File: OpenSwathChromatogramExtractor_input.TraML

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<?xml version="1.0" encoding="UTF-8"?>
<TraML version="0.9.2" xmlns="http://psi.hupo.org/ms/traml" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://psi.hupo.org/ms/traml TraML0.9.2.xsd">
  <cvList>
    <cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="unknown" URI="http://psidev.cvs.sourceforge.net/*checkout*/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo"/>
    <cv id="UO" fullName="Unit Ontology" version="unknown" URI="http://obo.cvs.sourceforge.net/obo/obo/ontology/phenotype/unit.obo"/>
  </cvList>
  <ProteinList>
    <Protein id="" >
      <Sequence></Sequence>
    </Protein>
  </ProteinList>
  <CompoundList>
    <Peptide id="tr_gr1" sequence="PEPTIDEA">
      <ProteinRef ref=""/>
      <RetentionTimeList>
       <RetentionTime>
          <cvParam cvRef="MS" accession="MS:1000896" name="normalized retention time" value="44"/>
       </RetentionTime>
      </RetentionTimeList>
    </Peptide>
    <Peptide id="tr_gr2" sequence="PEPTIDEB">
      <ProteinRef ref=""/>
      <RetentionTimeList>
       <RetentionTime>
          <cvParam cvRef="MS" accession="MS:1000896" name="normalized retention time" value="2"/>
       </RetentionTime>
      </RetentionTimeList>
    </Peptide>
  </CompoundList>
  <TransitionList>
    <Transition id="tr1" peptideRef="tr_gr1" >
      <cvParam cvRef="MS" accession="MS:1000045" name="collision energy" value="1"/>
      <cvParam cvRef="MS" accession="MS:1001226" name="product ion intensity" value="1"/>
      <cvParam cvRef="MS" accession="decoy" name="decoy" value="0"/>
      <Precursor>
       <cvParam cvRef="MS" accession="MS:1000827" name="isolation window target m/z" value="500" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
      </Precursor>
      <Product>
       <cvParam cvRef="MS" accession="MS:1000827" name="isolation window target m/z" value="628.45" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
      </Product>
    </Transition>
    <Transition id="tr2" peptideRef="tr_gr1" >
      <cvParam cvRef="MS" accession="MS:1000045" name="collision energy" value="1"/>
      <cvParam cvRef="MS" accession="MS:1001226" name="product ion intensity" value="2"/>
      <cvParam cvRef="MS" accession="decoy" name="decoy" value="0"/>
      <Precursor>
       <cvParam cvRef="MS" accession="MS:1000827" name="isolation window target m/z" value="500" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
      </Precursor>
      <Product>
       <cvParam cvRef="MS" accession="MS:1000827" name="isolation window target m/z" value="654.38" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
      </Product>
    </Transition>
    <Transition id="tr3" peptideRef="tr_gr2" >
      <cvParam cvRef="MS" accession="MS:1000045" name="collision energy" value="1"/>
      <cvParam cvRef="MS" accession="MS:1001226" name="product ion intensity" value="10000"/>
      <cvParam cvRef="MS" accession="decoy" name="decoy" value="0"/>
      <Precursor>
       <cvParam cvRef="MS" accession="MS:1000827" name="isolation window target m/z" value="501" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
      </Precursor>
      <Product>
       <cvParam cvRef="MS" accession="MS:1000827" name="isolation window target m/z" value="618.31" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
      </Product>
    </Transition>
  </TransitionList>
</TraML>