAR E A LLAT AMTT a A A rri LA When System Control has started for the first time the Star Assistant Communication Configuration Wizard will appear to guide you through the setup and network connections of your 3800 GC Use the following procedure for configuring the IP address for your GC The first time the Star Assistant guides you through the setup of your 3800 you will get the following messages Configuring Communications This Star Assistant will guide vou through the configuration of the hardware and software used for communications with your instrument modules IF you prefer to wait you can use the Setup commands in the Instrument Menu at any time Click the Mest button to conti
290. ning to Diagnostics mode The gate is pulsed to 120V during ionization and 120V otherwise so that electrons enter the trap only when they are needed for ionization lon Source External or Hybrid lon Source E mission 25 u mps Balance 195 usec Deviation 0 3 uA Filament Bias 70 0 Volts Filament 1 OF Filament 2 Untested On Ott Lens 2 A0 Volts 720 Volts Electron Lens 100 Volts 110 Volts Repeller Lens 99 Volts 99 Volks Lens 1 25 6 Volts Lens 3 19 7 Volts Ring Offset 7 4 Volts Endcap Offset 7 4 Volts When the system is in External or Hybrid configuration the emission current is set to a default value of 25 uAmps In negative CI External or Hybrid the emission current is set to a default of 250 uAmps The emission reading may vary by several Amps from this value Balance is a measure of how well balanced the 57 emission current is between ionization on and off Deviation is a measure of the total deviation of emission current as ionization turns on and off Deviation is an indication of the lens ability to provide a symmetrical pulse of electrons into the source If Deviation gt 5 Amps the electron lens needs to be tuned The filament bias is its voltage relative to ground The bias is always 70V in External and Hybrid modes The status of both filaments is indicated as OK Open or Untested If the Filament is untested you can determine its status by a
291. nue W Show this introduction nest time Cancel 83 Read the description presented in each window and click on the Next button to advance to the next step Configuring Communications Configuring Communications a a l B l E From the Setup Ethernet Ports dialog box click on Setup for IP Address Management BOOTP Server Setup Ethernet Ports for nabilB csb varian com 132 190 73 155 Click on the Setup button When the Setup BOOTP Server dialog box is displayed turn on the 3800 GC that has been connected to the network 84 NOTE If more than one Workstation is being connected on the same network only one Workstation should manage the IP addresses for all GCs connected all others should have the Manage IP addresses from this Workstation checkbox unchecked If more than one Workstation is managing IP addresses naming conflicts may arise As the GC is powered on an entry is added to the table For each entry an IP address is automatically assigned For each GC you provide a host name that will be used to identify it in the Varian MS Workstation Setup BOOTP Server at 10 2 129 1 10 0 132 14 4 00 60 93 00 84 0e at This Workstation will assign IP Addresses as 3600 GCs are powered on Use this feature when only Workstations and 3800 GCs are connected to the network You must enter a Host Mame for each 3800 GL after its IF Address i assigned before
292. o dissociation is observed reducing this amplitude may help However some ions with a higher m z than the precursor ion may not be ejected Dissociation Excitation Excitation Excitation Waveform Type Storage Amplitude Time Level m z volts 136 2 2000 Customize Dissociation Parameters Non Resonant Waveform Type The waveform type is either resonant or non resonant Resonant waveforms are harmonious with the frequencies of electrons held in 133 the ion trap Non resonant waveforms are not harmonious with the frequencies of the electrons held in the ion trap Excitation Storage Level m z The RF storage level in m z when the dissociation waveform is applied following isolation The excitation storage level range depends on the precursor mass but the lowest product ion must be more than several mass units above the excitation storage level A starting excitation storage level for a precursor ion can be calculated using the q calculator The q calculator is accessed by right clicking on any of the fields in the MS MS parameters table The optimum excitation storage level is a tradeoff between a storage level high enough to allow fragmentation of the precursor ion and a storage level low enough to allow efficient trapping of the lowest m z product ion A higher excitation storage level allows more energy to be imparted to the precursor ions by allowing a higher excitation amplitude Excitation Amplit
293. odules When an MS method is activated the GC method will not be downloaded To activate the GC and AutoSampler modules click drag drop the icons into the active field 96 Building GC MS Methods Using Star Assistant to Create a New Method Click the Method Builder button B on the Workstation Toolbar to open the Create Open Method File dialog box Create Open Method File Ea Select a method file action f Create a New Method File Open an Existing Method File Peace Do not display this dialog at startup If you choose Create a New Method File the Star Assistant Wizard will guide you in building this new method To avoid seeing this message again uncheck the box Show this introduction next time Configuring method This Star Assistant will guide you through adding instrument module control and any post run processing to the method Click the Nest button to continue 1 Select the instrument configuration for the method either Custom or Instrument 1 Use Custom configuration to create methods on a PC remote from the instrument 97 Select Configuration Select an existing instrument configuration for the method or elect a custom configuration for the method Then click Next to continue Select a Configuration Configuration Description The following screens will guide you in selecting a custom configuration for your method Instrument 1 lt Back Cancel
294. ogram display window Action Effect of Action Left mouse button Any section of the chromatogram display may be expanded to fill click and drag a the chromatogram window by clicking and dragging the cursor to selection enclose the area of interest on the display Whenever the display scaling is less than full scale in either axis the appropriate scroll bar s will be displayed at the right or bottom of the display to allow scrolling of the display Left mouse button Zooms out to full scale double click 264 Left mouse click Zooms isometrically from the mouse position or if you are and hold holding the control key down zooms out from that point Once PowerZooming begins you can move the mouse around while the mouse button is still down to change the point at which you are zooming 3800 Setup Dialog 3800 Setup Column Oven zone Temp Limit 325 C No Coolant one 1 Front 1177 Temp Limit 350 C No Coolant one 2 Wid 1079 Temp Limit 350 C LH 2 Coolant one 3 Rear 1041 Temp Limit 300 C No Coolant one 4 Front FID Temp Limit 400 C one 5 Mid FID Temp Limit 400 C Zone 6 Rear ECD Temp Limit 400 C Front Injector EFC Type 1 Outlet Atm Units psi Splitless Yent 10 ml min Gas Saver 20 ml min after 120 00 Mid Injector EFC Type 1 Outlet Atm Units psi Splitless Yent 10 mlrmin Gas Saver 20 ml min after 120 00 Rear Injector EFC Type 3 is Configured with Outlet Atm Units psi Front FID Det
295. ol Adjust the flow of reagent gas so that the ion gauge reading is between 50 and 80 uTorr Forming Reagent lons In the first step reagent gas ions are formed as the reagent gas is ionized by interaction with electrons emitted by the filament In external mode the Cl reagent can be either liquid or gas The most common reagents are methane and ammonia For ammonia the reagent ion is simply the protonated reagent NH4 NOTE Reagent ion formation can be a complex process For example when methane is used as the reagent gas reagent gas ions are formed as follows First methane is ionized to form two primary ions CH e CH 2e CH e CH e H These primary ions then react very rapidly to form predominantly the secondary ions CH and C H CH CH gt CH4 CH CH CH gt C H H The function of the reagent in negative Cl is to act as a source of electrons and then to thermalize or lower the kinetic energy of the electrons Only electrons with energies less than 1 2 eV can attach and form negative ions by electron capture Transferring Analyte lons to the lon Trap As chemical ionization occurs in the ion source product ions are continuously being directed toward the ion trap by the lenses between the source and the ion trap Loss of electrons from negative ions or fragmentation of positive ions can occur during this transfer process Lowering RF storage levels may reduce this effect but remembe
296. olenoids by clicking on the Cl Gas Control on the System Control page and allow the vapor flow from the reservoir to equilibrate If after allowing some time for equilibration there is not enough Cl gas entering the trap further open the needle valve by turning it clockwise 4 While observing the spectrum using Adjust Cl Gas checks and adjustments tab turn the Cl needle valve to increase or decrease the amount of reagent entering the trap until the resolution between M and M 1 just starts to degrade Forming Reagent lons In the first step reagent gas ions are formed as the reagent gas is ionized by interaction with electrons emitted by the filament The ion trap operates in a pulsed mode The supply of reagent ions is created during the ionization pulse and consumed during the reaction period to form analyte ions 194 In internal mode the Cl reagent can be either liquid or gas The most common reagents are methane methanol acetonitrile and isobutane NOTE Reagent ion formation can be a complex process For example when methane is used as the reagent gas reagent gas ions are formed as follows First methane is ionized to form two primary ions CH e CH 2e CH e CH e H These primary ions then react very rapidly to form predominantly the secondary ions CH and C H CH CH gt CH CH CH CH gt C H H PCI Reactions in the lon Trap Four main types of reactions occur in positive c
297. oltages are determined based on weighted intensities of the two ions RF Full Scale Adjust This routine should always be run before mass calibration and trap function calibration The RF Full Scale Adjust routine coarsely adjusts the mass calibration of the ion trap Successive adjustments are performed on PFTBA calibration gas ions at m z 69 414 and 614 For this algorithm to work properly it is important that the specified ions are stable and present in sufficient intensity gt 20 counts under normal scanning conditions Mass Calibration When you initiate this routine the calibration gas valve is opened and the electron multiplier filament and RF voltage are turned on The algorithm then uses the calibration compound ions at m z 69 131 264 414 464 and 614 to create a calibration curve The nitrogen peak m z 28 is not used for calibration A fixed offset at m z 0 has been empirically determined to give proper mass assignments between m z 10 and 69 The calibration is extrapolated from the highest observed calibration ion to the maximum mass m z 1000 Mass calibration is performed in both normal scanning 5 000 u sec and fast scanning 10 000 u sec modes Factors Affecting Mass Calibration For this routine to work properly the calibration ions must be present in sufficient intensity gt 20 counts and stable under normal scanning conditions Temperature changes can shift the mass calibration and this procedure should be
298. oltages are useful if an increase in the relative abundance at the low end of the mass range is desired Furthermore if your application involves more fragile compounds then a lower setting can produce a situation where less fragmentation of the molecular ion is observed Temperatures Tab a System Control Yarian 4000 GC M5 Not Ready File Edit Inject Aukomation Recalculate Instrument Windows Help alele E satupmh lal l lE jm Not Ready Manual Control Auto Tune Temperatures Diagnostics Startup Shutdown Acquisition Control and Status Conditions Analysis Start Bakeout State Ready Analysis Bakeout Operating Conditions Trap Temperature 1 00 E Manifold Temperature sa E Transfer Line Temperature 200 E Trap Temperature 101 C Manifold Temperature 37C Hold Time 0 00 hours Tiansterline Temperature 253 C lon Source Temperature ET C lon Source Temperature 221 C Save Restore Hide Keypad Event Messages Control and Status Control and Status Conditions Analysis Start Bakeout State Ready Hold Time 0 00 hours The Control and Status area has Temperature information and identifies if Analysis or Bakeout temperatures are active State tells if the system is Ready or Equilibrating If a bakeout has been started the Hold Time field shows the remaining time before the bakeout is complete NOTE Hold Time does not start counting down until bakeout temperat
299. olume ful Pre Inj Sample Flushes oll Strokes 1o ia Post Inj Solvent Flushes a 4utosample a Speed uL seck 5 0 HH Clean Solvent Source El Sample Delivery g Data Handling E Integration Parameters Peak Table Calibration Setup LE Verification Setup Time Events Table SA Standard Reports Print Options Results Format Chromatogram Format Calibration Block Report Format Column Oven End Time 20 00 min Default clean steps are used in the case that automation is stopped or a serious fault is detected Select Pre and Post injection syringe clean modes Injection Mode Injection Mode Std Split S plitl Std On Columr lean Wal Volume fuL User Defined ted The Injection Mode selection consists of five predefined injection modes Standard Split Splitless Standard On Column Neat Viscous and Volatile If any of these modes cannot satisfy your injection needs a sixth User Defined mode is available Selecting User Defined mode allows you access to all 8400 autosampler parameters to fine tune your injection Consult the Online Help for a detailed description of all Injection Mode parameters Auto Configuring the Method to Match the 3800 GC Hardware When you edit a 3800 GC Method while the corresponding GC is online in System Control you are warned if the Method configuration does not match the hardware on the GC 154 M
300. omplex rearrangements following collision induced dissociation The second method for increasing the precursor ion kinetic energy involves resonant excitation This method requires application of a high frequency supplemental dipole field to the end caps of the ion trap The frequency must match the oscillation frequency of the trapped ion The resonant frequency of the trapped ion depends on ion mass space charge within the ion trap RF trapping field amplitude and other instrumental factors Thus it is difficult to precisely calculate its value The amplitude of the RF trapping field is therefore modulated over a fixed range As the resonant frequency of the trapped ion depends on the magnitude of the RF field modulating the RF field amplitude results in a modulation of the resonant frequency of the ion Modulation of this frequency causes the frequency of the ion to periodically match that of the applied supplemental dipole field Thus the energy coupled to ion motion is maximized and the effects of shifts in the ion resonant frequency are minimized The resonant excitation method is selective to the mass range that is excited It permits coupling of energy to the motion of an ion having a particular m z value in a very controlled way Consequently at the correct excitation amplitude the rate that the amplitude of the ion motion increases is just balanced by the rate that energy is removed by collisions The ion is not ejected and energy can
301. omponents that will be monitored and tested The user may also select which filament is to be monitored Filament 1 or Filament 2 by selecting the appropriate radio button Diagnostic Tests Tab The Diagnostic Tests Tab provides a checklist of which diagnostic tests should be run There are currently three diagnostic tests that can be run System Verification Waveform Generator and the Scan and Acquisition Test There are Select All and Clear All buttons Display You may choose to display either Monitor Window and or Event Messages by choosing the desired display from the drop down menu next to the Keypad button Event Messages are a log of actions and events which have occurred during the Diagnostic and Monitoring process In most cases there will be messages indicating if certain tests Started Passed and Completed The Monitor Window displays the status and values of the following systems Vacuum Trap Waveform Temperatures and lon Source Have both Monitor Window and Event Messages selected at the start of any diagnostics and monitoring After you select which components to activate and diagnose click Start Diagnostic in the Control and Status Area The Monitor Window has the following areas that indicate the value and status of their respective components Vacuum System This indicates the status of the Turbo Pump lon Gauge and Foreline Pressure The Turbo Pump area indicates the pump status Stopped Running the pump speed
