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hendrikweisser/PAMI-176_Mouse_A-J_TMT_40ug_14pctACN_25cm_120min_20160223_OT.idXML Secret

Created March 15, 2024 16:01
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TMT6plex_idXML
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PAMI-176_Mouse_A-J_TMT_40ug_14pctACN_25cm_120min_20160223_OT.idXML
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<?xml version="1.0" encoding="UTF-8"?>
<?xml-stylesheet type="text/xsl" href="https://www.openms.de/xml-stylesheet/IdXML.xsl" ?>
<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">
<SearchParameters id="SP_0" db="/home/matteo/knime-workspace/Example_Data/IsobaricTMT/database/sprot_2015.07_mouse_for_decoy.fasta" db_version="" taxonomy="" mass_type="monoisotopic" charges="2-3" enzyme="trypsin/p" missed_cleavages="1000" precursor_peak_tolerance="10" precursor_peak_tolerance_ppm="true" peak_mass_tolerance="0" peak_mass_tolerance_ppm="false" >
<FixedModification name="Carbamidomethyl (C)" />
<FixedModification name="TMT6plex (N-term)" />
<FixedModification name="TMT6plex (K)" />
<FixedModification name="Label:13C(6)15N(4) (R)" />
<VariableModification name="Oxidation (M)" />
<UserParam type="string" name="MS:1001211" value=""/>
<UserParam type="string" name="MS:1001256" value=""/>
<UserParam type="string" name="ChargeCarrierMass" value="1.00727649"/>
<UserParam type="string" name="FragmentMethod" value="As written in the spectrum or CID if no info"/>
<UserParam type="string" name="Instrument" value="HighRes"/>
<UserParam type="string" name="MaxIsotopeError" value="1"/>
<UserParam type="string" name="MaxNumModifications" value="2"/>
<UserParam type="string" name="MaxPepLength" value="40"/>
<UserParam type="string" name="MinIsotopeError" value="0"/>
<UserParam type="string" name="MinPepLength" value="6"/>
<UserParam type="string" name="NumMatchesPerSpec" value="1"/>
<UserParam type="string" name="Protocol" value="TMT"/>
<UserParam type="string" name="TargetDecoyApproach" value="false"/>
<UserParam type="string" name="MSGFPlusAdapter:1:in" value="/home/matteo/knime-workspace/Example_Data/IsobaricTMT/dataset/PAMI-176_Mouse_A-J_TMT_40ug_14pctACN_25cm_120min_20160223_OT.mzML"/>
<UserParam type="string" name="MSGFPlusAdapter:1:out" value="/tmp/knime_Identification_13595/fs-ZipLo_3-5-35970/000/000/1_0_MSGFPlusAdapter_0/PAMI-176_Mouse_A-J_TMT_40ug_14pctACN_25cm_120min_20160223_OT.idXML"/>
<UserParam type="string" name="MSGFPlusAdapter:1:mzid_out" value="/tmp/knime_Identification_13595/fs-ZipLo_3-5-35970/000/000/2_0_MSGFPlusAdapter_1/PAMI-176_Mouse_A-J_TMT_40ug_14pctACN_25cm_120min_20160223_OT.mzid"/>
<UserParam type="string" name="MSGFPlusAdapter:1:executable" value="MSGFPlus.jar"/>
<UserParam type="string" name="MSGFPlusAdapter:1:database" value="/home/matteo/knime-workspace/Example_Data/IsobaricTMT/database/sprot_2015.07_mouse_for_decoy.fasta"/>
<UserParam type="float" name="MSGFPlusAdapter:1:precursor_mass_tolerance" value="10.0"/>
<UserParam type="string" name="MSGFPlusAdapter:1:precursor_error_units" value="ppm"/>
<UserParam type="string" name="MSGFPlusAdapter:1:isotope_error_range" value="0,1"/>
<UserParam type="string" name="MSGFPlusAdapter:1:fragment_method" value="from_spectrum"/>
<UserParam type="string" name="MSGFPlusAdapter:1:instrument" value="high_res"/>
