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HUPO-PSI / psi-mod-CV

Reactivated PSI-MOD ontology for molecular mass modifications
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Collagen-related mods #59

Open pmt706 opened 3 years ago

pmt706 commented 3 years ago

Glycosylation of collagens is a common PTM. Right now, many of the glyco modifications of hydroxylated amino acids have the naked amino acid as the origin, when this should be the hydroxylated amino acid.

Is this correct? My question is: For a MOD:01914 is it changing from lysine to galactosyl-hydroxy-lysine in a single step OR is the modification hydroxy-lysine being galactosylated to galactosyl-hydroxy-lysine?

pabinz commented 3 years ago

galactosyl-hydroxy-lysine is obtained as a two-step mod. But for all mods, one refers to the original one i.e. Lysine here. As we are allowed to put a MOD as Origin, we should be able to derive the successive steps. Alternatively, one can allow to have two Origin lines, to differentiate from an Origin that requires more than one origin residue (crosslinks for instance). But in this case, the definition must match both direct and indirect mods. PAB

De : Paul Thomas @.> Envoyé : mercredi 10 mars 2021 16:40 À : HUPO-PSI/psi-mod-CV @.> Cc : Subscribed @.***> Objet : [HUPO-PSI/psi-mod-CV] Collagen-related mods (#59)

Glycosylation of collagens is a common PTM. Right now, many of the glyco modifications of hydroxylated amino acids have the naked amino acid as the origin, when this should be the hydroxylated amino acid.

Is this correct? My question is: For a MOD:01914 is it changing from lysine to galactosyl-hydroxy-lysine in a single step OR is the modification hydroxy-lysine being galactosylated to galactosyl-hydroxy-lysine?

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