Varian 4000 GCMS Installation Procedures Manual Download Page 1

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03-914998-55:6

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Varian, Inc.
2700 Mitchell Drive
Walnut Creek, CA 94598-1675/USA

4000 GCMS SYSTEM

Installation Procedures

Summary of Contents for 4000 GCMS

Page 1: ...03 914998 55 6 1 of 63 Varian Inc 2700 Mitchell Drive Walnut Creek CA 94598 1675 USA 4000 GCMS SYSTEM Installation Procedures...

Page 2: ...ary Tuning 23 3 1 System Monitoring 23 3 2 RF Ramp Adjustment 24 3 3 Dipole Adjustment 26 3 4 Air Water Check 28 3 5 Cal Gas Adjustment 29 Section 4 Auto Tuning 31 4 1 Internal Auto Tuning 31 4 2 Exte...

Page 3: ...Achieving External PCI Specifications 57 8 1 Install Gaseous CI 57 8 2 Adjust Gaseous CI Reagent Flow 57 8 3 Methodology 59 8 4 BZP Acquisition 59 8 5 Signal to noise Calculation 60 Section 9 Achievi...

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Page 5: ...ours 4 EI ionization mode demo 1 hours 5 Additional customer familiarization 4 hours Option Installation 1 Autosampler installation check out familiarization 1 5 hours 2 CI ionization mode demo famili...

Page 6: ...tion ensure you have all the necessary samples or that they have been shipped to the customer from a local Varian office Installation engineers outside of the USA should confirm the availability of te...

Page 7: ...the MS The remaining FC 43 can be stored in the vials provided in the accessory kit Do not overfill the Cal Gas vial installed in the MS Overfilling can result in FC 43 contamination that interferes...

Page 8: ...S at J7 USB and to a USB port on the PC Connect the Ethernet cable to the GC and to the PC Be sure to connect the Ethernet cable using the side connector of the Tee and NOT the terminal end Install th...

Page 9: ...as described in Section 2 of this document The column shipped with the system must be installed to achieve the best results for acquisitions associated with the installation If an 1177 injector is in...

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Page 11: ...th the MS top cover to ON Turn on the main circuit breaker at the rear of the MS The mechanical pump will run loudly initially but should run quietly within 30 seconds If the mechanical pump continues...

Page 12: ...ed to the MS the Windows XP operating system may launch the Found New Hardware Wizard when first turning on the MS Configure the MS as new hardware by clicking through the pages of this wizard as show...

Page 13: ...03 914998 55 6 13 of 63 Select Install the software automatically Recommended and click Next Figure 2 2...

Page 14: ...03 914998 55 6 14 of 63 Click Finish to close the wizard Figure 2 3...

Page 15: ...hutdown refer to Figure 2 4 click Turn On for Pneumatics Set the Damping Gas Flow to 4 mL min on the Module Attributes tab in Manual Control refer to Figure 2 5 enter 4 0 mL min and click Activate Cha...

Page 16: ...le results until after auto tuning the system Go to Manual Control and click the Active Segment tab Enter a Mass Range of 15 to 45 m z refer to Figure 2 6 Full Scan Parameters tab Also enter a Fixed I...

Page 17: ...03 914998 55 6 17 of 63 Figure 2 6...

Page 18: ...03 914998 55 6 18 of 63 Figure 2 7...

Page 19: ...ot be a significant 28 m z peak visible Refer to Figure 2 8 If there is the system has a leak which needs to be found and fixed If the system has a significant leak the baseline will be flat or there...

Page 20: ...MS Int or Ext Service mth Turn on the trap and click on the words Ion Source to turn off the ion source The RF and Multiplier should remain on green is on black is off In this configuration refer to...

Page 21: ...or the column stationary phase and hold for 60 minutes From the Analysis tab on the Temperatures page set the Trap to 150 C Manifold to 40 C Transfer Line to 230 C and the Source to 150 C external mod...

Page 22: ...me familiarization could be done with the operator NOTE After bakeout reset the manifold bakeout temperature to 80 C and click Save A manifold bakeout temperature of 110 C is appropriate for the initi...

Page 23: ...ect the Ion Source Multiplier Dynode and Ion Gauge check boxes refer to Figure 3 1 and monitor the following Vacuum System Power should be 8 12 Watts with no damping gas 12 15 Watts with damping gas f...

Page 24: ...ghlight RF Ramp Adjustment and click Start refer to Figure 3 2 Adjust the RF tuning rod as shown in Figure 3 3 to minimize the Base Amount value displayed in the upper right corner of the spectral win...

Page 25: ...03 914998 55 6 25 of 63 Figure 3 2...

Page 26: ...x and select the RF radio button from the Monitoring tab as shown in Figure 3 4 Adjust the trapping field dipole inductors on the Upper Manifold PWA through the holes in the Manifold Electronics Enclo...

Page 27: ...03 914998 55 6 27 of 63 Figure 3 4 Figure 3 5...

Page 28: ...and water levels can also be checked with inclusion of the CI plumbing From the Checks and Adjustments tab in Manual Control highlight Air Water Check select the CI Plumbing Leak Check box and click S...

Page 29: ...cks and Adjustments tab in Manual Control highlight Cal Gas Adjustment and click Start refer to Figure 3 8 Adjust the Cal Gas needle valve behind the MS front door until the display indicates the Cal...

Page 30: ...03 914998 55 6 30 of 63 Figure 3 8...

Page 31: ...at the auto tunes should be re run after re adjusting the Cal Gas needle valve because each of these two features Cal Gas adjustment and auto tuning can affect the other 4 1 Internal Auto Tuning INTER...