<UserParam type="string" name="MSGFPlusAdapter:1:enzyme" value="Trypsin/P"/>
<UserParam type="string" name="MSGFPlusAdapter:1:protocol" value="automatic"/>
<UserParam type="string" name="MSGFPlusAdapter:1:tryptic" value="fully"/>
<UserParam type="int" name="MSGFPlusAdapter:1:min_precursor_charge" value="2"/>
<UserParam type="int" name="MSGFPlusAdapter:1:max_precursor_charge" value="3"/>
<UserParam type="int" name="MSGFPlusAdapter:1:min_peptide_length" value="6"/>
<UserParam type="int" name="MSGFPlusAdapter:1:max_peptide_length" value="40"/>
<UserParam type="int" name="MSGFPlusAdapter:1:matches_per_spec" value="1"/>
<UserParam type="string" name="MSGFPlusAdapter:1:add_features" value="true"/>
<UserParam type="int" name="MSGFPlusAdapter:1:max_mods" value="2"/>
<UserParam type="int" name="MSGFPlusAdapter:1:max_missed_cleavages" value="-1"/>
<UserParam type="int" name="MSGFPlusAdapter:1:tasks" value="0"/>
<UserParam type="stringList" name="MSGFPlusAdapter:1:fixed_modifications" value="[Carbamidomethyl (C),TMT6plex (N-term),TMT6plex (K),Label:13C(6)15N(4) (R)]"/>
<UserParam type="stringList" name="MSGFPlusAdapter:1:variable_modifications" value="[Oxidation (M)]"/>
<UserParam type="string" name="MSGFPlusAdapter:1:legacy_conversion" value="false"/>
<UserParam type="string" name="MSGFPlusAdapter:1:conf" value=""/>
<UserParam type="string" name="MSGFPlusAdapter:1:java_executable" value="java"/>
<UserParam type="int" name="MSGFPlusAdapter:1:java_memory" value="3500"/>
<UserParam type="int" name="MSGFPlusAdapter:1:java_permgen" value="0"/>
<UserParam type="string" name="MSGFPlusAdapter:1:reindex" value="true"/>
<UserParam type="string" name="MSGFPlusAdapter:1:log" value=""/>
<UserParam type="int" name="MSGFPlusAdapter:1:debug" value="0"/>
<UserParam type="int" name="MSGFPlusAdapter:1:threads" value="8"/>
<UserParam type="string" name="MSGFPlusAdapter:1:no_progress" value="false"/>
<UserParam type="string" name="MSGFPlusAdapter:1:force" value="false"/>
<UserParam type="string" name="MSGFPlusAdapter:1:test" value="false"/>
<UserParam type="string" name="MSGFPlusAdapter:1:decoy_string" value="DECOY"/>
<UserParam type="string" name="MSGFPlusAdapter:1:decoy_string_position" value="prefix"/>
<UserParam type="string" name="MSGFPlusAdapter:1:missing_decoy_action" value="error"/>
<UserParam type="string" name="MSGFPlusAdapter:1:write_protein_sequence" value="false"/>
<UserParam type="string" name="MSGFPlusAdapter:1:write_protein_description" value="false"/>
<UserParam type="string" name="MSGFPlusAdapter:1:keep_unreferenced_proteins" value="false"/>
<UserParam type="string" name="MSGFPlusAdapter:1:unmatched_action" value="error"/>
<UserParam type="int" name="MSGFPlusAdapter:1:aaa_max" value="3"/>
<UserParam type="int" name="MSGFPlusAdapter:1:mismatches_max" value="0"/>
<UserParam type="string" name="MSGFPlusAdapter:1:IL_equivalent" value="false"/>
<UserParam type="string" name="MSGFPlusAdapter:1:allow_nterm_protein_cleavage" value="true"/>
<UserParam type="string" name="MSGFPlusAdapter:1:name" value="auto"/>
<UserParam type="string" name="MSGFPlusAdapter:1:specificity" value="auto"/>
<UserParam type="string" name="EnzymeTermSpecificity" value="full"/>
<UserParam type="string" name="SE:MS-GF+" value="Release (v2023.01.12)"/>
<UserParam type="string" name="MS-GF+:db" value="/home/matteo/knime-workspace/Example_Data/IsobaricTMT/database/sprot_2015.07_mouse_for_decoy.fasta"/>
