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<?xml version="1.0" encoding="UTF-8"?>
<TraML version="1.0.0" xmlns="http://psi.hupo.org/ms/traml" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://psi.hupo.org/ms/traml TraML1.0.0.xsd">
<cvList>
<cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="2.31.0" 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"/>
<cv id="UNIMOD" fullName="UNIMOD CV for modifications" version="unknown" URI="http://www.unimod.org/obo/unimod.obo"/>
</cvList>
<SourceFileList>
<SourceFile id="sf1" name="OneTransition.tsv" location="file:///F:/data/Exp01">
<cvParam cvRef="MS" accession="MS:1000914" name="tab delimited text file" value=""/>
<cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="71be39fb2700ab2f3c8b2234b91274968b6899b1"/>
</SourceFile>
</SourceFileList>
<ContactList>
<Contact id="CS">
<cvParam cvRef="MS" accession="MS:1000586" name="contact name" value="Eric Deutsch"/>
<cvParam cvRef="MS" accession="MS:1000590" name="contact organization" value="Institute for Systems Biology"/>
<cvParam cvRef="MS" accession="MS:1000587" name="contact address" value="1441 NE 34th St, Seattle WA 98103, USA"/>
<cvParam cvRef="MS" accession="MS:1000588" name="contact URL" value="http://www.systemsbiology.org/"/>
<cvParam cvRef="MS" accession="MS:1000589" name="contact email" value="example@systemsbiology.org"/>
</Contact>
</ContactList>
<PublicationList>
<Publication id="PMID12748199">
<cvParam cvRef="MS" accession="MS:1000879" name="PubMed identifier" value="12748199"/>
</Publication>
</PublicationList>
<InstrumentList>
<Instrument id="LCQ_Deca">
<cvParam cvRef="MS" accession="MS:1000554" name="LCQ Deca"/>
</Instrument>
<Instrument id="QTRAP">
<cvParam cvRef="MS" accession="MS:1000870" name="4000 QTRAP"/>
</Instrument>
</InstrumentList>
<SoftwareList>
<Software id="MaRiMba" version="1.0">
<cvParam cvRef="MS" accession="MS:1000872" name="MaRiMba"/>
</Software>
<Software id="SSRCalc3.0" version="3.0">
<cvParam cvRef="MS" accession="MS:1000874" name="SSRCalc"/>
</Software>
<Software id="Skyline0.5" version="0.5">
<cvParam cvRef="MS" accession="MS:1000922" name="Skyline"/>
</Software>
</SoftwareList>
<!-- Note that the protein names, peptide sequences, modification and transition values are not all fully internally consistent, but are intended merely as examples here -->
<ProteinList>
<Protein id="Q12149">
<cvParam cvRef="MS" accession="MS:1000885" name="protein accession" value="Q00613"/>
<cvParam cvRef="MS" accession="MS:1000883" name="protein short name" value="HSF 1"/>
<cvParam cvRef="MS" accession="MS:1000886" name="protein name" value="Heat shock factor protein 1"/>
<Sequence>MSTEMETKAEDVETFAFQAEIAQLMSLIINTFYSNKEIFLRELISNSSDALDKIRYESLTDPSKLDNGKE</Sequence>
</Protein>
<Protein id="ENSP00000332698">
<cvParam cvRef="MS" accession="MS:1000885" name="protein accession" value="ENSP00000332698"/>
<cvParam cvRef="MS" accession="MS:1000883" name="protein short name" value="HSF 1"/>
<cvParam cvRef="MS" accession="MS:1000886" name="protein name" value="Heat shock factor protein 1"/>
<Sequence>MSTEMETKAEDVETFAFQAEIAQLMSLIINTFYSNKEIFLRELISNSSDALDKIRYESLTDPSKLDNGKEELISNSSDALDKI</Sequence>
</Protein>
</ProteinList>
<CompoundList>
<Peptide id="ADTHFLLNIYDQLR-M1" sequence="ADTHFLLNIYDQLR">
<cvParam cvRef="MS" accession="MS:1000891" name="heavy labeled peptide"/>
<cvParam cvRef="MS" accession="MS:1000893" name="peptide group label" value="G1"/>
<cvParam cvRef="MS" accession="MS:1000863" name="predicted isoelectric point" value="5.22"/>
<cvParam cvRef="MS" accession="MS:1001117" name="theoretical mass" value="1189.22" unitCvRef="UO" unitAccession="UO:0000221" unitName="dalton"/>
