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likelihood of different modifications at the same position accounting for the same mass difference
We have come upon this problem in Proteoform Suite, and they've come upon it in this paper.
In the text they give the example (with glycans): "For instance, assume that a given residual mass may be compatible with the glycoforms A2G0F/A2G2F and A2G1F/A2G1F, whose scores are 0.7 and 0.3, respectively. Then, the former permutation will account for 70% of the peak abundance, while the latter one will explain the remaining 30%."
How should we note this type of likelihood for two different modifications at the same position?
Can anyone think of more categories of scores?
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In an attempt at 2), I suppose the ambiguity grouping works nicely even for the same position: PRO[A2G0F|#glycan:70][A2G1F|#glycan:30]TEOFORM
And with two positions, that is also possible, where the probability for the glycan is 70/30 at each site and the position likelihood is 80/20: PRON[A2G0F|#glycanA:70|#position:40][A2G1F|#glycanA:30|#position:40]TEOFORN[A2G0F|#glycanB:70|#position:10][A2G1F|#glycanB:30|#position:10]
I'm actually confused by my own follow-up statement from last week. The # mark would usually be used for the same modification at several locations, indicating it could be at one of the set. The #position mark breaks that assumption, since it is used with a couple types of modifications, as does #glycanA and #glycanB.
I'm reading this MoFi paper right now, and it's reminding me of @veitveit's concern that we need to allow room for scores in PTMs.
I think we might need to formalize a solution for at least two categories of scores:
PROT[Phospho|#mod:20]EOFORMS[Phospho|#mod:80]
, as noted in Ambiguity of PTM localization #17Can anyone think of more categories of scores?
The text was updated successfully, but these errors were encountered: