inconsistency re. whether the "crosslink donor" CV term is accompanied by another CV term giving accession

[colin-combe]

in file the https://storage.jpostdb.org/JPST001851/membrane_5pc_1200IDs.mzid (xiFDR output I believe) there is inconsistency as to whether the "crosslink donor" CV term is accompanied by another CV term giving accession for the crosslinker. (It should do - "The cross-link donor peptide’s Modification element MUST have a suitably sourced cvParam for the crosslink.", p.20, mzId spec.)

E.g. in lines 2933169-2933196:

<Peptide id="187505_QLphl-loopATQLphl-hydSGVQR_187506_GEILGIAGLphl-loopVGAK_10_4_p0">
    <PeptideSequence>QLATQLSGVQR</PeptideSequence>
    <Modification location="2" residues="L" monoisotopicMassDelta="-16.0313">
      <cvParam cvRef="UNIMOD" accession="UNIMOD:604" name="Leu-&gt;Pro"></cvParam>
    </Modification>
    <Modification location="6" residues="L" monoisotopicMassDelta="1.9792646">
      <cvParam cvRef="PSI-MS" accession="MS:1001460" name="unknown modification"></cvParam>
    </Modification>
    <Modification location="10" monoisotopicMassDelta="-16.031300099999726">
      <cvParam cvRef="PSI-MS" accession="MS:1001460" name="unknown modification"></cvParam>
      <cvParam cvRef="PSI-MS" accession="MS:1002509" name="cross-link donor" value="157613"></cvParam>
    </Modification>
  </Peptide>
  <Peptide id="55123_LPADDKTAIESALTALETALKGEDKAAIEAK_119039_APGMoxTMFK_1_7_p1">
    <PeptideSequence>APGMTMFK</PeptideSequence>
    <Modification location="4" residues="M" monoisotopicMassDelta="15.99491">
      <cvParam cvRef="UNIMOD" accession="UNIMOD:35" name="Oxidation"></cvParam>
    </Modification>
    <Modification location="7" monoisotopicMassDelta="0.0">
      <cvParam cvRef="PSI-MS" accession="MS:1002510" name="cross-link acceptor" value="157614"></cvParam>
    </Modification>
  </Peptide>
  <Peptide id="55123_LPADDKTAIESALTALETALKGEDKAAIEAK_119039_APGMoxTMFK_1_7_p0">
    <PeptideSequence>LPADDKTAIESALTALETALKGEDKAAIEAK</PeptideSequence>
    <Modification location="1" monoisotopicMassDelta="-16.031299540000532">
      <cvParam cvRef="PSI-MS" accession="MS:1002509" name="cross-link donor" value="157614"></cvParam>
    </Modification>
  </Peptide>

so for peptide 187505_QLphl-loopATQLphl-hydSGVQR_187506_GEILGIAGLphl-loopVGAK_10_4_p0 it has it,
for peptide 55123_LPADDKTAIESALTALETALKGEDKAAIEAK_119039_APGMoxTMFK_1_7_p0 it doesn't

@lutzfischer
@Lars - this is what caused need for Rappsilber-Laboratory/xi-mzidentml-converter@1fa22d7
@grandrea

[colin-combe]

this came up again...