Introduction to Mass Spectrometry

This experiment was developed by S.E. Van Bramer for Chemistry 465 at Widener University.


Mass Spectrometry is one of the fastest growing instrumental techniques. At the simplest level a mass spectrometer is simply a very sensitive balance that makes it possible to "weigh" molecules. In addition to determining the mass, the fragmentation patterns are used to determine the structure of an unknown compound.

Mass spectrometers actually measure the mass to charge ratio (m/z) of an ion. During ionization many molecules undergo fragmentation. The mass spectrum is produced the different probabilities for the formation of each fragment ion. This provides a structural fingerprint of the molecule.

In this experiment you will use a Finnigan 4000 quadrupole mass spectrometer with a Teckinvent data system to identify several unknown organic compounds.


  1. Review parts of the instrument
    1. inlet
    2. source region
    3. mass analyzer
    4. vacuum system
    5. electronics cabinet
    6. data system

  2. Calibration of the mass spectrometer. The mass axis of the spectrometer is calibrated with perfluoro-tributyl-amine, (n- C4F9)3N, abbreviated PFTBA.
    1. Open: gc-gs_ei.u
    2. Execute; MS on
    3. Execute; spectrum scan
    4. Tune; quicktime

  • Setting up the experiment
    1. Open the data acquisition
    2. Open a method and Check/Set the following parameters
      1. Select the tune file
      2. Select the scan mode
      3. Set the GC temperatures
    3. Open the data analysis program to observe data.
      • Edit: Snapshot to update the data
      • Right double click on TIC to open a spectrum
      • Right drag on TIC to average spectrum
      • Left drag to zoom to a box
      • Left double click to zoom out
      • Double right click on MS for library search

  • Data to collect. For this experiment you will identify a set of unknown compounds. After the instrument is setup you will inject the compounds as neat liquids to obtain mass spectra.

    Laboratory Write-up:

    Your Laboratory write-up should include the following information
    1. (5 pts) An abstract for this experiment.

    2. (15 pts) Clearly labeled and annotated graphs that show the following:
      1. The mass spectrum of each unknown.
      2. The library report for THREE of your five unknowns.

    3. (15 pts, ea unknown) Analysis of your unknowns
      1. For three unknowns you may use the instrument software to run a library search. For each of these unknowns:
        1. report the results of the library search
        2. determine which search hit is your unknown
        3. interpret the fragmentation patterns observed.
        4. Look up unknowns in the Merck index and summarize the information found.
        5. Locate a MSDS of the unknown and summarize.
      2. For each of the remaining unknowns
        1. Interpret the mass spectrum by identifying the fragmentation patterns observed. Use this to identify the unknown.
        2. If you have an unknown with several possible structures. First identify the possible structures. Then print out the mass spectra for these compounds using the database on the cart 3 computer. Compare these spectra with your unknown to narrow the possible structures.
        3. Look up unknowns in the Merck index and summarize the information found.
        4. Locate a MSDS of the unknown and summarize.
    4. (5 pts) The Carbon pages from your laboratory manual.

    This page is maintained by
    Scott Van Bramer
    Department of Chemistry
    Widener University
    Chester, PA 19013

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    Last Updated Thursday, September 02, 1999 12:49:45 PM