| Previous changeset 20:837224ad1694 (2023-01-31) Next changeset 22:9c52362ae7bb (2024-03-18) |
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Commit message:
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 419e4f6608f60f0d73987b890d6b7f8854e874fb |
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modified:
macros.xml maxquant.xml maxquant_mqpar.xml test-data/01/combined/txt/msms.txt test-data/01/combined/txt/mzTab.mzTab test-data/01/combined/txt/parameters.txt test-data/01/mqpar.xml test-data/02/mqpar.xml test-data/03/mqpar.xml test-data/04/mqpar.xml test-data/05/mqpar.xml test-data/06/mqpar.xml test-data/07/mqpar.xml test-data/08/combined/txt/proteinGroups.txt test-data/08/mqpar.xml test-data/09/combined/txt/msmsScans.txt test-data/10/mqpar.xml test-data/mqpar/mqpar.xml test-data/mqpar/txt/allPeptides.txt test-data/mqpar/txt/mqpar.xml test-data/mqpar/txt/mzRange.txt test-data/mqpar/txt/parameters.txt test-data/mqpar/txt/summary.txt |
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removed:
test-data/01/combined/txt/allPeptides.txt test-data/01/combined/txt/evidence.txt test-data/01/combined/txt/modificationSpecificPeptides.txt test-data/01/combined/txt/msmsScans.txt test-data/01/combined/txt/mzRange.txt test-data/01/combined/txt/peptideSection.txt test-data/01/combined/txt/peptides.txt test-data/01/combined/txt/proteinGroups.txt test-data/01/combined/txt/summary.txt test-data/07/combined/txt/report_v1.0.10_combined.pdf |
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| diff -r 837224ad1694 -r 8934bc76bb52 macros.xml --- a/macros.xml Tue Jan 31 18:14:40 2023 +0000 +++ b/macros.xml Mon Jun 19 17:02:17 2023 +0000 |
| [ |
| b'@@ -1,9 +1,10 @@\n <?xml version="1.0" ?>\n <macros>\n- <token name="@VERSION@">1.6.17.0</token>\n- <token name="@VERSION_SUFFIX@">7</token>\n- <token name="@VERSION_SUFFIX_MQPAR@">2</token>\n- <token name="@VERSION_PTXQC@">1.0.10</token>\n+ <token name="@PROFILE@">21.05</token>\n+ <token name="@VERSION@">2.0.3.0</token>\n+ <token name="@VERSION_SUFFIX@">0</token>\n+ <token name="@VERSION_SUFFIX_MQPAR@">0</token>\n+ <token name="@VERSION_PTXQC@">1.0.16</token>\n <token name="@SUBSTITUTION_RX@">[^\\w\\-\\s\\.]</token>\n <token name="@TMT2PLEX@">\n - [TMT2plex-Lys126,TMT2plex-Nter126,0,0,0,0,True]\n@@ -90,8 +91,8 @@\n <xml name="requirements">\n <requirements>\n <requirement type="package" version="@VERSION@">maxquant</requirement>\n- <requirement type="package" version="3.7">python</requirement>\n- <requirement type="package" version="5.1.2">pyyaml</requirement>\n+ <requirement type="package" version="5.4.1">pyyaml</requirement>\n+ <requirement type="package" version="3.1.418">dotnet</requirement>\n <requirement type="package" version="@VERSION_PTXQC@">r-ptxqc</requirement>\n <requirement type="package" version="1.32">tar</requirement>\n </requirements>\n@@ -116,25 +117,25 @@\n AddPageNumbers: \'on\'\n File:\n Parameters:\n- #if $qc.do_it:\n+ #if $qc.do_it == "true":\n enabled: ${qc.parameters}\n #end if\n Summary:\n- #if $qc.do_it:\n+ #if $qc.do_it == "true":\n enabled: ${qc.summary}\n #end if\n IDRate:\n Thresh_bad_num: 20.0\n Thresh_great_num: 35.0\n ProteinGroups:\n- #if $qc.do_it:\n+ #if $qc.do_it == "true":\n enabled: ${qc.proteingroups}\n #end if\n RatioPlot:\n LabelIncThresh_num: 4.0\n IntensityThreshLog2_num: 25.0\n Evidence:\n- #if $qc.do_it:\n+ #if $qc.do_it == "true":\n enabled: ${qc.evidence}\n #end if\n ProteinCountThresh_num: 3500.0\n@@ -161,11 +162,11 @@\n firstSearch_outOfCalWarnSD_num: 2.0\n MQpar_mainSearchTol_num: 4.5\n MsMs:\n- #if $qc.do_it:\n+ #if $qc.do_it == "true":\n enabled: ${qc.msms}\n #end if\n MsMsScans:\n- #if $qc.do_it:\n+ #if $qc.do_it == "true":\n enabled: ${qc.msmsscans}\n #end if\n IonInjectionThresh_num: 10.0\n@@ -222,7 +223,10 @@\n </xml>\n <xml name="ptxqc-opts">\n <conditional name="qc">\n- <param name="do_it" label="Generate PTXQC (proteomics quality control pipeline) report? (experimental setting)" type="boolean" checked="false"/>\n+ <param name="do_it" label="Generate PTXQC (proteomics quality control pipeline) report? (experimental setting)" type="select">\n+ <option value="true">True</option>\n+ <option value="false" selected="true">False</option>\n+ </param>\n <when value="true">\n <param name="parameters" type="boolean" checked="true" label="use parameters.txt?" truevalue="yes" falsevalue="no"/>\n <param name="summary" type="boolean" checked="true" label="use summary.txt?" truevalue="yes" falsevalue="no"/>\n@@ -234,6 +238,18 @@\n <when value="false"/>\n </conditional>\n </xml>\n+\n+ <xml name="output" tokens="name,label" token_format="tabular">\n+ <data format="@FORMAT@" label="${on_string}: @LABEL@" name="@NAME@">\n+ <filter>\'@NAME@\' in output_opts[\'output\']</filter>\n+ </data>\n+ </xml>\n+ <xml name="output_from_wdir" tokens="name,label" toke'..b'bel="yaml config file"/>\n <data format="pdf" label="PTXQC report for ${on_string}" name="ptxqc_report">\n- <filter>qc[\'do_it\'] == True</filter>\n+ <filter>qc[\'do_it\'] == "true"</filter>\n </data>\n </outputs>\n </xml>\n@@ -853,6 +869,67 @@\n <expand macro="mod_option" value="TMTpro18plex-Lys134C"/>\n <expand macro="mod_option" value="TMTpro18plex-Lys135N"/>\n </xml>\n+\n+ <xml name="reporter_ion_macro">\n+ <conditional name="iso_labels">\n+ <param name="labeling" type="select" label="isobaric labeling"\n+ help="Select one of the standard labelings (correction factors are zero) or create a custom labeling.">\n+ <option value="custom">custom</option>\n+ <option value="tmt2plex">TMT2plex</option>\n+ <option value="tmt6plex">TMT6plex</option>\n+ <option value="tmt8plex">TMT8plex</option>\n+ <option value="tmt10plex">TMT10plex</option>\n+ <option value="tmt11plex">TMT11plex</option>\n+ <option value="tmtpro16plex">TMTpro16plex</option>\n+ <option value="tmtpro18plex">TMTpro18plex</option>\n+ <option value="itraq4plex">iTRAQ4plex</option>\n+ <option value="itraq8plex">iTRAQ8plex</option>\n+ <option value="iodotmt6plex">iodoTMT6plex</option>\n+ </param>\n+ <when value="tmt2plex"/>\n+ <when value="tmt6plex"/>\n+ <when value="tmt8plex"/>\n+ <when value="tmt10plex"/>\n+ <when value="tmt11plex"/>\n+ <when value="tmtpro16plex"/>\n+ <when value="tmtpro18plex"/>\n+ <when value="itraq4plex"/>\n+ <when value="itraq8plex"/>\n+ <when value="iodotmt6plex"/>\n+ <when value="custom">\n+ <repeat name="iso_label" title="Isobaric Label" min="1" default="1">\n+ <param name="internallabel" type="select" label="internal label" help="contains Lys">\n+ <expand macro="iso_labels"/>\n+ </param>\n+ <param name="terminallabel" type="select" label="terminal label" help="contains Nter">\n+ <option value="">None</option>\n+ <expand macro="iso_labels"/>\n+ </param>\n+ <param name="cm2" type="float" label="correction factor -2%" value="0.0"/>\n+ <param name="cm1" type="float" label="correction factor -1%" value="0.0"/>\n+ <param name="cp1" type="float" label="correction factor +1%" value="0.0"/>\n+ <param name="cp2" type="float" label="correction factor +2%" value="0.0"/>\n+ <param type="boolean" name="tmtlike" checked="false"\n+ label="TMT-like"\n+ truevalue="True" falsevalue="False"/>\n+ </repeat>\n+ </when>\n+ </conditional>\n+ <conditional name="filter_by_pif">\n+ <param name="filter_pif" type="select" label="Filter by PIF"\n+ help="If checked, quantified PSMs will be filtered by their precursor intensity fraction to avoid using peptides that clearly suffer from co-fragmentation with other peptide species.">\n+ <option value="True">True</option>\n+ <option value="False" selected="true">False</option>\n+ </param>\n+ <when value="True">\n+ <param name="reporter_pif" type="float" label="Minimum reporter PIF" value="0.75" min="0"\n+ max="1"\n+ help="MS/MS spectra with a lower value for the PIF will be discarded for isobaric label quantification."/>\n+ </when>\n+ <when value="False"/>\n+ </conditional>\n+ </xml>\n+\n <xml name="citations">\n <citations>\n <citation type="bibtex">\n' |