302. on distribution that results from the CID process depends on the characteristics of the precursor ion and the amount of energy that has been converted into internal vibrational energy The amount of energy that is converted to internal energy in the precursor ion depends on the number of collisions excitation time the relative energy of the collisions CID excitation amplitude and the rate that the internal energy is removed by collisional deactivation related to the excitation method Collision induced dissociation in the ion trap is always in competition with ion ejection If the CID excitation amplitude selected is too large the precursor ion will be 210 ejected to the trap electrodes before it can collide with background helium atoms If the CID excitation amplitude selected is too small the energy of the precursor ion will not exceed the internal energy threshold required to break the chemical bonds and form product ions This is because energy is constantly being removed by low energy collisional deactivation Therefore the CID excitation amplitude and the excitation time are both used to optimize the CID process in conjunction with an appropriate choice of excitation method The translational kinetic energy of the precursor ion can be increased using either of two methods Each method requires application of a waveform to the ion trap The waveform amplitude is called the CID excitation amplitude and the length of time that the w
303. one Workstation is being connected on the same network only one Workstation should manage the IP addresses for all GCs connected all others should have the Manage IP addresses from this Workstation checkbox unchecked The Workstation acting as BOOTP Server must remain running all the time to allow other Workstations to connect to GCs If more than one Workstation is managing IP addresses naming conflicts may arise Setup BOOTP Server at 132 190 73 155 Delete am Manually enter an IF Address and Host Mame corresponding to each Ethernet Address in the table Use this feature when individual IF Addresses and Host Names have been reserved for use by each 3800 GC but IF Address and Host Name management it not performed by a Network Administrator Assign IP addresses manually C Assign fo IP addresses starting from 0 0 0 0 This Workstation will assign these settings to each 3800 GC Subnet Mask 265 56 255 192 Gateway 132 190 73 129 Domain cab vaian com Check Manage IP addresses from this Workstation box to enable the BOOTP Server If 3800 or 3900 GCs are already connected to the network and powered on their Ethernet addresses will appear in the table You must enter a host name for each GC The IP address will not be assigned to the GC until a name is entered You may manually assign any IP address to any GC When this item is selected type the IP addresses directly into the table Select OK whe
304. ones of the 3800 GC The display is Fault if a fault occurs in the zone component or Off if the zone oven is off If the zone has not been configured by the 3800 GC then N A is displayed for the setpoints and actual temperature Clicking on one of the temperature zone entries will display the corresponding component status in the Component Status Display The LEDs indicate the status of each temperature zone If the zone is not configured or the zone oven is off the LED is gray If the temperature zone is Not Ready or there is a fault then the LED is red Otherwise the LED is green Component Status Display Column Oven Status Ready Yes Fault No Oven Power On Coolant OFf Setpoint 5C Actual 65C Stabilization Time 0 50 min Enable Column Oven Coolant at 50 C Timeout 20 00 min Timed Quk No Column Oven Status Front Injector Status Middle Injector Status Rear Injector Status Front Flow Pressure Status Middle FlowPressure Status Rear Flow Pressure Status Column Oven Status Front Detector Status Middle Detector Status Rear Detector Status Front Detector EFC Status Middle Detector EFC Status Rear Detector EFC Status Aubosampler Status The Component Status display is in the right portion of the 3800 Status and Control window Select the component status to view with the drop down list box below the display area 251 Column Oven Status tem Desoription Ready Yes or No The colu
305. onization mode e Internal Electron lonization on page 191 e Internal Positive Chemical lonization on page 194 e External Electron lonization on page 199 e External Positive or Negative Chemical lonization on page 202 e Hybrid Positive or Negative Chemical lonization on page 206 Internal Electron lonization About Internal Electron lonization Electron ionization is the most common mode of operation of the 4000 MS All of the sample ionization fragmentation storage and scanning steps occur within the confines of the ion trap Electron ionization generates fragments that are specific to the compound providing fingerprint spectra It is however not selective and will show ions for all compounds present El is sensitive but the sensitivity can be improved by reducing the interfering ions using ion preparation techniques In the El mode electrons are gated into the ion trap cavity during the ionization period These electrons collide with the neutral sample molecules A removing an additional electron to create energetically excited molecular ions A Some of the excited molecular ions equilibrate through collisions with helium but others undergo unimolecular decomposition to create various fragment ions fy This set of fragment ions characteristic of the sample molecule makes up the mass spectrum A e gt At 2e lonization A is excited He At gt At Equilibration At ff n Fragmentation
306. onization Storage Level Target Factor lon Time Factor and Waveform Scale Factor can be adjusted for each of the mass segments The Waveform Scale Factor can be autoscaled based on the calibration or explicitly set NOTE There is a minimum gap of 10 m z between the end of one segment and the start of the next segment Single lon Mode Single lon Mode is where a single ion is selected for storage a aaau Low Mass High Hass m z EE SIS Single lon Mode 2B Lt The Single lon mode of SIS has the advantage of removing all of the background noise from the analysis However since there is only one ion there is no secondary information and therefore no confirmation of the compound NOTE Unit mass isolation can only take place at low mass at higher masses a range of ions is stored even when a single mass is entered 143 Multiple lon Mode S15 1 Low Mass High Mass m z ia 276 276 414 414 so e SIS Multiple lon Mode The Multiple lon Mode is used to collect several ions from a single analyte This allows for confirmation of compound identity through ion ratio confirmation Up to six 6 ions can be specified in a single time segment Range Mode i Low Mass High Mass m z zie 150 350 460 SIS Range Mode The Range Mode is good at eliminating sections of the spectra where high background ions are present such as column bleed at 207 m z Up to 6 ranges can be analyzed in a
307. optimize trapping of the ions of interest a notched waveform is applied during ionization for internal El mode For external El amp external Cl mode a notched waveform is applied after the ions are trapped The ions are analyzed by applying a radio frequency RF voltage to the ring electrode encircling the trap cavity As the voltage increases on the ring electrode ions are sequentially ejected from the trap according to their mass to charge ratio Supplemental waveform voltages are applied to the end cap electrodes during the analysis to improve mass resolution and mass axis stability The ions scanned out of the trap strike the conversion dynode ejecting electrons which are repelled to the electron multiplier The conversion dynode is held at 10 KV and the voltage on the multiplier is adjusted to provide an enhancement of 10 The signal is then sent through an integrator to collect an intensity reading for each m z MS data are stored as sets of ion intensity pairs for each m z over the acquired mass range A complete mass spectrum is stored for each analytical scan Hybrid Positive or Negative Chemical lonization Hybrid Cl Scan Function In the Hybrid Cl configuration the external ion source is installed but the transfer line directs the sample into the ion trap Cl reagent ions are generated in the external source and only those reagent ions which are selected are stored in the ion trap These trapped reagent ions are allowed to react w
308. or build a new method appropriate to the new ionization configuration 105 The ionization configuration is selected in the MS Acquisition Method section of the method in the Instrument Configuration list box If you change the ionization configuration in a method all the previous Time Segment information will be replaced with a default section appropriate to the new ionization configuration Internal Configuration Options In Internal configuration you can create a method to collect El or Cl data alone or you can build a method with multiple time segments to collect either El or Cl data Cl in internal configuration can only be performed on positive ions This is also known as PCI External Configuration Options In External configuration create an External El method or an External Cl method but not a method with both El and Cl segments However in Cl mode you can collect either positive Cl PCI or negative Cl NCI data on a segment by segment basis When an External Cl method is active the Cl ion volume in the external ion source is automatically inserted except when Auto Tune methods are being run Hybrid Configuration Options Hybrid methods can be performed only in positive or negative ion Cl modes PCI or NCI except when Auto Tune methods requiring El mode are being run For both these methods Cl reagent ions are formed in the external ion source and drawn into the ion trap to react with compounds eluting from the GC column
309. ork Logon Client for Microsoft Networks File and Print Sharing Description TCP IP ts the protocol you use to connect to the Internet and wide area networks 4 Select Protocol and click Add TT Select Network Component ype EAE Add Cancel Click the type of network component you want to install Protocol i a language a computer uses Computers must use the same protocol to communicate 5 Select Microsoft as the manufacturer Select Network Protocol Ed Click the Network Protocol that you want to install then click OF IF you have i an installation disk for this device click Have Disk Manufacturers Network Protocals IPSS Pe compatible Protocol Microsoft OLC ra Digital Equipment DEC F NetBEUI 4 SunSoft Have Disk Cea 6 Select TCP IP as the protocol Click OK The protocol is added to your installed network Component list NOTE If you are not connecting your Workstation to a company network that is you are not assigned an IP address by a Network Administrator follow the next three steps If you are connecting your Workstation to a company network skip to Configuring the GC for a Company Network on page 85 78 Configuring TCP IP Parameters with no Company Network The following three steps assume you have completed steps 1 through 3 from the previous procedure 1 Select TCP IP from the network components list and click
310. ormance Range Internal El 10 65 000 microseconds Range Internal PCI 10 2 500 microseconds The Internal El Cl Parameters Tab will display an editable field for Emission Current When in Cl mode additional fields for editing Reagent Gas parameters are available 275 tem Description S Emission Current Reagent Parameters Reagent Low Mass Reagent High Mass Customize Reaction Storage Level The Emission Current uAmps is the current of electrons produced by the filament and it controls the number of electrons that enter the trap By increasing the emission current so that the ion time for the baseline is approximately the maximum ion time the maximum number of ions will be present In certain cases a high emission current can be used to increase the sensitivity One of these is EI MS MS where the MS MS isolation step eliminates the higher background that would normally arise from a high emission current This option appears in both El and CI Methods Range 10 100 microAmps Internal El CI Range 5 250 microAmps External El Cl Hybrid Cl When you select a standard reagent i e Acetonitrile Isobutane Methane or Methanol the Cl parameters for the selected reagent are set automatically and you do not need to change the default values of the Cl parameters However the Cl parameters Reaction Storage Level Ejection Amplitude V and Max Reaction time can be optimized for sensitivity by
311. orsey 132 790 73 756 3000 pilot 2 Available 132 790 75 154 3800 pilot 6 Available 132 190 735 153 3800 pilot Available 132 190 735 152 3500 pilot Available 132 190 73 182 Ok Cancel Select the GC that you wish to connect to the address 44 Click on OK to make the selection NOTE If you are running on a company network only GCs on the same local subnet appear in the Select Available Modules dialog box To connect to a GC in a different subnet type its IP Address directly into the IP address field in the Setup Ethernet Ports dialog box Consult your Network Administrator about subnets on your network After you have completed your selection the Setup Ethernet Ports Dialog Box shows the 3800 GC connected to your Workstation 92 Setup Ethernet Ports for Nabil B csb yarian com 132 190 73 155 Address Module Type IP Address or Domain Name Status Actual IP J fso a fot oo Available 132 190 73 182 5 Nore A f No Address 48 Nore A f No Address s Noe A f No Address IP Address Management BOOTP Server No IP Addresses are being assigned from this Workstation Setup M Prompt for Setup if needed lt Back OK Cancel This 3800 GC is connected to Port 44 The status indicates the availability of the GC The IP address of the GC is shown here Click on the OK button to close the dialog box and wait for the 3800 to connect When the GC connects to System Control it will be indicate
312. ot Ready DER Edit Inject Automation Recalculate Instrument Windows Help ca mal Si rele Mel aol m Not Ready 4000 01 Not Ready Ee anual Control Auto Tune Temperatures Diagnostics Startup Shutdown Acquisition ontrol and Status Method Active Segment Checks and Adjustments Module Attributes 4s ource Internal Edit Method Cal Gas Adjustment Aa W ater Check lethod Internal Upload MS Method Last Check Date Not Applicab A acuum System OK emperstures OK Source OK m Gauge Pressure 0 0 uTorn Fill Valid Trap Parameters T Cl Plumbing Leak Check CI Plumbing Leak Check Results Last Check Date Not Applicab lt gt canning E sie m Calibration Gas Active Method Segment Scan Function Channels I CG 2 co Rese he 12 FIL MUL DELAY FF Cycle brat IN aj o S 1i m Sean Number 1 Time 0 000 min Base Peak 20 Base Amount 409 RIC 75280 lon Range 13 40 miz lon 25000 us Segment 1 Channel 500 000 Pad 500 000 jia 500 4 0 0 20 Acquired Range miz Instrument 1 Jul 11 14 34 39 Module 4000 01 5 1 1 1 1 Method Active Segment Checks and Adjustments Module Attributes Filament r High Mass Calibration 1 3 Adjust high mass calibration Enable Sno pE CAUTION Enabing Disaing Lon Mass Electron Multiplier 1 ras Enhancement requires new Mass Cabbration Last Set Not Applicable Resut Default Values Vetoge 1200 vots
313. ou will learn how to edit a SampleList and inject multiple samples from System Control Edit Inject Automation Recalculate Activate Method Upload Active Method from Modules New SampleList Open SampleList New RecalcList Open RecalcList New SequenceList Open SequenceList Print Printer Setup Exit Choose to open either a New SampleList or an existing SampleList from the File menu The SampleList window for the open SampleList is displayed It contains fields that are specific to the sampling device configured in the instrument In this case if a sampling device such as the 8400 AutoSampler is configured the corresponding SampleList is used 167 8400 SampleList New_Samples smp Ioj x ae Injection Injectors Amount Std E Sample Name i Injection Notes AutoLink Valua Used IS NZ only Add Default Name Analysis 7 1 none none 0 1 0 Pos1 1 Insert Delete Fill Down Add Lines Defaults 1 2 3 4 5 6 T 8 9 alalalalalalalafa a _ Data Files RecalcList Size spreadsheet columns by dragging their border using the left mouse button Right click on the column headers for formatting options When the table is scrolled to the right the Sample Name column does not scroll so you can easily tell for which sample you are entering additional parameters Defining the Fields in the Table The top of the SampleList window
