Mass spectrometry

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  1. Using mass spectrometry.
  2. What is mass spectrometry?
  3. Stages of mass spectrometry analysis.
  4. Reading an organic mass spectrum.
  5. Mass spectrum of chlorine, Cl2
  6. Example: Calculating relative atomic mass of boron.
  7. Example 2: Calculating atomic mass of molybdenum.
  1. The mass spectrum of butane (C4H10) is shown below:
    1. Identify the molecular ion peak (M+) and suggest the identity of the other three major peaks on the spectrum.
    2. Explain why a small peak at m/z = 59 is present in the mass spectrum. Suggest the most likely cause of this peak.
    Topic Notes

    In this lesson, we will learn:

    • How mass spectrometry works and the stages involved in producing a mass spectrum.
    • How to analyze mass spectra to find evidence of organic structure.
    • How to work out relative atomic mass from mass spectrum data.


    • Mass spectrometry is, in a sentence, a weighing scale for molecules. It can produce data for the molecular weight of molecules that are put into it. The process works as follows:
      • Ionization: A pure sample of a substance is placed in the spectrometer and bombarded by high-energy electrons. This causes the molecules to lose an electron and become a positive ion.
        • These ions are highly unstable. Many break up into two fragments: a neutral fragment and a fragment ion. This is important later!

      • Acceleration: the ion fragments are passed through an electric field which causes positively charged ions to accelerate. The higher their charge, the faster they accelerate.
        The neutral radical molecules or any unionized molecules do not accelerate as they are uncharged – they are lost at this point, and removed by vacuum.

      • Deflection: the accelerated ions pass through a magnetic field which causes them to deflect off of a straight path according to their mass and charge:
        • The higher the charge of the ion, the more deflection occurs.
        • The lower the mass of the ion, the more deflection occurs.

      • Detection: The deflection turns the ions towards a detector and by the time they reach it, the ions have separated out and arrive at separate times according to the mass to charge ratio (m/z): The lower the mass-to-charge ratio, the earlier the fragment ion arrives at the detector. The spectrometer can then produce a graph showing the m/z of all the ions and the relative abundance (how much of the sample ions had this m/z). An example of a mass spectrum is below:
        • When ions fragment, they do so because they are unstable. The resulting ions are usually relatively more stable fragments of the hydrocarbon chain (such as CH3+ or C2H5+). With a charge of +1, knowing the mass of these fragments makes identifying these fragments very easy and noticeable on a mass spectrum!

    • A mass spectrum displays an x-axis plotting mass-to-charge ratio (m/z) against a y-axis plotting relative abundance (it is relative – like in other spectroscopy, the y-axis normally isn’t graduated/scaled.) The spectrum itself has some key features:
      • A molecular ion peak (symbol M+). This is the largest m/z peak of significant abundance (not one of the very small peaks) on the x-axis. The molecular ion peak is just the whole molecule intact, but with the electron knocked off of it from the ionization process. This m/z peak is good evidence for the molecular mass of the substance being analyzed. This applies to electron impact (EI) mass spectrometry – other methods have peaks larger than the molecular ion.
      • Isotope peaks – these are most of the small peaks on the spectrum. Mass spectrometry measures molecular mass of individual atoms or molecules. This means that isotopes are fairly easily seen on a mass spectrum – the most obvious ones are the small peaks just after the molecular ion peak. These could be the peaks where one of the hydrogens is 2H, or a carbon atom is 13C.
      • Ion fragments – these are the large peaks throughout the mass spectrum. These are where the molecular ion has fragmented on its way to the detector; into a smaller fragment ion and a neutral fragment that is lost in the spectrometer as it can’t be accelerated or detected.