| b |
| diff -r 837224ad1694 -r 8934bc76bb52 maxquant.xml --- a/maxquant.xml Tue Jan 31 18:14:40 2023 +0000 +++ b/maxquant.xml Mon Jun 19 17:02:17 2023 +0000 |
| [ |
| b'@@ -1,15 +1,5 @@\n-<tool id="maxquant" name="MaxQuant" version="@VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">\n+<tool id="maxquant" name="MaxQuant" version="@VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">\n <macros>\n- <xml name="output" token_format="tabular" token_label="default description" token_name="default">\n- <data format="@FORMAT@" label="@LABEL@ for ${on_string}" name="@NAME@">\n- <filter>\'@NAME@\' in output_opts[\'output\']</filter>\n- </data>\n- </xml>\n- <xml name="output_from_wdir" token_ext="txt" token_format="tabular" token_label="default description" token_name="default">\n- <data format="@FORMAT@" from_work_dir="combined/txt/@NAME@.@EXT@" label="@LABEL@ for ${on_string}" name="@NAME@">\n- <filter>\'@NAME@\' in output_opts[\'output\']</filter>\n- </data>\n- </xml>\n <import>macros.xml</import>\n </macros>\n <expand macro="requirements"/>\n@@ -20,12 +10,6 @@\n #import re\n maxquant -c mqpar.xml 2>/dev/null ## MQ writes success of creation to stderr\n \n- ## Workaround for wrong MQ version in MaxQuantCmd.exe created mqpar.xml (1.6.5.0 instead of 1.6.17.0)\n- ## Should be removed as soon as MQ is updated with a fixed version\n- &&\n- sed -i -E \'s:(maxQuantVersion>)1.6.5.0(<):\\1\'1.6.17.0\'\\2:\' mqpar.xml\n- ## ==============================================================================================\n-\n #if \'config\' in $output_opts.output:\n &&\n cp \'$mq_conf\' \'$config\'\n@@ -70,7 +54,7 @@\n tar -zcf \'$output_all\' ./combined/txt\n #end if\n \n- #if $qc.do_it:\n+ #if $qc.do_it == \'true\':\n &&\n Rscript \'$qr\' \'$qr_yaml\'\n #if \'log\' in $output_opts.output:\n@@ -513,118 +497,10 @@\n </param>\n </when>\n <when value="reporter_ion_ms2">\n- <conditional name="iso_labels">\n- <param name="labeling" type="select" label="isobaric labeling"\n- help="Select one of the standard labelings (correction factors are zero) or create a custom labeling.">\n- <option value="custom">custom</option>\n- <option value="tmt2plex">TMT2plex</option>\n- <option value="tmt6plex">TMT6plex</option>\n- <option value="tmt8plex">TMT8plex</option>\n- <option value="tmt10plex">TMT10plex</option>\n- <option value="tmt11plex">TMT11plex</option>\n- <option value="tmtpro16plex">TMTpro16plex</option>\n- <option value="tmtpro18plex">TMTpro18plex</option>\n- <option value="itraq4plex">iTRAQ4plex</option>\n- <option value="itraq8plex">iTRAQ8plex</option>\n- <option value="iodotmt6plex">iodoTMT6plex</option>\n- </param>\n- <when value="tmt2plex"/>\n- <when value="tmt6plex"/>\n- <when value="tmt8plex"/>\n- <when value="tmt10plex"/>\n- <when value="tmt11plex"/>\n- <when value="tmtpro16plex"/>\n- <when value="tmtpro18plex"/>\n- <when value="itraq4plex"/>\n- <when value="itraq8plex"/>\n- <when value="iodotmt6plex"/>\n- <when value="custom">\n- <repeat name="iso_label" title="Isobaric Label" min="1" default="1">\n- <param name="internallabel" type="select" label="internal label" help="contains Lys">\n- <expand macro="iso_labels"/>\n- </param>\n- <param name="terminallabel" typ'..b'True" />\n </assert_contents>\n </output>\n- <output name="mqpar" file="05/mqpar.xml" lines_diff="4">\n+ <output name="mqpar" file="05/mqpar.xml" lines_diff="6">\n <assert_contents>\n <has_text_matching expression=".matchBetweenRuns.True.\\/matchBetweenRuns." />\n </assert_contents>\n </output>\n </test>\n- <!-- silac + fractions with experimental design template, testing yaml conf file and mqpar.xml only -->\n+ <!-- 6 silac + fractions with experimental design template, testing yaml conf file and mqpar.xml only -->\n <test expect_num_outputs="2">\n <param name="ftype" value=".mzxml" />\n <param name="fasta_files" value="bsa.fasta" />\n@@ -914,7 +827,7 @@\n <output name="config" file="04/config.yml" lines_diff="2" />\n <output name="mqpar" file="04/mqpar.xml" lines_diff="12" />\n </test>\n- <!-- PTXQC Test -->\n+ <!-- 7 PTXQC Test -->\n <test expect_num_outputs="3">\n <param name="ftype" value=".mzxml" />\n <param name="fasta_files" value="tmt_data.fasta" />\n@@ -931,14 +844,20 @@\n </conditional>\n </conditional>\n </repeat>\n- <param name="do_it" value="True" />\n+ <param name="do_it" value="true" />\n <param name="output" value="config,mqpar" />\n <output name="config" file="07/config.yml" lines_diff="2" />\n <!-- high difference due to unconsistant xml formatting in MQ -->\n- <output name="mqpar" file="07/mqpar.xml" lines_diff="4" />\n- <output name="ptxqc_report" file="07/combined/txt/report_v1.0.10_combined.pdf" compare="sim_size" />\n+ <output name="mqpar" file="07/mqpar.xml" lines_diff="6" />\n+ <output name="ptxqc_report">\n+ <assert_contents>\n+ <has_line line="%PDF-1.4"/>\n+ <!-- was 50k for older versions, now 88K (for 30-pages) -->\n+ <has_size min="40K" max="100K"/>\n+ </assert_contents>\n+ </output>\n </test>\n- <!-- TMTpro16plex test -->\n+ <!-- 8 TMTpro16plex test -->\n <test expect_num_outputs="3">\n <param name="ftype" value=".mzxml" />\n <param name="fasta_files" value="tmt_data_16.fasta" />\n@@ -955,14 +874,14 @@\n </conditional>\n </conditional>\n </repeat>\n- <param name="do_it" value="False" />\n+ <param name="do_it" value="false" />\n <param name="output" value="config,mqpar,proteinGroups" />\n <output name="config" file="08/config.yml" lines_diff="2" />\n <!-- high difference due to unconsistant xml formatting in MQ -->\n <output name="mqpar" file="08/mqpar.xml" lines_diff="24" />\n <output name="proteinGroups" file="08/combined/txt/proteinGroups.txt" />\n </test>\n- <!-- TMTpro18plex test -->\n+ <!-- 9 TMTpro18plex test -->\n <test expect_num_outputs="2">\n <param name="ftype" value=".mzxml" />\n <param name="fasta_files" value="tmt_data_18.fasta" />\n@@ -979,7 +898,7 @@\n </conditional>\n </conditional>\n </repeat>\n- <param name="do_it" value="False" />\n+ <param name="do_it" value="false" />\n <param name="output" value="msmsScans" />\n <output name="msmsScans" file="09/combined/txt/msmsScans.txt">\n <assert_contents>\n@@ -987,7 +906,7 @@\n </assert_contents>\n </output>\n </test>\n- <!-- Thermo RAW file test -->\n+ <!-- 10 Thermo RAW file test -->\n <test expect_num_outputs="2">\n <param name="ftype" value=".thermo.raw" />\n <param name="fasta_files" value="bsa.fasta" />\n' |
| b |
| diff -r 837224ad1694 -r 8934bc76bb52 maxquant_mqpar.xml --- a/maxquant_mqpar.xml Tue Jan 31 18:14:40 2023 +0000 +++ b/maxquant_mqpar.xml Mon Jun 19 17:02:17 2023 +0000 |
| [ |
| @@ -1,15 +1,5 @@ -<tool id="maxquant_mqpar" name="MaxQuant (using mqpar.xml)" version="@VERSION@+galaxy@VERSION_SUFFIX_MQPAR@" profile="21.05"> +<tool id="maxquant_mqpar" name="MaxQuant (using mqpar.xml)" version="@VERSION@+galaxy@VERSION_SUFFIX_MQPAR@" profile="@PROFILE@"> <macros> - <xml name="output" token_format="tabular" token_label="default description" token_name="default"> - <data format="@FORMAT@" label="@LABEL@ for ${on_string}" name="@NAME@"> - <filter>'@NAME@' in output</filter> - </data> - </xml> - <xml name="output_from_wdir" token_ext="txt" token_format="tabular" token_label="default description" token_name="default"> - <data format="@FORMAT@" from_work_dir="combined/txt/@NAME@.@EXT@" label="@LABEL@ for ${on_string}" name="@NAME@"> - <filter>'@NAME@' in output</filter> - </data> - </xml> <import>macros.xml</import> </macros> <expand macro="requirements"/> @@ -50,7 +40,7 @@ tar -zcf '$output_all' ./combined/txt #end if - #if $qc.do_it: + #if $qc.do_it == 'true': && Rscript '$qr' '$qr_yaml' #if 'log' in $output: @@ -148,7 +138,7 @@ <param name="identifier_parse_rule" value=">([^\s]*)" /> <param name="description_parse_rule" value=">(.*)" /> <param name="mqpar_input" value="mqpar/mqpar.xml" /> - <param name="output" value="evidence,msms,mzTab,allPeptides,msmsScans,mzRange,parameters,peptides,peptideSection,proteinGroups,summary,modificationSpecificPeptides,mqpar,output_all" /> + <param name="output" value="evidence,msms,mzTab,allPeptides,msmsScans,mzRange,parameters,peptides,proteinGroups,summary,modificationSpecificPeptides,mqpar,output_all" /> <output name="evidence"> <assert_contents> <has_text text="AEFVEVTK" /> |
