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Haverford College
Department of Chemistry

Instructions for HP mass spectrometer

Unless otherwise noted, all clicks use the left hand button on mouse. The mass spectrum is run with windows software.

1. Turn on computer and screen. When the cow in space screen appears, double click on HP Chem Station Icon

2. In Utilities Menu, choose Start, and click on only choice, 5899, then click OK.

3. The Window should say 5988 Top. In the Method Menu, choose Load and Run Method. Scroll through methods, and choose Supscan.m. Click OK.

4. In the Start Run window, type in your name, same name and any misc. information you want. Click OK.

For a typical organic chemistry analysis, you will be using the gc inlet, scan mode. There are two ways that you can modify the conditions for any mass spec run: In the Method Menu under Edit Entire Method, where one can go through a long list of menus to edit the two of importance, Normal Scan Acquisition and Temp Information. Changes made here will change the Supscan program for everyone who follows you. It is better to modify the conditions to Supscan.m using the methods described below.

5. In the Acquire Data Menu, choose Main Panel (only option). Then choose Edit Parameters. In this menu there are two windows you should call up:

1. SIM/Scan: [The window is similar to the Normal Scan Acquisition in the Edit Entire Menu mention above.] In this window you may want to adjust three parameters:

a. Solvent delay. This tells the mass spec when to start detecting. One wants the solvent to have come off the gc before any efluent is sent to the ms source. A one minute solvent delay is good of diethyl ether; a two minutes solvent delay for solvents with bp's below 100°C and a higher solvent delay for solvents like DMSO.

b. Mass ranges. You should define the mass ranges you will search. Mass of 35 is a good low range. The upper range can be adjusted depending on the masses of the compounds you are analyzing or expecting. For the upper level choose a mass about 50 or 100 amu higher than the MM of your heaviest compound. Set Threshhold to about 50 or 100. (this sets the lower limit for the number of ions that the ms will detect.)

c. Types of plots that appear during analysis. Set Plot #1 to Total- This give a total ion chromatograph, which looks like a gc trace. Set Plot #2 to Extracted, which can be adjusted to look at a different mass range from the Total plot.

2. GC Temperatures: [This window is similar to the Temp Information in the Edit Entire Menu mentioned above.] Here you set the temperatures of the injector, detector and oven. We use injector and detector B. For most organic work they should be set between 200-250°C. Generally the best separation of a mixture of compounds results with a programmed temperature gradient for the oven. A typical gradient might be Initial Temperature 40°C and Initial Time, 1 - 2 minutes (how long the oven stays at initial temp.), with a Rate (how fast the oven heats up) of 20 - 30°/minutes) to a Final Temperature of 200 - 250°C, and Final Time (how long it stays at the final temp) of 5 minutes. The Run Time should then automatically calculate what your run time is based on your gradient.

6. When the Method is modified, go to the Acquire Data Menu and choose Acquire Data. Fill in the Data file name (8 digits) of your choice, the operators name etc and click OK. [For the file name I like to use my initials and the page number from lab book containing the experiment that led to the solution being analyzed.]

7. Now you are ready to make your injection. When the temperatures are ready the red "not ready" light on the gc will go off. When that happens, make your injection and press the start button on the gc button pad. [ A window on the computer will remind you of these instructions if you wait a minute.] When it asks if you want to override the solvent delay click NO.

8. When the run is complete, go to the Top Menu Window, and choose the Data Analysis Menu, in which you choose Main Panel.

10. In the Chromatograph Menu, choose Draw Chromatograph. Click OK. The TIC (Total Ion Chromatograph- which looks like a gc trace)will appear. With the arrow you can double click on any peak with the right button and the mass spectrum of that peak will appear below.

11. To Zoom in on peaks, Click with the left button and holding it down, frame the peaks of interest. Double click on the screen to return to the TIC.

12. To integrate the peaks, in the Chromatograph Menu, choose Autointegrate. To view the results, in the Chromatograph Menu, choose List Results.

13. To tabulate the results of mass and abundance choose the Spectrum Menu and choose Tabulate.

Generally any screen can by printed by choosing Print under the File Menu.