<userParam name="isomerization potential" value="0.583" type="xsd:float"/> <!-- Additional information may be added as a userParams if it is not possible and not appropriate to encode the information as a cvParam -->
<ProteinRef ref="Q12149"/>
<ProteinRef ref="ENSP00000332698"/>
<Modification location="0" monoisotopicMassDelta="127.063324">
<cvParam cvRef="UNIMOD" accession="UNIMOD:29" name="SMA"/>
</Modification>
<Modification location="1" monoisotopicMassDelta="15.994919">
<cvParam cvRef="UNIMOD" accession="UNIMOD:35" name="Oxidation"/>
</Modification>
<RetentionTimeList>
<RetentionTime softwareRef="SSRCalc3.0">
<cvParam cvRef="MS" accession="MS:1000897" name="predicted retention time" value="44.07" unitCvRef="UO" unitAccession="UO:0000031" unitName="minute"/>
</RetentionTime>
<RetentionTime>
<cvParam cvRef="MS" accession="MS:1000896" name="normalized retention time" value="38.43" unitCvRef="UO" unitAccession="UO:0000031" unitName="minute"/>
<cvParam cvRef="MS" accession="MS:1000902" name="H-PINS retention time normalization standard"/>
</RetentionTime>
</RetentionTimeList>
<Evidence>
<cvParam cvRef="MS" accession="MS:1001100" name="confident peptide" value="6"/>
</Evidence>
</Peptide>
<Peptide id="PEPTIDEC" sequence="PEPTIDEC"/>
<Peptide id="PEPTIDEM" sequence="PEPTIDEM"/>
<Compound id="glyoxylate">
<cvParam cvRef="MS" accession="MS:1001117" name="theoretical mass" value="423.39" unitCvRef="UO" unitAccession="UO:0000221" unitName="dalton"/>
<cvParam cvRef="MS" accession="MS:1000866" name="molecular formula" value="C2HO3"/>
<cvParam cvRef="MS" accession="MS:1000868" name="SMILES string" value="[CH](=[O])[C](=[O])[O-]"/>
<RetentionTimeList>
<RetentionTime>
<cvParam cvRef="MS" accession="MS:1000896" name="normalized retention time" value="22.34" unitCvRef="UO" unitAccession="UO:0000031" unitName="minute"/>
<cvParam cvRef="MS" accession="MS:1000902" name="H-PINS retention time normalization standard"/>
</RetentionTime>
</RetentionTimeList>
</Compound>
</CompoundList>
<TransitionList>
<Transition id="ADTHFLLNIYDQLR-M1-T1" peptideRef="ADTHFLLNIYDQLR-M1">
<Precursor>
<cvParam cvRef="MS" accession="MS:1000827" name="isolation window target m/z" value="862.9467" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
<cvParam cvRef="MS" accession="MS:1000041" name="charge state" value="2"/>
</Precursor>
<Product>
<cvParam cvRef="MS" accession="MS:1000827" name="isolation window target m/z" value="1040.57" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
<cvParam cvRef="MS" accession="MS:1000041" name="charge state" value="1"/>
<InterpretationList>
<Interpretation>
<cvParam cvRef="MS" accession="MS:1000926" name="product interpretation rank" value="1"/>
<cvParam cvRef="MS" accession="MS:1001220" name="frag: y ion"/>
<cvParam cvRef="MS" accession="MS:1000903" name="product ion series ordinal" value="8"/>
<cvParam cvRef="MS" accession="MS:1000904" name="product ion m/z delta" value="0.03" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
</Interpretation>
<Interpretation>
<cvParam cvRef="MS" accession="MS:1000926" name="product interpretation rank" value="2"/>
<cvParam cvRef="MS" accession="MS:1001222" name="frag: b ion - H2O"/>
<cvParam cvRef="MS" accession="MS:1000903" name="product ion series ordinal" value="9"/>
<cvParam cvRef="MS" accession="MS:1000904" name="product ion m/z delta" value="-0.43" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
</Interpretation>
</InterpretationList>
<ConfigurationList>
<Configuration instrumentRef="QTRAP" contactRef="CS">
<cvParam cvRef="MS" accession="MS:1000502" name="dwell time" value="0.12" unitCvRef="UO" unitAccession="UO:0000010" unitName="second"/>
<cvParam cvRef="MS" accession="MS:1000045" name="collision energy" value="26" unitCvRef="UO" unitAccession="UO:0000266" unitName="electronvolt"/>
