Question about Guanidination

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The Guanidination is contemplated in PSI-MOD in the entry MOD:00445 (L-homoarginine). Two other terms in PSI-MOD, with different specificities (TermSpec and Origin) have exactly the same MassDiff: MOD:00340 (S-amidino-L-cysteine) and MOD:00442 (protonated omega-N,omega-N'-dimethylated L-arginine with secondary neutral loss of N,N'-carbodiimide). Should these terms be considered related to the first mentioned modification?

Reported by: dovelleiro

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There are two problems you have found here. The first is that "process names" can be based either on the group that is reacting to make the modification, or on the group that results from the modification. When cysteine forms S-amidino-L-cysteine it is equivalent to the lysine reaction with O-methylisourea to form homoarginine. The latter happens to have the process name "guanidination" because a guandino group is formed, but the first reaction despite being equivalent is not called "guanidination". People do manage to confuse things tiyh their inconsistent naming.
The second problem is that I think MOD:00442, being a neutral loss, should be
the negative of what is there now, that is C -1 H -2 N -2. The case being that an expected Arg in a peptide is observed to be 42.021798 lighter than it should be, because it was symmetrically dimethylated and then lost dimethylcarbodiimide (the neutral loss). So it looks like a "deguanidination". This is diagnostic for the symmetric dimethylation, because the asymmetric dimethylation undergoes a different neutral loss.
If you agree with this I will change it.

Original comment by: jsgaravelli

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• assigned_to: nobody --> jsgaravelli

Original comment by: jsgaravelli