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Julianus Pfeuffer
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added idXML notebook
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+288
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‎MSGFPlusAdapter_1_out.idXML

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<?xml version="1.0" encoding="UTF-8"?>
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<?xml-stylesheet type="text/xsl" href="https://www.openms.de/xml-stylesheet/IdXML.xsl" ?>
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<IdXML version="1.5" xsi:noNamespaceSchemaLocation="https://www.openms.de/xml-schema/IdXML_1_5.xsd" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
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<SearchParameters id="SP_0" db="/Users/pfeuffer/git/OpenMS-fixes-src/src/tests/topp/THIRDPARTY/proteins.fasta" db_version="" taxonomy="" mass_type="monoisotopic" charges="1-3" enzyme="trypsin/p" missed_cleavages="1000" precursor_peak_tolerance="10" precursor_peak_tolerance_ppm="true" peak_mass_tolerance="0" peak_mass_tolerance_ppm="false" >
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<VariableModification name="Oxidation (M)" />
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<UserParam type="string" name="MS:1001211" value=""/>
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<UserParam type="string" name="MS:1001256" value=""/>
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<UserParam type="string" name="ChargeCarrierMass" value="1.00727649"/>
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<UserParam type="string" name="FragmentMethod" value="As written in the spectrum or CID if no info"/>
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<UserParam type="string" name="Instrument" value="HighRes"/>
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<UserParam type="string" name="MaxIsotopeError" value="1"/>
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<UserParam type="string" name="MaxNumModifications" value="2"/>
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<UserParam type="string" name="MaxPepLength" value="40"/>
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<UserParam type="string" name="MinIsotopeError" value="0"/>
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<UserParam type="string" name="MinPepLength" value="6"/>
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<UserParam type="string" name="NumMatchesPerSpec" value="1"/>
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<UserParam type="string" name="Protocol" value="Standard"/>
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<UserParam type="string" name="TargetDecoyApproach" value="false"/>
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<UserParam type="string" name="MSGFPlusAdapter:1:in" value="C:/Development/OpenMS/src/tests/topp/THIRDPARTY/spectra.mzML"/>
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<UserParam type="string" name="MSGFPlusAdapter:1:out" value="MSGFPlusAdapter_1_out1.tmp"/>
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<UserParam type="string" name="MSGFPlusAdapter:1:mzid_out" value="MSGFPlusAdapter_1_out2.tmp.mzid"/>
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<UserParam type="string" name="MSGFPlusAdapter:1:executable" value="C:/Development/analysis_executables/msgf+/MSGFPlus.jar"/>
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<UserParam type="string" name="MSGFPlusAdapter:1:database" value="C:/Development/OpenMS/src/tests/topp/THIRDPARTY/proteins.fasta"/>
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<UserParam type="string" name="MSGFPlusAdapter:1:add_decoys" value="false"/>
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<UserParam type="float" name="MSGFPlusAdapter:1:precursor_mass_tolerance" value="10.0"/>
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<UserParam type="string" name="MSGFPlusAdapter:1:precursor_error_units" value="ppm"/>
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<UserParam type="string" name="MSGFPlusAdapter:1:isotope_error_range" value="0,1"/>
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<UserParam type="string" name="MSGFPlusAdapter:1:fragment_method" value="from_spectrum"/>
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<UserParam type="string" name="MSGFPlusAdapter:1:instrument" value="high_res"/>
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<UserParam type="string" name="MSGFPlusAdapter:1:enzyme" value="Trypsin/P"/>
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<UserParam type="string" name="MSGFPlusAdapter:1:protocol" value="none"/>
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<UserParam type="string" name="MSGFPlusAdapter:1:tryptic" value="fully"/>
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<UserParam type="int" name="MSGFPlusAdapter:1:min_precursor_charge" value="1"/>
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<UserParam type="int" name="MSGFPlusAdapter:1:max_precursor_charge" value="3"/>
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<UserParam type="int" name="MSGFPlusAdapter:1:min_peptide_length" value="6"/>
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<UserParam type="int" name="MSGFPlusAdapter:1:max_peptide_length" value="40"/>
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<UserParam type="int" name="MSGFPlusAdapter:1:matches_per_spec" value="1"/>
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<UserParam type="string" name="MSGFPlusAdapter:1:add_features" value="false"/>
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<UserParam type="int" name="MSGFPlusAdapter:1:max_mods" value="2"/>
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<UserParam type="int" name="MSGFPlusAdapter:1:max_missed_cleavages" value="-1"/>
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<UserParam type="int" name="MSGFPlusAdapter:1:tasks" value="0"/>
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<UserParam type="stringList" name="MSGFPlusAdapter:1:fixed_modifications" value="[]"/>
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<UserParam type="stringList" name="MSGFPlusAdapter:1:variable_modifications" value="[Oxidation (M)]"/>
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<UserParam type="string" name="MSGFPlusAdapter:1:legacy_conversion" value="false"/>
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<UserParam type="string" name="MSGFPlusAdapter:1:conf" value=""/>
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<UserParam type="string" name="MSGFPlusAdapter:1:java_executable" value="java"/>
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<UserParam type="int" name="MSGFPlusAdapter:1:java_memory" value="512"/>
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<UserParam type="int" name="MSGFPlusAdapter:1:java_permgen" value="0"/>
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<UserParam type="string" name="MSGFPlusAdapter:1:log" value=""/>
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<UserParam type="int" name="MSGFPlusAdapter:1:debug" value="0"/>
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<UserParam type="int" name="MSGFPlusAdapter:1:threads" value="1"/>
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<UserParam type="string" name="MSGFPlusAdapter:1:no_progress" value="false"/>
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<UserParam type="string" name="MSGFPlusAdapter:1:force" value="false"/>