| b |
| diff -r 837224ad1694 -r 8934bc76bb52 test-data/01/combined/txt/allPeptides.txt --- a/test-data/01/combined/txt/allPeptides.txt Tue Jan 31 18:14:40 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| b'@@ -1,159 +0,0 @@\n-Raw file\tType\tCharge\tm/z\tMass\tUncalibrated m/z\tNumber of data points\tNumber of scans\tNumber of isotopic peaks\tPIF\tMass fractional part\tMass deficit\tMass precision [ppm]\tMax intensity m/z 0\tRetention time\tRetention length\tRetention length (FWHM)\tMin scan number\tMax scan number\tIdentified\tReverse\tMS/MS IDs\tSequence\tLength\tModifications\tModified sequence\tProteins\tScore\tPEP\tIntensity\tIntensities\tIsotope pattern\tMS/MS Count\tMSMS Scan Numbers\tMSMS Isotope Indices\n-BSA_min_23\tMULTI\t3\t710.69967\t2129.0772\t710.69967\t5\t3\t2\t\t0.0771934\t0.0578179145768445\t1.19977\t711.033930698172\t0.0366\t8.26\t0\t1\t25\t\t\t-1\t\t0\t\t\t\t0\tNaN\t27774\t0;16823.720703125;10726.12109375;6644.5966796875;0\t7737.3974609375;9086.3232421875\t0\t\t\n-BSA_min_23\tMULTI\t3\t1567.4354\t4699.2845\t1567.4354\t5\t3\t2\t\t0.284515\t0.0828443190730468\t8.12054\t1568.10387245715\t0.0671\t8.26\t0\t1\t25\t\t\t-1\t\t0\t\t\t\t0\tNaN\t137800\t0;23479.5932617188;59085.9194335938;20990.259765625;0\t0;0;53540.3203125;7305.36279296875\t0\t\t\n-BSA_min_23\tMULTI\t2\t466.26818\t930.5218\t466.26818\t6\t4\t2\t\t0.521798\t0.0537578274037287\t1.5007\t466.26850803291\t0.107\t10.3\t0\t1\t31\t\t\t-1\t\t0\t\t\t\t0\tNaN\t33623\t0;16896.8359375;13251.4482421875;29638.681640625;21903.5859375;0\t22962.34375;6676.337890625\t0\t\t\n-BSA_min_23\tMULTI\t2\t835.80692\t1669.5993\t835.80692\t7\t4\t2\t\t0.599289\t-0.208726671340173\t1.21705\t835.807035746435\t0.107\t10.3\t0\t1\t31\t\t\t-1\t\t0\t\t\t\t0\tNaN\t35433\t0;14611.8764648438;18125.6357421875;25099.0166015625;15365.583984375;0\t16483.943359375;8615.0732421875\t0\t\t\n-BSA_min_23\tMULTI\t2\t889.42648\t1776.8384\t889.42648\t6\t3\t2\t\t0.8384\t-0.01894535091742\t2.99291\t889.927320499287\t0.107\t8.26\t0\t1\t25\t\t\t-1\t\t0\t\t\t\t0\tNaN\t24724\t0;9125.99072265625;13286.1201171875;16742.716796875;0\t7208.8173828125;9533.8994140625\t0\t\t\n-BSA_min_23\tMULTI\t2\t378.70717\t755.39979\t378.70717\t4\t2\t2\t\t0.399787\t0.0123026053665853\t2.94983\t378.7066995797\t0.119\t6.22\t0\t13\t31\t\t\t-1\t\t0\t\t\t\t0\tNaN\t17167\t0;15764.96875;12169.2568359375;0\t9865.826171875;5910.52587890625\t0\t\t\n-BSA_min_23\tMULTI\t6\t456.58136\t2733.4445\t456.58136\t6\t5\t2\t\t0.444506\t0.147121855573914\t1.38811\t456.748107866223\t0.139\t12.6\t0\t7\t43\t\t\t-1\t\t0\t\t\t\t0\tNaN\t36615\t0;9077.5439453125;13902.0874023438;19992.689453125;13010.4306640625;0;0\t0;13844.125;6148.564453125\t1\t8\t1\n-BSA_min_23\tMULTI\t2\t701.87367\t1401.7328\t701.87367\t4\t2\t2\t\t0.732781\t0.0479841303626927\t2.12222\t701.87287295525\t0.139\t6.22\t0\t13\t31\t\t\t-1\t\t0\t\t\t\t0\tNaN\t19734\t0;11736.2470703125;14934.2939453125;0\t8433.541015625;6500.7529296875\t0\t\t\n-BSA_min_23\tMULTI\t2\t903.84665\t1805.6788\t903.84665\t14\t5\t3\t\t0.678752\t-0.191860390769989\t0.59721\t903.846381489202\t0.128\t12.5\t0\t1\t37\t\t\t-1\t\t0\t\t\t\t0\tNaN\t90093\t0;22660.5712890625;48080.4096679688;66770.5043945312;78759.361328125;39740.7744140625;0\t39216.41796875;30181.7421875;16944.533203125\t1\t27\t0\n-BSA_min_23\tMULTI\t3\t487.53462\t1459.582\t487.53462\t16\t8\t3\t\t0.582038\t-0.129370140185074\t0.666208\t487.53461224021\t0.133\t19\t0\t1\t55\t\t\t-1\t\t0\t\t\t\t0\tNaN\t85737\t0;7211.73095703125;32638.8959960938;79787.74609375;74581.1875;40743.359375;31912.87890625;10748.6064453125;5496.4296875;0\t40288.40234375;32200.93359375;13735.64453125\t1\t33\t1\n-BSA_min_23\tMULTI\t3\t583.22015\t1746.6386\t583.22015\t7\t4\t2\t\t0.638627\t-0.204827158799844\t2.32471\t583.220239813966\t0.176\t10.5\t0\t7\t37\t\t\t-1\t\t0\t\t\t\t0\tNaN\t42691\t0;4036.83081054688;17411.11328125;19834.8046875;29221.802734375;0\t17431.560546875;11790.2421875\t0\t\t\n-BSA_min_23\tMULTI\t2\t730.79903\t1459.5835\t730.79903\t10\t6\t2\t\t0.583509\t-0.127899819310187\t0.552215\t730.799136547346\t0.151\t14.7\t0\t1\t43\t\t\t-1\t\t0\t\t\t\t0\tNaN\t78416\t0;5839.765625;27434.9599609375;42471.279296875;58278.560546875;32345.4384765625;15650.7568359375;0\t39553.00390625;19513.171875\t1\t29\t0\n-BSA_min_23\tMULTI\t2\t996.94429\t1991.874\t996.94429\t15\t13\t2\t\t0.874035\t-0.0822274555589502\t0.962151\t997.446155697545\t0.123\t28.7\t0\t7\t87\t\t\t-1\t\t0\t\t\t\t0\tNaN\t45220\t0;20391.6489257812;28769.4560546875;39230.09765625;19622.400390625;13010.86328125;12843.5712890625;12676.279296875;15763.220703125;13381.2666015625;18258.947265625;16122.5546875;0;0;0\t20617.05859375;21871.28515625\t0\t\t\n-BSA_min_23\tMULTI\t1\t553.54774\t552.54046\t553.54774\t5\t4\t2\t\t0.540462\t0.2'..b'\t121882.3984375;41811.76171875\t0\t\t\n-BSA_min_23\tMULTI\t2\t609.30165\t1216.5887\t609.30165\t5\t3\t2\t\t0.588749\t-0.0108816439892507\t3.20128\t609.801905531048\t0.578\t6.09\t0\t87\t99\t\t\t-1\t\t0\t\t\t\t0\tNaN\t18598\t0;6848.39208984375;14504.1098632812;15519.5483398438;0\t5654.28662109375;10022.16015625\t0\t\t\n-BSA_min_23\tMULTI\t2\t626.82568\t1251.6368\t626.82568\t8\t5\t2\t\t0.636812\t0.021059465134158\t1.01648\t627.327160354538\t0.556\t10.1\t0\t75\t99\t\t\t-1\t\t0\t\t\t\t0\tNaN\t20589\t0;7513.7216796875;15837.8994140625;13457.0910644531;10665.5668945312;6652.02783203125;0\t7548.9072265625;10244.0595703125\t0\t\t\n-BSA_min_23\tMULTI\t3\t635.60201\t1903.7842\t635.60201\t11\t4\t3\t\t0.784198\t-0.131542440920157\t0.776339\t635.601854227925\t0.587\t8.25\t0\t81\t99\t\t\t-1\t\t0\t\t\t\t0\tNaN\t110200\t0;11539.9194335938;49907.1435546875;64455.1904296875;94715.8671875;0\t41372.8828125;37360.796875;15982.1875\t1\t93\t0\n-BSA_min_23\tMULTI\t2\t722.29286\t1442.5712\t722.29286\t11\t4\t3\t\t0.571174\t-0.132409118188889\t0.62138\t722.794557009268\t0.587\t8.25\t0\t81\t99\t\t\t-1\t\t0\t\t\t\t0\tNaN\t89007\t0;19382.1572265625;29263.3842773438;56304.751953125;72047.59765625;0\t31798.40625;40249.19140625;9051.69140625\t2\t94;97\t0;0\n-BSA_min_23\tMULTI\t2\t731.29826\t1460.582\t731.29826\t9\t5\t2\t\t0.581962\t-0.129906048768817\t1.03253\t731.799523381077\t0.526\t10.1\t0\t75\t99\t\t\t-1\t\t0\t\t\t\t0\tNaN\t29515\t0;10700.2763671875;21935.4814453125;17981.1000976562;13056.220703125;17802.30078125;0\t11073.208984375;11301.125\t1\t90\t0\n-BSA_min_23\tMULTI\t2\t772.82766\t1543.6408\t772.82766\t5\t3\t2\t\t0.640774\t-0.109301011002572\t1.18653\t772.827340413045\t0.587\t6.09\t0\t87\t99\t\t\t-1\t\t0\t\t\t\t0\tNaN\t33591\t0;6804.890625;12703.8696289062;24380.708984375;0\t15360.51953125;9020.189453125\t0\t\t\n-BSA_min_23\tMULTI\t3\t776.67069\t2326.9902\t776.67069\t7\t3\t3\t\t0.990247\t-0.120168276232107\t2.2861\t777.004331643663\t0.571\t6.09\t0\t87\t99\t\t\t-1\t\t0\t\t\t\t0\tNaN\t37369\t0;6977.5546875;29906.751953125;25277;0\t9063.5791015625;14645.7783203125;12678.326171875\t0\t\t\n-BSA_min_23\tMULTI\t1\t837.43636\t836.42908\t837.43636\t7\t4\t2\t\t0.429084\t0.00432657079568344\t1.1961\t837.436103089852\t0.587\t8.25\t0\t81\t99\t\t\t-1\t\t0\t\t\t\t0\tNaN\t73507\t0;8795.1123046875;28166.4892578125;33590.7690429688;65961.154296875;0\t53311.69140625;12649.462890625\t0\t\t\n-BSA_min_23\tMULTI\t2\t882.84611\t1763.6777\t882.84611\t12\t7\t3\t\t0.677666\t-0.173625559149741\t0.52725\t882.846072087715\t0.563\t13.8\t0\t65\t99\t\t\t-1\t\t0\t\t\t\t0\tNaN\t1184700\t0;10685.890625;57645.44140625;185231.5625;292455.5625;750275.78125;1040647.75;871335.640625;0\t494015.65625;379948.71875;166683.375\t1\t100\t0\n-BSA_min_23\tMULTI\t2\t886.81224\t1771.6099