Ammonium?

[rfellers]

Hey all,

I'm looking for a mapping for Unimod:989 Ammonium. Does such a thing exist in PSI-MOD? My searching led nowhere.

Thanks,
Ryan

[pmt706]

It's not in there now... but related... there is a monosodium adduct MOD:00423 and a protonated residue MOD:01699. We should add it, but I think it should be in the mold of MOD:00423 where you have a H -1 N 1 H 4 (or a net N 1 H3)... then it's neutral, so the user would add in any ionization-related charges to it. The "PSI-MOD-way" is to have the N-term and C-term separate as well as any charging...

Thoughts?

[edeutsch]

+1 on adding ammonium modeled after MOD:00423.

[pabinz]

Sodium Adduct is adding Na+, non covalently, that's all. Nothing to do with a removal of H+compensated with an addition of Na+. But in PSI-MOD a diff of H-1 Na 1 is defined as one assumes, when a peptide is analysed as (singly or multiply) protonated, one adds a H 1 to the neutral mass.
Similarly, Ammonium adduct is a non covalent addition of NH4+ (a N 1 H 4). Therefore the diff of N 1 H 3 can be ok. It is an artefactual mod.