I recognized that there is some controversy about the average mass of amino acid masses in different online sources.

Expasy and Wikipedia report the same masses, but UWPR and Mascot report different ones. However, the monoisotopic masses are always the same.

Does anyone know where these differences come from or where to find a definite source for the masses?

In the end, the question boils down to the average masses of single atoms. The UWPR names UniMod as a source for their calculation. What different ways of calculation for average mass exist and who defined them?


I guess confusion comes from either:

  1. Inclusion vs exclusion of H2O (free AA vs in chain)

  2. Averaging with equal weight between all AA vs weight of their relative occurrence

Does this help?

  • 1
    $\begingroup$ 1. cannot be the cause, the differences are minimal, nothing like 18 Da. 2. No average is calculated over AA. The average weight is calculated out of the relative occurrence of different stable isotopes of the atoms. I guess that there are different reports of the relative occurrence of stable isotopes that lead to the difference in AA average mass. $\endgroup$ – DaRealHonk Nov 18 '20 at 19:16
  • $\begingroup$ Your question sounded like isotopes were the only point you could successfully exclude. $\endgroup$ – KaPy3141 Nov 19 '20 at 20:17

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