Beginner’s Guide to Varian GC/MS
Conventions used: Icons to be clicked are bolded
Menu screen names are italicized
Warnings are bolded/underlined
Right mouse clicks are <right> click
Files are enclosed in [brackets]
Part I: Start-up and Injecting Samples
1. For the most part, the MS Workstation should be pre-loaded on the desktop and you can skip to step 3. If the software isn’t loaded, doubleclick on Varian WS icon, followed by clicking the System Control key on top left corner.
2. This will load the system control screen. The system will pop up a message about configuring the communications. This has already been done so just hit Cancel.
3. The System Control screen has three sub-screens that you can navigate between by minimizing or maximizing. The Status screen shows what is going on now and is not really necessary to watch. The 3800 menu monitors the GC and autoloader. In this screen, just make sure all the lights are green. The 2000 screen is the important screen to watch.
Things to note: underneath the task bar ( File...Edit...Inject...) is the method selector (currently set to [Charlie.mth]). If you have your own method, change it here before injecting. More about methods are discussed later on. For normal operation, use EI_NormalMethod.mth by clicking on the folder to the right. All methods are found in the D:\ directory.
4. For samples, please prepare sample concentrations of 1mg/ml in vials with septa (available in stockroom) in organic solvents (halogenated, aliphatic, aromatic, and dry ethers are all ok). The instrument will inject a 1 ul sample for analysis. Do not inject the following: water, acetone, strong acids (HBr included), strong bases, or heavy metals. Please do not overload the column. If you’re having trouble with solubility or signal intensity, there are other methods that fine tune the instrument to your needs, just ask for assistance.
5. Ready to inject. Place vial in autoloader tray and click on the Acquisition key in the 2000 menu screen. When the system is ready, two green lights appear on the left side of the menu. There are two methods of injecting, single injection or batch injections
a) To single inject, click on the Inject icon or select inject at the top of the System Control menu and select single injection.
This will pop up an information window. In this windows, put the position of your sample under 
Vial and hit enter key. The default is vial 1. Under Injectors Used, make sure it reads “Pos 1”. Any other position will z-fold (damage and break) the $yringe. Now, click on the Data Files icon. Put the name that you want the file to be saved as ( e.g., decane, myfile, CR1-190B) in the blank on the right. The file will be saved with a [*.sms] extension. Select the directory you want your data to save to on the D:\ drive. If you do not redirect files to your folder you will have to look for them. When you are ready, click Ok and the Inject icon.
b) To perform a batch injection, you must create a sample list file, [mylist.smp]. To do this, select File from then New Sample List. The 8410 Sample List table will pop up. This file can be reused and reedited for each batch injection. Save it in your folder on the D:\ drive. The sample list works just like above. Type in Sample Names that you want your data to be saved as. Enter the vial positions for each sample. If you do not do this, vial 1 will be reinjected each time. Make sure the Injectors Used reads “Pos 1” all the way down. Choose your save directory with the Data Files icon. In a batch job, all the files are saved to one directory. If you are doing samples for someone else, they will be saved to the same directory as your samples. When you are ready for batch automation, click the Begin icon.
6. The instrument will begin its automation. The syringe will be cleaned once, your sample will then be injected, and then the syringe will be cleaned 3 more times after injection. Occasionally the wash solvents will have to be filled. A high grade, moderate boiling point (70°-80° C) solvent like toluene should be used. Please label all vials.
7. A word on usage and etiquette. Please limit large batch injections to late evenings or overnights. Secondly, the MS software is available to all groups and the computer is networked. Data that has been saved can be retrieved and printed in ones lab if the computer is in use. Methods can be fine tuned for each user: with that, runs should take in general 20 to 30 minutes (See Part III: Methods). The mass range is 40 to 650 amu and the temperature limit is 325° C. We ask you not to go above 320° C. Again, do not overload the column. This instrument is more sensitive then the previous one and picks up the smallest signals (See Part II: Data Reviewing). Please remember to retrieve your samples.
Part II: Reviewing Data
1. If you followed the steps above, you should be collecting data (system should say Running in the menu bar). Both a chromatogram and its spectrum should be seen. The system monitors base peak intensities and auto adjusts the scale to fit the chromatogram. A proper sample should range between baseline and 1 million counts (Mcounts on y-axis) and should not exceed 5 million counts. A slider bar on the right of the chromatogram allows you to rescale and see really small peaks. The green cross-hairs (circled on the left) returns the screen to normal. The last icon (circled in picture) allows you to enter the MS Data Review screen used for retrieving spectra and printing. Data can be reviewed as it is being collected
2. In the MS Data Review, you can blow up areas of your chromatogram by clicking and dragging a box over the area. Again the green cross hairs take you back to full screen. Clicking on the peaks gives you their spectra. To view multiple spectra at the same time, select the first peak by a left click. Next, go to second peak and <right> click and highlight the first command line: Create new spectrum window. This adds a second spectra. You can now print these by clicking on File the selecting Print All Chromatograms and Spectra Plots. The <right> click menu screen gives lots of options, such as adding labels to plots or exporting spectra.
3. Libraries. The software is packaged with a library of NIST spectra. Click on a peak in the chromatogram, then push the “L” key on the keyboard. The software will try to match your spectra with its own. It lists its best guess first with a spectral comparison on the right. The red is your sample, the green is the guess. This is good for identifying known compounds. Personal libraries can be made as well, please ask for assistance.
Part III: Methods
1. Method editing should only occur on rare occasions. The method determines how the GC/MS performs its tasks. Editing the method can cause confusion, bad data acquisition, or damage to the GC/MS.
2. The top right corner of the GC/MS toolbar lists the current method. By clicking on this icon, a small menu appears. Select View/Edit Method to enter the method editor.
3. The Method Builder screen will pop up and will have a tree format for each section of the method. Only concern yourself with the following sections:
a) MS Method Editor – This is where delay times and acquisition times can be changed. Also, this is where the instrument can be switched from EI mode to CI mode.
b) Compound Table – Import your own library from a [*.sms] file. (Still working out kinks, please ask for help).
c) Column Oven – Change heat ramping on the column, only when needed. Do not exceed 320° C.
4. Again, if the instrument isn’t broke, don’t fix it. For most samples the [EI_NormalMethod.mth] works fine and gives good data with in a 35 minute work window. Other methods have been developed for use with the chromatoprobe, high boiling solvents, and long delays.