<UserParam type="string" name="MS-GF+:db_version" value=""/>
<UserParam type="string" name="MS-GF+:taxonomy" value=""/>
<UserParam type="string" name="MS-GF+:charges" value="2-3"/>
<UserParam type="string" name="MS-GF+:fixed_modifications" value="Carbamidomethyl (C),TMT6plex (N-term),TMT6plex (K),Label:13C(6)15N(4) (R)"/>
<UserParam type="string" name="MS-GF+:variable_modifications" value="Oxidation (M)"/>
<UserParam type="int" name="MS-GF+:missed_cleavages" value="1000"/>
<UserParam type="float" name="MS-GF+:fragment_mass_tolerance" value="0.0"/>
<UserParam type="string" name="MS-GF+:fragment_mass_tolerance_unit" value="Da"/>
<UserParam type="float" name="MS-GF+:precursor_mass_tolerance" value="10.0"/>
<UserParam type="string" name="MS-GF+:precursor_mass_tolerance_unit" value="ppm"/>
<UserParam type="string" name="MS-GF+:digestion_enzyme" value="Trypsin/P"/>
<UserParam type="int" name="MS-GF+:enzyme_term_specificity" value="2"/>
<UserParam type="string" name="feature_extractor" value="TOPP_PSMFeatureExtractor"/>
<UserParam type="string" name="extra_features" value="MS:1002049,MS:1002050,MSGF:ScoreRatio,MSGF:Energy,MSGF:lnEValue,isotope_error,MSGF:lnExplainedIonCurrentRatio,MSGF:lnNTermIonCurrentRatio,MSGF:lnCTermIonCurrentRatio,MSGF:lnMS2IonCurrent,MSGF:MeanErrorTop7,MSGF:sqMeanErrorTop7,MSGF:StdevErrorTop7"/>
<UserParam type="int" name="Percolator:peptide_level_fdrs" value="0"/>
<UserParam type="int" name="Percolator:protein_level_fdrs" value="0"/>
<UserParam type="int" name="Percolator:generic_feature_set" value="0"/>
<UserParam type="float" name="Percolator:testFDR" value="0.01"/>
<UserParam type="float" name="Percolator:trainFDR" value="0.01"/>
<UserParam type="int" name="Percolator:maxiter" value="10"/>
<UserParam type="int" name="Percolator:subset_max_train" value="0"/>
<UserParam type="int" name="Percolator:quick_validation" value="0"/>
<UserParam type="int" name="Percolator:static" value="0"/>
<UserParam type="string" name="Percolator:weights" value="/tmp/knime_Identification_13595/fs-ZipLo_3-5-35970/000/000/9_0_PercolatorAdapter_6/PAMI-176_Mouse_A-J_TMT_40ug_14pctACN_25cm_120min_20160223_OT.tsv"/>
<UserParam type="string" name="Percolator:init_weights" value=""/>
<UserParam type="string" name="Percolator:default_direction" value=""/>
<UserParam type="float" name="Percolator:cpos" value="0.0"/>
<UserParam type="float" name="Percolator:cneg" value="0.0"/>
<UserParam type="int" name="Percolator:unitnorm" value="0"/>
<UserParam type="int" name="Percolator:override" value="0"/>
<UserParam type="int" name="Percolator:seed" value="1"/>
<UserParam type="int" name="Percolator:doc" value="0"/>
<UserParam type="int" name="Percolator:klammer" value="0"/>
<UserParam type="string" name="Percolator:fasta" value=""/>
<UserParam type="string" name="Percolator:decoy_pattern" value="random"/>
<UserParam type="int" name="Percolator:post_processing_tdc" value="0"/>
<UserParam type="int" name="Percolator:train_best_positive" value="0"/>
<UserParam name="EnzymeTermSpecificity" type="string" value="full" />
</SearchParameters>
<IdentificationRun date="2024-03-15T13:14:58" search_engine="Percolator" search_engine_version="3.05" search_parameters_ref="SP_0" >
<ProteinIdentification score_type="" higher_score_better="true" significance_threshold="0" >