\t886.81224\t8\t5\t2\t\t0.609921\t-0.245019278866494\t1.59077\t887.31412154531\t0.576\t10.1\t0\t75\t99\t\t\t-1\t\t0\t\t\t\t0\tNaN\t29285\t0;5249.1533203125;6298.3564453125;13226.2900390625;17856.4375;20045.5546875;0\t8890.65234375;11784.896484375\t0\t\t\n-BSA_min_23\tMULTI\t1\t899.44874\t898.44147\t899.44874\t10\t6\t2\t\t0.441465\t-0.0118176683625961\t0.574049\t899.44868329937\t0.563\t11.9\t0\t71\t99\t\t\t-1\t\t0\t\t\t\t0\tNaN\t93690\t0;10259.021484375;11104.9755859375;38988.1611328125;51494.2109375;83477.83203125;72926.943359375;0\t61125.3359375;22352.49609375\t0\t\t\n-BSA_min_23\tMULTI\t2\t973.90466\t1945.7948\t973.90466\t7\t4\t2\t\t0.794758\t-0.140307405074736\t1.26096\t973.904958275679\t0.587\t8.25\t0\t81\t99\t\t\t-1\t\t0\t\t\t\t0\tNaN\t67411\t0;22343.408203125;30602.4375;39709.193359375;30783.283203125;0\t30783.283203125;12774.3359375\t0\t\t\n-BSA_min_23\tMULTI\t1\t1012.4647\t1011.4574\t1012.4647\t10\t6\t2\t\t0.457398\t-0.0478720617985573\t0.652247\t1012.46465963589\t0.58\t11.9\t0\t71\t99\t\t\t-1\t\t0\t\t\t\t0\tNaN\t45820\t0;6566.83447265625;5892.9794921875;22179.6865234375;26302.4379882812;35693.482421875;39795.4755859375;0\t31461.541015625;12683.193359375\t0\t\t\n-BSA_min_23\tMULTI\t2\t1044.9323\t2087.8501\t1044.9323\t6\t4\t2\t\t0.850139\t-0.150272249905811\t2.18201\t1045.43259299012\t0.587\t8.25\t0\t81\t99\t\t\t-1\t\t0\t\t\t\t0\tNaN\t22421\t0;6181.01806640625;6017.2158203125;11961.13671875;13880.3842773438;0\t6740.865234375;7139.51904296875\t0\t\t\n-BSA_min_23\tMULTI\t1\t1164.5167\t1163.5094\t1164.5167\t6\t4\t2\t\t0.509441\t-0.0657732965746618\t0.927403\t1164.51651446826\t0.569\t8.25\t0\t81\t99\t\t\t-1\t\t0\t\t\t\t0\tNaN\t30441\t0;5882.703125;19118.6171875;25656.2758789062;16791.0786132812;0\t19902.078125;6989.12060546875\t0\t\t\n' |
| b |
| diff -r 837224ad1694 -r 8934bc76bb52 test-data/01/combined/txt/evidence.txt --- a/test-data/01/combined/txt/evidence.txt Tue Jan 31 18:14:40 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,7 +0,0 @@ -Sequence Length Modifications Modified sequence Oxidation (M) Probabilities Oxidation (M) Score Diffs Oxidation (M) Missed cleavages Proteins Leading proteins Leading razor protein Type Raw file Experiment MS/MS m/z Charge m/z Mass Uncalibrated - Calibrated m/z [ppm] Uncalibrated - Calibrated m/z [Da] Mass error [ppm] Mass error [Da] Uncalibrated mass error [ppm] Uncalibrated mass error [Da] Max intensity m/z 0 Retention time Retention length Calibrated retention time Calibrated retention time start Calibrated retention time finish Retention time calibration Match time difference Match m/z difference Match q-value Match score Number of data points Number of scans Number of isotopic peaks PIF Fraction of total spectrum Base peak fraction PEP MS/MS count MS/MS scan number Score Delta score Combinatorics Intensity Reverse Potential contaminant id Protein group IDs Peptide ID Mod. peptide ID MS/MS IDs Best MS/MS Oxidation (M) site IDs Taxonomy IDs -DSFDIIK 7 Unmodified _DSFDIIK_ 0 0 CON__ENSEMBL:ENSBTAP00000016046 CON__ENSEMBL:ENSBTAP00000016046 CON__ENSEMBL:ENSBTAP00000016046 MULTI-MSMS BSA_min_23 BSA_min_23.mzXML 419.221313476563 2 419.221268 836.427984 0 0 0.51923 0.00021767 0.51923 0.00021767 419.22139467134 0.58669 0.13742 0.58669 0.46121 0.59862 0 11 4 3 0 0 0 0.010549 1 96 0 0 1 769840 + 0 1 0 0 0 0 -LLESEECR 8 Unmodified _LLESEECR_ 0 0 CON__Q14CN4-1;CON__Q3SY84;CON__Q9R0H5 CON__Q14CN4-1 CON__Q14CN4-1 MSMS BSA_min_23 BSA_min_23.mzXML 518.238220214844 2 518.242406 1034.47026 NaN NaN NaN NaN NaN NaN NaN 0.50957 1 0.50957 0.0095717 1.0096 0 0 0 0 0.0075205 1 86 1.6313 1.6313 1 + 1 5 1 1 1 1 -LVTDLTK 7 Unmodified _LVTDLTK_ 0 0 bsa;CON__P02769;CON__P02768-1 bsa bsa MSMS BSA_min_23 BSA_min_23.mzXML 395.239288330078 2 395.239461 788.46437 NaN NaN NaN NaN NaN NaN NaN 0.010013 1 0.010013 -0.48999 0.51001 0 0 0 0 0.0046553 1 2 0 0 1 + 2 3 2 2 2 2 -QLELEKQLEK 10 Unmodified _QLELEKQLEK_ 0 1 CON__ENSEMBL:ENSBTAP00000001528 CON__ENSEMBL:ENSBTAP00000001528 CON__ENSEMBL:ENSBTAP00000001528 MULTI-SECPEP BSA_min_23 BSA_min_23.mzXML 419.221313476563 3 419.906482 1256.69762 0 0 0.05222 2.1927E-05 0.05222 2.1927E-05 419.9067499241 0.32847 0.47559 0.32847 0.12303 0.59862 0 25 14 2 0 0 0 0.011549 1 96 0 0 1 57896 + 3 0 3 3 3 3 -SLSAIRER 8 Unmodified _SLSAIRER_ 0 1 CON__Q03247 CON__Q03247 CON__Q03247 MULTI-SECPEP BSA_min_23 BSA_min_23.mzXML 465.766693115234 2 466.269616 930.524678 0 0 -3.0889 -0.0014403 -3.0889 -0.0014403 466.26850803291 0.10674 0.17216 0.10674 -0.014552 0.15761 0 6 4 2 0 0 0 0.011549 1 17 0 0 1 33623 + 4 4 4 4 4 4 -TLGPWGQR 8 Unmodified _TLGPWGQR_ 0 0 CON__ENSEMBL:ENSBTAP00000018574 CON__ENSEMBL:ENSBTAP00000018574 CON__ENSEMBL:ENSBTAP00000018574 MULTI-MSMS BSA_min_23 BSA_min_23.mzXML 457.746032714844 2 457.745776 913.477 0 0 -0.28247 -0.0001293 -0.28247 -0.0001293 457.745456355006 0.4547 0.40477 0.4547 0.19386 0.59862 -5.5511E-17 18 12 2 0 0 0 0.01108 1 72 0 0 1 62116 + 5 2 5 5 5 5 |
| b |
| diff -r 837224ad1694 -r 8934bc76bb52 test-data/01/combined/txt/modificationSpecificPeptides.txt --- a/test-data/01/combined/txt/modificationSpecificPeptides.txt Tue Jan 31 18:14:40 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,7 +0,0 @@ -Sequence Modifications Mass Mass Fractional Part Protein Groups Proteins Unique (Groups) Unique (Proteins) Oxidation (M) Missed cleavages Experiment BSA_min_23.mzXML Retention time Calibrated retention time Charges PEP MS/MS scan number Raw file Score Delta score Reverse Potential contaminant Intensity Intensity BSA_min_23.mzXML id Protein group IDs Peptide ID Evidence IDs MS/MS IDs Best MS/MS Oxidation (M) site IDs MS/MS Count Taxonomy IDs -DSFDIIK Unmodified 836.42798 0.42798405 1 CON__ENSEMBL:ENSBTAP00000016046 yes yes 0 0 1 0.58669 0.58669 2 0.010549 96 BSA_min_23 0 0 + 769840 769840 0 1 0 0 0 0 1 -LLESEECR Unmodified 1034.4703 0.47025958 5 CON__Q14CN4-1;CON__Q3SY84;CON__Q9R0H5 yes no 0 0 1 0.50957 0.50957 2 0.0075205 86 BSA_min_23 1.6313 1.6313 + 0 0 1 5 1 1 1 1 1 -LVTDLTK Unmodified 788.46437 0.46436956 3 bsa;CON__P02769;CON__P02768-1 yes no 0 0 1 0.010013 0.010013 2 0.0046553 2 BSA_min_23 0 0 + 0 0 2 3 2 2 2 2 1 -QLELEKQLEK Unmodified 1256.6976 0.69761697 0 CON__ENSEMBL:ENSBTAP00000001528 yes yes 0 1 1 0.32847 0.32847 3 0.011549 96 BSA_min_23 0 0 + 57896 57896 3 0 3 3 3 3 0 -SLSAIRER Unmodified 930.52468 0.52467841 4 CON__Q03247 yes yes 0 1 1 0.10674 0.10674 2 0.011549 17 BSA_min_23 0 0 + 33623 33623 4 4 4 4 4 4 0 -TLGPWGQR Unmodified 913.477 0.47699993 2 CON__ENSEMBL:ENSBTAP00000018574 yes yes 0 0 1 0.4547 0.4547 2 0.01108 72 BSA_min_23 0 0 + 62116 62116 5 2 5 5 5 5 1 |
| b |
| diff -r 837224ad1694 -r 8934bc76bb52 test-data/01/combined/txt/msms.txt --- a/test-data/01/combined/txt/msms.txt Tue Jan 31 18:14:40 2023 +0000 +++ b/test-data/01/combined/txt/msms.txt Mon Jun 19 17:02:17 2023 +0000 |
| [ |