314. ows the resulting frequency in Hz The base frequency is 40 HZ Bunching points causes the frequency to decrease by 40 bunch rate With increased bunch rates less disk space is required for storing the data With decreased rates more data is collected Bunch rate should be set appropriately for the narrowest peak of interest in your chromatogram 20 points peak 16 to 128 bunched points Sets the number of points collected during the monitoring period shows the resulting time in seconds Used to set the number of data points used to calculate the baseline noise Generally a larger value entered here will yield a lower noise calculation 1V 10V 100V 1000V Specifies the maximum detector value that will be processed by the Varian MS Workstation The dynamic range of the FID and TSD detectors are equivalent to 1000V full scale but if your peaks of interest fall significantly below this value you may wish to limit the full scale value here Since the attenuation setting used by the Standard Report application to scale the chromatogram printout is based on the detector s full scale value a lower full scale value will allow you to scale smaller peaks with greater resolution 310 Automation File Editor Command Reference Menus S Automation File Editor CI_MSMS rcl File Edit Help aleme S cele File Menu Satelit e A sub menu displays RecalcList SampleList and Sequence Selecting one of them displays the
315. oximately 10 electrons per ion The multiplier voltage needed for this gain is determined automatically by the Set Electron Multiplier method in Auto Tune Changing the multiplier voltage will change the gain of the MS calibration and analysis runs should always be run at constant gain to achieve valid results Under certain circumstances low background small signal increasing the electron multiplier gain by 100 or 200 volts above the 10 gain can improve the detection limit As noted above the same multiplier gain must be used for determining the calibration curve and analyzing unknown samples Emission Current The emission current is an adjustable parameter in Internal configuration only It is set at a fixed 25 uAmps for Hybrid and External configurations As a Starting point for Internal configuration full scan analyses the emission current should be set so that the ionization time is slightly less than the Maximum lonization Time for the method Then the instrument will have its best dynamic range when data are automatically scaled to account for adjustable ionization time If the ionization time is already lower than the max ion time when it is set for 10 Amps no sensitivity enhancement as reflected by signal to noise enhancement will result from increasing the emission current In certain cases a high emission current can be used to improve sensitivity One example is El MS MS in Internal configuration where the MS MS isolat
316. pectra Colors Spectra Aves Report Header IY Show Spectra Header Report Features IY Show Spectrum lon Intensity Pairs IY Show Spectra Comparison IY Show Difference Spectrum IY Show Difference lon Intensity Pairs Thick Line Harrow Help Reset to Defaults Reset All to Defaults Cancel 33 Use General Preferences to change the way numbers and fonts appear Lf anara Praterances I Taaa Serie Haan bnlomabon List Foris Font ej phas no decmal skort 1 ea Arial Select Lisi Fari gt Font uoed where deoma erai i aa e COMELec Hey Je lert Alignment Font iain Plecet to Defaults Repet All to Cet outs DE Cancel Configuring the Real Time Chromatogram Display Before doing an analysis place the MS module window in acquisition mode If you are in a different mode and start a SampleList or Inject a Single Sample the mode automatically changes to Acquisition During an analysis you can see the chromatogram Select the information you wish to view Click Default View to display the Spectrum and Chromatogram side by side Manual Control Auto Tune Temperatures Diagnostics startup Shutde Status And Control M5 Method Run Time 0 00 minutes Start Acquisition Segment Number End Time 10 00 minutes Edit tdethad Segment Descripti Scan Description Ready No Fault Wait For Readyln scan Farge Hide Hide Keypad ce slice and eee D
317. plays in mL min the programmed and actual channel 2 flow Set Actual rate The Chromatogram Display toolbar contains the following controls Full Scale button Resets the X axis scale from 0 to the end time of the current chromatogram and the Y axis to include the full range of the selected detector signal This effect may also be achieved by double clicking in the lower left corner outside the chromatogram display T Vertical Full Scale Resets the Y axis to include the full range of the selected detector signal within the selected range of the X axis This effect may also be achieved by double clicking in the left margin outside the chromatogram display Horizontal Full Scale resets the X axis from 0 to the end time of the currently displayed chromatogram This effect may also be achieved by double clicking in the margin below the chromatogram display Previous Scaling restores the scaling previously applied to the chromatogram display Repeated use of this button allows you to step back through a number of sequential scaling changes F E Next Scaling is only active after one or more Previous Scaling selections have been made This button allows you sequentially to restore chromatogram scaling previously accessed by the Previous Scaling button to display the full range of the selected detector signal while the chromatogram is running Auto Scaling Selecting this button allows the system to adjust the scaling In addit
318. plays the secular frequency values for the two trap function calibration points Nominal values are 249 kHz and 248 kHz respectively These values can vary up to 4 kHz between instruments Trap DC Offset Voltage The trap offset is a DC voltage applied to the ion trap electrodes end caps and ring electrode to facilitate the injection of the externally generated ions into the trap The intensity of the m z 414 ion from FC 43 is used to maximize the signal thus optimizing for the midpoint of the mass range The trap offset has a range from 3 to 15 volts Lower voltages are useful if an increase in the relative abundance at the low end of the mass range is desired Furthermore if your application involves more fragile compounds then a lower setting can produce a situation where less fragmentation of the molecular ion is observed The Temperatures tab allows you to set the temperature zones of the mass spectrometer for both normal operation and Bakeout and to initiate and terminate Bakeout The Status display can be set to display either Event messages regarding the execution of the temperature commands or Module Attributes detailing the instrument configuration temperature setpoints and results of manual and Autotune procedures a 4000 56 Not Ready Manual Control Auto Tune Temperatures Diagnostics Startup Shutdown Acquisition Control and Status Operating Conditions Analysis Bakeout Conditions Analysis Stark B
319. pleList begins 162 Monitoring the Status of the Run After an injection is performed the status of the run can be monitored in the instrument window SRAM lil ses nae ae piem Costral Yarian 4000 GEOH Runny eee Eat E File ESQ iht Su onatin Feces Inetrurank Windows the leja Erca ni tel me al jem Ranaing a ADELE Funnie Hered Coie dada Tame Temperate Ciagrontion Siahaan Aan Soba ted Cerir MS Haha yp Dasig Dorion Flan Tie O3 aai Slop Acquistion papah la Daafie iH Lir Cir Tes 1 oar Seger Pei Senats Sd E Aang Son Decii Bil Ashe FULL losizatice Tira 7657 Hs Fen Pater Fece Scan fanga 2 20 lon Count 1117 Heda Empa ipc ared maaan 4 6 al a AEE E J Elm TELLE its hm Bili Fade air Emina oe es fats ee ka Fu a i ia ma baii GESE eari i Canil i kopini tay mi 5 ir Ele Al a kais H A QO n eann eril Shi i LEI Lt f 35 si ino 4 Wadulera Inetument li Jan 12 1E2423 Madule 4000 56 Filament 2 nod OK daa E a E Ej reese pcrioecu fretted 2 E r es ee The module status is shown in the status and control windows and on the Toolbar Automation actions and errors are logged in the Message Log the latest line of this log is shown at the bottom of the screen When you double click on the status bar at the bottom of the instrument window the entire Message Log window is displayed Message Log MSGLOG1 MLG Mi
320. pproximately 100 agitation strokes per minute of adsorption required 1 000 agitation strokes would be typical 0 to 999 99 minutes The adsorb time is executed for each Agitation Stroke specified For Headspace sampling or liquid sampling without agitation enter the total desired adsorption time for example 10 0 minutes divided by the number of agitation strokes typically 1 For liquid sampling with agitation enter a value of 0 which will allow the maximum agitation rate 293 3800 GC Sample Delivery Front Valve Oven Middle Valve Oven Rear Valve Oven Front Yale Oven Installed Yes C Mo Temperature C 1 00 OFF sles Add Inget Delete Sat Ro Column Oven End Time 20 00 min Description Front Valve Oven The 3800 GC can have up to three valve ovens installed front Middle Valve Oven middle and rear The tabs at the top of the window select the Rear Valve Oven _ Valve oven position Valve Oven Indicate whether or not the Valve Oven at each position is Installed installed by clicking on the Yes or No radio buttons Valve Oven on off Indicate whether or not you will use the installed Valve Oven by clicking on the ON or Off radio buttons C Temperature C Specifies the isothermal temperature of each Valve Oven Time Time settings to program how each valve is used initially and at the indicated time Valve 1 7 Use the first row to indicate how each valve is used Click on t
321. precursor ion trajectory More stable trajectories allow higher excitation voltages to be applied before ions are ejected from the trap It has been empirically observed that a q value of 0 4 provides an optimum yield of product ions This calculator utility determines the corresponding CID storage RF value m z following user entry of an ion mass m z and desired 19 7 q value Customize Clicking the Customize button displays parameters to customize user settings for set points ionization parameters or scan function parameters Clicking the button again will hide the customizable parameters lonization Storage This column appears when you click on the Customize button This Level RF Storage value is the m z value at which the RF is maintained during Level ionization and the coarse isolation step The typical range is 35 to 100 m z with a default value of 35 m z Range 8 150 m z full range Low Offset This column appears when you click on the Customize button The Low Edge Offset Low Edge Offset is the mass offset to optimize the ejection of the mass just below the precursor ion mass The default value is 0 Low Edge Offset affects the isolation window on the low mass side of the precursor ion Increasing the mass offset increases the isolation window on the low mass side of the precursor ion Decreasing the offset decreases the window on the low mass side The offset should be adjusted to minimize the amplit
322. quent transfer of ions to the trap by a set of lenses The newly formed sample ions are then permitted to stabilize in their orbits at the storage voltage This stabilization period is referred to as the cool time The length of this period is fixed 205 Fourth stage The dynode and electron multiplier are made ready and the RF voltage is ramped quickly from the storage voltage to a value appropriate to begin the mass scanning of the segment Scan Segment Scanning Period During the scanning period the RF voltage is steadily increased causing ions of increasing m z to be ejected from the trap to be detected by the dynode and electron multiplier The AGC software automatically selects an ionization time from 10 usec to 65 000 usec for each of the scan segments of the microscan depending on the amount of analyte in the ion trap and the tuning parameters An estimate of the number of ions formed in the ion trap is provided by a prescan with a varying ionization period 10 to 2 500 usec For low levels e g for baseline or small GC peaks the maximum ionization time of 65 milliseconds is selected which offers maximum sensitivity As the amount of analyte increases the ionization time is decreased automatically in order to prevent overloading of the ion trap with ions The ion signals in each microscan are scaled automatically to correct for the variation in ionization time Microscans are averaged to improve the spectral quality To
323. quickly Edit Notes Opens the Edit Notes dialog box to permit editing of the notes associated with the currently open automation file Help Menu Menu ttem Description Help Topics Displays the help you are now viewing Product If you have Internet access and a web browser installed on your Support computer this option will automatically open the Varian MS Web Site Workstation Product Support Web Site Here you will find the latest software and documentation updates for the Varian MS Workstation suite of products along with additional notes tips and answers to frequently asked questions You may wish to visit this site periodically to see if new information is available that may be pertinent to you About Displays the About Box for the Automation File Editor application Automation The About Box contains information about the software version File Editor installation information and a list of the instrument control modules that you have installed You can validate the installed workstation files from this dialog alelmlel al ele vel New Automation File A sub menu displays RecalcList SampleList and SequenceList Selecting one of them displays the Create a New Automation File dialog box to name a new file of the selected type 2 Open Automation File A sub menu displays RecalcList SampleList and SequenceList Selecting one of them displays the Open an Automation File dialog box to open an existing automatio
324. r of use When you select a Data File from this list the Data File currently displayed in the Quick Link button is changed to the selected file Pick Method for Quick Link Button This hierarchical menu item lists the eight most recently used Methods in order of use When you select a Method from this list the Method currently displayed in the Quick Link button is changed to the selected file Help on Workstation Toolbar Displays the help for the open application Product Support Web Site If you have Internet access and a web browser installed on your computer this option will automatically open the 4000 GC MS Workstation Product Support Web Site This has the latest software and documentation updates for the 4000 GC MS Workstation products along with additional notes tips and answers to frequently asked questions Visit this site periodically to see if new information is available that may be pertinent to you About Workstation Toolbar The About box for the Workstation Toolbar contains information about the software version installation information and a list of the instrument control modules that you have installed Quit Closes the Workstation Toolbar application If you elected to run the Workstation Toolbar automatically when Windows starts the Workstation Toolbar will reappear the next time you start Windows 15 16 System Control Overview This section introduces the features of System Control Later sections
325. r Middle Detector Rear Detector Middle Detector Type ECD Detector Over On C Off Temperature C Electronics On C Off Autozero Add lnsert Delete Ee Sort Adjustments Time Constant Slow amp Fast EFC Type Type 13 Cell Current CAP Make up Flow ml min Contact Potential rm tem Description Detector Oven On or off Electronics On or Off 50 to 450 C Initial 0 00 to 999 99 min Autozero Yes or No Yes at initial time means that the ECD Autozero is on continuously before the run starts Adds a line to the spreadsheet Inserts a line above the currently selected row in the spreadsheet Deletes the currently selected row s in the spreadsheet Sorts the spreadsheet rows by time Slow or Fast N2 High N2 Std CAP Ar CH4 Zero Make up Flow mL min 0 to 50 mL min 307 PFPD Detector Front Detector Middle Detector Fear Detector Rear Detector Type PFPD Detector Oven On C Off Temperature C Electronics On C Off Square Root Mode C On Off Add ngert ea Delete am Adjustments Fhotomultiplher Voltage M Gate Delay mzec Gate Width msec Trigger Level mv da 05 mE oo 20 E 12 EFC Type Type 15 Ar 1 Flow ml min ES Ie Foek E ARECA Gain Factor Use Auto Gain Factor Yes No tem Description Photomultiplier Voltage V Gate Delay msec Gate Width msec Trig
