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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will contain historical references to Varian.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. 2004-2009
4000 MS Users Guide
Internal Ionization
Printed in U.S.A.
www.angeldans.com
Varian, Inc.
2700 Mitchell Drive
Walnut Creek, CA 94598-1675/USA
4000 MS
03-954032-00:Rev. 4
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Table of Contents
Related Manuals for Varian 4000 MS
Summary of Contents for Varian 4000 MS
- Page 1 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 This document is provided as a courtesy but is no longer kept current and thus will contain historical references to Varian.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 Varian, Inc. 2700 Mitchell Drive information, go to www.agilent.com/chem.
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Page 3: Table Of Contents
Contents Overview of Internal Configuration ..................5 Scan Functions Control MS Processes ........................6 Steps to Create a Mass Spectrum ..........................6 Sample Introduction ............................. 6 Ionization ................................6 Fragmentation ..............................7 Ion Storage ................................7 ... - Page 4 Preparing an MS Method for Data Acquisition ......................22 Building a New MS Method ..........................22 Name the Method ............................24 Set the 4000 MS Instrument Configuration ....................24 Select the Acquisition Data Type ......................... 25 Edit Chromatographic Time Segments ....................... 25 ...
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Page 5: Overview Of Internal Configuration
Overview of Internal Configuration The Internal configuration is one of the three operational configurations of the 4000 GC/MS system. In this configuration, it is possible to collect either electron ionization or positive chemical ionization (EI or PCI) data. Unlike the External Ionization configuration, it is possible to collect EI or PCI data during different time segments of a single chromatographic acquisition. -
Page 6: Scan Functions Control Ms Processes
The scan function controls the variations in time of the RF potential applied to the ring electrode as well as any supplementary waveforms applied to the endcap electrodes. The 4000 MS module has two techniques, Electron Ionization (EI) and Chemical Ionization (CI), for generating sample ions in the external source. -
Page 7: Fragmentation
Fragmentation Depending on the structure of the molecular ion and the excess internal energy remaining after electron impact, there may be further unimolecular decomposition of some of the molecular ions to form various fragment ions and neutrals. Unimolecular decomposition happens in picoseconds, the time scale of a few molecular vibrations, effectively occurring at the same time as ionization. -
Page 8: Ion Preparation Options
Ion 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. -
Page 9: Library Searching And Data Handling
DFTPP and BFB. Library Searching and Data Handling The mass spectra collected from the MS are analyzed through Varian MS Data Review. The identity of most compounds is determined by the comparison of the collected spectrum with a reference library. The mass and intensity listing is compared to results collected on other instruments. -
Page 10: Chemical Ionization Reactions In Pci
Ion Preparation Options The 4000 MS uses a combination of waveforms and RF to isolate, or remove, specific ions after they are formed and are stored in the trap. Selected Ion Storage (SIS) and Tandem Mass Spec (MS/MS) can be performed on the ions... -
Page 11: Scanning Ions To Collect Mass Spectra
Using CI, the molecular weight is obvious and the most intense ion is M+1. Because the 4000 MS is able to switch between EI and CI in a single run, the best analytical conditions can be used for a given compound. -
Page 12: Conversion From External To Internal Configuration
Conversion from External to Internal Configuration Converting the 4000 MS from External to Internal configuration involves changing both the ion source and the column position. The External ion source assembly is removed from the trap assembly and replaced with the Internal ion source assembly. -
Page 13: Starting The Instrument
Open System Control and the Startup/Shutdown page opens. Check the Vacuum Status The vacuum readings tell a lot about the state of the MS after pump down (and during operation). Typical operating ranges for the 4000 MS in Internal mode are: • Speed 100% •... -
Page 14: Diagnostic Tests
Perform hardware checks on the 4000 MS using the Diagnostics tab. For more details on the diagnostic tests, seethe Diagnostics section in the 4000 MS Ion Trap Software Operation Manual. -
Page 15: Setting System Temperatures
System Bakeout To remove water adsorbed on the manifold while the 4000 MS was vented, perform a Bakeout from the Temperatures tab in System Control. Perform a system bakeout to remove chemical background after running samples. -
Page 16: Startup And Shutdown
Manual. Shutting Down the System To shut down the 4000 MS, click the Shut Down button in the upper left corner of the Startup/Shutdown dialog. The heaters will be turned off and the speed of the turbo pump will be gradually reduced to 35% of full speed. -
Page 17: Adjusting The Rf Ramp
2. Click Cal Gas Adjustment in the Checks and Adjustments tab in Manual Control. 3. Turn the Cal Gas valve inside the front door of the 4000 MS either clockwise to decrease the flow or counterclockwise to increase the flow. Adjust the flow... -
Page 18: Ci Gas Adjustment
CI Gas Adjustment Before performing chemical ionization, adjust the reagent gas pressure. The next section explains the set up of the most common reagent gases. Air/Water Check Too high a pressure of air or water in the system because of an air leak or a need to bake out the system will result in poor performance. -
Page 19: Installing A Liquid Reagent
Installing a Liquid Reagent To connect a liquid reagent reservoir to the liquid reagent inlet block, do the following: 1. Connect a liquid reagent reservoir containing the chosen liquid to the liquid reagent inlet block. 2. Open the CI needle valve 6-7 turns clockwise. 3. -
Page 20: Installing A Gaseous Reagent
1. Connect the regulator of the gas cylinder to the back of the instrument using a 4 mL/min restrictor. 2. See the 4000 MS Ion Trap Hardware Operation Manual for more details. Auto Tune Depending on your configuration and settings, you may not see all the available Auto Tune routings. -
Page 21: Ion Lens Tuning
the imbalance. If the balance is outside the range of 200 to 300 µA, 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. -
Page 22: Preparing An Ms Method For Data Acquisition
Preparing an MS Method for Data Acquisition Building a New MS Method From the Workstation Toolbar, open the Method Builder The ‘Create/Open Method File’ dialog will be displayed. You may choose to create a new method or open an existing method. If you do not need to see this dialog again, check the box labeled ‘Do not display this dialog at startup.’... - Page 23 Select which detectors (MS and/or GC) will have data handling. Select what data analysis sections are required; Standard MS Reports and/or MS Data Handling.