<cvParam cvRef="MS" accession="MS:1000875" name="declustering potential" value="64" unitCvRef="UO" unitAccession="UO:0000218" unitName="volt"/>
<cvParam cvRef="MS" accession="MS:1000419" name="collision gas" value="argon"/>
<cvParam cvRef="MS" accession="MS:1000869" name="collision gas pressure" value="12" unitCvRef="UO" unitAccession="UO:0000110" unitName="pascal"/>
<cvParam cvRef="MS" accession="MS:1000876" name="cone voltage" value="1200" unitCvRef="UO" unitAccession="UO:0000218" unitName="volt"/>
<cvParam cvRef="MS" accession="MS:1000880" name="interchannel delay" value="0.01" unitCvRef="UO" unitAccession="UO:0000010" unitName="second"/>
<cvParam cvRef="MS" accession="MS:1000877" name="tube lens voltage" value="23" unitCvRef="UO" unitAccession="UO:0000218" unitName="volt"/>
<ValidationStatus>
<cvParam cvRef="MS" accession="MS:1000910" name="transition optimized on specified instrument"/>
<cvParam cvRef="MS" accession="MS:1000139" name="4000 QTRAP"/>
<cvParam cvRef="MS" accession="MS:1000042" name="peak intensity" value="4072" unitCvRef="MS" unitAccession="MS:1000905" unitName="percent of base peak times 100"/>
<cvParam cvRef="MS" accession="MS:1000906" name="peak intensity rank" value="2"/>
<cvParam cvRef="MS" accession="MS:1000907" name="peak targeting suitability rank" value="1"/>
</ValidationStatus>
</Configuration>
</ConfigurationList>
</Product>
<RetentionTime softwareRef="Skyline0.5">
<cvParam cvRef="MS" accession="MS:1000895" name="local retention time" value="40.02" unitCvRef="UO" unitAccession="UO:0000031" unitName="minute"/>
<cvParam cvRef="MS" accession="MS:1000916" name="retention time window lower offset" value="3.0" unitCvRef="UO" unitAccession="UO:0000031" unitName="minute"/>
<cvParam cvRef="MS" accession="MS:1000917" name="retention time window upper offset" value="3.0" unitCvRef="UO" unitAccession="UO:0000031" unitName="minute"/>
</RetentionTime>
<Prediction softwareRef="MaRiMba" contactRef="CS">
<cvParam cvRef="MS" accession="MS:1000912" name="transition purported from an MS/MS spectrum on a different, specified instrument"/>
<cvParam cvRef="MS" accession="MS:1000291" name="linear ion trap"/>
<cvParam cvRef="MS" accession="MS:1000042" name="peak intensity" value="10000" unitCvRef="MS" unitAccession="MS:1000905" unitName="percent of base peak times 100"/>
<cvParam cvRef="MS" accession="MS:1000906" name="peak intensity rank" value="1"/>
<cvParam cvRef="MS" accession="MS:1000907" name="peak targeting suitability rank" value="1"/>
</Prediction>
</Transition>
<Transition id="ADTHFLLNIYDQLR-M1-T2" peptideRef="ADTHFLLNIYDQLR-M1">
<Precursor>
<cvParam cvRef="MS" accession="MS:1000827" name="isolation window target m/z" value="862.9467" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
<cvParam cvRef="MS" accession="MS:1000828" name="isolation window lower offset" value="1.0" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
<cvParam cvRef="MS" accession="MS:1000829" name="isolation window upper offset" value="1.0" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
<cvParam cvRef="MS" accession="MS:1000041" name="charge state" value="2"/>
</Precursor>
<IntermediateProduct>
<cvParam cvRef="MS" accession="MS:1000827" name="isolation window target m/z" value="1040.57" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
<cvParam cvRef="MS" accession="MS:1000041" name="charge state" value="1"/>
<InterpretationList>
<Interpretation>
<cvParam cvRef="MS" accession="MS:1000926" name="product interpretation rank" value="1"/>
<cvParam cvRef="MS" accession="MS:1001220" name="frag: y ion"/>
<cvParam cvRef="MS" accession="MS:1000903" name="product ion series ordinal" value="8"/>