| @@ -1,7 +1,7 @@ Raw file Scan number Scan index Sequence Length Missed cleavages Modifications Modified sequence Oxidation (M) Probabilities Oxidation (M) Score diffs Oxidation (M) Proteins Charge Fragmentation Mass analyzer Type Scan event number Isotope index m/z Mass Mass error [ppm] Mass error [Da] Simple mass error [ppm] Retention time PEP Score Delta score Score diff Localization prob Combinatorics PIF Fraction of total spectrum Base peak fraction Precursor full scan number Precursor Intensity Precursor apex fraction Precursor apex offset Precursor apex offset time Matches Intensities Mass deviations [Da] Mass deviations [ppm] Masses Number of matches Intensity coverage Peak coverage Neutral loss level ETD identification type Reverse All scores All sequences All modified sequences Reporter PIF Reporter fraction id Protein group IDs Peptide ID Mod. peptide ID Evidence ID Oxidation (M) site IDs -BSA_min_23 96 77 DSFDIIK 7 0 Unmodified _DSFDIIK_ 0 CON__ENSEMBL:ENSBTAP00000016046 2 CID FTMS MULTI-MSMS 1 0 419.22127 836.42798 0.51923 0.00021767 NaN 0.57043 0.010549 0 0 NaN NaN 1 0 0 0 95 346270.625 0.704625040984097 -1 0.0243583333333334 0 0 0 None Unknown 0 DSFDIIK _DSFDIIK_ 0 1 0 0 0 +BSA_min_23 96 77 DSFDIIK 7 0 Unmodified _DSFDIIK_ 0 CON__ENSEMBL:ENSBTAP00000016046 2 CID FTMS MULTI-MSMS 1 0 419.22127 836.42798 0.51923 0.00021767 NaN 0.57043 0.010549 0 0 NaN NaN 1 0 0 0 95 346270.625 0.704625040984097 -1 0.0243583333333334 0 0 0 None Unknown 0 DSFDIIK _DSFDIIK_ 0 2 0 0 0 BSA_min_23 86 70 LLESEECR 8 0 Unmodified _LLESEECR_ 0 CON__Q14CN4-1;CON__Q3SY84;CON__Q9R0H5 2 CID FTMS MSMS 5 518.24241 1034.4703 NaN NaN NaN 0.50957 0.0075205 1.6313 1.6313 NaN NaN 1 0 0 0 81 10271.2001953125 1 0 0 y6 10 0.0135096433999706 16.6930827476743 809.2958984375 1 0.00309955136291107 0.00847457627118644 None Unknown 1.63126590808724;0;0 LLESEECR;LGSDMEDLR;QLNQEMEK _LLESEECR_;_LGSDMEDLR_;_QLNQEM(Oxidation (M))EK_ 1 5 1 1 1 -BSA_min_23 2 0 LVTDLTK 7 0 Unmodified _LVTDLTK_ 0 bsa;CON__P02769;CON__P02768-1 2 CID FTMS MSMS 1 395.23946 788.46437 NaN NaN NaN 0.010013 0.0046553 0 0 NaN NaN 1 0 0 0 -1 NaN NaN 0 NaN 0 0 0 None Unknown 0;0 LVTDLTK;DSLLTLK _LVTDLTK_;_DSLLTLK_ 2 3 2 2 2 -BSA_min_23 96 77 QLELEKQLEK 10 1 Unmodified _QLELEKQLEK_ 0 CON__ENSEMBL:ENSBTAP00000001528 3 CID FTMS MULTI-SECPEP 1 -2 419.90648 1256.6976 0.05222 2.1927E-05 NaN 0.57043 0.011549 0 0 NaN NaN 1 0 0 0 95 346270.625 0.704625040984097 -1 0.0243583333333334 0 0 0 None Unknown 0 QLELEKQLEK _QLELEKQLEK_ 3 0 3 3 3 +BSA_min_23 2 0 LVTDLTK 7 0 Unmodified _LVTDLTK_ 0 CON__P02769;bsa;CON__P02768-1 2 CID FTMS MSMS 1 395.23946 788.46437 NaN NaN NaN 0.010013 0.0046553 0 0 NaN NaN 1 0 0 0 -1 NaN NaN 0 NaN 0 0 0 None Unknown 0;0 LVTDLTK;DSLLTLK _LVTDLTK_;_DSLLTLK_ 2 0 2 2 2 +BSA_min_23 96 77 QLELEKQLEK 10 1 Unmodified _QLELEKQLEK_ 0 CON__ENSEMBL:ENSBTAP00000001528 3 CID FTMS MULTI-SECPEP 1 -2 419.90648 1256.6976 0.05222 2.1927E-05 NaN 0.57043 0.011549 0 0 NaN NaN 1 0 0 0 95 346270.625 0.704625040984097 -1 0.0243583333333334 0 0 0 None Unknown 0 QLELEKQLEK _QLELEKQLEK_ 3 1 3 3 3 BSA_min_23 17 13 SLSAIRER 8 1 Unmodified _SLSAIRER_ 0 CON__Q03247 2 CID FTMS MULTI-SECPEP 4 -1 466.26962 930.52468 -3.0889 -0.0014403 NaN 0.096553 0.011549 0 0 NaN NaN 1 0 0 0 -1 NaN NaN 0 NaN 0 0 0 None Unknown 0 SLSAIRER _SLSAIRER_ 4 4 4 4 4 -BSA_min_23 72 58 TLGPWGQR 8 0 Unmodified _TLGPWGQR_ 0 CON__ENSEMBL:ENSBTAP00000018574 2 CID FTMS MULTI-MSMS 1 0 457.74578 913.477 -0.28247 -0.0001293 NaN 0.42593 0.01108 0 0 NaN NaN 1 0 0 0 71 32936.3203125 0.758644306612328 -2 0.0615566666666666 0 0 0 None Unknown 0;0 TLGPWGQR;IHVFNER _TLGPWGQR_;_IHVFNER_ 5 2 5 5 5 +BSA_min_23 72 58 TLGPWGQR 8 0 Unmodified _TLGPWGQR_ 0 CON__ENSEMBL:ENSBTAP00000018574 2 CID FTMS MULTI-MSMS 1 0 457.74578 913.477 -0.28247 -0.0001293 NaN 0.42593 0.01108 0 0 NaN NaN 1 0 0 0 71 32936.3203125 0.758644306612328 -2 0.0615566666666666 0 0 0 None Unknown 0;0 TLGPWGQR;IHVFNER _TLGPWGQR_;_IHVFNER_ 5 3 5 5 5 |
| b |
| diff -r 837224ad1694 -r 8934bc76bb52 test-data/01/combined/txt/msmsScans.txt --- a/test-data/01/combined/txt/msmsScans.txt Tue Jan 31 18:14:40 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,82 +0,0 @@\n-Raw file\tScan number\tRetention time\tIon injection time\tTotal ion current\tCollision energy\tSummations\tBase peak intensity\tElapsed time\tIdentified\tMatched\tReverse\tMS/MS IDs\tSequence\tLength\tFiltered peaks\tm/z\tMass\tCharge\tType\tFragmentation\tMass analyzer\tParent intensity fraction\tFraction of total spectrum\tBase peak fraction\tPrecursor full scan number\tPrecursor intensity\tPrecursor apex fraction\tPrecursor apex offset\tPrecursor apex offset time\tScan event number\tModifications\tModified sequence\tProteins\tScore\tPEP\tExperiment\tReporter PIF\tReporter fraction\tIntens Comp Factor\tCTCD Comp\tRawOvFtT\tAGC Fill\tScan index\tMS scan index\tMS scan number\n-BSA_min_23\t2\t0.010013\t-1\t35863\t35\t0\t15154\t-1\t+\t\t\t2\tLVTDLTK\t7\t103\t395.239288330078\tNaN\t0\tPEAK\tCID\tFTMS\t0\t0\t0\t-1\tNaN\tNaN\t0\tNaN\t1\tUnmodified\t_LVTDLTK_\tbsa;CON__P02768-1;CON__P02769\t0\t0.00465525978542915\tBSA_min_23.mzXML\t\t\tNaN\tNaN\tNaN\t0\t0\t0\t1\n-BSA_min_23\t3\t0.01458\t-1\t30585\t35\t0\t3755\t-1\t-\t\t+\t-1\tEHGLGSSHGSGSEYPR\t16\t164\t552.918823242188\tNaN\t0\tPEAK\tCID\tFTMS\t0\t0\t0\t-1\tNaN\tNaN\t0\tNaN\t2\tUnmodified\t_EHGLGSSHGSGSEYPR_\tREV__CON__Q86YZ3;REV__CON__Q86YZ3;REV__CON__Q86YZ3\t0\t0.0407221938552647\tBSA_min_23.mzXML\t\t\tNaN\tNaN\tNaN\t0\t1\t0\t1\n-BSA_min_23\t4\t0.020265\t-1\t11886\t35\t0\t5306.3\t-1\t-\t\t+\t-1\tIKNLDEITLHR\t11\t126\t676.387463660037\tNaN\t0\tPEAK\tCID\tFTMS\t0\t0\t0\t-1\tNaN\tNaN\t0\tNaN\t3\tUnmodified\t_IKNLDEITLHR_\tREV__CON__Q148H6;REV__CON__Q7Z3Y7\t0\t0.0187034863713379\tBSA_min_23.mzXML\t\t\tNaN\tNaN\tNaN\t0\t2\t0\t1\n-BSA_min_23\t5\t0.025633\t-1\t12813\t35\t0\t1425.6\t-1\t-\t\t\t-1\tEYEATLEECCAK\t12\t146\t751.810668945313\tNaN\t0\tPEAK\tCID\tFTMS\t0\t0\t0\t-1\tNaN\tNaN\t0\tNaN\t4\tUnmodified\t_EYEATLEECCAK_\tbsa;CON__P02769\t0\t0.0238166743936118\tBSA_min_23.mzXML\t\t\tNaN\tNaN\tNaN\t0\t3\t0\t1\n-BSA_min_23\t6\t0.031253\t-1\t10791\t35\t0\t2980.7\t-1\t-\t\t+\t-1\tCLNCFERWR\t9\t124\t670.800842285156\tNaN\t0\tPEAK\tCID\tFTMS\t0\t0\t0\t-1\tNaN\tNaN\t0\tNaN\t5\tUnmodified\t_CLNCFERWR_\tREV__CON__P06868\t0\t0.0115486780155693\tBSA_min_23.mzXML\t\t\tNaN\tNaN\tNaN\t0\t4\t0\t1\n-BSA_min_23\t8\t0.044372\t-1\t7950.3\t35\t0\t925.49\t-1\t-\t\t+\t-1\tTPLQYLHEFLSGILRAHVAPAVNGM\t25\t111\t456.581360854681\t2733.44450632849\t6\tMULTI\tCID\tFTMS\t0\t0\t0\t-1\tNaN\tNaN\t0\tNaN\t1\tUnmodified\t_TPLQYLHEFLSGILRAHVAPAVNGM_\tREV__CON__REFSEQ:XP_092267\t0\t0.0735193037455702\tBSA_min_23.mzXML\t\t\tNaN\tNaN\tNaN\t0\t5\t1\t7\n-BSA_min_23\t9\t0.049315\t-1\t13730\t35\t0\t3362.2\t-1\t-\t\t\t-1\tTSCSNANLEK\t10\t120\t562.257629394531\tNaN\t0\tPEAK\tCID\tFTMS\t0\t0\t0\t-1\tNaN\tNaN\t0\tNaN\t2\tUnmodified\t_TSCSNANLEK_\tCON__Q1A7A4\t0\t0.0144386597183341\tBSA_min_23.mzXML\t\t\tNaN\tNaN\tNaN\t0\t6\t1\t7\n-BSA_min_23\t10\t0.05446\t-1\t8774.7\t35\t0\t723.28\t-1\t-\t\t\t-1\t \t0\t121\t589.203415053777\t588.196138587177\t1\tMULTI\tCID\tFTMS\t0\t0\t0\t-1\tNaN\tNaN\t0\tNaN\t3\t \t \t \tNaN\tNaN\tBSA_min_23.mzXML\t\t\tNaN\tNaN\tNaN\t0\t7\t1\t7\n-BSA_min_23\t11\t0.06018\t-1\t4436.2\t35\t0\t280.8\t-1\t-\t\t\t-1\t \t0\t115\t828.876770019531\tNaN\t0\tPEAK\tCID\tFTMS\t0\t0\t0\t-1\tNaN\tNaN\t0\tNaN\t4\t \t \t \tNaN\tNaN\tBSA_min_23.mzXML\t\t\tNaN\tNaN\tNaN\t0\t8\t1\t7\n-BSA_min_23\t12\t0.065908\t-1\t3625.8\t35\t0\t189.9\t-1\t-\t\t\t-1\tGSCGIGGGIGGGSSR\t15\t112\t639.798400878906\tNaN\t0\tPEAK\tCID\tFTMS\t0\t0\t0\t-1\tNaN\tNaN\t0\tNaN\t5\tUnmodified\t_GSCGIGGGIGGGSSR_\tCON__P02533;CON__P08779\t1.5870418381875\t0.0369296140263621\tBSA_min_23.mzXML\t\t\tNaN\tNaN\tNaN\t0\t9\t1\t7\n-BSA_min_23\t14\t0.078957\t-1\t13236\t35\t0\t4982.4\t-1\t-\t\t\t-1\t \t0\t137\t883.333060315928\t1764.65156769866\t2\tMULTI\tCID\tFTMS\t0\t0\t0\t13\t171569.53125\t0.0583552615411773\t-4\tNaN\t1\t \t \t \tNaN\tNaN\tBSA_min_23.mzXML\t\t\tNaN\tNaN\tNaN\t0\t10\t2\t13\n-BSA_min_23\t15\t0.084805\t-1\t6304.6\t35\t0\t393.58\t-1\t-\t\t\t-1\t \t0\t120\t602.8994140625\tNaN\t0\tPEAK\tCID\tFTMS\t0\t0\t0\t-1\tNaN\tNaN\t0\tNaN\t2\t \t \t \tNaN\tNaN\tBSA_min_23.mzXML\t\t\tNaN\tNaN\tNaN\t0\t11\t2\t13\n-BSA_min_23\t16\t0.090573\t-1\t12119\t35\t0\t1996\t-1\t-\t\t\t-1\t \t0\t135\t648.602725656856\t1942.78634757077\t3\tMULTI\tCID\tFTMS\t0\t0\t0\t13\t52074.7734375\t0.102435594507697\t-16\tNaN\t3\t \t \t \tNaN\tNaN\tBSA_min_23.mzXML\t\t\tNaN\tNaN\tNaN\t0\t12\t2\t13\n-BSA_min_23\t17\t0.096553\t-1\t5932.3\t35\t0\t1047.4\t-1\t-\t\t+\t-1\tSAAKLPSEK\t9\t110\t465.766693115234\tNaN\t0\tPEAK\tCID\tFTMS\t0\t0\t0\t-1\tNaN\tNaN\t0\tNaN\t4\tUnmodified\t_SAAKLPSEK_\tREV__CON__REFSEQ:XP_585019\t0\t0.0115486780155693\tBSA_min_23.mzXML\t\t\tNaN\tNaN\tNaN\t0\t13\t2\t13\n-BSA_min_23\t18\t0.10154\t-1\t4161.5\t35\t0\t213.29\t-1\t-\t\t\t-1\t \t0\t108\t605.75811767'..b'zXML\t\t\tNaN\tNaN\tNaN\t0\t64\t13\t75\n-BSA_min_23\t80\t0.4736\t-1\t1227.2\t35\t0\t58.422\t-1\t-\t\t+\t-1\tTTHISVNQMGSERLSEEGELK\t21\t96\t1173.07641230313\t2344.13827167306\t2\tMULTI\tCID\tFTMS\t0\t0\t0\t75\t23081.546875\t1\t0\t0\t5\tUnmodified\t_TTHISVNQMGSERLSEEGELK_\tREV__CON__Q9H552\t0\t0.0521844715306576\tBSA_min_23.mzXML\t\t\tNaN\tNaN\tNaN\t0\t65\t13\t75\n-BSA_min_23\t82\t0.48722\t-1\t6556.1\t35\t0\t1271.7\t-1\t-\t\t\t-1\tQLELEKQLEK\t10\t116\t629.356567222744\t1256.69858151229\t2\tMULTI\tCID\tFTMS\t0\t0\t0\t81\t28788.931640625\t1\t0\t0\t1\tUnmodified\t_QLELEKQLEK_\tCON__ENSEMBL:ENSBTAP00000001528\t0\t0.0119676768621359\tBSA_min_23.mzXML\t\t\tNaN\tNaN\tNaN\t0\t66\t14\t81\n-BSA_min_23\t83\t0.4925\t-1\t6615.3\t35\t0\t545.34\t-1\t-\t\t\t-1\t \t0\t116\t559.768784960153\t1117.5230169871\t2\tMULTI\tCID\tFTMS\t0\t0\t0\t81\t35334.84765625\t0.949368528711517\t-1\t0.0369099999999999\t2\t \t \t \tNaN\tNaN\tBSA_min_23.mzXML\t\t\tNaN\tNaN\tNaN\t0\t67\t14\t81\n-BSA_min_23\t84\t0.49762\t-1\t6183.7\t35\t0\t2375.9\t-1\t-\t\t\t-1\t \t0\t125\t972.401410989102\t1942.788269045\t2\tMULTI\tCID\tFTMS\t0\t0\t0\t81\t19756.91796875\t0.347354270628424\t7\tNaN\t3\t \t \t \tNaN\tNaN\tBSA_min_23.mzXML\t\t\tNaN\tNaN\tNaN\t0\t68\t14\t81\n-BSA_min_23\t85\t0.50353\t-1\t3559.8\t35\t0\t122.14\t-1\t-\t\t\t-1\t \t0\t116\t681.999312814333\t2042.9761090432\t3\tMULTI\tCID\tFTMS\t0\t0\t0\t81\t11550.4775390625\t0.629091502669348\t2\t-0.0587916666666667\t4\t \t \t \tNaN\tNaN\tBSA_min_23.mzXML\t\t\tNaN\tNaN\tNaN\t0\t69\t14\t81\n-BSA_min_23\t86\t0.50957\t-1\t5114.2\t35\t0\t640.76\t-1\t+\t\t\t1\tLLESEECR\t8\t118\t518.240989833781\tNaN\t0\tPEAK\tCID\tFTMS\t0\t0\t0\t81\t10271.2001953125\t1\t0\t0\t5\tUnmodified\t_LLESEECR_\tCON__Q14CN4-1;CON__Q3SY84;CON__Q9R0H5\t1.63126590808724\t0.00752050293704335\tBSA_min_23.mzXML\t\t\tNaN\tNaN\tNaN\t0\t70\t14\t81\n-BSA_min_23\t88\t0.52259\t-1\t44411\t35\t0\t18940\t-1\t-\t\t\t-1\t \t0\t134\t385.207384246749\t384.200107780149\t1\tMULTI\tCID\tFTMS\t0\t0\t0\t87\t5929296.5\t0.739051055541228\t-3\t0.0963616666666667\t1\t \t \t \tNaN\tNaN\tBSA_min_23.mzXML\t\t\tNaN\tNaN\tNaN\t0\t71\t15\t87\n-BSA_min_23\t89\t0.52681\t-1\t3749.8\t35\t0\t351.63\t-1\t-\t\t\t-1\t \t0\t100\t597.066145240602\t2980.29434387001\t5\tMULTI\tCID\tFTMS\t0\t0\t0\t87\t19359.11328125\t0.820197080002651\t2\t-0.04811\t2\t \t \t \tNaN\tNaN\tBSA_min_23.mzXML\t\t\tNaN\tNaN\tNaN\t0\t72\t15\t87\n-BSA_min_23\t90\t0.53279\t-1\t3364.5\t35\t0\t196.99\t-1\t-\t\t\t-1\t \t0\t128\t731.298257293396\t1460.58196165359\t2\tMULTI\tCID\tFTMS\t0\t0\t0\t87\t10634.3564453125\t0.960368079417471\t-1\t0.0350400000000001\t3\t \t \t \tNaN\tNaN\tBSA_min_23.mzXML\t\t\tNaN\tNaN\tNaN\t0\t73\t15\t87\n-BSA_min_23\t92\t0.54611\t-1\t4680.5\t35\t0\t301.84\t-1\t-\t\t+\t-1\tGNMIMYTYR\t9\t116\t582.760859148704\t1163.50716536421\t2\tMULTI\tCID\tFTMS\t0\t0\t0\t91\t46220.83984375\t0.762103661377976\t-2\t0.0587916666666667\t1\tOxidation (M)\t_GNM(Oxidation (M))IMYTYR_\tREV__CON__Q2UVX4\t0\t0.0115486780155693\tBSA_min_23.mzXML\t\t\tNaN\tNaN\tNaN\t0\t74\t16\t91\n-BSA_min_23\t93\t0.55132\t-1\t3773.2\t35\t0\t552.59\t-1\t-\t\t\t-1\t \t0\t106\t635.602009230031\t1903.78419829029\t3\tMULTI\tCID\tFTMS\t0\t0\t0\t91\t24284.580078125\t0.586968526901584\t-2\t0.0587916666666667\t2\t \t \t \tNaN\tNaN\tBSA_min_23.mzXML\t\t\tNaN\tNaN\tNaN\t0\t75\t16\t91\n-BSA_min_23\t94\t0.55721\t-1\t4670.5\t35\t0\t438.63\t-1\t-\t\t\t-1\t \t0\t143\t722.292863277439\t1442.57117362168\t2\tMULTI\tCID\tFTMS\t0\t0\t0\t91\t14970.0166015625\t0.470778833500893\t-2\t0.0587916666666667\t3\t \t \t \tNaN\tNaN\tBSA_min_23.mzXML\t\t\tNaN\tNaN\tNaN\t0\t76\t16\t91\n-BSA_min_23\t96\t0.57043\t-1\t15235\t35\t0\t3357.3\t-1\t+\t\t\t0\tDSFDIIK\t7\t110\t419.221486165858\t836.428419398517\t2\tMULTI\tCID\tFTMS\t0\t0\t0\t95\t346270.625\t0.704625040984097\t-1\t0.0243583333333334\t1\tUnmodified\t_DSFDIIK_\tCON__ENSEMBL:ENSBTAP00000016046\t0\t0.010549248059121\tBSA_min_23.mzXML\t\t\tNaN\tNaN\tNaN\t0\t77\t17\t95\n-BSA_min_23\t97\t0.57533\t-1\t4806.4\t35\t0\t539.18\t-1\t-\t\t\t-1\t \t0\t129\t722.292863277439\t1442.57117362168\t2\tMULTI\tCID\tFTMS\t0\t0\t0\t95\t26752.708984375\t0.841322322069994\t-1\t0.0243583333333334\t2\t \t \t \tNaN\tNaN\tBSA_min_23.mzXML\t\t\tNaN\tNaN\tNaN\t0\t78\t17\t95\n-BSA_min_23\t98\t0.58084\t-1\t3667\t35\t0\t164.63\t-1\t-\t\t\t-1\t \t0\t113\t595.224647156549\tNaN\t0\tPEAK\tCID\tFTMS\t0\t0\t0\t95\t6964.16259765625\t0.341923515563021\t-1\t0.0243583333333334\t3\t \t \t \tNaN\tNaN\tBSA_min_23.mzXML\t\t\tNaN\tNaN\tNaN\t0\t79\t17\t95\n-BSA_min_23\t100\t0.59414\t-1\t44171\t35\t0\t23670\t-1\t-\t\t\t-1\t \t0\t176\t882.846109550244\t1763.67766616729\t2\tMULTI\tCID\tFTMS\t0\t0\t0\t99\t379571.375\t0.768338756470332\t1\tNaN\t1\t \t \t \tNaN\tNaN\tBSA_min_23.mzXML\t\t\tNaN\tNaN\tNaN\t0\t80\t18\t99\n' |
| b |
| diff -r 837224ad1694 -r 8934bc76bb52 test-data/01/combined/txt/mzRange.txt --- a/test-data/01/combined/txt/mzRange.txt Tue Jan 31 18:14:40 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| b'@@ -1,1881 +0,0 @@\n-Raw file\tm/z\tPeaks / Da\tSingle peaks / Da\tIsotope patterns / Da\tSingle isotope patterns / Da\tSILAC pairs / Da\tIdentified SILAC pairs / Da\tSILAC identification rate [%]\tMS/MS / Da\tIdentified MS/MS / Da\tIdentification rate 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|
| b |
| diff -r 837224ad1694 -r 8934bc76bb52 test-data/01/combined/txt/mzTab.mzTab --- a/test-data/01/combined/txt/mzTab.mzTab Tue Jan 31 18:14:40 2023 +0000 +++ b/test-data/01/combined/txt/mzTab.mzTab Mon Jun 19 17:02:17 2023 +0000 |
| [ |
| b'@@ -3,7 +3,7 @@\n MTD\tmzTab-type\tIdentification\n MTD\ttitle\tnull\n MTD\tdescription\tnull\n-MTD\tsoftware[1]\t[MS, MS:1001583, MaxQuant,1.6.17.0]\n+MTD\tsoftware[1]\t[MS, MS:1001583, MaxQuant,2.0.3.0]\n COM\t[, CHEMMOD:57.0214637236, Carbamidomethyl (C),]\t\n MTD\tfixed_mod[1]\t[, , CHEMMOD:57.0214637236,]\n MTD\tfixed_mod[1]-site\tC\n@@ -17,26 +17,26 @@\n MTD\tpsm_search_engine_score[1]\t[MS, MS:1002338, Andromeda:score, ]\n MTD\tpsm_search_engine_score[2]\t[MS, MS:1002995, Andromeda PEP, ]\n MTD\tms_run[1]-format\t[MS, , ,]\n-MTD\tms_run[1]-location\tfile:///tmp/tmp9jbmb6lc/job_working_directory/000/3/working/BSA_min_23.mzXML\n+MTD\tms_run[1]-location\tfile:///tmp/tmphsgikyer/job_working_directory/000/3/working/BSA_min_23.mzXML\n MTD\tms_run[1]-id_format\t[MS, , ,]\n \n PRH\taccession\tdescription\ttaxid\tspecies\tdatabase\tdatabase_version\tsearch_engine\tbest_search_engine_score[1]\tsearch_engine_score[1]_ms_run[1]\tnum_psms_ms_run[1]\tnum_peptides_distinct_ms_run[1]\tnum_peptides_unique_ms_run[1]\tambiguity_members\tmodifications\tprotein_coverage\n-PRT\tCON__P02769\tnull\tnull\tnull\t/tmp/tmp9jbmb6lc/files/7/5/d/dataset_75d9a22a-c00d-4c98-b445-0f54e57ec138.dat;\tnull\t[MS, MS:1002337, Andromeda, 1.6.17.0]\t6.33205607832812\tnull\tnull\tnull\tnull\tCON__P02769, bsa, CON__P02768-1\tnull\t0.012\n-PRT\tCON__ENSEMBL:ENSBTAP00000001528\tnull\tnull\tnull\t/tmp/tmp9jbmb6lc/files/7/5/d/dataset_75d9a22a-c00d-4c98-b445-0f54e57ec138.dat;\tnull\t[MS, MS:1002337, Andromeda, 1.6.17.0]\t5.93746772688895\tnull\tnull\tnull\tnull\tCON__ENSEMBL:ENSBTAP00000001528\tnull\t0.008\n-PRT\tCON__ENSEMBL:ENSBTAP00000016046\tnull\tnull\tnull\t/tmp/tmp9jbmb6lc/files/7/5/d/dataset_75d9a22a-c00d-4c98-b445-0f54e57ec138.dat;\tnull\t[MS, MS:1002337, Andromeda, 1.6.17.0]\t5.97677849538172\tnull\tnull\tnull\tnull\tCON__ENSEMBL:ENSBTAP00000016046\tnull\t0.01\n-PRT\tCON__ENSEMBL:ENSBTAP00000018574\tnull\tnull\tnull\t/tmp/tmp9jbmb6lc/files/7/5/d/dataset_75d9a22a-c00d-4c98-b445-0f54e57ec138.dat;\tnull\t[MS, MS:1002337, Andromeda, 1.6.17.0]\t5.95544937626172\tnull\tnull\tnull\tnull\tCON__ENSEMBL:ENSBTAP00000018574\tnull\t0.016\n-PRT\tCON__Q03247\tnull\tnull\tnull\t/tmp/tmp9jbmb6lc/files/7/5/d/dataset_75d9a22a-c00d-4c98-b445-0f54e57ec138.dat;\tnull\t[MS, MS:1002337, Andromeda, 1.6.17.0]\t5.93746772688895\tnull\tnull\tnull\tnull\tCON__Q03247\tnull\t0.025\n-PRT\tCON__Q14CN4-1\tnull\tnull\tnull\t/tmp/tmp9jbmb6lc/files/7/5/d/dataset_75d9a22a-c00d-4c98-b445-0f54e57ec138.dat;\tnull\t[MS, MS:1002337, Andromeda, 