326. r ionization trapping and ion preparation steps ions are scanned out to the conversion dynode and electron multiplier Mass scanning is implemented by increasing the RF voltage on the ring electrode the mass spectrum is collected in order from low to high mass over the user designated scan range In positive mode electrons are ejected from the conversion dynode held at 10000V and repelled to the electron multiplier In negative mode positive ions are ejected from the 10000V dynode and repelled toward the multiplier The signal is enhanced by 10 by the multiplier and sent through an integrator to collect an intensity for each m z MS data are stored as sets of ion intensity pairs for each m z over the acquired mass range A complete mass spectrum is stored for each analytical scan External Electron lonization Chemical Information for External El lonization Energy Positive ions are formed in electron ionization by the impact of energetic electrons 70 eV on neutral molecules The minimum energy necessary to remove an electron from the neutral to create a positive molecular ion is called the ionization energy or the ionization potential of the molecule Thus for molecule A Ate gt At 2e lonization 10 eV Unimolecular Decomposition For most organic molecules the ionization potential is between 10 11 electron volts eV If the energy of the electrons striking molecule A is higher than this by several eV the collision of th
327. r mass assignments between m z 10 and 69 The calibration is extrapolated from the highest observed calibration ion to the maximum mass m z 1000 Mass calibration is performed in both normal scanning 5 000 u sec and fast scanning 10 000 u sec modes Factors Affecting Mass Calibration For this routine to work properly the calibration ions must be present in sufficient intensity gt 20 counts and stable under normal scanning conditions Temperature changes can shift the mass calibration and this procedure should be initiated after the trap has reached its equilibrium point approximately 2 hours after the set point temperature has been established For External and Hybrid modes changing the trap damping gas flow may require both Mass Calibration Trap Frequency Calibration There could also be subtle effects on mass assignments after ion source temperature changes 238 Temperature s Trap Frequency Calibration When the mass calibration has been completed the trap frequency calibration must be performed This routine determines resonant frequencies required for the generation of notched waveforms used in most modes of operation In particular the resonant frequencies for FC 43 ions at m z 69 and 414 are determined The method takes several minutes to complete NOTE Trap Frequency Calibration should be performed each time a mass calibration is done Upon completion of Trap Frequency Calibration the Event Message Window dis
328. r that using too low an RF storage level will reduce trapping efficiency for high mass ions PCI Reactions in the lon Source Four main types of reactions occur in positive chemical ionization Symbolizing the sample analyte by A with mass M and the neutral reagent by R these are Proton Transfer The reagent ion donates a proton to the sample molecule to produce a protonated analyte sometimes called a pseudomolecular ion with mass M 1 RH A gt AH R 203 This is the most commonly recognized PCI reaction Note that the AH ion may fragment to lower mass ions because of excess energy deposited during the PCI reaction Charge Transfer The Cl reagent may transfer only charge to the analyte molecule by electron transfer to the reagent RH A gt A RH Adduct lon Formation The Cl reagent ion may bond in its entirety to the sample molecule to create an adduct ion RH A gt ARH Hydride Abstraction Some reagent ions have a tendency to remove a hydrogen atom to create an analyte product ion that is still positively charged but having a weight of M 1 Rt A gt A H RH NCI Reactions in the lon Source A variety of reactions occur in negative chemical ionization First the reagent is ionized by Electron lonization to create thermalized or low energy electron e 70 eV R gt e lt 1eV R Using CH Methane as an example e 70 eV CH gt e lt 1eV CH These low energy electrons react with th
329. r when the auxiliary flow is turned off in Startup Shutdown mode In Internal configuration the pressure should be lt 10 uTorr The foreline pressure is determined with a thermocouple gauge detector its reading is strongly influenced by the auxiliary Helium flow as well Trap Tap Multiplier 1342 Volts ynode 1 0360 Volts tons Readings for multiplier and conversion dynode voltages are displayed only when Multiplier Dynode is checked in the Monitoring tab dialog in the keypad above The multiplier reading is always negative and reflects the voltage drop between ground and the entrance of the multiplier The dynode voltage should be close to 10 000V the polarity is opposite that of the ions being detected Waveform System Waveform System T Entrance Endcap Trapping Field Dipole 100 Exit Endcap Trapping Field Dipole 100 Dipole Supplemental yy avetorn Had a Quadrupole Supplemental Wavetormn 444 3z The readings for Entrance Exit End Cap Trapping Field Dipole are activated when RF control is checked and the RF radio button is checked in the Monitoring tab dialog The values should be 100 1 Waveform System Entrance Endcap Trapping Field Dipole 0 3 Exit Endcap Trapping Feld Dipole Tp Dipole Supplemental waveform LEA Quadrupole Supplemental Waveform 100 2 Dipole and Quadrupole Supplemental Waveform readings are activated when RF control is checked and the Waveform radio button is checked in t
330. rate DC offset voltage lens voltages etc If a massive air peak is present turn off the Damping Gas flow and run Air Water Check again If no peaks are present with the damping gas off then the most likely cause of a massive nitrogen peak m z 28 is inadequate flushing of filters and or helium line rather than a leak in the mass spectrometer If the nitrogen peak m z 28 is observed with the damping gas off please see the Troubleshooting section for more information on finding air leaks The Cl Plumbing Leak Test is run automatically after the Air Water Test The Cl solenoid valve is opened and air water levels are checked It is not unusual for these values to be initially high Generally the Cl valve should be opened and flushed or left under vacuum several minutes before this test is done The Air Water Check will give advice on the levels of these background components High water level is indicated both by the intensity of the ion at m z 18 but also by the percentage of m z 19 H30 relative to m z 18 The water level is high after the instrument is first pumped down after maintenance Baking the instrument overnight should bring the level to an acceptable level A high air level as shown in the example suggests that there may be a leak in the vacuum system or GC Consult the troubleshooting section in the 4000 GC MS Hardware Operation Manual for advice on locating sources of air leaks 43 System Control Varian 4000 MS N
331. re repelled to the electron multiplier The conversion dynode is held at 10 KV and the voltage on the multiplier is adjusted to provide an enhancement of 10 The signal is then sent through an integrator to collect an intensity reading for each m z MS data are stored as sets of ion intensity pairs for each m z over the acquired mass range A complete mass spectrum is stored for each analytical scan External Positive or Negative Chemical lonization About External Chemical lonization Chemical ionization Cl provides mass spectral data that complement electron ionization El data for the analysis of complex compounds The generation of ions in chemical ionization is a two step process A Cl reagent gas is introduced into the ion source For chemical ionization a special Cl ion source volume of the reagent gas is ionized by El Then the sample molecules are ionized by ion molecule reactions with the reagent gas ions Cl is a softer ionization technique than El That is Cl imparts less energy to the sample molecules than does El Thus the ionized sample molecule undergoes less fragmentation and an ion indicative of the molecular weight is more likely to be observed In addition to molecular weight confirmation Cl mass spectra often provide other significant structural information that may not be available from El mass spectra 202 Adjusting Cl Pressure We recommend setting flows by observing the ion gauge pressure in Manual Contr
332. re the flow rate to the set point in the Current Set Points field This does not appear when the instrument is in Internal configuration Getter Control If the instrument is in External or Hybrid configuration and the Damping Gas and Getter Heater are turned on the getter temperature is displayed Compare this temperature to the set point of 400 C in the Current Set Points field This does not appear when the instrument is in Internal configuration 61 Shutting Down the System To shut down the 4000 MS click Shut Down in the upper left corner of the screen The heaters are turned off and the speed of the turbo pump is gradually reduced to 35 of full speed In the following the shutdown command was activated Notice that the turbo pump speed is being reduced as the heated zones are being cooled After the temperature zones are cooled turn OFF the main power using the switch at rear of system Manually vent the system for at least 5 minutes by opening the vent valve on the front panel one turn counterclockwise NOTE Retract the transfer line before lifting the analyzer assembly from the vacuum manifold Failing to retract the transfer line can cause damage to the transfer line tip and to the trap assembly a 4000 56 Not Ready Manual Control Auto Tune Temperatures Diagnostics 9 Startup Shutdown Acquisition Operating Conditions Heated ones Current Set Points Heated ones Status and Control Conditions Sh
333. rel Cancel Notes Recent Files gt Save in Lists the available folders and files To see how the current folder fits in the hierarchy on your computer click the down arrow To see what s inside a folder click it The box below shows the folders and files in the selected location You can also double click a folder or file in that box to open it To open the folder one level higher click the up arrow button on the toolbar To open a new folder in the current directory click on the Create New Folder button click the up arrow button on the toolbar Shows the currently specified file Save as type Specifies the type of file to save Recent Files Click on this button to display a list of recently selected files When you select a file from this list its name is displayed in the File name File list Lists the folders and files in the selected location To see what s inside a folder double click it You can also use the Save In box to see the hierarchy of folders To open the folder one level higher box 314 ttem Description Notes When checked displays any notes and or revision log associated with the currently selected file Saves the file with the specified name Cancels file saving Print Setup Dialog Box This dialog box is used to specify the printers that will be used by Varian MS Workstation applications both interactively and during automation Star Printer Setup Default Star Printer U
334. rmed in Auto mode the prescan is followed by Target Factor an ionization time and scan of each segment needed to cover the Mass Range designated to the left of the segment table The actual lon Time for each segment is the AGC lon Time multiplied by the percentage in the lon Time Factor field If needed adjust the lon Time Factor for particular segments to increase or decrease the abundance of key ions For Full Scan the lon Time Factor is specified for both fixed ionization and AGC ionization For SIS the lon Time Factor is specified for fixed ionization and the Target Factor is specified for AGC ionization Range 1 999 Save Save allows any modification to the tune parameters to be saved so that the tune parameters can be referenced in other methods Add This button adds a segment to the end of the Scan Segment table The range of the previously final segment is divided between that segment and the added segment For example if the final segment covered m z 400 to 1000 that segment will now cover m z 400 to 700 and the added segment will cover m z 701 to 1000 2 7 tem Description S Insert This button inserts a segment after the currently selected row of the Scan Segment table Inserting a segment will essentially split the currently selected segment into two segments of equal mass range Delete This button deletes one or more selected segments from the Scan Segment table However there must always be at leas
335. rrent set between 10 and 100 Amps Settings above 10 Amps do not improve performance unless the ion time in the baseline of the chromatogram is at the Max lon Time this value can be viewed by clicking the Customize button in the lonization Control tab dialog Setting the emission current so that the ion time in the baseline is just below the Max lon Time will give the widest dynamic range for the CI method nternal Cl Parameters Emission Curent 104 Wmps Reagent Parameters Reagent Methanol z Acetonitrile Isobutane Reagent ER Methane g Methanol Select Parameters for any of four internal PCI reagents from list If you design parameters for a new reagent or change the parameters for one of these reagents you may save these changes under a new name that will then be added to your list of selections Internal CI Reagent Parameters x Create update or delete user defined parameter sets Delete Cancel The default values for Reagent Low Mass and Reagent High Mass vary depending on the selected Cl reagent When the Customize button is clicked note that the Reaction Storage Level and the Ejection Amplitude are also reagent dependent These features are all discussed in more detail in Internal Positive Chemical lonization on page 194 in the section 4000 MS lonization Techniques Briefly Reagent Low Mass must be low enough so that the reagent ions can be created and stored For example formation of the me
336. s Manifold Aa Lens 3 17 8 Volts Transterline 174C RAimg Offset 7 4 Wols Source 154C Endcap Offset 7 5 Volts 241 Control and Status The Control and Status area indicates the state of the Diagnostics system Idle or Running as well as the function the Diagnostics system is currently in The normal function is Monitoring Status but cycles through various test functions once the Start Diagnostics button is clicked Monitoring Tab This tab provides the user with choices for which lon Trap and lon Gauge components will be monitored Selecting the lon Source checkbox activates the Emission Balance and Deviation parameters in the lon Source data area lower Monitor Window section Selecting the Multiplier Dynode checkbox activates the Multiplier and Dynode parameters in the Trap data area lower Monitor Window section Selecting the RF Control checkbox activates the Waveform System data area lower Monitor Window section Underneath the RF Control checkbox there are two radio buttons RF and Waveform that indicate which elements of the Waveform System the user wishes to monitor Selecting the RF radio button activates the Entrance End Cap Trapping Field Dipole percentage and Exit End Cap Trapping Field Dipole percentage Selecting the Waveform radio button activates the Dipole Supplemental Waveform percentage monitor and the Quadrupole Supplemental Waveform percentage monitor Selecting the lon Gauge checkbox adds the lon Gauge to the c
