Hewlett Packard 5971A Gas Chromatograph - Mass Spectrometer


Quadrupole mass spectrometer with gas chromatograph inlet. Electron impact ionization. Chemical ionization source is also available.


Hewlett Packard Corporation, Palo Alto, California


5971A (Mass Spectrometer) / 5890 (Gas Chromatograph)/7673A (Autosampler)

Data System

Intel Pentium 3; Windows 95; quadrupolaris.chem.washington.edu

Installation Date

May 1989


Bagley 83

Serial Number


Assset Number




From the Start menu select Programs>GC_MS Instrument #1>GC_MS Instrument #1 or double click on the HP5971A GC-Mass Spec icon on the desktop.

Two windows will appear on the desktop, one titled GC/MS Instrument #1 MS Top and the other titled simply GC/MS Instrument #1. A third window titled HP Chemstation is minimized and since you will not work in this window, ignore it.

Go to the MS Top window and under the Sequence drop down menu select Edit Sample Log Table (if you wish to edit a previously saved sequence table make sure that it is loaded by clicking Sequence>Load first).

The top half of the window which opens shows the current contents of the sequence table being edited. Click on line one to select it and enter the appropriate information into the fields in the bottom half of the window. Type is always Sample. Vial is the location in the autosampler tray where you put the vial containing your sample. Data File is whatever name you want the data acquired under (max 8 characters, no extension). Method is the name of the method that you wish to use to run this sample (no .m extension). Sample Name and Miscelaneous Information can be used for any descriptive information that you wish to include. The sequence table must have one line for each sample that you wish to run. The Repeat, Cut, Copy and Paste buttons can be used to assist in creating your sequence table.

Once the sequence table is complete click on the OK button and then click Sequence>Run. In the window which opens make sure that Full Method is selected under Method Sections to Run. The Data File Directory should be C:\USERFI~1\USERS\XXXXXXXX\ where the X's are replaced with the name of your data directory. To save this sequence table click the OK button and then click Sequence>Save. To run the sequence click Sequence>Run and then click the Run Sequence button (make sure that your samples are in the autosampler tray at the locations specified in the sequence table).

The program will download the acquisition parameters to the gas chromatograph and the mass spectrometer. Once the instrument has equilibrated the autosampler will fetch the first vial from the tray and inject that sample into the instrument. The progress of the acquisition can be monitored in the GC_MS Instrument #1 window. The program will display a prompt inquiring if you want to override the solvent delay. You do not need to respond to this prompt - it will go away after the solvent delay period has elapsed.

The process of download, equilibrate, fetch, inject and acquire will be repeated for each line in the sequence table.


From the Start menu select Programs>GC_MS Instrument #1>Data Analysis #1 or double click on the GC-MS Data Analysis icon on the desktop. To analyze data from a run that is still being acquired, select Take Snapshot from the File menu of the data analysis program to load the data from the current acquisition. To analyze data from a run for which the acquisition is complete, select Load Data File from the File menu of the data analysis program and select the data file that you want to look at. The last data file analyzed will be selected by default.

The total ion chromatogram from the acquisition will be displayed when the data file has loaded. To zoom in on a selected area of the TIC, drag a box over the plot with the left mouse button. Double click with the left mouse button to display the previously selected region.

To display a selected mass spectrum, double click with the right mouse button on the TIC over the desired scan. Drag the right mouse button over a retention time range on the TIC to display the average of several scans.

To subtract the background from the displayed spectrum, drag the right mouse button over the TIC baseline adjacent to the peak displayed, then select Subtract from the Tuner menu.

To remove noise peaks from the display, activate the white command line at the bottom of the data analysis window if necessary with the Tools selection on the Options menu, then enter the command mstrunc x,1. This will remove all peaks less than 1% of the base peak. Enter the command draw 1,x to display the truncated spectrum.

To print a copy of the displayed spectrum select Print... from the File menu, choose Selected Window then enter 1 as the window to print.

To generate a tabulated mass list of the displayed spectrum, select Tabulate from the Spectrum menu. Select Print in the Tabulate window for a printed copy of the mass list, and Done to clear the window.

Quit the data analysis program when you are done by selecting Exit from the File menu. Quit the MSTop program when you are done unless someone else is ready to use the instrument.



Rate per hour

  • Subsidized
  • Full


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