1.6.17.0]\t6.1237531147968\tnull\tnull\tnull\tnull\tCON__Q14CN4-1, CON__Q3SY84, CON__Q9R0H5\tnull\t0.016\n+PRT\tCON__P02769\tnull\tnull\tnull\t/tmp/tmphsgikyer/files/9/e/a/dataset_9ea3021f-0686-4675-87e9-a4e4f55afbd2.dat;\tnull\t[MS, MS:1002337, Andromeda, 2.0.3.0]\t6.33205607832812\tnull\tnull\tnull\tnull\tCON__P02769, bsa, CON__P02768-1\tnull\t0.012\n+PRT\tCON__ENSEMBL:ENSBTAP00000001528\tnull\tnull\tnull\t/tmp/tmphsgikyer/files/9/e/a/dataset_9ea3021f-0686-4675-87e9-a4e4f55afbd2.dat;\tnull\t[MS, MS:1002337, Andromeda, 2.0.3.0]\t5.93746772688895\tnull\tnull\tnull\tnull\tCON__ENSEMBL:ENSBTAP00000001528\tnull\t0.008\n+PRT\tCON__ENSEMBL:ENSBTAP00000016046\tnull\tnull\tnull\t/tmp/tmphsgikyer/files/9/e/a/dataset_9ea3021f-0686-4675-87e9-a4e4f55afbd2.dat;\tnull\t[MS, MS:1002337, Andromeda, 2.0.3.0]\t5.97677849538172\tnull\tnull\tnull\tnull\tCON__ENSEMBL:ENSBTAP00000016046\tnull\t0.01\n+PRT\tCON__ENSEMBL:ENSBTAP00000018574\tnull\tnull\tnull\t/tmp/tmphsgikyer/files/9/e/a/dataset_9ea3021f-0686-4675-87e9-a4e4f55afbd2.dat;\tnull\t[MS, MS:1002337, Andromeda, 2.0.3.0]\t5.95544937626172\tnull\tnull\tnull\tnull\tCON__ENSEMBL:ENSBTAP00000018574\tnull\t0.016\n+PRT\tCON__Q03247\tnull\tnull\tnull\t/tmp/tmphsgikyer/files/9/e/a/dataset_9ea3021f-0686-4675-87e9-a4e4f55afbd2.dat;\tnull\t[MS, MS:1002337, Andromeda, 2.0.3.0]\t5.93746772688895\tnull\tnull\tnull\tnull\tCON__Q03247\tnull\t0.025\n+PRT\tCON__Q14CN4-1\tnull\tnull\tnull\t/tmp/tmphsgikyer/files/9/e/a/dataset_9ea3021f-0686-4675-87e9-a4e4f55afbd2.dat;\tnull\t[MS, MS:1002337, Andromeda, 2.0.3.0]\t6.1237531147968\tnull\tnull\tnull\tnull\tCON__Q14CN4-1, CON__Q3SY84, CON__Q9R0H5\tnull\t0.016\n \n PSH\tsequence\tPSM_ID\taccession\tunique\tdatabase\tdatabase_version\tsearch_engine\tsearch_e'..b'an=2\tK\tV\t257\t263\t2\t0\n-PSM\tLVTDLTK\t3\tbsa\t0\t/tmp/tmp9jbmb6lc/files/7/5/d/dataset_75d9a22a-c00d-4c98-b445-0f54e57ec138.dat;\tnull\t[MS, MS:1002338, Andromeda:score, 1.6.17.0]\t0\t0.00465525978542915\tnull\t0.0100133333333333\t2\t395.2393\t395.2395\tms_run[1]:scan=2\tK\tV\t257\t263\t2\t0\n-PSM\tLVTDLTK\t3\tCON__P02768-1\t0\t/tmp/tmp9jbmb6lc/files/7/5/d/dataset_75d9a22a-c00d-4c98-b445-0f54e57ec138.dat;\tnull\t[MS, MS:1002338, Andromeda:score, 1.6.17.0]\t0\t0.00465525978542915\tnull\t0.0100133333333333\t2\t395.2393\t395.2395\tms_run[1]:scan=2\tK\tV\t257\t263\t2\t0\n-PSM\tQLELEKQLEK\t4\tCON__ENSEMBL:ENSBTAP00000001528\t1\t/tmp/tmp9jbmb6lc/files/7/5/d/dataset_75d9a22a-c00d-4c98-b445-0f54e57ec138.dat;\tnull\t[MS, MS:1002338, Andromeda:score, 1.6.17.0]\t0\t0.0115486780155693\tnull\t0.570428333333333\t3\t419.9065\t419.9065\tms_run[1]:scan=96\tR\tQ\t408\t417\t96\t0\n-PSM\tSLSAIRER\t5\tCON__Q03247\t1\t/tmp/tmp9jbmb6lc/files/7/5/d/dataset_75d9a22a-c00d-4c98-b445-0f54e57ec138.dat;\tnull\t[MS, MS:1002338, Andromeda:score, 1.6.17.0]\t0\t0.0115486780155693\tnull\t0.0965533333333333\t2\t466.2696\t466.2696\tms_run[1]:scan=17\tR\tF\t190\t197\t17\t0\n-PSM\tTLGPWGQR\t6\tCON__ENSEMBL:ENSBTAP00000018574\t1\t/tmp/tmp9jbmb6lc/files/7/5/d/dataset_75d9a22a-c00d-4c98-b445-0f54e57ec138.dat;\tnull\t[MS, MS:1002338, Andromeda:score, 1.6.17.0]\t0\t0.0110802771561295\tnull\t0.425933333333333\t2\t457.746\t457.7458\tms_run[1]:scan=72\tR\tD\t20\t27\t72\t0\n+PSM\tDSFDIIK\t1\tCON__ENSEMBL:ENSBTAP00000016046\t1\t/tmp/tmphsgikyer/files/9/e/a/dataset_9ea3021f-0686-4675-87e9-a4e4f55afbd2.dat;\tnull\t[MS, MS:1002338, Andromeda:score, 2.0.3.0]\t0\t0.010549248059121\tnull\t0.570428333333333\t2\t419.2213\t419.2213\tms_run[1]:scan=96\tR\tR\t646\t652\t96\t0\n+PSM\tLLESEECR\t2\tCON__Q14CN4-1\t0\t/tmp/tmphsgikyer/files/9/e/a/dataset_9ea3021f-0686-4675-87e9-a4e4f55afbd2.dat;\tnull\t[MS, MS:1002338, Andromeda:score, 2.0.3.0]\t1.63126590808724\t0.00752050293704335\tnull\t0.509571666666667\t2\t518.2382\t518.2424\tms_run[1]:scan=86\tK\tM\t430\t437\t86\t0\n+PSM\tLLESEECR\t2\tCON__Q3SY84\t0\t/tmp/tmphsgikyer/files/9/e/a/dataset_9ea3021f-0686-4675-87e9-a4e4f55afbd2.dat;\tnull\t[MS, MS:1002338, Andromeda:score, 2.0.3.0]\t1.63126590808724\t0.00752050293704335\tnull\t0.509571666666667\t2\t518.2382\t518.2424\tms_run[1]:scan=86\tK\tM\t430\t437\t86\t0\n+PSM\tLLESEECR\t2\tCON__Q9R0H5\t0\t/tmp/tmphsgikyer/files/9/e/a/dataset_9ea3021f-0686-4675-87e9-a4e4f55afbd2.dat;\tnull\t[MS, MS:1002338, Andromeda:score, 2.0.3.0]\t1.63126590808724\t0.00752050293704335\tnull\t0.509571666666667\t2\t518.2382\t518.2424\tms_run[1]:scan=86\tK\tM\t430\t437\t86\t0\n+PSM\tLVTDLTK\t3\tCON__P02769\t0\t/tmp/tmphsgikyer/files/9/e/a/dataset_9ea3021f-0686-4675-87e9-a4e4f55afbd2.dat;\tnull\t[MS, MS:1002338, Andromeda:score, 2.0.3.0]\t0\t0.00465525978542915\tnull\t0.0100133333333333\t2\t395.2393\t395.2395\tms_run[1]:scan=2\tK\tV\t257\t263\t2\t0\n+PSM\tLVTDLTK\t3\tbsa\t0\t/tmp/tmphsgikyer/files/9/e/a/dataset_9ea3021f-0686-4675-87e9-a4e4f55afbd2.dat;\tnull\t[MS, MS:1002338, Andromeda:score, 2.0.3.0]\t0\t0.00465525978542915\tnull\t0.0100133333333333\t2\t395.2393\t395.2395\tms_run[1]:scan=2\tK\tV\t257\t263\t2\t0\n+PSM\tLVTDLTK\t3\tCON__P02768-1\t0\t/tmp/tmphsgikyer/files/9/e/a/dataset_9ea3021f-0686-4675-87e9-a4e4f55afbd2.dat;\tnull\t[MS, MS:1002338, Andromeda:score, 2.0.3.0]\t0\t0.00465525978542915\tnull\t0.0100133333333333\t2\t395.2393\t395.2395\tms_run[1]:scan=2\tK\tV\t257\t263\t2\t0\n+PSM\tQLELEKQLEK\t4\tCON__ENSEMBL:ENSBTAP00000001528\t1\t/tmp/tmphsgikyer/files/9/e/a/dataset_9ea3021f-0686-4675-87e9-a4e4f55afbd2.dat;\tnull\t[MS, MS:1002338, Andromeda:score, 2.0.3.0]\t0\t0.0115486780155693\tnull\t0.570428333333333\t3\t419.9065\t419.9065\tms_run[1]:scan=96\tR\tQ\t408\t417\t96\t0\n+PSM\tSLSAIRER\t5\tCON__Q03247\t1\t/tmp/tmphsgikyer/files/9/e/a/dataset_9ea3021f-0686-4675-87e9-a4e4f55afbd2.dat;\tnull\t[MS, MS:1002338, Andromeda:score, 2.0.3.0]\t0\t0.0115486780155693\tnull\t0.0965533333333333\t2\t466.2696\t466.2696\tms_run[1]:scan=17\tR\tF\t190\t197\t17\t0\n+PSM\tTLGPWGQR\t6\tCON__ENSEMBL:ENSBTAP00000018574\t1\t/tmp/tmphsgikyer/files/9/e/a/dataset_9ea3021f-0686-4675-87e9-a4e4f55afbd2.dat;\tnull\t[MS, MS:1002338, Andromeda:score, 2.0.3.0]\t0\t0.0110802771561295\tnull\t0.425933333333333\t2\t457.746\t457.7458\tms_run[1]:scan=72\tR\tD\t20\t27\t72\t0\n \n' |
| b |
| diff -r 837224ad1694 -r 8934bc76bb52 test-data/01/combined/txt/parameters.txt --- a/test-data/01/combined/txt/parameters.txt Tue Jan 31 18:14:40 2023 +0000 +++ b/test-data/01/combined/txt/parameters.txt Mon Jun 19 17:02:17 2023 +0000 |
| [ |
| @@ -46,8 +46,9 @@ Write allPeptides table True Write mzRange table True Write DIA fragments table False +Write DIA fragments quant table False Write pasefMsmsScans table True -Write accumulatedPasefMsmsScans table False +Write accumulatedMsmsScans table True Max. peptide mass [Da] 4600 Min. peptide length for unspecific search 8 Max. peptide length for unspecific search 25 |
| b |