337. s 501 502 and 503 m z would be isolated If there is a need to reduce the window because of interfering ions this should be done in a later step because the customized parameters may require optimization Some ions are easily dissociated during the isolation step Increasing the width of the isolation window will reduce the ion loss by premature dissociation at the expense of selectivity Range 1 0 14 0 m z full range Waveform Type Select the Waveform Type by selecting non resonant or resonant excitation from the list box The non resonant method is usually the first choice for reasons of simplicity of operation Resonant excitation involves exciting the target ions by an RF field of the resonant frequency of the trapped ions Non resonant excitation involves exciting the precursor ions using an RF field not at the resonant frequency of the trapped ions Excitation Storage The Excitation Storage Level is the RF storage level in m z applied Level m z while the dissociation waveform is applied following isolation The Excitation Storage level depends on the precursor mass but the lowest product ion must be more than 2 mass units above the excitation storage level The excitation storage level for the precursor ion can be calculated using the q calculator The q calculator is accessed by right clicking on any of the fields in the MS MS parameters table NOTE Set the excitation storage level to avoid ejection of the lowe
338. s electronic noise The Integrator zero is adjusted such that the average value of electronic noise is slightly greater than zero The acceptance range is between 0 3 and 0 5 counts The integrator then records signals only when ions actually strike the dynode and electrons emitted from the dynode strike the electron multiplier 47 Set Electron Multiplier 1400 ion time 65000 usec ion time 10000 usec gt EM voltage Vv 21 16 07 25 EM voltage 1500 V Nay 21 16 07 27 EM voltage 1500 V ion time 65000 usec May 21 16 07 28 EM voltage 1525 V ion time 6S000 usec May 21 16 07 29 EM voltage i550 V ion time 65000 usec May 21 16 07 30 EM voltage 1575 V ion time 65000 usec Mey 21 16 07 31 EM voltage i600 V ion time 65000 usec Nay 21 16 07 32 EM voltage 1625 VY ion time 65000 usec May 21 16 07 33 EM voltege 1650 V ion time 65000 usec May 21 16 07 34 EM voltage 1675 V ion time 65000 usec May 21 16 07 34 Electron Nultiplier gain is 3 71 May 21 16 07 34 Electron Nuitiplier voltage setting is 1675 May 21 16 07 34 Electron MNuitiplier Gain Adj completed May 21 16 07 34 Auto Tune Passed May 21 16 07 34 Electron Nultiplier Voltage 1675 PASS May 21 16 07 34 Auto Tune Passed Before starting the EM gain algorithm the RF Full Scale is adjusted to calibrate the cal gas ion at m z 502 Set Electron Multiplier adjusts the multiplier voltage and ion time to look at low mass fragments from the unstable m z 502 ion The multip
339. s entry pou want and then click Display 8200 SampleList window Extensions 4 chivake Method Dialog Bor ADC Board States Adding 3600 GCs to Instruments in System Control _ Address IP Address AutoLink Parameters Dialog Bor Automation Mena 4ubomit Aoutines Dialog Box Subotampler Carrousel Gisplay 4S ubosampler Cigplay BOOTP Server dialog bos From a company nebework Carousel Dialog Bor Changing Default S ampleList Entries Changing the Method in the S ampleList 26 To use the Find dialog type in a key word or phrase to get help topics Help Topics System Control H E Contents Indes Find 1 Type the wordia you want to find able aborts about About above 3 Click a topic then click Display Activate Method Dialog Box ADC Board States Adding 3800 GCs to Instruments in System Control AutoLink Parameters Dialog Box Automation Menu Autom Routines Dialog Box Autosampler Carousel Display 185 Topics Found All words Begin Auto Pause Display rift Cancel System Control Toolbar The system control toolbar is near the top of the screen Bas Borso s me AE njem 27 Create a new automation file The first icon opens an existing automation file The second icon opens the Message Log file startup nth View edit or print a Method Open a Method Edit notes for an automation file Edit Module information for any online Module Open Instrument 1 Status E
340. sed by all Star Workstation applications for interactive printing HP Laserdet Ill on W s dev printq_O Instrument Printers Used during automated printing by System Control Instrument 1 HP Lasenlet 551 551 Me on S Serverl Charge Instrument 2 HF Laserlet 551551 Ma on S Serverl Change Instrument 3 HP Laserlet 551 551 Me on Serverl Change Instrument 4 HF Lasenet 551551 Ma on S Serverl Change hem Description Default Printer Displays the printer that is used when printing interactively from Varian MS Workstation applications Click on the Change button to select a different printer Instrument Displays the printer that is used when printing under automation Printers from System Control Since the Varian MS Workstation is a single instrument workstation the printer specifications for instruments 2 4 will be ignored Edit Notes Dialog Box This dialog box allows you to enter descriptive notes associated with an automation file These notes can be viewed when selecting the file and are included in the file s printout 315 Notes C Yarian W S i MP9 Septun S EPTA2 RCL Tutorial fle calibration block These notes will be displayed in the Open File dialog box and in automation file printouts men em Description ooo Notepad Area Shows any notes attached to the file The notes may describe the contents of the file its uses restrictions etc The Notepad Area is scro
341. segment by segment basis The Count Threshold is normally 1 count a value of 2 3 counts will reduce the number of low level ions reported in the mass spectrum This approach may 126 improve library searches and reduce data file size at the cost of somewhat less detailed information in the mass spectra The count threshold is shown only if the Customize button is active lonization Control General Parameters lonization Control Hybrid Farar Automatic Gain Control Target TIC SOOO counts The default Target TIC for positive or negative chemical ionization is 5 000 The target can be set as high as 65 000 General Parameters lonization Control Hybrid Pare Automatic Gain Control Target TIC nogi H courts lonization Time Fired lonization Time lonizaton Time ino Useconds Max lon Time 25004 useconds Click Customize to run fixed ion time experiments with ion times as high as 65 000 usec or to change the Maximum lon Time for Cl Auto experiments One can turn on the Cl Gas and the ion trap in Manual Control and check the ion time in Cl Auto mode Hybrid Parameters General Parameters lanization Control Hybrid Parameters Full Scan Parameters Hybrid lonization Parameters Reagent Gas Acetonitrile Save Reagent Low Mass s4 miz 9 oe Reagent High Mass eo miz GR Ejection Amplitude BEE Wols a OU Mas Reaction Time w miec Start Mass se 15 Reaction Storage Lev
342. single time segment Cluster Mode 5 Low Mass High Mass m z 1 200 SIS Cluster Mode The Cluster Mode is a combination of the Range and the Multiple lon Modes The Cluster Mode is set up to store only the ion clusters of a selected compound This is useful when looking at chlorinated or brominated compounds The Cluster Mode retains all of the isotope ratio information but removes most of the background ions for better sensitivity The clusters of octachlorobiphenyl ether at 201 372 and 442 are shown in the above example 144 3800 GC Method Section The 3800 GC Method Windows The 3800 GC entry specifies the Varian MS Workstation module address of the GC that the method uses The module address in the parameter window can be changed so that a method developed for an instrument using one module address can be easily modified for use on another instrument at a different module address E Method Builder startup1 mth C Eile Edit view Window Help 8 x asale Anm E ld 4 gt gt i ee 5 aS Detector 3800 GC Address 144 X m Detector Control Parameters startup1 mth Ea Method Notes 2900 GC Address 4 Detector Control Parameters 2 Autosampler aa Sample Delivery oa Injector aa Flow Pressure P Column Oven Detector Autosampler Sample Delivery ja 4000 Mass Spec Address 56 E 1 4000 Mass Spec Control Last Modified Tuesday
343. solation window on the low mass side of the precursor ion larger Decreasing the offset decreasing from the default O to 0 5 m z decreases the window on the low mass side The offset should be adjusted to minimize the amplitude of the adjacent masses below the precursor ion Initially adjust in 0 2 m z increments High Edge Offset The mass offset to optimize the ejection of the mass just above the precursor ion mass The High Edge Offset range is 0 5 m z to 0 5 m z The default value is 0 High Edge Offset affects the isolation window on the high mass side of the precursor ion Increasing the mass offset increasing the default from 0 to 0 1 m z makes the isolation window on the high mass side of the precursor ion larger Decreasing the offset decreasing from the default O to 0 1 m z decreases the window on the high mass side The offset should be adjusted to minimize the amplitude of the adjacent masses below the precursor ion Initially adjust in 0 2 m z increments High Mass Ejection Amplitude of broadband waveform used to eject masses above the isolated precursor ion Default is 35 volts If precursor ions are lost due to dissociation reducing this amplitude may help However some ions with a m z higher than the precursor ion may not be ejected Dissociation CID Excitation Excitation Modulate Resonant Customize Dissociation Parameters Resonant Excitation Waveform Type Storage Ampli
344. ssure psi Pulse Duration min 0 95 jE Column Oven End Time 20 00 min If Constant Column Flow mode is selected the pressure table is grayed out since the pressure will be calculated by the system to increase with column temperature to maintain the selected column flow In addition the option of a Pressure Pulse injection will be presented Pressure Pulse injection is used to minimize the expansion of the solvent vapor cloud in the injector and enhance transfer of the sample to the column usually in conjunction with a splitless injection If you click on the Yes button you may enter a pressure and pulse duration for the injection The system will stabilize all the temperature zones then increase the pressure to the pulse pressure stabilize and hold until the injection is made and the run starts The pulse pressure will be held for the pulse duration period and will then be dropped to the pressure computed for the constant column flow selected 299 Type 4 EFC for valved systems Front EFC Middle EFC Rear EFC Middle EFC Type Type 4 for Valved Systems Rate Hold min Total min psi min 10 0 1 00 1 00 Add E OS 2 00 20 06 ee Delete Add Insert ddu Delete Sart tem Desoription S Pressure psi Pressure spreadsheet 0 1 to 100 0 psi Rate psi min 0 1 to 100 0 psi min The first line is devoted to initial conditions so a rate cannot be entered For subsequen
345. st Set Date Not Applicable Result Complete Reagent Methane Ionization Time 0O Total Ion Count O Cancel Action Initializing Adjustment Results Adjust the reagent gas pressure so that the ratio of peak heights at m z 17 and 29 are between 1 1 and 1 4 The jratio of the ions at m z 17 to m z 16 should be about 10 1 The ton at m z 41 should be visible 41 RF Ramp Adjustment When you select RF Ramp Adjustment a screen opens that displays if the RF voltage is in tune over the entire mass range of the 4000 MS After opening the screen use a screwdriver to adjust the RF coil screw inside the front door of the 4000 MS Follow the instructions in the Adjustment Results field until the value of the highest part of the graph is at a minimum Manual Control Auto Tune Temperatures Diagnostics Startup Shutdown Acquisition nd Statues Method Active Seqment Checks and Adjustments Module Alt sie ethod Active Segment Module A Method E xtemal El Upload MS Method ee Last Set Date 12 2 2005 9415 AM Result OR Highest Count 742 Vacum System OF Demping Gas OK Temperatures OK Source OF lon Gauge Pressure OO uTee Fill Vahd Ti Bere carcet Action Measuring Ads RF cod tuning to obtar a straight Ine in the lsplectial display and minimize the size of the bar graph r pe Adjust Rf voltage until rradtaglies y minimum s
346. st mass product ion If for example a precursor ion of 403 m z dissociated to product ions with m z values of 350 200 and 131 you would not want to use an excitation storage level above 126 m z 278 item Description S Excitation The amplitude range for non resonant excitation is 0 to 120 volts Amplitude volts For resonant excitation the range is O to 60 volts The default values are 20 volts for non resonant excitation and 0 2 volts for resonant excitation Range Resonant Excitation 0 59 79 volts Range Non resonant Excitation 0 119 58 volts Product lon Start Set up the Product lon Start and End Masses or Low and High Mass m z masses to cover the mass range required Product lon End Mass m z More Ranges More Ranges allows you to have multiple Product lon Start and End Masses in a single segment Clicking on the More Ranges square spawns the Product lon Mass Ranges Dialog box with a Mass Ranges table and buttons to Add Insert and Delete Product lon Start and End Masses Add This button adds a line to the end of the Mass Ranges Table Insert This button inserts a line after the currently selected row of the Mass Ranges table Delete This button deletes one or more selected rows from the Mass Ranges table q Calculator In scientific literature storage RF values are often reported in terms of the Mathieu q parameter The value of the q parameter determines the stability of the
347. st vial will be injected on the first injection and the next vial location will be sampled for the second injection Injection Volume 0 1 to 5 0 uL or 0 1 to 10 uL or 1 to 100 uL depending on syringe volume Sets the injection volume of the sample in microliters When the SampleList is edited in System Control the maximum value allowed is set to the syringe size currently configured in the 3800 GC setup During operation if the sample volume plus solvent volume internal standard addition volume and air gaps volume specified in the active method on the 3800 exceed the syringe volume a 3800 hardware fault will occur This will cause the Star Workstation to halt automation and reset the 3800 After changing the method settings and or the injection volume to reduce the total below the installed syringe volume shown in the 3800 setup screen you should begin the SampleList at the selected line to bypass the samples that have already been run 2nd Inj Volume 0 1 to 5 0 uL or 0 1 to 10 uL or 1 to 100 uL depending on Duplicate Mode or Dual syringe volume Mode operation only Sets the injection volume in microliters for the second injection of the sample in Duplicate Mode or the injection of the second sample in Dual Mode When the SampleList is edited in System Control the maximum value allowed is set to the syringe size currently configured in the 3800 GC setup During operation if the sample volume plus solvent volume internal st
348. t values in the section being built regardless of the values placed in the Default mth To change Methods click Activate a Method on the System Control Toolbar or choose Activate Method from the File menu 67 T System Control Varian 4000 MS Not Ready File Edit Inject Automation Recalculate Instrument dow aala Pystatupt mth cas E S BR dl aol An gt mm Not Ready 4000 01 Not Ready Manual Control Auto Tune Temperatures Diagnostics Startup Shutdown Acquisition Control and Status Method Active Segment Checks and Adjustments Module Attributes Source Intermal Edit Method Method intemal Upload MS Method Instrument Configuration Acquisition Data Type Vacuum System OK internal EI and Cl z Centroid Profile Temperatures OK Source OK Chromatographic Time Segments lon Gauge Pressure 0 0 uTon Fill Valid a Trap Segment Description Scan Description 1 FILMUL DELAY 0 00 3 00 lonization Off re 3 00 10 00 El Auto Full ni I Trap Calibration Gas Method Active Method Segment Scan Function Channels AES T lon Gauge CI Gas Acti ctivate B r Number 14 FIL MUL DELAY Cycle nnel 1 UEA Spem H a Changes Restore j _t j Scan Number 762 Time 10 692 min Base Ped RIC 7 lon Range 10 5 1000 0 m z lon 1674 us Seqment Editing Methods from the 4000 MS Status and Control Window You can edit the method in Manual Control and save the changes immediately by c
349. t TIL 200004 counts The Target Total lon Current or TIC is specified here The Automatic Gain Control AGC algorithm uses the ion count from a prescan at fixed ion time along with this target value to calculate an ion time necessary to fill the ion trap with the target number of ions during the analytical scan The objective is to fill the trap with an optimal number of ions during each analytical scan The Target 111 TIC is usually not set below 10 000 for full scan acquisitions but it should also not be set too high or spectral distortions due to space charge loss of MS resolution and or shift in mass assignments for strong chromatographic peaks may result Typically a Target TIC between 20 000 and 40 000 counts gives the best results General Parameters lonization Control Internal El f Automatic Gain Control Target TIL 20000 counts lonization Time Fixed lonization Time lonization Time me seconds Max lon Time J 2500024 Useconds Customize If one activates the Customize features it becomes possible to run fixed ion time experiments and or to change the Maximum lon Time for Automatic Gain Control Fixed ion time experiments are generally limited to diagnostic tests and are not advised for qualitative or quantitative analysis in the ion trap Changing the Maximum lon Time can improve the sensitivity of techniques such as MS MS or SIS This parameter can be increased to 65 000 usec If the ion time in the b
