TCNJ Chemistry Instrumentation

Operating Instructions

Varian Saturn GCMS (Basic)

NOTE: Only use these instructions when you are performing manual injections. The autosampler must not be attached to the gas chromatograph.

Creating a GC-MS Method

1) On the instrument toolbar (top of screen), click the Method Builder icon (second from the left) that looks like a paper and pencil.

2) Click FileOpen an Existing Method File. Click OK. Choose an existing method file. Click OK. A "directory tree" will appear on the left side of the screen.

3) Click FileSave As. Type a new name for your method and click Save.

MS Method

1) Click on MS Method Editor in the directory tree.

2) You will see a table with two segments.

a. The first segment is a Filament/Multiplier Delay segment. This segment will be acquired with the filament and multiplier turned off to protect the instrument until after the elution of the solvent peak and/or undesired impurities. Type in the desired end time for this segment (usually between 1-3 minutes).

b. The second segment is used to acquire data. Enter the segment description, start time (same as the end time for the first segment), end time, low mass, and high mass values. Choose EI Auto for the Ionization Mode and None for the Ion Preparation. Do not change any of the parameters that appear at the bottom of the screen.

GC Method

1) Click on Flow/Pressure in the directory tree.

a. Select Type 1 (for 1079 injectors) as the Front EFC Type using the pull-down list.

b. Enter your carrier gas pressure, as well as the hold time (typically the same as your total analysis time).

OR

c. To acquire data in constant flow mode, select On in the Constant Column Flow Mode field and enter a flow rate between 0.5-1.5mL/min.

2) Click on Injector in the directory tree.

a. Make sure the injector type is 1079, the injector oven is on, and the injector coolant is off.

b. Enter your injector temperature, as well as the hold time (typically the same as your total analysis time). It is very important that this temperature is higher than the boiling point of your analyte of interest. If it isn't, your analyte will never make it onto the GC column!

c. Click on the split ratio button. Make sure the split state in the first row is turned off. Turn the split state on in the second row using the pull-down list. Type in the time and split ratio. (For example, a split ratio value of 20 means that 1/20 of your sample will end up on the GC column.)

3) Click on Column Oven in the directory tree.

a. Make sure the column oven coolant is off.

b. Select a stabilization time (usually 0.5-1 min.).

c. Enter your column oven temperature program segments.

Note: The end of an analysis is determined by the column oven end time. If the total time that appears in the Injector (or Flow/Pressure) window is greater than the column oven end time, the software will alert you. Make sure the total injector and flow/pressure times are the same as your column oven end time.

When you are finished creating your GC-MS Method, remember to save it! Then close the Method Builder window.

Activating the GC-MS Method

1) On the instrument toolbar, click the System Control icon on the far left that looks like a computer to get to the system control screen.

2) In the instrument pull-down menu, choose Saturn GC/MS #1.

3) Click on the Acquisition button.

4) Activate your GC-MS Method by clicking FileActivate Method. Highlight your saved method, and then click Open. At the top of the screen, you should see the word "Waiting" in flashing yellow letters.

5) Look for two green circles on the left side of the screen indicating that the GC and MS are ready. An orange light should also appear on the GC itself if the GC is ready.

Manually Injecting a Sample

1) Manually inject your sample using a 10uL syringe. Make sure you push down on the injection port to trigger the start of your run. (Inject ~1uL or less.)

2) If you want to stop the analysis prior to the column oven end time specified in your GC Method, press the Stop button on the GC, and press Reset in the Data Acquisition tab located on the left side of the screen.

Looking at Your Data

NOTE: When performing manual injections, the data file name is created automatically. To determine the name of your data file, you can check the system log by double clicking on the message banner at the bottom of the screen. The data file name should also appear on the "Most Recently Used Data File" icon. (This icon is the second from the right. It looks like two chromatograms and includes a data file name.)

1) There are two ways to open your data file:

a. The name of you data file should appear on the "Most Recently Used Data File" icon. (This icon is second from the right. It looks like two chromatograms and includes a data file name.) If you see the name of your data file, click the icon, and click "View/Edit MS Chromatogram".

b. If you do not see the name of your data file, click the "Review/Process MS Data" icon (fourth from the left, also looks like two chromatograms). Choose the file you want to open and click the Add/Replace button. Click Open File(s).

2) To look at a selected ion chromatogram, click the "Review/Process MS Data" icon (fourth from the left, also looks like two chromatograms). Choose the file you want to open and click the Add/Replace button. In the data pull-down menu, select "ion(s)". Enter the ion or range of ions of interest. Click OK. Click Open File(s).

3) To zoom into your chromatogram, draw a box around the desired region with the left mouse button. To zoom out of the chromatogram, click the Full Scale icon (looks like a bowtie).

4) To see a mass spectrum, left click on any peak in your chromatogram.

5) To print you data, click File Print Chromatogram or File Print Spectra.