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commented
13 years ago The molecular ionic form most commonly found in mass-spectrometry is used in PSI-MOD. The correction to "phosphono group" has been made in the definition and will appear in the next release. But because most people would probably think first of searching for "phosphate", that word in quotes and the difference formula as it is normally written as if it were an acid, are included in the definition.
Original comment by: jsgaravelli
Dear PSI-MOD workgroup,
I am currently working with Rhea (http://www.ebi.ac.uk/rhea) trying to implement macromolecules, which make it difficult to check the reaction stoichiometry. To that end we decided to use residues and chemical groups from ChEBI, which could provide the formula needed to check mass and charge balance. Besides, we wish to use BioPAX level 3 and ontologies like MOD. One common case is phosphorylation, for which I found the following definition: "A protein modification that effectively replaces a hydrogen atom with a phosphate group." According to ChEBI nomenclature, and after consulting ChEBI curators, we think that it would be more accurate to use "phosphono group" (CHEBI:48108) - or even "phosphonate group" (CHEBI.30931) in physiological conditions - rather than "phosphate group" (CHEBI:32958). Otherwise, the phosphorylation of a serine residue, for example, would lead to a peroxide which is not the case.
Best regards, and merry Christmas!
Reported by: ralcantara