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HUPO-PSI / ProForma

HUPO-PSI Standardized peptidoform notation
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Potential error in monosaccharide list #7

Closed douweschulte closed 8 months ago

douweschulte commented 8 months ago

According to the ProForma monosaccharide list the chemical formula of a Neu5Ac is H17C11N1O8. But according to most other sources the formula is H17C11N1O9 (note the additional oxygen) (PubChem glyco mass calc wikipedia).

I assume this is just an error in the list, or is there something else going on?

(For ease of checking I reference @mobiusklein, as he made the list)

douweschulte commented 8 months ago

Sorry error in my own code. (The discrepancy is thanks to the lost H2O in MS)

mobiusklein commented 8 months ago

All the monosaccharides in that list are presented with their residual composition (-H2O), just like amino acid residues. If you were to express it as a free glycan composition, you'd need to add water to represent the free reducing end.

It's not MS-specific. The assumption is that the reducing end is covalently bound to an amide or hydroxyl group on an amino acid, which would also result from a dehydration reaction, so representing all monosaccharides in their residual form requires no extra book-keeping.