TCNJ Chemistry Instrumentation

Operating Instructions

Varian Saturn GCMS

Autotuning

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) Set the GC column oven temperature to the initial value that you will be using for your analysis using the keypad on the GC. (Press the Column Oven button, type in the temperature, then press enter.)

4) Set the carrier gas pressure or flow value to the initial value you will be using for your analysis. (Press the Pressure/Flow button. Type in the pressure on page 1 of the display window, or scroll to page two using the arrow keys to select constant flow mode and type in the flow value. Press enter.)

NOTE: If you choose to enter a flow value, this value will represent the column flow rate NOT the total flow rate.

5) In the System Control window, click the Manual Control button. Then click on the Adjustments tab. Click Adjust Cal Gas.

6) Open the door on the right side on the instrument. Slowly turn the Cal Gas Adjustment Knob counterclockwise until the blue bars begin to appear in the lower end of the region labeled "OK" on the left side of the screen. (The ion time will be between 300 and 1000us in the Operating Conditions field on the right side of the screen.) Close the door.

NOTE: Do not turn the calibration gas up too high. The calibration gas is very slow to respond. If the calibration gas is turned up too high, the instrument will not complete the autotune procedure.

7) Click on the Autotune button. Check the Air/Water Check, Electron multiplier Tune, and FC-43 Mass Calibration boxes. Then click Start Autotune. The instrument will run through a series of tests. When the autotune procedure is finished, the message "Calibration Complete" will appear at the bottom of the screen.

8) Open the door on the right side on the instrument. Turn the Cal Gas Adjustment knob clockwise until you feel resistance (approximately 5-6 turns).

Creating a GC-MS Method

1) In the System Control window, click File Upload Active Method from Modules.

2) Type in a new name for your method and click Save.

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

4) Click Open an Existing Method File. Click OK. Choose your method file. Click OK. A directory tree will appear on the left side of the screen.

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. (Note: If you change this value after the autotune is performed, you must rerun the mass calibration.)

2) Click on Injector in the directory tree.

a. A message will appear that says "Creating Default Split Ratio Program". Click OK.

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

c. 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!

d. 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 windows 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.

Autosampler Parameters

1) Click on Autosampler Configuration in the directory tree.

2) Choose 48 vials as the carousel type.

3) Do not check the Prep Ahead box.

4) In the Sampling Modes field, select Standard Mode.

5) For the Liquid Sampling Options, select Solvent A Wash and 10uL Syringe.

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

Starting the GC-MS Run

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, the flashing words "Not Ready (red)" will change to "Ready (green)".

Injecting a Single Sample

1) Click InjectInject Single Sample

2) Enter your name or initials in the operator field and click OK.

3) In the Inject Single Sample Window, enter a name for your sample.

4) Choose Analysis as the Sample Type.

5) Enter 1 in the injection field if you want to inject the sample one time.

6) Enter the vial position.

7) Enter injection notes.

8) Click the Browse button to select your method if it does not appear in the box.

9) Click the Data Files button to specify a data file path and name.

10) Click the Inject button.

11) Check the status of the GC and Saturn MS Modules by maximizing each Module if they are minimized at the bottom of the System Control screen. (Minimize one Module to maximize the other Module.)

12) Check the instrument status by clicking InstrumentStatus on the System Control Screen.

Injecting Multiple Samples

1) Click FileNew Sample List.

2) Specify a filename for your Sample List and click Save.

3) In the Sample List Window, enter your sample names.

4) Choose Analysis as the Sample Type.

5) Enter 1 in the injection field if you want to inject the sample one time.

6) Enter the vial position for each sample vial.

7) Enter injection notes.

8) Click the Data Files button to specify a data file path and name.

9) Click Begin. (Note: The Sample List saves automatically.)

10) In the Begin Sample List Window, click the Browse button to select your method if it does not appear in the box.

11) Check the status of the GC and Saturn MS Modules by maximizing each Module if they are minimized at the bottom of the System Control screen. (Minimize one Module to maximize the other Module.)

12) Check the instrument status by clicking InstrumentStatus on the System Control Screen.

Using More Than One Method in Your Sample List

1) To use another method in your Sample List, you must activate it in the Sample List.

a. Select Activate Method from the Sample Type cell in your Sample List.

b. Click on the Auto Link cell.

c. In the Activate Method window, click the Browse button to select the desired method. The method name will appear in the Auto Link cell. (Note: All of the samples injected after the new method is activated will be injected using the new method.)

Looking at Your Data

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, highlight the desired peaks 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, click on any peak in your chromatogram.

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