Varian 4000 MS, User Manual

Page 1: ...Varian Inc 2700 Mitchell Drive Walnut Creek CA 94598 1675 USA Varian Inc 2004 2009 Printed in U S A 03 954032 00 Rev 4 4000 MS 4000 MS Users Guide Internal Ionization www angeldans com...

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Page 3: ...Mass Spectra 11 Library Searching 11 Selectivity Considerations 11 Type of Matrix 11 Using EI and PCI to Get More Information 11 Conversion from External to Internal Configuration 12 Checklist 12 Con...

Page 4: ...uisition Data Type 25 Edit Chromatographic Time Segments 25 Edit the 4000 MS Method Segments 25 Scan Function Settings 26 General Parameters Tab 26 Ionization Control 27 EI Ionization Parameters 27 Se...

Page 5: ...age SIS or with optional software and equipment Tandem Mass Spectrometry Automated Methods Development AMD MS MS MSn and Multiple Reaction Monitoring MRM Refer to the 4000 GC MS Software Operation Man...

Page 6: ...function These scan functions are discussed in more detail in the 4000 GC MS Software Operation Manual RF Voltage Steps to Create a Mass Spectrum Sample analysis with an ion trap analyzer may be divid...

Page 7: ...kground noise and increased selectivity Ion Analysis The stored ions are analyzed by ramping the RF voltage applied to the ring electrode to a high value during which time ions from low to high mass a...

Page 8: ...ns within the stored mass range and fill the trap only with ions in the mass range s of interest In MS MS a parent ion is isolated and then dissociated by energetic collisions with helium buffer gas t...

Page 9: ...nalysis of complex compounds The generation of ions in chemical ionization is a two step process A CI reagent gas is introduced into the ion trap analyzer The reagent gas is ionized by EI Then the sam...

Page 10: ...mong the common liquid CI reagents methanol has a proton affinity of 180 3 kcal mol while acetonitrile is 1862 kcal mol By choosing a suitable reagent gas you can obtain high specificity i e less effi...

Page 11: ...has small CI libraries generated using internal configuration ion trap GC MS systems The libraries are organized by the CI reagent which include methane methanol and isobutane Selectivity Considerati...

Page 12: ...ation only requires changing the ion source The column position and transfer line are already directed to the trap and do not need to be adjusted Outline 1 Change the ion source 2 Move the heat shield...

Page 13: ...k 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 Current 200 30...

Page 14: ...b Monitor the vacuum system the electron multiplier the waveform system temperatures and the ion source Perform hardware checks on the 4000 MS using the Diagnostics tab For more details on the diagnos...

Page 15: ...hours for the trap to stabilize The temperature of the trap affects mass calibration and therefore the trap frequency calibration Set the transfer line temperature so there are no cold spot between t...

Page 16: ...Operation 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 th...

Page 17: ...t line and the intensity is at a minimum The Status Bar in the Adjustment Results field should be just below OK Adjusting the Calibration Gas To adjust the calibration gas do the following 1 Check the...

Page 18: ...anual setting After replacing the electron multiplier auto tune of Electron Multiplier before performing the Air Water Check Setting Up CI Reagents Before running CI experiments adjust the CI gas pres...

Page 19: ...open the needle valve clockwise 5 While observing the spectrum use the Adjust CI Gas and turn the CI needle valve to increase or decrease the amount of reagent entering the trap until the resolution b...

Page 20: ...tomatic setup tuning and calibration program for Hybrid CI Integrator Zero Integrator Zero obtains the average value of the signal level from the integrator circuitry when the filament is off When the...

Page 21: ...the correct mass assignment for high mass ions in the calibration gas spectrum This routine should always be run before Mass Calibration and Trap Frequency Calibration Mass Calibration Mass Calibrati...

Page 22: ...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...

Page 23: ...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...

Page 24: ...a name for the method and save it either in the default folder or another folder you select Set the 4000 MS Instrument Configuration The GC and the MS will be set to the configuration of the instrumen...

Page 25: ...able allows you to time 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 ther...

Page 26: ...st Fastest 50 1000 1 Segment 3 0 76 sec 0 47 sec 0 41 sec 50 1000 4 Segment 3 1 08 sec 0 79 sec N A 50 400 DFTPP 3 0 70 sec 0 59 sec N A General Parameters Tab Scan Time Scans Averaged and Data Rate a...

Page 27: ...f somewhat less detailed information in the mass spectra The count threshold is shown only if the Customize button is active Ionization Control The Target Total Ion Current or TIC is specified here Th...

Page 28: ...ed in the trap during ionization All masses above this mass are ejected during the ionization step This reduces the number of EI generated ions that are in the trap The combination of Reagent Low and...

Page 29: ...r details on how to optimize these parameters or on how to set up for non standard reagents refer to the 4000 GC MS Software Operation Manual NOTE Be aware that if you do change a CI parameter and set...

Page 30: ...ion mass range For example adjusting four or five segments appropriately allows the system to pass DFTPP or BFB tune requirements for US EPA environmental methods Setting Parameters for an MS MS Metho...

Page 31: ...Using the AMD Automated Method Development mode is the easiest way to determine this voltage The Product Ion Mass range during method development encompasses the range from Excitation Storage Level to...

Page 32: ...gment 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 Change to an ionization segment 2 Click the Trap check box to...

Page 33: ...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...

Page 34: ...4 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...

Page 35: ...l be given the option to save these changes or discard them NOTE If you leave System Control by starting automation or choosing Inject Single Sample you are prompted to save the method Click Yes the i...

Page 36: ...ntrol Before an acquisition has been started the Status and Control field is similar to the following figure The Run Time is 0 00 minutes The End Time is the run length specified in the active method...

Page 37: ...Inject Single Sample do the following 1 Click Inject Single Sample from the Inject menu 2 After the Inject Single Sample window opens do the following a Type a sample name b Enter the vial number of...

Page 38: ...s from System Control do the following 1 Click either New SampleList or Open SampleList from the File menu 2 The SampleList window for the open SampleList opens It contains fields that are specific to...

Page 39: ...itor 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 d...