search

HUPO-PSI / psi-mod-CV

Reactivated PSI-MOD ontology for molecular mass modifications
Creative Commons Attribution 4.0 International
8 stars 13 forks source link

Missing PSI-MS-label on MOD:01458 #71

Open dtabb73 opened 2 years ago

dtabb73 commented 2 years ago

All the acetylated side chains carry this note: "Acetyl" RELATED PSI-MS-label

N-terminal acetylation (MOD:01458), however, lacks this note.

Is this intentional, or is it an omission?

pabinz commented 2 years ago

Reverse engineering result : These PSI-MS-labels are the Unimod PSI-MS labels. This is badly and non-explicitly expressed as such in PSI-MOD. However, here is the historical reason, as seen in the Unimod documentation: PSI-MS Name: The standard short name for a modification, agreed by members of the protein modification workgrouphttp://www.psidev.info/node/92 of the Proteomics Standards Initiative. This field is display only, and may sometimes be copied from the interim name suggested by the record curator. Must be unique within the database.

We should either replace RELATED PSI-MS-label [] by something else, such as PSI MOD shortname or something else. Maybe useful to have such terms for similar mod types, but would that be redundant to a common parent term (here MOD_00394 mono-acetylated residue)?

Pierre-Alain

De : dtabb73 @.> Envoyé : jeudi 12 mai 2022 13:49 À : HUPO-PSI/psi-mod-CV @.> Cc : Subscribed @.***> Objet : [HUPO-PSI/psi-mod-CV] Missing PSI-MS-label on MOD:01458 (Issue #71)

All the acetylated side chains carry this note: "Acetyl" RELATED PSI-MS-label

N-terminal acetylation (MOD:01458), however, lacks this note.

Is this intentional, or is it an omission?

— Reply to this email directly, view it on GitHubhttps://github.com/HUPO-PSI/psi-mod-CV/issues/71, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AESGSRSKEBPWWT4OKJT6F7LVJTVZDANCNFSM5VX7MJFA. You are receiving this because you are subscribed to this thread.Message ID: @.**@.>>

edeutsch commented 2 years ago

These appear to be two different topics?

Dave's comment still seems unaddressed. should:

id: MOD:01458
name: alpha-amino acetylated residue

also include this:

synonym: "Acetyl" RELATED PSI-MS-label []

like all the other acetylated residues.

I'm thinking it should.

In fact, if one had to pick one PSI-MOD term that matches the UNIMOD:1, then MOD:01458 would be it, right?