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HUPO-PSI / ProForma

HUPO-PSI Standardized peptidoform notation
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Consider how to support non-standard amino acids #10

Open edeutsch opened 3 months ago

edeutsch commented 3 months ago

A user asked me how to specify some custom amino acids: Ahx (amino hexanoic acid): C6H13NO2 residue mass = 113.08406 lysyl biotin (aka biocytin): C16H28N4O4S residue mass = 354.17256

We found workarounds for this one, but this seems like a more generic issue that we will face, especially with synthetic peptides.

Ideas?

javizca commented 3 months ago

One possible way would be to have one custom 1 letter-3 letters for an unusual/synthetic amino acid, and that that letter needs to be followed by the formula or the mass of the amino acid with some extra character that we have not used before.

Something like X^C6H13NO2^ or X^113.08406^

I know X does not have this meaning, we probably would need to find the right letter-three letters for this case.

The other option is what we have discussed before (and probably not practical) is that to have some metadata associated file highlighting special rules in these very rare cases. But this would only work internally within the same software environment or similar.