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MSGFPlus / msgfplus

MS-GF+ (aka MSGF+ or MSGFPlus) performs peptide identification by scoring MS/MS spectra against peptides derived from a protein sequence database.
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Identical <SpectrumIdentificationItem>in mzid file #92

Open pigeonwei opened 4 years ago

pigeonwei commented 4 years ago

Hi, I wonder why my result mzid file from MS-GF+ does contain identical of the same spectrum which are both ranked as '1'. How should I choose between them?

  <SpectrumIdentificationItem chargeState="3" experimentalMassToCharge="485.64434814453125" calculatedMassToCharge="485.9692687988281" peptide_ref="Pep_FVFHAVK" rank="1" passThreshold="true" id="SII_735628_1">
      <PeptideEvidenceRef peptideEvidence_ref="PepEv_3394722_FVFHAVK_361"/>
      <cvParam cvRef="PSI-MS" accession="MS:1002049" name="MS-GF:RawScore" value="27"/>
      <cvParam cvRef="PSI-MS" accession="MS:1002050" name="MS-GF:DeNovoScore" value="44"/>
      <cvParam cvRef="PSI-MS" accession="MS:1002052" name="MS-GF:SpecEValue" value="2.7998803E-7"/>
      <cvParam cvRef="PSI-MS" accession="MS:1002053" name="MS-GF:EValue" value="5.8170533"/>
      <cvParam cvRef="PSI-MS" accession="MS:1002054" name="MS-GF:QValue" value="0.5088999"/>
      <cvParam cvRef="PSI-MS" accession="MS:1002055" name="MS-GF:PepQValue" value="0.6275891"/>
      <userParam name="IsotopeError" value="-1"/>
      <userParam name="AssumedDissociationMethod" value="CID"/>
    </SpectrumIdentificationItem>
    <SpectrumIdentificationItem chargeState="3" experimentalMassToCharge="485.64434814453125" calculatedMassToCharge="485.3044128417969" peptide_ref="Pep_FITHISK" rank="1" passThreshold="true" id="SII_735628_2">
      <PeptideEvidenceRef peptideEvidence_ref="PepEv_9639660_FITHISK_1331"/>
      <cvParam cvRef="PSI-MS" accession="MS:1002049" name="MS-GF:RawScore" value="27"/>
      <cvParam cvRef="PSI-MS" accession="MS:1002050" name="MS-GF:DeNovoScore" value="44"/>
      <cvParam cvRef="PSI-MS" accession="MS:1002052" name="MS-GF:SpecEValue" value="2.7998803E-7"/>
      <cvParam cvRef="PSI-MS" accession="MS:1002053" name="MS-GF:EValue" value="5.8170533"/>
      <cvParam cvRef="PSI-MS" accession="MS:1002054" name="MS-GF:QValue" value="0.5088999"/>
      <cvParam cvRef="PSI-MS" accession="MS:1002055" name="MS-GF:PepQValue" value="0.6275891"/>
      <userParam name="IsotopeError" value="1"/>
      <userParam name="AssumedDissociationMethod" value="CID"/>
    </SpectrumIdentificationItem>
    <cvParam cvRef="PSI-MS" accession="MS:1000796" name="spectrum title" value="File123794 Spectrum735628 scans: 35028"/>
    <cvParam cvRef="PSI-MS" accession="MS:1001115" name="scan number(s)" value="35028"/>
    <cvParam cvRef="PSI-MS" accession="MS:1000016" name="scan start time" value="2926.0" unitAccession="UO:0000010" unitName="second" unitCvRef="UO"/>
  </SpectrumIdentificationResult>
FarmGeek4Life commented 4 years ago

The identical rank is according to the mzid specification for the rank - if 2 different peptide results for the same spectrum have the same score, then the rank for those 2 results is the same.

These also have SpecEValue scores that are somewhat low, so these matches aren't particularly reliable.