350. t in a SampleList file that may contain more than one section tem Description S SampleList section Selects a section type to use in building a new SampleList type list box opens the appropriate SampleList window SampleLists may contain sections for multiple types of sample handling devices depending upon which module drivers have been installed Creates a SampleList section of the specified type Cancels the SampleList section creation 324 Data File Generation Dialog Box Data File Generation Specify the names for Data Files generated by detector modules using this SampleList Numbers will be appended to file names if the file already exists Do not include the file extension in the Data File name Directory for Data Files Data File names HESS Fo modulel Exarnple Sample 11 Use the following symbols to enter the E corresponding variable data to the file New Folder Drives EP e Sawe_devvole users rovle Cancel Injection number Date Detector Module name tem Description Directory for Data Files Shows the currently selected directory where Data Files will be generated New Folder Allows you to create and name a new folder in the currently displayed directory Drives Allows you to specify the drive where Data Files will be generated Data File Names Allows you to enter the Data File name specification You may enter as many characters as you wish but the final file name
351. t lines the rate defines how quickly the pressure entered in the Pressure column will be attained Hold min 0 to 999 99 min Total program time cannot exceed 999 99 min Defines how long the pressure entered in the Pressure column will be held constant once that pressure is achieved Total min Calculated by system based upon user entries in the previous 3 columns Time Flow program spreadsheet Initial to 999 99 min Flows are executed as step changes at the programmed times Commonly used to increase flow just before a valve is switched Total Flow mL min 1 to 1000 mL min Be sure that total flow is adequate to support any pressure program steps you have entered Add Adds a line to the spreadsheet This button appears next to both the top and bottom spreadsheet Inserts a line above the currently selected row in the spreadsheet This button appears next to both the top and bottom spreadsheet Deletes the currently selected row s in the spreadsheet This button appears next to both the top and bottom spreadsheet Sorts the spreadsheet rows by time This button appears next to the bottom spreadsheet 300 3800 GC Column Oven Column Oven Coolant On C Off Enable Coolant at C Coolant Timeout min Po 00 Stabilization Time min Hold min Total min 1 00 180 20 0 a00 O O Insert ttem Description Column Oven Coolant On or Off SAORA cer tr or rote cto csi used Enable Coolant at 3
352. t one segment in the table To delete multiple segments the entire row for each segment must be selected Customize Clicking the Customize button displays the Scan Segment table and the associated controls Clicking the button again will hide the customizable parameters AMD MRM If you choose any of these MS MS type ion preparation modes you MS MS MS Scan will see a Table that shows all of the available MS MS parameters Parameters set out in tabular form Each of the three steps of MS MS isolation dissociation and scanning follows across the table Precursor lon Integer mass values may be used if the mass isolation window next column is greater than 1 5 m z If the window size is less than 1 5 m z or if the mass defect of the precursor ion is greater than approximately 0 3 m z use the exact fractional mass Range 50 1000 m z Isolation Window The full mass isolation window range is 1 0 to 14 0 m z The actual range is dependent on the precursor ion The default value is 3 0 m z Both integral and fractional mass isolation windows are accepted If an isolation window smaller than 1 5 m z is used then the exact mass of the precursor ion should be entered in the Precursor lon column When first developing a method you may wish to start with a mass isolation window of 3 m z to ensure that the ion is centered in the window e g given a precursor ion mass of 502 m z and a mass isolation window of 3 m z ions of masse
353. t the Start Time The Start Time you enter will also be entered as the End Time of the preceding segment if one exists End min This cell indicates the time at which the particular segment will end Clicking in this cell allows you to edit the End Time The End Time you enter will also be entered as the Start Time of the succeeding segment if one exists Scan Description This indicates the Scan Type and lonization Type You don t edit this cell but instead edit the Scan Type and lonization Type in the lower Method Segment window by choosing the desired Scan Type and lonization from the appropriate drop down menus Changing these drop down menu values will cause the Scan Descriptions in the upper window to change 2 2 tem Description S Add This button adds a chromatographic time segment to the end of the Chromatographic Time Segment Table Adding a segment will copy all of the parameters from the last segment into the newly created segment The default duration for the newly created segment is 1 00 minute Insert This button inserts a chromatographic time segment before the currently selected row of the Chromatographic Time Segment table Inserting a segment will copy all of the parameters from the currently selected segment into the newly created segment Inserting a segment will essentially split the currently selected segment into two segments of equal duration Delete This button deletes one or more selected segments
354. tailed status information including ready and fault status for the selected component You can change the component being displayed using the selection box below the display area or by clicking on the corresponding temperature zone entry in the temperature zone status display 3800 GCs that have an 8400 AutoSampler or 8410 Autolnjector installed will have another display area the 8400 8410 Carrousel display that shows a 249 graphical representation of the 8400 or 8410 Carrousel This display graphically shows which vials are to be sampled which vials have been sampled which vial is currently being sampled Below these display areas is the Chromatogram display A selection box above the chromatogram allows you to select the channels for which you want to view the real time chromatogram 3800 Operation Display The 3800 Operation display is in the left portion of the 3800 Status and Control window 3000 Operation RunTime 0 00 min Start EndTime 4 50 mir Reset D Ready Method 2 No Fault Valves 1 2 3 4 5 6 7 mem Description O Run Time Shows the elapsed time in minutes since the beginning of the run The maximum run time is 999 99 minutes Shows the time at which the run will end State Ready Running Stabilizing Equilibrating Computing Needs Monitor Monitoring Sampling Connecting or Not Ready Shows the state of the GC The light appears green if the GC is Ready or Running Otherwise the light is red
355. talled Workstation files from this dialog 225 226 4000 MS System Control Command Reference Display The 4000 MS status and control window is available for display whenever a 4000 MS module is configured in System Control It may be displayed in the System Control Status window by selecting the Windows menu item and clicking the 4000 xx menu item or by expanding the 4000 xx icon which appears at the lower left of the System Control window a System Control Ferguson_1 Waiting for Instrument Modules File Edit Inject Automation Recalculate Instrument Windows Help al serial al Show Module Windows Tinie Module Wind ots Show Automation Windows Innes Guba eatin ovina Arrange Icons SampleList 1200cat smp Instrument 1 Status Message Log w 4000 01 Not Ready Instrument 1 Dec 22 13 50 45 Module 4 227 System Control Tabs T System Control VarianWS_1 Not Ready File Edit Inject Automation Recalculate Instrument Windows Help Biss Banh l Boles Si vB Fel 11 gt mt Not Ready a 4000 01 Not Ready Manual Control Auto Tune Temperatures Diagnostics Stattup Shutdown Acquistion Control and Status Method Active Segment Checks and Adustments Module Attributes Source Internal Edit Method Method Internal Upload MS Method ges Segment IV lonization On Scan Type Full z Ionization fel Scan Mode Normal xl Selpoints Vacuum System OK
356. tatus information 247 Chromatogram Toolbar Aj o 11 m sk BB i P al Clicking on the green arrow will hide the toolbar Clicking on the upper left of the full screen display restores the toolbar bc Clicking on the full scale button will cause the chromatogram to be normalized in the vertical and horizontal directions Double clicking on the lower left corner of the scale has the same effect Clicking on the previous scale button will restore previous settings Id l Clicking on the scale button allows you to choose between Auto Scale Intensity and Fixed Scale Intensity Al When selected this button allows you to click on a feature in the chromatogram and have the spectrum at that point displayed in the Spectrum window When this button is not selected the Spectrum window will display and continuously update the most recently acquired spectrum This links MS Data Review If an acquisition is running when the button is pressed MSDR will be opened with the current acquisition as the active chromatogram if MSDR was already open the current acquisition will be added as the active chromatogram If no acquisition is running and the chromatogram window is blank when this button is pressed MSDR will be opened with a file select dialog to select the active file EF lin Click to display a plot of the Intensity of the Base Peak To display the RIC trace and the Intensity of Base Peak plot at same time enter IBP in the lons fi
357. ternal ionization modes all Auto Tune routines should be run Some routines should be run after changing operating conditions such as trap temperature or helium buffer gas flow rate Specific routines may be run periodically as part of a system check a 4000 56 Not Ready Sele Manual Control Auto Tune Temperatures Diagnostics Startup Shutdown Acquisition Control and Status Auto Tune Method Action Mass Calibration State Calibrating NORMAL V Auto select prerequisite tuning functions Ea O Integrator Zero O Electron Lens Tuning C Set Electron Multiplier O lon Lens Tuning O FF Full Scale Adjust Mass Calibration O Trap Frequency Calibration J Trap DC Offset Voltage Hide Keypad Spectrum and Event Messages v 4 11 17 E E Scan Number 3 Time 0 032 min RIC 4378 lon Range 80 6 181 5 m z Base Peak 129 8 Base Amount 986 lon 333 us Segment 1 Channel 1 i 150 125 125 Acamea Bande m z Mar 15 16 37 39 QuickVerify Started ar 15 16 37 39 QuickVerify Completed Aar 15 16 37 40 ar 15 16 37 40 Mar 15 16 37 40 Mass Calibration started Mar 15 16 37 40 Calibrating on mass 69 0 Mar 15 16 38 06 Centered on mass 69 0 rf dac 662 9 Mi Ahma AL AS DS 1 alil om hia nm ma toe aa 1AA A The Auto Tune window has three sections Control and Status Spectrum and Event Messages and Auto Tune Method 45 Control and Status Cl
358. tes the Bakeout temperature setpoints and enables the Bakeout timer when the setpoints are reached Stop Bakeout resets the temperature setpoints to the Analysis values and resets the Bakeout timer The Diagnostics tab provides control and status for monitoring and diagnosing nearly every system in the Mass Spectrometer ele Manual Control Auto Tune Temperatures Diagnostics StartupS hutdown Acquisition Control and Status State Idle Function Monitoring Status Vacuum System Turbo Pump Status Marmal Speed 100 Current 242 mAmpe Power 10 Watts Temp 260 lon Gauge Pressure 21 8 uTorr Filament 1 OF Filament 2 Untested Roughing Line Pressure 18 mT orr Start Diaanasti Hide Keypad Monitor Window and Event Messages Trap Damping Gas Flow 1 0 miLrrun Monitoring Diagnostic Tests Trap On Off lon Gauge Fie ll Parcs f Filament 1 f Filament 1 C Filament 2 C Filament 2 i MMultiplier Dynode i RF Control RF f Waveform Trap lon Source Multiplier 2152 Volts Emission 24 umpa Dyrnode 10374 Volts iona Balance 1244 Deviation 1 4 uA Waveform System Filament Bias 70 6 Volts Filament 1 OF Filament 2 Untested Dipole Supplemental Waveform 103 On Off Quadrupole Supplemental Waveform 101 Lens 2 g0 Vols 120 Walts Temperatures Electron Lens 95 Volts 95 Volts Entrance Endcap 100 C Repeller Lens 171 Volts 159 Volts Exit Endcap 100 C Lens 1 26 4 Volt
359. thane reagent 117 ions at m z 17 29 and 41 requires that the CH and CH precursor ions be stored Therefore the default Reagent Low Mass for methane is 15u Methanol has its reagent ions at m z 33 and 47 so a higher default Reagent Low Mass value of 25u is appropriate The Reagent High Mass value may be lowered to exclude one of the Cl reagent ions For example you could set the value to 40u to exclude the 41u reagent ion of methane However since there are still neutral methane molecules in the ion trap the m z 41 ion can be recreated by reactions of stored 29u ions with methane General Parameters lonization Control Internal Cl Parameters Full Internal Cl Parameters Emission Current Da u mps Reagent Parameters Reagent MHethanal r Save Reagent Low Mass Reagent High Mass 25 A Al Reaction Storage Levet 25 54 100 rz mz miz Valks Ejection Amplitude moecs Max Reaction Time With the Customize button active you can change the Reaction Storage Level or the Ejection Amplitude The Ejection Amplitude is applied at the end of the ionization time to eject unwanted high mass EIl artifact ions The default value for each reagent usually does not need adjustment The Reaction Storage Level affects the storage efficiency for high mass ions When this value is set below 25u storage of ions above m z 200 will be poor This is one reason that ammonia PCI is not a de
360. the conditions for dissociation of that product ion entered as the second precursor ion You may need to make sequential injections using the MS method If the second or third generation product ion is in the original El or Cl spectrum then you can use AMD to find the optimum conditions Selected lon Storage Selected lon Storage SIS may be used with either External El or Internal El Using the Selected lon Storage SIS option you may selectively accumulate or store specific ions in the ion trap Success with this technique requires that there be no excessive space charge build up Optimum mass resolution is achieved by controlling the number of ions in the trap SIS eliminates unwanted ions by ejecting them from the trap Given the optimum number of ions that can be stored in the trap SIS enriches the sample ions relative to the unwanted matrix ions by ejecting the latter throughout ionization The unwanted ions are ejected from the trap by a technique known as resonant ion ejection Operational Modes for SIS SIS is enabled using the scan Type Group drop down list box SIS can operate in several mode Single lon Multiple lon Range and Cluster Each is described below 142 General Parameters lonization Control Internal El Parameters 315 Parameters lonization Storage Target Factor Waveform Scale Level m z Factor MW AutoS cale Waveform Insert Add Delete Customize SIS mode Customize The l
361. the instrument When the Electron Lens Tuning Box is clicked an additional Turn on Cl gas flow during tune option appears For Cl methods in External or Hybrid mode the electron repeller lens must be tuned with the CI plunger CI volume in place and the Cl gas turned on The user should adjust the Cl gas flow in Manual Control before this tune function is done lon Lens Tuning The lon Lens system consists of three lenses Lens 1 2 amp 3 These lenses are tuned using Cal Gas ions at m z 131 and 414 Optimum voltages are determined based on weighted intensities of the two ions RF Full Scale Adjust This routine should always be run before mass calibration and trap function calibration The RF Full Scale Adjust routine coarsely adjusts the mass calibration of the ion trap Successive adjustments are performed on PF TBA calibration gas ions at m z 69 414 and 614 For this algorithm to work properly it is important that the specified ions are stable and present in sufficient intensity gt 20 counts under normal scanning conditions Mass Calibration When you initiate this routine the calibration gas valve is opened and the electron multiplier filament and RF voltage are turned on The algorithm then uses the calibration compound ions at m z 69 131 264 414 464 and 614 to create a calibration curve The nitrogen peak m z 28 is not used for calibration A fixed offset at m z 0 has been empirically determined to give prope
