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The Mass Spectrometry Experiment

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  • ms schematic.gif
    Figure MS2. A very approximate schematic of a typical mass spectrometry experiment.

    Mass spectrometry only works with ions, not with neutral molecules. That means a neutral molecules must become charged in order to do this experiment. It is common to generate a cation from the molecule by removing one electron. The electron is knocked off the molecule in a collision. The collision can be caused in two different ways:

    • The molecule can be sent through a stream of high-energy electrons. This method is called electron ionization.
    • The molecule is sent through a stream of small molecules, such as ammonia or methane. This method is called chemical ionization.
    • Electron ionization frequently results in the molecule falling to pieces because of the high energy of the electrons.
    • Chemical ionization results in a "softer" collision because momentum can be dissipated through various bonds in both colliding molecules. Chemical ionization results in less fragmentation of the target molecule.
    • However, after chemical ionization, the ionizing molecule sometimes sticks to the target molecule, leading to a greater "molecular" mass. For example, if ammonia is used for ionization, an extra mass may be observed at 17 amu higher than expected.

    The reason the x-axis on a mass spectrum is labeled m/z (mass-to-charge ratio) is to acknowledge that there are really two factors contributing to the experiment.

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