#40 query: proteolytic cleavage

[Midori Harris]

Another question has arisen from our legacy vocabulary mapping effort:

Are proteolytic cleavages that contribute to protein maturation (as opposed to degradation) within the scope of MOD? If so, are there existing terms?

(If it's out of scope, we can use GO and SO terms, but would like to know whether we'll be able to map 'modification, proteolytic cleavage' to MOD.)

Thanks,
Midori

[John S. Garavelli]

Although proteolytic cleavages are certainly considered protein modifications (they are, in fact, the most frequent protein modification) they are "invisible" to PSI-MOD because the molecular mass changes they produce for mass-spectrometry purposes are automatically taken into account within the set of peptide products. I have considered making a general term with a mass-difference of +18 for "top-down" MS purposes, but have been hard pressed to come up with a definition that would be workable in the current ontology.
Going in the other direction, there are terms for formation of isopeptide bonds. However because of unresolved problems with the annotation of non-ribosomal peptide bonds and cyclopeptide bonds in UniProt, I have pursued all the other annotation issues more likely to be productive.
If someone involved in "top-down" proteomics can send me a use case for a PSI-MOD term for proteolytic cleavage, I would certainly have the motivation to add it.