362. ther Parameters Browse Click Hardware to select parameters for the AutoSampler This is the dialog if an 8400 AutoSampler is configured 1 6400 Hardware amp Configuration Ed Sampling Device Injectors Used Bul Syringe Fos 1 E Between Injechons 100 ul Syringe Duplicate 2nd Inj Yolume fi D Injection Delay fo T Second Sample Name a He Second Sample Notes OF Cancel Enter sampling information This information is specific to the type of sampling device installed Note that Factor Multiplier and Divisor fields apply only to data acquired with standard GC detectors not MS data files Level is the Calibration level if that is the sample type Vial H Injects Yolume Amount Factor Hultiplier Divisor 1 TAAT Level Click Help for more information about QuickStart 166 Help Topics Reference Help Quick Start E Contents Indes Find Click a book and then click Open Or click another tab such as Index Overview g gt Menus cS Dialog Boxes co Customizing Quick Start g gt Quick Start loons Print Cancel Injecting Multiple Samples Introduction Before injecting multiple samples the 3800 GC 4000 MS and AutoSampler must be configured and a GC MS Method must be created Using a SampleList in System Control You can create and edit a SampleList in the Automation File Editor or in System Control In this section y
363. tion Channels Ristore Number 1 2 FIL MUL DELAY 4 Channel N 38 In this image the Active Segment tab dialog is shown with some method related controls in the lower pane The information in the top row shows that lonization is on the Scan Type lonization mode and the Scan Mode The Scan Type choices are as follows Scan Type Full The Scan Mode choices are as follows Scan Mode Noma Hormal Fast Fastest fi You can examine and edit the parameters in the active MS method and observe the effects of these changes on the mass spectra being acquired The tab dialogs available depend on the ionization and ion preparation modes in the current method segment After you edit a parameter implement the change by clicking Activate Changes To save changes to the method click the Upload MS Method button above the lon Trap icon You can also edit the method in Method Builder by clicking the Edit Method Control and Status Source External Edit Method Method External El Upload MiS Method Vacuum System OF Damping Gas UF Temperatures OK Source OK lon Gauge Pressure 11 6 uTorr Fill Valid NOTE Details about editing the MS method are in the relevant section of Building GC MS Methods 39 Checks and Adjustments Four adjustments may be made in the Checks and Adjustments tab dialog In each case one clicks the Start button to begin the adjustment and the Done button when the a
364. tion Time for each segment is the AGC lon Time multiplied by the percentage in the Target Factor field If needed adjust the Target Factor for particular segments to increase or decrease the abundance of key ions For SIS the lon Time Factor is specified for fixed ionization and the Target Factor is specified for AGC ionization 280 item Description S Waveform Scale This parameter only appears in SIS Scan Type while in Customize Factor mode The Waveform Scale Factor is a relative scaling factor applied to the amplitude of the SIS ejection waveform Range 1 999 Count Threshold The Count Threshold setting appears in the General Parameters Customize option of all Scan Types Any ions with less intensity than the selected Count Threshold will be regarded as noise and will not be saved during the run External El e 25 Amps emission current default e 10 000 count AGC target default External Cl e NosIs e Fewer options in Reagent Parameters e Positive Negative Cl option e Single scan segment default Hybrid Cl e Emission current default 25 Amps in positive mode 250 uAmps in negative mode 281 282 3800 GC Method Command Reference 3800 GC AutoSampler Autoganmpler Syringe Size uL 110 uL z Sample Depth Injection Mode User Defined solvent Depth 2 Clean Mode Default Clean Vial Volurne uL Strokes Speed uLzec Pre Inj Solvent Flushes Pre Inj Sample Flushes
365. tions Moving the Workstation Toolbar The Workstation Toolbar can be moved to any edge of the Windows screen Click on a portion of the Workstation Toolbar that does not contain application or Quick Link buttons and drag the toolbar to the edge of the screen that you desire When you release the mouse the toolbar will remain on that edge The Workstation Toolbar remembers its location the next time it is started Additionally you can display the Workstation Toolbar as a Windows Taskbar icon To do so select Move to Windows Taskbar from the Workstation Toolbar options menu Taskbar icons appear in the lower right or bottom of the Windows Taskbar the bar on which the Start button appears When displayed as a Taskbar icon the toolbar no longer takes up space on the screen When you click on the Workstation Toolbar icon the options menu is displayed The Workstation Toolbar Options Menu RESP SYR S500 b A orotic When you move the mouse over an area of the Workstation Toolbar not containing application or QuickLink buttons right click to display the Toolbar option menu Move to Windows Task Bar Show Hide Applications on Toolbar Enable Disable Instrument Modules Application Descriptions Small Buttons an Toolbar Run Application Help on Pick Data File For Quick Link Button Pick Method For Quick Link Button Help on Workstation Toolbar Product Support Web Site About workstation Toolbar Cit Move to
366. to Forward Backflush Detector Backflush to vent Forward Backflush Column Selection Column 1 Column 2 Injection to detector Backflush Inject Injection to vent Backflush Inject Alternate injection Column 1 Column 2 Simultaneous Injection Fill Inject Methanizer Bypass Series Bypass Sample Preconcentration Trap SPT Desorb SPT Trap External Event A Off External Event B Off External Event C Off External Event D Off 254 1177 Injector Status tem Description Ready Yes or No The 1177 injector oven is Ready Yes if the setpoints have been achieved and stabilized Fault Yes or No Sos tateak 17 cor npr oe 1177 Oven On or Off al Displays if the 1177 injector oven component is turned off or on at the 3800 GC The 1177 injector is an isothermal injector Setpoint 50 to 450 C Displays the 1177 injector oven programmed temperature setting in the active method Actual 50 to 450 C ae Displays the actual temperature of the 1177 injector oven at the 3800 GC Split State On or Off Pen bay cre te 7 erm Split Ratio 1 to 10000 or Off Displays the current split ratio of the 1177 injector method The split ratio is defined as the Column Flow the Split Flow the Column Flow 1079 Injector Status tem Description Ready Yes or No The 1079 injector oven is Ready Yes if the setpoints have been achieved and stabilized Fault Yes or No fo ip Ya tautine or entr comonertasocoure 1
367. toLink Activate Method Sets the sample type or automation action of each line in the RecalcList Cal Level 1 to 10 Sets the calibration level of each calibration or verification sample in the RecalcList Inj Cannot be edited Shows the number of injections made of each sample in the RecalcList Recalc Notes Up to 180 characters Opens the Notes window for the selected record to edit or create a note about the sample This note is stored separately from the original injection notes AutoLink Two AutoLink commands when Sample Type is Baseline Analysis Calibration or Verification One AutoLink command when Sample Type is AutoLink One Activate Method Command when Sample Type is Activate Method Opens the AutoLink Parameters dialog box to set the options for linking to a remote application during automation through System Control Opens the Activate Method Dialog Box to set the path name for activating a new method during automation of a RecalcList through System Control Unid Peak 0 to 1 000 000 0 Factor Sets a calibration factor for unidentified peaks Not used by calibration samples Multiplier 0 000001 to 1 000 000 0 Sets a value for the multiplier Results for the sample are multiplied by this value Not used by calibration samples Divisor 0 000001 to 1 000 000 0 Sets a value for the divisor Results for the sample are divided by this value Not used by calibration samples Amount 0 000001 to 1 0
368. tor EFC Status tem Description Type 13 Displays the Detector EFC type Detector EFC Type 13 has 1 channel and is used for either ECD or TCD detector gas control Ch 1 Make up Set Displays in mL min the programmed and actual channel 1 flow Actual rate for ECD or TCD detector gas control Type 14 Detector EFC Status tem Description 14 Displays the Detector EFC type Detector EFC Type 14 has 2 channels and is used for TCD detector gas control for Helium Nitrogen or Argon Ch 1 Make up Set Displays in mL min the programmed and actual channel 1 flow Actual rate Ch 2 Reference Set Displays in mL min the programmed and actual channel 2 flow Actual rate Type 15 Detector EFC Status Type 15 Displays the Detector EFC type Detector EFC Type 15 has 3 channels and is used for PFPD detector gas control Ch 1 Air 1 Set Displays in mL min the programmed and actual channel 1 flow Actual rate Ch 2 H2 Set Displays in mL min the programmed and actual channel 2 flow Actual rate Ch 3 Air 2 Set Displays in mL min the programmed and actual channel 3 flow Actual rate Type 16 Detector EFC Status tem Description 16 Displays the Detector EFC type Detector EFC Type 16 has 2 channels and is used for TCD detector gas control for hydrogen 262 tem Description Ch 1 Make up Set Displays in mL min the programmed and actual channel 1 flow Actual rate Ch 2 Reference Dis
369. trap If the value was too small the precursor ion spectrum will be dominant and the product ion spectrum will be weak or missing Increase or decrease the CID excitation amplitude until a change in the spectra is observed In the case of non resonant CID use 10 volt steps for resonant CID use 0 2 volt steps Continue to increase or decrease the CID excitation amplitude but in smaller increments until suitable ion spectra are obtained Adjust the excitation time in 10 ms steps to optimize the spectra NOTE If the precursor ion is ejected instead of forming a product ion increase the excitation storage level and adjust the excitation amplitude In general increasing the excitation storage level necessitates the use of higher amplitude to dissociate the ions Do not raise the excitation storage level above the storage level where the product ions will not be stored Customize the Resonant Excitation Method For practice you can use a fixed sample source such as perfluorotributylamine PF TBA calibration gas or the column bleed obtained by raising the gas chromatograph oven temperature lteratively adjust the excitation storage level excitation amplitude and excitation time to optimize precursor to product ion conversion The optimum excitation amplitude will be slightly different when RF modulation is selected NOTE If the amplitude used is sufficiently large the precursor ion should be ejected Precursor ion ejection indicates t
370. trum Report to preview the spectrum report which can then be printed aH Click Scale to choose between Auto Scale and Fixed Mode Intensity w Auto Scale Fixed Mode hmi E Click Display Options to choose Plot lon Intensity List or Summary Information for the display Ws l Click the Display Type to choose between graphical and text displays of mass spectra or to display additional information about the spectrum Spectrum Preferences Right click the spectrum window to open a menu From this menu you can select Spectra Plot Preferences Report Preferences or General Preferences Spectra Plot Preferences Report Preferences General Preferences Use Spectra Plot Preferences to modify the appearance of the plot 32 Spectra Plot Preferences Colors Labels Axes Font Profile Plots Features Labeling and Comparisons Scales Spectra Features Background Corect Spectra Dio not show masses below joo 2 of the base peak Display Features IY Show Toolbar Display Format Show Gain Controls Plot Interaction Features Click and Drag Action Single Click Action Help Reset to Defaults Save All as Defaults Reset All toa Defaults Use Report Preferences to select chromatogram and spectrum report options Report Preferences Chro Reports Chro Markers Chro Colors Chro Aves Cal Curves Fonts Spooler Misc Spectra Reports Spectra Plots S
371. ts of the top cell in a series of highlighted cells to be copied to the cells below it Used to edit all the cells in a column quickly Edit Notes Opens the Edit Notes Dialog Box to permit editing of the notes associated with the SequenceList SampleList RecalcList or Method file displayed in the active window Edit Module Info Opens the Module Information Editor Dialog Box to permit editing of the Module Information associated with the module displayed in the active window Inject Menu yzi System Control Ferguson_1 Not File Edit Inject Automation Recalculal Inject Single Opens the appropriate Inject Single Sample Dialog Box for your Sample system Used to inject a single sample without building a SequenceList and SampleList manually Inject Single Sample Cal Amount Std Unid Peak ae sate Tne S w saa OES nat 1 1 Default Sample JAnalsis none Injection Hotes hone HultiChannel Hults tandard Hane Inject the Sample using the Method C Variant S M PIONS PME mth Browse Defaults Clear Coefficients before Calibrating Cancel Data Files RecaleList For more information on the Inject Single Sample dialog see Acquiring GC MS Data Injecting a Single Sample on page 159 219 Automation Menu a System Control Ferguson_1 Not Ready File Edit Inject Automation Recalculate Instrument Wi alele B a 4000 01 Rez Man
372. tude Time its ae Frequency Level m z volts q Offset kHz 198 2 0 20 0 E 1 0 0 Waveform Type The waveform type is either resonant or non resonant Resonant waveforms are harmonious with the frequencies of electrons held in 135 the ion trap Non resonant waveforms are not harmonious with the frequencies of the electrons held in the ion trap Excitation Storage Level m z The RF storage level in m z when the dissociation waveform is applied following isolation The excitation storage level range depends on the precursor mass but the lowest product ion must be more than several mass units above the excitation storage level A starting excitation storage level for a precursor ion can be calculated using the q calculator The q calculator is accessed by right clicking on any of the fields in the MS MS parameters table The optimum excitation storage level is a tradeoff between a storage level high enough to allow fragmentation of the precursor ion and a storage level low enough to allow efficient trapping of the lowest m z product ion A higher excitation storage level allows more energy to be imparted to the precursor ions by allowing a higher excitation amplitude Excitation Amplitude volts Voltage used to excite the precursor ion causing it to dissociate into product ions The amplitude range for non resonant excitation is O to 120 volts For resonant excitation the range is O to 60 volts The default values ar
373. ual Control l f Status 4nd Contr Aun Time 0 00 End Time 10 0 O Ready gt No Fault Begin SarnpleList Begin Sequence Begin 4t Selected SarmpleList Line Begin At Selected Sequence Line suspend ect nett ot Resume SUboTTabion Stop Automation Reset Modules Enable Automated Printing Mmenunem pescipn Begin SampleList Begin Sequence Begin at Selected SampleList Line Begin at Selected Sequence Line Suspend Automation Resume Automation Stop Automation Reset Modules Enable Automated Printing Begins execution of the currently open SampleList The currently active method will be downloaded to the instrument s which will begin to equilibrate and stabilize Begins execution of the currently open Sequence The method specified in the first line of the sequence will be downloaded to the instrument s and the corresponding Sample List will be activated Begins the open SampleList at the selected SampleList line This item is enabled when a SampleList is open Upon selecting this menu item a prompt for the line in the SampleList appears This is useful when recovering from a power failure that interrupted automation in progress Begins the open Sequence at the selected Sequence line This item is enabled when a Sequence is open Upon selecting this menu item a prompt for the line in the Sequence appears This is useful when recovering from a power failure that interrupted
