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16 years ago Response from John S. Garavelli: Because of the difficulty of classifying things that are the result of multistep processes, we have not made many entries for such things. There is no single entry for the process of either N-terminal methionine removal (the negative of MOD:00022) or N-formylmethionine removal (the negative of MOD:00030), combined with the process of N-terminal acetylation (the positive of MOD:00408). The only entries we have made for multistep modifications like this are for secondary neutral losses in MS.
I think most of the analysis programs consider Met or fMet removal as being a separate process that can be combined with other modification processes. Certainly, Met removal does not always happen - we have one documented case of fMet deformylation followed by acetylation of the Met (PMID:7250376).
The alpha-amino acetylation of the amino acids (not all of them are natural) are classified chemically as N-acetylations, "a protein modification that effectively replaces a residue amino group with an acetamido group." We will have to find a solution for the ontological problem of how to classify a residue that is being modified by the replacement of something that is not really a part of it, the neighboring residue. Tomorrow, I will post this on the MOD Controlled Vocabulary Changes list and see if anyone has some ideas on how to deal with this as a single entry, or whether it should be left as two entries.
Original comment by: jsgaravelli
We're working again on our list of post-translational modifications as we plan to search for N-termini of which the methionine was cleaved off and which were afterwards acetylated. This is supposed to be a very common modification of the N-terminus (see review by Polevoda B and Sherman F, J. Biol. Chem., Vol. 275, Issue 47, 36479-36482, November 24, 2000) and should come with a deltamass of -89.03 Da. In the MOD Ontology Browser I could not find an entry for this type of modification. Is there a reason why it's not in there, or did I just look in the wrong place?
Reported by: jsgaravelli