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Page 24: Name The Method
The GC and the MS will be set to the configuration of the instrument connected to the Varian MS Workstation. For the 4000 MS Internal configuration, both EI and CI can be performed during the same run and so there is only one internal... -
Page 25: Select The Acquisition Data Type
Edit Chromatographic Time Segments When the 4000 MS is in Internal Configuration, it can do EI, CI, EI/MS/MS, and CI/MS/MS in a single run. The Chromatographic Time Segments table allows you to time-program analysis conditions to get the best results for each segment in the analysis. -
Page 26: Scan Function Settings
MS/MS, Multiple Reaction Monitoring (MRM), or Selected Ion Storage (SIS). Scan Function selection The 4000 MS has three scan modes - normal speed (5,000 u/sec), fast speed (10,000 u/sec), or fastest (10,000 u/sec without a prescan). The Fastest speed only allows acquisition with single-segment mass ranges. -
Page 27: Ionization Control
NIST library reports molecular weights to the nearest integer mass unit only. The Varian MS Workstation software must decide to which mass to assign measured intensity. If the exact mass of an ion happens to fall close to the dividing line between integer masses, the software may make an incorrect mass assignment. -
Page 28: Setting Parameters For Chemical Ionization
Setting Parameters for Chemical Ionization After selecting a standard reagent (methane, isobutane, acetonitrile, or methanol), the CI parameters for the selected reagent are set automatically so you do not need to change the default values of the CI parameters. However, the remaining CI parameters (Reaction Storage Level, Ejection Amplitude (V), and Max Reaction Time) can be optimized for sensitivity. -
Page 29: Full Scan Parameters
Mass Range area (upper left), enter Low Mass and High Mass values to specify the full scan mass range. This is the most common scan type for the 4000 MS. The mass range also determines the scan range of the AGC calculation. -
Page 30: Setting Parameters For An Ms/Ms Method Segment
When DFTPP and BFB tune types are selected, mass segments and ion time factors, which will be good starting points for meeting US EPA semivolatile and volatile tuning requirements, are displayed in the mass segment table. Each mass segment has its own RF Storage Level. This is the RF voltage used to hold ions in the trap during the ionization period and is specified in mass units. -
Page 31: Viewing Method Parameters In Manual Control
The Precursor Ion is usually an intense ion in the full scan mass spectrum. Usually, the Isolation Window is the parent ion mass ±1.0 (3.0 mass units wide). Waveform Type is either Resonant or Non-resonant. The Excitation Storage Level is the lowest mass stored during collision-assisted dissociation. A good value can be calculated using the “q”... -
Page 32: Displaying Ions
4. The active method is displayed in the toolbar. Displaying Ions To view ions do the following: 1. Select an ionization segment in which the ionization is on. You cannot turn on the ion trap in a segment where ionization is OFF as in the Fil/Mul Delay segment #1. -
Page 33: Viewing Method Parameters
Viewing Method Parameters In the following figure, the Method Segment tab dialog is shown with method related controls in the lower pane. The information in the top row of the Method Segment tab indicates if the trap is on, the Scan Type, Ionization mode, and Scan Mode. Editing a Method in Manual Control Examine and edit all the parameters in the active MS method and observe the changes on the mass spectra being acquired. - Page 34 After editing a parameter, implement the change by clicking the Activate Changes button. The changes are reflected in the spectrum. The example here is a change in the Start Mass from 50 m/z to 100 m/z:...
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Page 35: Saving A Method
Saving a Method To save changes to the method, click the Upload MS Method button above the Ion Trap icon. Click Edit Method to open the Method Builder and make other changes. If you do not upload changes, the method is still checked to see if changes are made when the segment is changed or when you leave Manual Control or the Method Segment. -
Page 36: Status And Control
If the GC is not ready, you will see a Not Ready message at the top of the screen. After 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 see the top pull down menu under Windows and see the states for the 4000, 3800, and Combi PAL modules. -
Page 37: Activating A Method
Activating a Method To activate a GC/MS method, do the following: 1. Click the File menu. 2. Click Activate Method. 3. Select a method by doing one of the following: • Click Recent Files to display the eight most recent methods. •... -
Page 38: Injecting Using A Samplelist
• If the MS is not in Acquisition mode, it changes to that mode automatically. • If an AutoSampler is doing the injection, it begins after the instrument modules are Ready. • If you are doing a manual injection, wait until the System Control title bar reads “Waiting for Injection of Sample”... -
Page 39: Monitoring The Status Of Runs
Monitoring the Status of Runs Monitor the status of the run in the instrument window. The Status and Control window and the Toolbar show the run status. Monitor the chromatogram and spectra in System Control, or click the far right button in the Chromatogram toolbar to open MS Data Review, where you can perform operations like library searching while the data file is being acquired.