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Varian 3800/2000 GC/MS Operating Instructions
General Notes:
* All mouse functions are accomplished with the left button unless specified.
* The function of each icon can be listed by placing the cursor over the icon and waiting a second
or two. The icon label will be listed on the screen.
* Don't use the go-away box on the 3800.44 or 2000.40 control windows. Minimize them
instead.
* Do use the go-away box for the Review/Process Data- SatView window.
Procedure:
1. Check that the helium pressure gauge on the wall reads 80 psi.
3. On the computer, note the Varian Star Toolbar. This is a wide toolbar that runs down the left
side of the screen. If the Varian Star toolbar runs across the bottom of the screen, click on the
background of the toolbar and drag it to the left. Click on the System Control icon. This icon is at
the top.
4. Pull down the Windows menu and select 3800.44 to display the GC control panel.
5. To select the desired method, click on the "Activate a Method" icon. This icon is an "open file
folder" icon in the middle of the top icon bar, just to the right of the method pull down list. Find
the folder for your course or research group; you may need to go up a level. In this folder, the
methods "m50t200m12", "m50t200m12CI", or "m50t200m12mw" are good general methods.
See the notes at the end of these instructions for a discussion of molecular weight determination.
This method runs a temperature gradient from 50 to 200°C in 12 minutes. Click Open to
continue.
6. Check the GC temperature zones, which are listed in the middle of the screen. The column
oven should be 50°C, the front injector 225°C, and the middle injector 50°C. We will use the
front injector for this lab. The oven temperature gradient is set for 50-200°C at 15°C/min. With
an initial hold at 50°C for 2.0 min, the total run time is 12 min. Check for the total run time,
which is listed as the "End Time." Note the two status indicator lights: the Equilibrating/Ready
light and the Fault/No Fault lights should both be green before beginning a run. These status
indicators are in the upper left-hand block of the control window.
7. Minimize the 3800 control window.
8. Pull down the Windows menu and select 2000.40 to display the MS control panel.
9. Click on the Auto Tune button.
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Summary of Contents for Agilent Technologies Varian 3800 GC
- Page 1 Varian 3800/2000 GC/MS Operating Instructions General Notes: * All mouse functions are accomplished with the left button unless specified. * The function of each icon can be listed by placing the cursor over the icon and waiting a second or two. The icon label will be listed on the screen. * Don’t use the go-away box on the 3800.44 or 2000.40 control windows.
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Page 2: Running A Sample
Deuterium Exchange 9. The tuning procedure calibrates the mass axis. Choose the “FC-43 mass calibration” tuning mode in the pull-down list box in the middle of the window. Make sure the check box to the left of the pull-down list box is checked, and the other three check boxes are cleared. Click on Start Auto Tune. - Page 3 Deuterium Exchange 7. To view the data while it is being taken, click on the Hide Keypad button, which is on the left side in the middle of the control window. Pull down the adjacent list box and select Spectrum and Chromatogram.
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Page 4: Shutdown Procedure
Deuterium Exchange 14. To prepare for printing, press the right mouse button with the mouse in the mass spectrum window and slide right on Options. If you want a listing of the ion fragments and their abundances, make sure “print ions and intensities” is checked. Normally, we don’t need a listing and “print ions and intensities”... - Page 5 Deuterium Exchange Note on Molecular Weight Determination Compounds often don’t give a large parent ion, M , peak. Alcohols, for example readily loose O and give no parent ion. Auto-ionization also can give a parent peak for the protonated molecular ion, MH , which occurs at 1 m/z higher than the parent mass, M .
- Page 6 Deuterium Exchange parameters may be easily controlled. In addition to auto-ionization, overfilling the trap decreases mass resolution. Ion traps have an automatic mechanism for controlling the number of ions in the trap, called automatic gain control, or AGC. The system does a pre-scan to determine the signal strength and then adjusts the hold time in the trap to avoid filling the trap with too many ions.