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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?

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    $\begingroup$ This is chemistry not biology. If there is still any interest in the topic it should be reposted on SE Chemistry. Otherwise it is best closed. $\endgroup$
    – David
    Aug 14, 2021 at 20:14

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A bit more link following reveals on the UniMod site: "All mass values in Unimod are calculated from the IUPAC atomic weights and isotopic abundances tabulated by WebElements:"

So, the answer is the isotope abundances are from the IUPAC; you can find links to references at webelements.com by drilling down in the periodic table there.

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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

(EDIT) The Wikipedia link states:

  • Alanine A Ala 89.09404

ExPASy link:

  • Alanine (A) 71.03711

So ExPASy lists the weight without H2O, 18 Dalton lighter due to the condensation reaction in the form you would find the amino-acids in a peptide.

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    $\begingroup$ 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, 2020 at 19:16
  • $\begingroup$ I keep this answer because it might be relevant for people, who arrive here via search engines. $\endgroup$
    – KaPy3141
    Feb 28, 2022 at 16:16

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