<ProteinHit id="PH_0" accession="sp|Q9Z2X1|HNRPF_MOUSE" score="0.0" sequence="" >
<UserParam type="string" name="target_decoy" value="target"/>
</ProteinHit>
<ProteinHit id="PH_1" accession="sp|Q9Z2S7|T22D3_MOUSE" score="0.0" sequence="" >
<UserParam type="string" name="target_decoy" value="target"/>
</ProteinHit>
<ProteinHit id="PH_2" accession="sp|Q9Z2I0|LETM1_MOUSE" score="0.0" sequence="" >
<UserParam type="string" name="target_decoy" value="target"/>
</ProteinHit>
<ProteinHit id="PH_3" accession="sp|Q9Z2D0|MTMR9_MOUSE" score="0.0" sequence="" >
<UserParam type="string" name="target_decoy" value="target"/>
</ProteinHit>
<ProteinHit id="PH_4" accession="sp|Q9Z204|HNRPC_MOUSE" score="0.0" sequence="" >
<UserParam type="string" name="target_decoy" value="target"/>
</ProteinHit>
<ProteinHit id="PH_5" accession="sp|Q9Z1F9|SAE2_MOUSE" score="0.0" sequence="" >
<UserParam type="string" name="target_decoy" value="target"/>
</ProteinHit>
<ProteinHit id="PH_6" accession="sp|Q9Z1D1|EIF3G_MOUSE" score="0.0" sequence="" >
<UserParam type="string" name="target_decoy" value="target"/>
</ProteinHit>
<ProteinHit id="PH_7" accession="sp|Q9Z0X1|AIFM1_MOUSE" score="0.0" sequence="" >
<UserParam type="string" name="target_decoy" value="target"/>
</ProteinHit>
<ProteinHit id="PH_8" accession="sp|Q9Z0P4|PALM_MOUSE" score="0.0" sequence="" >
<UserParam type="string" name="target_decoy" value="target"/>
</ProteinHit>
<ProteinHit id="PH_9" accession="sp|Q9Z0F7|SYUG_MOUSE" score="0.0" sequence="" >
<UserParam type="string" name="target_decoy" value="target"/>
</ProteinHit>
<ProteinHit id="PH_10" accession="sp|Q9WTQ5|AKA12_MOUSE" score="0.0" sequence="" >
<UserParam type="string" name="target_decoy" value="target"/>
</ProteinHit>
<ProteinHit id="PH_11" accession="sp|Q9R269|PEPL_MOUSE" score="0.0" sequence="" >
<UserParam type="string" name="target_decoy" value="target"/>
</ProteinHit>
<ProteinHit id="PH_12" accession="sp|Q9R1Q7|PLP2_MOUSE" score="0.0" sequence="" >
<UserParam type="string" name="target_decoy" value="target"/>
</ProteinHit>
<ProteinHit id="PH_13" accession="sp|Q9R1P4|PSA1_MOUSE" score="0.0" sequence="" >
<UserParam type="string" name="target_decoy" value="target"/>
</ProteinHit>
<ProteinHit id="PH_14" accession="sp|Q9QZZ6|DERM_MOUSE" score="0.0" sequence="" >
<UserParam type="string" name="target_decoy" value="target"/>
</ProteinHit>
<ProteinHit id="PH_15" accession="sp|Q9QZE7|TSNAX_MOUSE" score="0.0" sequence="" >
<UserParam type="string" name="target_decoy" value="target"/>
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<ProteinHit id="PH_16" accession="sp|Q9QXS6|DREB_MOUSE" score="0.0" sequence="" >
<UserParam type="string" name="target_decoy" value="target"/>
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<UserParam type="string" name="target_decoy" value="target"/>
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<UserParam type="string" name="target_decoy" value="target"/>
</ProteinHit>
<ProteinHit id="PH_19" accession="sp|Q9JL35|HMGN5_MOUSE" score="0.0" sequence="" >
<UserParam type="string" name="target_decoy" value="target"/>
</ProteinHit>
<ProteinHit id="PH_20" accession="sp|Q9JKX6|NUDT5_MOUSE" score="0.0" sequence="" >
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<UserParam type="string" name="target_decoy" value="target"/>
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