mzIdentML validator: residue-pair-level score pairing and ambiguity

[lutzfischer]

The validator flags residue level scores up as not paired - but this disregards ambiguity. I.e. I have a case where I have a link from peptide XXXXXKXR to PEPTIDEKR and the protein actually contains the sequence ...PEPTIDEKRPEPTIDEKR... - therefore I get an ambiguous residue pair. Now in the resulting mzIdentML contains:

  <ProteinAmbiguityGroup id="PAG_13">
    <ProteinDetectionHypothesis dBSequence_ref="dbseq_XXXXX_target" passThreshold="false" id="PAG_13_PDH_0">
      ...
      <cvParam cvRef="PSI-MS" accession="MS:1002677" name="residue-pair-level global FDR" value="151808167.a:214:0.0:true"></cvParam>
      <cvParam cvRef="PSI-MS" accession="MS:1002677" name="residue-pair-level global FDR" value="151808167.b:141:0.0:true"></cvParam>
      <cvParam cvRef="PSI-MS" accession="MS:1002677" name="residue-pair-level global FDR" value="151808167.b:149:0.0:true"></cvParam>

But the validator comes back with:

Message 14497:
    Level: ERROR
    --> Interaction score is not paired for XL interaction ID 151810610 and score 0.0 (has only 1 entries for : PAG: PAG_13 and PDH: PAG_13_PDH_0

but it is paired - only that 151808167.b: turns up twice (as that side is the ambiguous).