<cvParam cvRef="MS" accession="MS:1000904" name="product ion m/z delta" value="0.03" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
</Interpretation>
</InterpretationList>
<ConfigurationList>
<Configuration instrumentRef="QTRAP" contactRef="CS">
<cvParam cvRef="MS" accession="MS:1000045" name="collision energy" value="26" unitCvRef="UO" unitAccession="UO:0000266" unitName="electronvolt"/>
</Configuration>
</ConfigurationList>
</IntermediateProduct>
<Product>
<cvParam cvRef="MS" accession="MS:1000827" name="isolation window target m/z" value="543.2" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
<cvParam cvRef="MS" accession="MS:1000041" name="charge state" value="1"/>
<InterpretationList>
<Interpretation>
<cvParam cvRef="MS" accession="MS:1000926" name="product interpretation rank" value="1"/>
<cvParam cvRef="MS" accession="MS:1001220" name="frag: y ion"/>
<cvParam cvRef="MS" accession="MS:1000903" name="product ion series ordinal" value="4"/>
<cvParam cvRef="MS" accession="MS:1000904" name="product ion m/z delta" value="0.03" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
</Interpretation>
</InterpretationList>
<ConfigurationList>
<Configuration instrumentRef="QTRAP" contactRef="CS">
<cvParam cvRef="MS" accession="MS:1000502" name="dwell time" value="0.12" unitCvRef="UO" unitAccession="UO:0000010" unitName="second"/>
<cvParam cvRef="MS" accession="MS:1000045" name="collision energy" value="20.4" unitCvRef="UO" unitAccession="UO:0000266" unitName="electronvolt"/>
</Configuration>
</ConfigurationList>
</Product>
<RetentionTime softwareRef="Skyline0.5">
<cvParam cvRef="MS" accession="MS:1000895" name="local retention time" value="40.02" unitCvRef="UO" unitAccession="UO:0000031" unitName="minute"/>
<cvParam cvRef="MS" accession="MS:1000916" name="retention time window lower offset" value="3.0" unitCvRef="UO" unitAccession="UO:0000031" unitName="minute"/>
<cvParam cvRef="MS" accession="MS:1000917" name="retention time window upper offset" value="3.0" unitCvRef="UO" unitAccession="UO:0000031" unitName="minute"/>
</RetentionTime>
</Transition>
</TransitionList>
<TargetList>
<cvParam cvRef="MS" accession="MS:1000920" name="includes supersede excludes"/>
<TargetIncludeList>
<Target id="PEPTIDEC2+" peptideRef="PEPTIDEC">
<Precursor>
<cvParam cvRef="MS" accession="MS:1000827" name="isolation window target m/z" value="862.9467" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
<cvParam cvRef="MS" accession="MS:1000041" name="charge state" value="2"/>
</Precursor>
<RetentionTime softwareRef="Skyline0.5">
<cvParam cvRef="MS" accession="MS:1000895" name="local retention time" value="27.44" unitCvRef="UO" unitAccession="UO:0000031" unitName="minute"/>
<cvParam cvRef="MS" accession="MS:1000916" name="retention time window lower offset" value="4.0" unitCvRef="UO" unitAccession="UO:0000031" unitName="minute"/>
<cvParam cvRef="MS" accession="MS:1000917" name="retention time window upper offset" value="4.0" unitCvRef="UO" unitAccession="UO:0000031" unitName="minute"/>
</RetentionTime>
<ConfigurationList>
<Configuration instrumentRef="LCQ_Deca" contactRef="CS">
<cvParam cvRef="MS" accession="MS:1000045" name="collision energy" value="26" unitCvRef="UO" unitAccession="UO:0000266" unitName="electronvolt"/>
</Configuration>
</ConfigurationList>
</Target>
</TargetIncludeList>
<TargetExcludeList>
<Target id="PEPTIDEM3+" peptideRef="PEPTIDEM">
<Precursor>
<cvParam cvRef="MS" accession="MS:1000827" name="isolation window target m/z" value="698.3443" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
<cvParam cvRef="MS" accession="MS:1000041" name="charge state" value="3"/>
</Precursor>
</Target>
</TargetExcludeList>
</TargetList>
</TraML>
|