374. ude volts Voltage used to excite the precursor ion causing it to dissociate into product ions The amplitude range for non resonant excitation is O to 120 volts For resonant excitation the range is 0 to 60 volts The default values are 0 2 volts for the resonant excitation method and 20 volts for the non resonant excitation method If the excitation amplitude used is too large the precursor ion and product ion spectra will be absent because both ions will be ejected from the trap If the value is too small the precursor ion spectrum will be dominant and the product ion spectrum will be weak or missing Excitation Time The excitation time is the time required for collision induced dissociation CID by ion excitation The excitation time range is 0 to 650 msec The default excitation time is 20 msec for both resonant and non resonant excitation Customize a Resonant Method The parameters in the MS MS lon Prep Method Editor window are the basic ones needed to create a MS MS lon Prep Method file for most application However some applications may require further customization Customize Parameters is separated into three sections lonization Isolation and Dissociation These parameters are hidden by default but can be modified by clicking the Customize button High Mass Ejection volts Precursor a am nies Level m 2z i Customize lonization and Isolation Parameters lonization Precursor lon m z
375. ude of the adjacent masses below the precursor ion Initially adjust in 0 2 m z increments Range 0 5 to 0 5 m z 279 tem Description S High Offset High Edge Offset High Mass Ejection Excitation Time msec Modulate RF Number of Frequencies CID Frequency Offset Defaults Target Factor This column appears when you click on the Customize button The High Edge Offset is the mass offset to optimize the ejection of the mass just above the precursor ion mass The default value is 0 High Edge Offset affects the isolation window on the high mass side of the precursor ion Increasing the mass offset increases the isolation window on the high mass side of the precursor ion Decreasing the offset decreases the window on the high mass side The offset should be adjusted to minimize the amplitude of the adjacent masses below the precursor ion Initially adjust in 0 2 m z increments Range 0 5 to 0 5 m z This column appears when you click on the Customize button The High Mass Ejection is the amplitude of the broadband waveform used to eject masses above the isolated precursor ion The default High Mass Ejection value is 35 volts Range 0 59 7 volts This column appears when you click on the Customize button The Excitation Time is the time allotted for collision induced dissociation CID by ion excitation The default excitation time is 20 msec for both resonant and non resonant excitation Range
376. ular fragmentation occurs immediately The sample molecular and fragment ions are transferred to the ion trap by a set of lenses The ions are stored and stabilized in the ion trap cavity by an RF field applied to the ring electrode of the ion trap The ion trap has a maximum storage capacity beyond which mass resolution and spectral quality deteriorate The number of ions created is proportional to the ionization time with more ions being produced the longer the ionization time AGC controls the ionization time in order to maintain the number of ions in the trap at the optimum level 200 Four modes of operation Internal El External El External Cl and Hybrid Cl use a similar scanning sequence involving AGC to scan ions out of the trap The AGC scan function consists of a prescan and up to six scan segments The prescan uses a fast scan rate and the number of ions detected in the prescan is used to calculate the ionization time for the subsequent scan segments The figure below illustrates the AGC prescan and four scan segments corresponding to the following four portions of the mass range default values 10 to 99 m z 100 to 249 m z 250 to 399 m z and 400 to 1000 m z One scan involves one complete ramping of the RF voltage over the mass range selected by the user The RF voltage is ramped at a constant rate of approximately 5000 daltons sec for normal scan and 10000 daltons sec for fast scan One complete scan at this fixed rate produces a
377. ule Information Editor to keep a record of performance maintenance hours used or other comments A Module Information Editor C WarianWS MODULEO1 MDF File Help Add Edit Delete Help Done Description 7 Serial Humber Date Installed 7 Date Last Serviced 7 Use the Add Edit and Delete buttons to record your comments Inject Single Sample Menu E System Control Varian 4000 GC MS Fie Edit Mias Automation Recalculate Inject Single Sample alal tSr same Use Inject Single Sample o to enter sample information before making an injection The 4000 Module window must be in acquisition mode for the system Not Ready to convert to Ready before making an injection To process the sample by either a manual injection or an autosampler click Inject in the bottom left corner of the dialog box Ins 20 Inject Single Sample mine seine i a Default Sample Analysis ow 1 none none Injection Injectors Amount Std Unid Peak MultiChannel Volume IS N only Factor MultiStandard 1 0 Pos 1 x 1 0 1 1 none gt Divisor Multiplier Inject the Sample using the Method c Warianw S startup1 mth Defaults J Clear Coefficients before Calibrating Inject Cancel Data Files RecalcList From the menu select the Sample Type The following shows the choices Inject Single Sample Sample Name Sample nan Default Sampl
378. ured Valve 1 is Unused Default is Off Energized is On Valve 2 is Unused Default is Off Energized is On Valve 3 is Unused Default is Off Energized is On Valve 4 is Unused Default is Off Energized is On Valve 5 is Unused Default is Off Energized is On Valve 6 is Unused Default is Off Energized is On Valve 7 is Unused Default is Off Energized is On The Installed hardware is listed The setup is changed from the 3800 GC front panel The Real Time Chromatogram Display All detectors installed on the 3800 GC display their chromatographic signals in real time Configuration of the chromatogram display for all detectors is the same ag 3800 44 Equilibrating Mie Es 3800 Operation Set Actual Column Oven Status Temp ones Col Over 30 210 Ready No Fault No D Front 1079 96 98 Oven Power On Coolant Off Start Runtime 0 00 min ee ie ot ney eT picid 1073 Of 71 Setpoint 90C Actual 210 C Equilbrating Coolable N A NA Stabilization Time 0 00 min No Faut E Front FID 260 260 gt Mid TSO Of 69 gt Enable Column Oven Coolant at 60 C NAA NAL Timeouk 20 00 min Timed Out No Slee cys ey Valves ajaj Show only the chromatogram display Continue to view the signal after the run Select the detector s to view 73 Front FID 0 048 mY E Hide unhide the Toolbar G Set both the amplitude and time axes to full sca
379. ures have been reached or until the system has warmed up for 20 minutes 50 Operating Conditions Readbacks of the current temperatures in each zone Operating Conditions Trap Temperature 100 C Manifold Temperature 53C Transterline Temperature 253 C lon Source Temperature 221 C Event Messages and Module Attributes Display After a change the event log at the bottom of the screen updates with the time and identity of the event You can also look at the Module Attributes Hide Keypad Event Messages z Jan OF 10 Mo ETIE ETA acted Trap 220 Source 200 Manifold 120 Transferline 250 Jan 07 10 39 33 Bakeout Cancelled by User Returning to Analysis Temperatures Setting Analysis and Bakeout Temperatures Clicking in the fields and changing the values will change temperature settings After changing a setting click save The Restore button will return the settings prior to your changes The allowed temperature ranges in degrees and the default temperatures for either Internal or External Hybrid configurations or bakeout are entered in the following table All temperature units are C The ion source temperature zone will not appear when the instrument is in Internal configuration Temp Zone Default Default Default External Internal or Bakeout Hybrid on Trap e f po fee A C E e 2 E a a fensouce fo san fm i fae NOTE If the manifold temperature is 70 C or higher the source temperature is limit
380. use the Browse button to pick the Method from a list of files When this line is encountered during automated injections the specified Method is activated You may specify any number of Methods to be used in the SampleList 183 Creating or Editing a Sequence S i Automation File Editor Edit Help RecalcList Open j SampleList SAVE Sequence Creve AE Erit Printer Setup Exit Click New Sequence or Open to open an existing Sequence from the File menu E Automation File Editor File Edit Help Als El s S sleek or click New or Open Automation File button on the toolbar The Sequence window opens Untitled seq SequenceList OF x Action Click Add to add lines to the SequenceList You may enter any number of Sequence lines Choose the action for the selected step of the Sequence from the drop down box Browse for a Method and SampleList file in the active cells 184 Automated MS Report Generation Overview Once you have added Report sections to your Method automated reports can be generated from System Control after each injection after Recalculations or by the use of any of the Print actions in the Sequence window You may choose to disable automated Report printing during the course of an automated sequence of injections or Recalculations You can do this by disabling automated printing from the Automation menu in the Instrument window Automation Beg
381. ut Down State Shutting Down Trap Temperature OFF Trap Temperature 100 C Manifold Temperature 49C Manifold Temperature OFF Transterline Temperature OFF Transterline Temperature 234 C Source Temperature A120 Source Temperature OFF Vacuum System Pump Spin Speed fos Current 140 m mpe Preumatics Flow Rate 0 0 mL min Inlet Pressure a4 PSI Getter Control Temperature 390 Vacuum System Pump Spin Speed OFF Pneumatics Flow Rate 4 0 mLrnun Getter Control Temperature OFF Vacuum System Status Mot Ready Preumatics Damping Gas Off On Getter Control Heater OFF Or Hide Keypad Event Messages 08 14 57 37 Turning Getter OFF Jan 0S 14 57 37 Turning Damping Gas OFF Jan O8 14 57 37 Shutdown Pump Heated Zones are shutting down Jan O8 14 57 37 DO WOT PERFORM MAINTENANCE UNTIL SHUTDOWN IS COMPLETE Jan To restart the system after activating the shutdown click Start Up on the left side of the screen This restarts the pumps and turn on the heaters 62 Acquisition Tab Starting Up the System Status and Control Current Set Points Operating Conditions m Heated Zones Heated Zones Conditions Start Up Trap Temperature 100C Trap Temperature SIC State Starting Up Manifold Temperature 50C Manifold Temperature 51 C Transf
382. ve configured your computer s network settings start System Control SWAN CIN ET eee OND e ADAE AANRY a a a e ANKE org aie analyst run hE Defauttinth gt Eas Mine eles p AAA i i Pi TES pate ki Shins carrey ie N LAMINAT E MT T LLA LDAA T E LAAT ARINC s i TAA MLA TAREE Le EA LO nl HC CE ACR ANA ERARAS Ss Click on the System Control Automation button on the Workstation Toolbar to start System Control When System Control has started for the first time the Star Assistant Communication Configuration Wizard will appear to guide you through the setup and network connections of your GC NOTE Before proceeding with this section consult your Network Administrator about whether a central BOOTP Server is available on the network 1 If IP addresses are managed by a central BOOTP Server then proceed to Specifying IP Addresses from a Central BOOTP Server 2 IfIP addresses are specified by a Network Administrator but not centrally managed then continue reading Specifying IP Addresses from System Control Specifying IP Addresses from System Control The Varian MS Workstation can be used to specify IP addresses to 3800 and 3900 GCs attached to the network Use the following procedure to manage IP addresses from System Control The first time the Star Assistant guides you through the setup of your GC the following opens This Star Assistant will guide you through the configuration of the
383. with the currently active method Edit Method Click Edit Method to open the Method Builder application and loads the currently active method Wait for Readyin If this box is checked the state of the Readyln sync port is included in the checks the system performs to determine if the system is Ready The Readyln port typically would be used to interface to an external device such as a Purge and Trap sampler End Time The End Time is initially set equal to the end time of the active method You may change the end time to either shorten or prolong the end time of the data acquisition Note that this does not affect the end time of the GC method 246 Status Display Spectrum Toolbar tle a a a A Click the green arrow to hide the toolbar Clicking on the upper left of the full screen display restores the toolbar eee Click the full scale button to cause the spectrum to be normalized in the vertical and horizontal directions Double clicking on the lower left corner of the scale has the same effect Click the previous scale button to restore previous scalings Click the spectrum plot button to open a window with the spectrum ENEI Click the scale button to choose between Auto Scale Intensity and Fixed Scale Intensity hrm Click the mass range button to choose between Acquired Mass Range Fixed Mass Range or Maximum E Click this to switch between graphics and text displays of ion intensity and s
384. ws adjustment of Cl gas and Cal gas flow RF ramp and a check of air water levels Cl Gas Adjustment RF Ramp Adjustment An ater Check Last Set Date Mot Applicable Result Mot Adjusted Ionization Time O Total Ion Count O Start Cancel Actor Idle For the Cal Gas and Cl reagent adjustments the MS parameters are set up to produce and collect characteristic ions of the gas being adjusted The software then monitors the amplitude and resolution of these ions as the needle valve controlling gas flow is adjusted The system contains built in criteria for adjustment of the common Cl reagents methane iso butane ammonia methanol and acetonitrile A gauge display shows whether the flow is too high too low or OK and the spectrum of the gas is displayed to allow the user to judge for himself based on any special needs of his analysis Use RF Ramp Adjustment to fine tune the RF by adjusting the tuning screw that is in the front panel of the 4000 MS while observing a graphical display of the RF ramp Proper adjustment will give a smooth linear ramp with minimum amplitude Use the air water check to diagnose the state of the vacuum system Generally a narrow peak for the nitrogen ion at m z 28 indicates you do not have a vacuum leak problem A broad nitrogen peak may indicate an air leak but it might also indicate nitrogen contamination in the helium carrier supply The water level in the system can be estimat
385. you see fields where you can enter information about the sample The following define the fields and buttons in this dialog sample Hame Enter the sample name here The final name of the file depends on settings accessed by clicking the Data Files button If only s is listed in the Data Files dialog the sample name will be as you entered it here Sample Type There are several choices available from the Sample Type drop down list box Use the scroll bar to see all the options Sample Type Analysis Sample Type Analysis Print Calib New Cali Block Autolink Activate Method Print Summar Calibration Vertication Baseline Print Calib New Calib Block Cal level If you designate the sample type as calibration you can designate which calibration level you are injecting You can enter up to ten levels Ini Specify here the number of injections of this sample You may make up to nine replicate injections at each calibration level Injection Notes Enter notes about the sample 168 In the Vial Injection Volume and Injectors Used fields enter information about the sample The fields beginning with Amt Std are used only for data files acquired with standard GC detectors Inject the Sample using the Method E walan Colkest External mth Browse Select the Method to use for the run Click the Browse key to select a file using Windows Explorer What the Buttons Do Add o Add Adds a new line to t

Agilent Technologies 4000 GC/MS Version 6 Software Operation Manual

Contents

Download Pdf Manuals

Related Search

Related Contents