Mod scores - problem reporting a combined score for multiple sites

[andrewrobertjones]

Ville Koskinen is working on mzIdentML 1.2 export from Mascot and reports this issue:

we're looking at what changes are needed to export mzIdentML 1.2 from Mascot Server. One problem we've encountered so far is with site localisation scores. Here's an example query with two modifications and multiple permutations (scroll to the bottom of page):
http://www.matrixscience.com/cgi/peptide_view.pl?file=..%2Fdata%2F20190108%2FF001291.dat;_msresflags=3138;_msresflags2=266;ave_thresh=17;db_idx=2;hit=1;index=TRAP_PLAFA;px=1;query=8118;section=5
The confidence percentages are based on the score difference between adjacent ranks. There is no site-specific score; the percentage is for the joint assignment confidence of Oxidation and dHex(1)Hex(1).

1. One possibility is to have the same modification index for different elements. For example:

<Peptide Id="8118_1"> <PeptideSequence>TASCGVWDEWSPCSVTCGK</PeptideSequence> <Modification monoisotopicMassDelta="15.994915" location="7" residues="M"> <cvParam cvRef="PSI-MS" accession="MS:1002504" name="modification index" value="1"/> </Modification> <Modification monoisotopicMassDelta="308.110732" location="16" residues="T"> <cvParam cvRef="PSI-MS" accession="MS:1002504" name="modification index" value="1"/> </Modification> </Peptide>

Then, under , the line referring to modification index 1 means a simultaneous assignment. We could then encode the 10 different permutations like:

<cvParam cvRef="PSI-MS" accession="MS:xxxxx" name="yyyy" value="1:19.39:7|16:true" /> <cvParam cvRef="PSI-MS" accession="MS:xxxxx" name="yyyy" value="1:19.39:7|14:true" /> ... <cvParam cvRef="PSI-MS" accession="MS:xxxxx" name="yyyy" value="1:0.61:10|3:true" /> <cvParam cvRef="PSI-MS" accession="MS:xxxxx" name="yyyy" value="1:0.61:10|1:true" />

This is assuming the site alternation is in the same order as the elements (oxidation|dhex). Is this allowed, and is this the intended encoding?
2) If there must be a one-to-one mapping between modification index and modification name/delta, another possibility is to extend the regular expression constraint. Maybe something like this would work?

<cvParam cvRef="PSI-MS" accession="MS:xxxxx" name="yyyy" value="1:19.39:7:true,2:19.39:16:true" />
The least ambiguous syntax would be the following, but I realise this is a big departure from the existing syntax:

<cvParam cvRef="PSI-MS" accession="MS:xxxxx" name="yyyy" value="(1:7,2:16):19.39:true" />

[vrkosk]

What mzIdentML software is able to read and display localisation scores using the 1.2.0 syntax? Is there any?