Mass Spectrometry - Interpretation

Mass Spectrometry - Interpretation

Here are a list of steps to follow when interpreting a mass spectrum. This simplified list will help you to interpret many spectra, however there are other mechanisms of fragmentation which cannot be covered in this brief tutorial.


  1. Look for the molecular ion peak:
    • This peak (if it appears) will be the highest mass peak in the spectrum, except for isotope peaks.
    • Nominal MW (meaning=rounded off) will be an even number for compounds containing only C, H, O, S, Si.
    • Nominal MW will be an odd number if the compound also contains an odd number of N (1,3,...).
  2. Try to calculate the molecular formula:
    • The isotope peaks can be very useful, and are best explained with an example.
      • Carbon 12 has an isotope, carbon 13. Their abundances are 12C=100%, 13C=1.1%. This means that for every 100 (12)C atoms there are 1.1 (13)C atoms.
      • If a compound contains 6 carbons, then each atom has a 1.1% abundance of (13)C.
      • Therefore, if the molecular ion peak is 100%, then the isotope peak (1 mass unit higher) would be 6x1.1%=6.6%.
      • If the molecular ion peak is not 100% then you can calculate the relative abundance of the isotope peak to the ion peak. For example, if the molecular ion peak were 34% and the isotope peak 2.3%: (2.3/34)x100 = 6.8%. 6.8% is the relative abundance of the isotope peak to the ion peak. Next, divide the relative abundance by the isotope abundance: 6.8/1.1=6 carbons.
    • Follow this order when looking for information provided by isotopes: (A simplified table of isotopes is provided in the introduction, more detailed tables can be found in chemistry texts.)
      • Look for A+2 elements: O, Si, S, Cl, Br
      • Look for A+1 elements: C, N
      • "A" elements: H, F, P, I
  3. Calculate the total number of rings plus double bonds:
    • For the molecular formula:  CxHyNzOn
      • rings + double bonds = x - (1/2)y + (1/2)z + 1
  4. Postulate the molecular structure consistent with abundance and m/z of fragments.

Written by Dr. Linda Breci (retired).

If you have comments or suggestions, email Dr. Michael Marty at