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Rappsilber-Laboratory / xiFDR

Generic FDR-Calculation for cross-linked PSMs and resulting peptide pairs, links and protein pairs
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invalid <cvParam></cvParam> in mzIdentML output #39

Open colin-combe opened 5 months ago

colin-combe commented 5 months ago

in the Peptide elements there can be invalid Modification elements like:

    <Modification location="24" monoisotopicMassDelta="-77.98878522000018">
      <cvParam></cvParam>
      <cvParam cvRef="PSI-MS" accession="MS:1002509" name="cross-link donor" value="127"></cvParam>
    </Modification>

(don't think the empty cv param is allowed)

do you need the whole file? (its not mine but i can ask)

lutzfischer commented 5 months ago

I am not sure what exactly went wrong. I think having at least the whole peptide defintion might shed some light on what goes on. Ideally an mzIdentML and a csv-result file would be good. Or just the whole peptide defintion plus a line from the CSV file containing said peptide would be good.

colin-combe commented 5 months ago

this is an whole peptide:

  <Peptide id="581_ADYEKHKsda-hydVYACcmEVTHQGLSSPVTK_281_QpgluLTCcmRLDCcmADGGATVQWR_5_4_p0">
    <PeptideSequence>ADYEKHKVYACEVTHQGLSSPVTK</PeptideSequence>
    <Modification location="7" residues="K" monoisotopicMassDelta="100.05243">
      <cvParam cvRef="PSI-MS" accession="MS:1001460" name="unknown modification"></cvParam>
    </Modification>
    <Modification location="11" residues="C" monoisotopicMassDelta="57.021466">
      <cvParam cvRef="UNIMOD" accession="UNIMOD:4" name="Carbamidomethyl"></cvParam>
    </Modification>
    <Modification location="5" monoisotopicMassDelta="-77.9887854349995">
      <cvParam></cvParam>
      <cvParam cvRef="PSI-MS" accession="MS:1002509" name="cross-link donor" value="4"></cvParam>
    </Modification>
  </Peptide>

i can't find the line in the csv file, i'll ask about providing whole files

colin-combe commented 5 months ago

actually, i just emailed them to you

lutzfischer commented 5 months ago

looks like it is a problem with the second crosslinker. Still need to track that down what exactly is going wrong there.

colin-combe commented 5 months ago

https://github.com/Rappsilber-Laboratory/xiview/issues/561#issuecomment-2037414437

WeiqiangChen commented 4 months ago

I replaced the whole cvParam line with empty in Notepad++. Now it works to load the UV-XL XiSearch result to XiView.

XiFDR should just remove this lines when exporting the result.