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<UserParam type="string" name="MSGFPlusAdapter:1:test" value="true"/>
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<UserParam name="EnzymeTermSpecificity" type="string" value="full" />
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</SearchParameters>
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<IdentificationRun date="2020-05-20T23:45:50" search_engine="MS-GF+" search_engine_version="Release (v2020.03.14)" search_parameters_ref="SP_0" >
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<ProteinIdentification score_type="" higher_score_better="true" significance_threshold="0" >
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<ProteinHit id="PH_0" accession="BSA3" score="0.0" sequence="" >
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<UserParam type="string" name="isDecoy" value="false"/>
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</ProteinHit>
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<ProteinHit id="PH_1" accession="BSA2" score="0.0" sequence="" >
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<UserParam type="string" name="isDecoy" value="false"/>
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</ProteinHit>
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<ProteinHit id="PH_2" accession="" score="0.0" sequence="" >
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<UserParam type="string" name="isDecoy" value="false"/>
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</ProteinHit>
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<UserParam type="stringList" name="spectra_data" value="[/Users/pfeuffer/git/OpenMS-fixes-src/src/tests/topp/THIRDPARTY/spectra.mzML]"/>
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</ProteinIdentification>
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<PeptideIdentification score_type="SpecEValue" higher_score_better="false" significance_threshold="0.0" MZ="1063.2098388671875" RT="4587.668999999999869" spectrum_reference="spectrum=1" >
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<PeptideHit score="2.3492372e-26" sequence="IALSRPNVEVVALNDPFITNDYAAYM(Oxidation)FK" charge="3" aa_after="E" start="1" end="28" protein_refs="PH_1" >
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<UserParam type="float" name="MS:1002049" value="164.0"/>
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<UserParam type="float" name="MS:1002050" value="199.0"/>
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<UserParam type="float" name="MS:1002052" value="2.3492372e-26"/>
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<UserParam type="float" name="MS:1002053" value="9.678856999999999e-24"/>
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<UserParam type="string" name="AssumedDissociationMethod" value="HCD"/>
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<UserParam type="float" name="calcMZ" value="1063.2093505859375"/>
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<UserParam type="int" name="pass_threshold" value="1"/>
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<UserParam type="int" name="start" value="1"/>
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<UserParam type="int" name="end" value="28"/>
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<UserParam type="string" name="target_decoy" value="target"/>
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<UserParam type="string" name="isotope_error" value="0"/>
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</PeptideHit>
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</PeptideIdentification>
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<PeptideIdentification score_type="SpecEValue" higher_score_better="false" significance_threshold="0.0" MZ="775.38720703125" RT="4923.777299999999741" spectrum_reference="spectrum=2" >
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<PeptideHit score="1.6242718e-19" sequence="RPGADSDIGGFGGLFDLAQAGFR" charge="3" aa_after="A" start="1" end="23" protein_refs="PH_0" >
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<UserParam type="float" name="MS:1002049" value="151.0"/>
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<UserParam type="float" name="MS:1002050" value="188.0"/>
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<UserParam type="float" name="MS:1002052" value="1.6242718e-19"/>
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<UserParam type="float" name="MS:1002053" value="6.513329300000001e-17"/>
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<UserParam type="string" name="AssumedDissociationMethod" value="HCD"/>
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<UserParam type="float" name="calcMZ" value="775.38543701171875"/>
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<UserParam type="int" name="pass_threshold" value="1"/>
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<UserParam type="int" name="start" value="1"/>
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<UserParam type="int" name="end" value="23"/>
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<UserParam type="string" name="target_decoy" value="target"/>
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<UserParam type="string" name="isotope_error" value="0"/>
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</PeptideHit>
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</PeptideIdentification>
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<PeptideIdentification score_type="SpecEValue" higher_score_better="false" significance_threshold="0.0" MZ="520.2628173828125" RT="2655.095699999999852" spectrum_reference="spectrum=0" >
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<PeptideHit score="4.652130499999999e-19" sequence="DFASSGGYVLHLHR" charge="3" aa_after="E" start="1" end="14" >
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<UserParam type="float" name="MS:1002049" value="123.0"/>
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<UserParam type="float" name="MS:1002050" value="125.0"/>
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<UserParam type="float" name="MS:1002052" value="4.652130499999999e-19"/>
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<UserParam type="float" name="MS:1002053" value="1.63755e-16"/>
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<UserParam type="string" name="AssumedDissociationMethod" value="HCD"/>
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<UserParam type="float" name="calcMZ" value="520.2635498046875"/>
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<UserParam type="int" name="pass_threshold" value="1"/>
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<UserParam type="int" name="start" value="1"/>
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<UserParam type="int" name="end" value="14"/>
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<UserParam type="string" name="target_decoy" value="target"/>
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<UserParam type="string" name="isotope_error" value="0"/>
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</PeptideHit>
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</PeptideIdentification>
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</IdentificationRun>
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</IdXML>

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