Page 32: ...cluded with the CI option for details Turn the CI needle valve CCW until it stops From the Manual Control page Checks and Adjustments tab highlight CI Gas Adjustment select Methane as the Reagent and...

Page 33: ...egrator Zero Set Electron Multiplier Trap DC Offset Voltage Electron Lens Tuning and Ion Lens Tuning Run the following auto tunes as needed for mass assignment RF Full Scale Adjust Mass Calibration an...

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Page 35: ...odology NOTE The 4000 GCMS system will arrive with a Test Files CD containing factory test method and data files These method files can be used to pass the sensitivity tests associated with the instal...

Page 36: ...void sample loss through the tip of the needle Ensure the syringe plunger is not forced out of the syringe barrel if a Pressure Pulse is used in the method 5 3 Library Search and Signal to Noise Calcu...

Page 37: ...03 914998 55 6 37 of 63 Figure 5 2 In the MSDR window type 272 into the IONS field and press Enter to display a single ion chromatogram of the m z 272 ion signal see Figure 5 3 Figure 5 3...

Page 38: ...03 914998 55 6 38 of 63 Click and drag a zoom highlight box around the m z 272 ion from OFN see Figure 5 4 Figure 5 4...

Page 39: ...o see Figure 5 5 Figure 5 5 Note that the RMS signal to noise is calculated using 5 point Savitsky Golay smoothing How to manually set these Chromatogram Plot Preferences from the Chromatogram Plot an...

Page 40: ...03 914998 55 6 40 of 63 Figure 5 6...

Page 41: ...03 914998 55 6 41 of 63 Figure 5 7...

Page 42: ...03 914998 55 6 42 of 63 Figure 5 8...

Page 43: ...03 914998 55 6 43 of 63 From the Chromatogram pull down menu set Select Spectra to Average to 3 see Figure 5 9 Figure 5 9...

Page 44: ...4 of 63 From the Chromatogram pull down menu select Edit Background Correction see Figure 5 10 Figure 5 10 Click Auto Background Correction and Done in the Background Correction dialog box see Figure...

Page 45: ...e m z 272 single ion chromatogram to generate the spectrum Note the BC in the upper right corner of the spectral window which indicates a background corrected spectrum see Figure 5 12 Figure 5 12 3 sp...

Page 46: ...03 914998 55 6 46 of 63 From the Search pull down menu select Library Search a Spectrum 1A see Figure 5 13 Figure 5 13...

Page 47: ...03 914998 55 6 47 of 63 Figure 5 14 shows Octafluoronaphthalene with a match score of 500 Note that OFN is in the Tutorial library Figure 5 14 OFN match found in the Tutorial library...

Page 48: ...55 6 48 of 63 Click the Do NIST Search button and select Spectrum Search to edit the library search parameters and re search if necessary Suggested library search parameters are shown in Figure 5 15 F...

Page 49: ...914998 00 and parts ordering Troubleshooting including Manual Control Diagnostics the Troubleshooting section of the Hardware Manual and calling Technical Support Warranty issues such as the system in...

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Page 51: ...ty 99 95 methanol 6 1 Install Liquid CI Before introducing methanol into the CI plumbing it may be necessary to condition the CI plumbing to remove air and water by opening the CI solenoids in Manual...

Page 52: ...ethanol as shown in Figure 6 2 and click Start Figure 6 2 Open the 4000 MS front door and adjust the CI needle until the ratio between the m z 33 and m z 31 ions is approximately 10 1 33 31 10 1 Click...

Page 53: ...method and data files These method files can be used to pass the sensitivity tests associated with the installation Retain the test files CD for your records Ensure the MS temperatures are set for th...

Page 54: ...the syringe barrel before depressing the syringe plunger 6 5 Signal to noise Calculation Use the quick load option shown in Figure 5 2 to load the BZP data file into MSDR Plot a single ion chromatogra...

Page 55: ...ry a 10 1 dilution can be done using customer supplied glassware and 2 2 4 trimethylpentane isooctane to reduce the amount of OFN from 5 pg to 500 fg In addition a background corrected spectrum should...

Page 56: ...quiring the data file calculate the S N and run a library search Use this opportunity to demonstrate data analysis to the customer The sms data file can be loaded into Mass Spectra Data Review MSDR us...

Page 57: ...hane gas is recommended to minimize source contamination 8 2 Adjust Gaseous CI Reagent Flow Turn the CI needle valve behind the MS front door counter clockwise CCW until it stops Go to the Checks and...

Page 58: ...03 914998 55 6 58 of 63 Figure 8 1...

Page 59: ...le found on the Test Files CD included with the system The Damping Gas flow rate can also be found in the Data File Information dialog in the Module Attributes section Set the MS damping gas flow rate...

Page 60: ...n m z 183 Click the apex scan to display the spectrum Refer to Figures 5 10 and 5 11 and background correct the spectrum Right mouse click the apex scan and select Calculate Noise refer to Figure 5 5...

Page 61: ...your records Ensure the MS temperatures are set for this acquisition Trap 150 C Manifold 40 C Transfer Line 230 C Source 150 C In System Control activate the external NCI method from the Test Files CD...

Page 62: ...n m z 362 Click the apex scan to display the spectrum Refer to Figures 5 10 and 5 11 and background correct the spectrum Right mouse click the apex scan and select Calculate Noise refer to Figure 5 5...

Page 63: ...126 01 2 pg L OFN 5 pg uL BZP 5 pg BZP 183 50 1 N A Internal EI with a Quick Switch Valve in the GC 10 1 split or dilution of 03 931126 01 2 pg L OFN 5 pg uL BZP 200 fg OFN 272 10 1 500 External EI 10...

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