| diff -r 837224ad1694 -r 8934bc76bb52 test-data/01/combined/txt/peptides.txt --- a/test-data/01/combined/txt/peptides.txt Tue Jan 31 18:14:40 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,7 +0,0 @@ -Sequence N-term cleavage window C-term cleavage window Amino acid before First amino acid Second amino acid Second last amino acid Last amino acid Amino acid after A Count R Count N Count D Count C Count Q Count E Count G Count H Count I Count L Count K Count M Count F Count P Count S Count T Count W Count Y Count V Count U Count O Count Length Missed cleavages Mass Proteins Leading razor protein Start position End position Unique (Groups) Unique (Proteins) Charges PEP Score Experiment BSA_min_23.mzXML Intensity Intensity BSA_min_23.mzXML Reverse Potential contaminant id Protein group IDs Mod. peptide IDs Evidence IDs MS/MS IDs Best MS/MS Oxidation (M) site IDs Taxonomy IDs MS/MS Count -DSFDIIK NHADIIFDITDGNLRDSFDIIKRYMDGMTV DITDGNLRDSFDIIKRYMDGMTVGVVRQVR R D S I K R 0 0 0 2 0 0 0 0 0 2 0 1 0 1 0 1 0 0 0 0 0 0 7 0 836.42798 CON__ENSEMBL:ENSBTAP00000016046 CON__ENSEMBL:ENSBTAP00000016046 646 652 yes yes 2 0.010549 0 1 769840 769840 + 0 1 0 0 0 0 1 -LLESEECR SLKLALDMEIATYRKLLESEECRMSGEYPN EIATYRKLLESEECRMSGEYPNSVSISVIS K L L C R M 0 1 0 0 1 0 3 0 0 0 2 0 0 0 0 1 0 0 0 0 0 0 8 0 1034.4703 CON__Q14CN4-1;CON__Q3SY84;CON__Q9R0H5 CON__Q14CN4-1 430 437 yes no 2 0.0075205 1.6313 1 0 0 + 1 5 1 1 1 1 1 -LVTDLTK LSQKFPKAEFVEVTKLVTDLTKVHKECCHG AEFVEVTKLVTDLTKVHKECCHGDLLECAD K L V T K V 0 0 0 1 0 0 0 0 0 0 2 1 0 0 0 0 2 0 0 1 0 0 7 0 788.46437 bsa;CON__P02769;CON__P02768-1 bsa 257 263 yes no 2 0.0046553 0 1 0 0 + 2 3 2 2 2 2 1 -QLELEKQLEK QERKERERQEQERKRQLELEKQLEKQRELE QERKRQLELEKQLEKQRELERQREEERRKE R Q L E K Q 0 0 0 0 0 2 3 0 0 0 3 2 0 0 0 0 0 0 0 0 0 0 10 1 1256.6976 CON__ENSEMBL:ENSBTAP00000001528 CON__ENSEMBL:ENSBTAP00000001528 408 417 yes yes 3 0.011549 0 1 57896 57896 + 3 0 3 3 3 3 0 -SLSAIRER RLAVYQAGASEGAERSLSAIRERFGPLVEQ ASEGAERSLSAIRERFGPLVEQGQSRAATL R S L E R F 1 2 0 0 0 0 1 0 0 1 1 0 0 0 0 2 0 0 0 0 0 0 8 1 930.52468 CON__Q03247 CON__Q03247 190 197 yes yes 2 0.011549 0 1 33623 33623 + 4 4 4 4 4 4 0 -TLGPWGQR LRPLLLALLLASACRTLGPWGQRDDGGGEP LLASACRTLGPWGQRDDGGGEPESMEPRWG R T L Q R D 0 1 0 0 0 1 0 2 0 0 1 0 0 0 1 0 1 1 0 0 0 0 8 0 913.477 CON__ENSEMBL:ENSBTAP00000018574 CON__ENSEMBL:ENSBTAP00000018574 20 27 yes yes 2 0.01108 0 1 62116 62116 + 5 2 5 5 5 5 1 |
| b |
| diff -r 837224ad1694 -r 8934bc76bb52 test-data/01/combined/txt/proteinGroups.txt --- a/test-data/01/combined/txt/proteinGroups.txt Tue Jan 31 18:14:40 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,7 +0,0 @@ -Protein IDs Majority protein IDs Peptide counts (all) Peptide counts (razor+unique) Peptide counts (unique) Fasta headers Number of proteins Peptides Razor + unique peptides Unique peptides Peptides BSA_min_23.mzXML Razor + unique peptides BSA_min_23.mzXML Unique peptides BSA_min_23.mzXML Sequence coverage [%] Unique + razor sequence coverage [%] Unique sequence coverage [%] Mol. weight [kDa] Sequence length Sequence lengths Q-value Score Sequence coverage BSA_min_23.mzXML [%] Intensity Intensity BSA_min_23.mzXML MS/MS count Only identified by site Reverse Potential contaminant id Peptide IDs Peptide is razor Mod. peptide IDs Evidence IDs MS/MS IDs Best MS/MS Oxidation (M) site IDs Oxidation (M) site positions Taxonomy IDs -CON__ENSEMBL:ENSBTAP00000001528 CON__ENSEMBL:ENSBTAP00000001528 1 1 1 1 1 1 1 1 1 1 0.8 0.8 0.8 137.98 1222 1222 0 5.9375 0.8 57896 57896 0 + 0 3 True 3 3 3 3 -1 -CON__ENSEMBL:ENSBTAP00000016046 CON__ENSEMBL:ENSBTAP00000016046 1 1 1 1 1 1 1 1 1 1 1 1 1 77.456 706 706 0 5.9768 1 769840 769840 1 + 1 0 True 0 0 0 0 -1 -CON__ENSEMBL:ENSBTAP00000018574 CON__ENSEMBL:ENSBTAP00000018574 1 1 1 1 1 1 1 1 1 1 1.6 1.6 1.6 55.207 496 496 0 5.9554 1.6 62116 62116 1 + 2 5 True 5 5 5 5 -1 -bsa;CON__P02769;CON__P02768-1 bsa;CON__P02769;CON__P02768-1 1;1;1 1;1;1 1;1;1 bsa sp|P02769|ALBU_BOVIN Serum albumin OS=Bos taurus OX=9913 GN=ALB PE=1 SV=4;; 3 1 1 1 1 1 1 1.2 1.2 1.2 69.293 607 607;607;609 0 6.3321 1.2 0 0 1 + 3 2 True 2 2 2 2 -1;-1;-1 -CON__Q03247 CON__Q03247 1 1 1 1 1 1 1 1 1 1 2.5 2.5 2.5 35.979 316 316 0 5.9375 2.5 33623 33623 0 + 4 4 True 4 4 4 4 -1 -CON__Q14CN4-1;CON__Q3SY84;CON__Q9R0H5 CON__Q14CN4-1;CON__Q3SY84;CON__Q9R0H5 1;1;1 1;1;1 1;1;1 ;; 3 1 1 1 1 1 1 1.6 1.6 1.6 55.877 511 511;523;524 0 6.1238 1.6 0 0 1 + 5 1 True 1 1 1 1 -1;-1;-1 |
| b |
| diff -r 837224ad1694 -r 8934bc76bb52 test-data/01/combined/txt/summary.txt --- a/test-data/01/combined/txt/summary.txt Tue Jan 31 18:14:40 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,3 +0,0 @@ -Raw file Experiment Enzyme Enzyme mode Enzyme first search Enzyme mode first search Use enzyme first search Variable modifications Fixed modifications Multi modifications Variable modifications first search Use variable modifications first search Requantify Multiplicity Max. missed cleavages Labels0 LC-MS run type Time-dependent recalibration MS MS/MS MS3 MS/MS Submitted MS/MS Submitted (SIL) MS/MS Submitted (ISO) MS/MS Submitted (PEAK) MS/MS Identified MS/MS Identified (SIL) MS/MS Identified (ISO) MS/MS Identified (PEAK) MS/MS Identified [%] MS/MS Identified (SIL) [%] MS/MS Identified (ISO) [%] MS/MS Identified (PEAK) [%] Peptide Sequences Identified Peaks Peaks Sequenced Peaks Sequenced [%] Peaks Repeatedly Sequenced Peaks Repeatedly Sequenced [%] Isotope Patterns Isotope Patterns Sequenced Isotope Patterns Sequenced (z>1) Isotope Patterns Sequenced [%] Isotope Patterns Sequenced (z>1) [%] Isotope Patterns Repeatedly Sequenced Isotope Patterns Repeatedly Sequenced [%] Recalibrated Av. Absolute Mass Deviation [ppm] Mass Standard Deviation [ppm] Av. Absolute Mass Deviation [mDa] Mass Standard Deviation [mDa] -BSA_min_23 BSA_min_23.mzXML Trypsin/P Specific False Oxidation (M) Carbamidomethyl (C) False False 1 1 Standard 19 81 0 112 50 0 62 4 2 0 2 3.6 4 0 3.2 6 1200 57 4.8 4 7 158 38 34 24 27 10 26 + 0.40179 0.41895 0.17349 0.17902 -Total 19 81 0 112 50 0 62 4 2 0 2 3.6 4 0 3.2 6 1200 158 38 34 24 27 10 26 0.40179 0.41895 0.17349 0.17902 |
| b |
| diff -r 837224ad1694 -r 8934bc76bb52 test-data/01/mqpar.xml --- a/test-data/01/mqpar.xml Tue Jan 31 18:14:40 2023 +0000 +++ b/test-data/01/mqpar.xml Mon Jun 19 17:02:17 2023 +0000 |
| b |
| @@ -23,6 +23,7 @@ <separateLfq>False</separateLfq> <lfqStabilizeLargeRatios>True</lfqStabilizeLargeRatios> <lfqRequireMsms>True</lfqRequireMsms> + <lfqBayesQuant>False</lfqBayesQuant> <decoyMode>revert</decoyMode> <boxCarMode>all</boxCarMode> <includeContaminants>True</includeContaminants> @@ -55,9 +56,22 @@ <avalon>False</avalon> <nModColumns>3</nModColumns> <ibaqLogFit>False</ibaqLogFit> + <ibaqChargeNormalization>False</ibaqChargeNormalization> <razorProteinFdr>True</razorProteinFdr> <deNovoSequencing>False</deNovoSequencing> - <deNovoVarMods>True</deNovoVarMods> + <deNovoVarMods>False</deNovoVarMods> + <deNovoCompleteSequence>False</deNovoCompleteSequence> + <deNovoCalibratedMasses>False</deNovoCalibratedMasses> + <deNovoMaxIterations>0</deNovoMaxIterations> + <deNovoProteaseReward>0</deNovoProteaseReward> + <deNovoProteaseRewardTof>0</deNovoProteaseRewardTof> + <deNovoAgPenalty>0</deNovoAgPenalty> + <deNovoGgPenalty>0</deNovoGgPenalty> + <deNovoUseComplementScore>True</deNovoUseComplementScore> + <deNovoUseProteaseScore>True</deNovoUseProteaseScore> + <deNovoUseWaterLossScore>True</deNovoUseWaterLossScore> + <deNovoUseAmmoniaLossScore>True</deNovoUseAmmoniaLossScore> + <deNovoUseA2Score>True</deNovoUseA2Score> <massDifferenceSearch>False</massDifferenceSearch> <isotopeCalc>False</isotopeCalc> <writePeptidesForSpectrumFile/> @@ -97,11 +111,12 @@ <writeMsScansTable>False</writeMsScansTable> <writeMsmsScansTable>True</writeMsmsScansTable> <writePasefMsmsScansTable>True</writePasefMsmsScansTable> - <writeAccumulatedPasefMsmsScansTable>False</writeAccumulatedPasefMsmsScansTable> + <writeAccumulatedMsmsScansTable>True</writeAccumulatedMsmsScansTable> <writeMs3ScansTable>True</writeMs3ScansTable> <writeAllPeptidesTable>True</writeAllPeptidesTable> <writeMzRangeTable>True</writeMzRangeTable> <writeDiaFragmentTable>False</writeDiaFragmentTable> + <writeDiaFragmentQuantTable>False</writeDiaFragmentQuantTable> <writeMzTab>True</writeMzTab> <disableMd5>False</disableMd5> <cacheBinInds>True</cacheBinInds> @@ -112,10 +127,9 @@ <variationMode>none</variationMode> <useSeriesReporters>False</useSeriesReporters> <name>templateSession</name> - <maxQuantVersion>1.6.17.0</maxQuantVersion> + <maxQuantVersion>2.0.3.0</maxQuantVersion> <pluginFolder/> <numThreads>1</numThreads> - <batchSize>1</batchSize> <emailAddress/> <smtpHost/> <emailFromAddress/> @@ -151,6 +165,11 @@ <intensPred>False</intensPred> <intensPredModelReTrain>False</intensPredModelReTrain> <lfqTopNPeptides>0</lfqTopNPeptides> + <diaJoinPrecChargesForLfq>False</diaJoinPrecChargesForLfq> + <diaFragChargesForQuant>1</diaFragChargesForQuant> + <timsRearrangeSpectra>False</timsRearrangeSpectra> + <gridSpacing>0.5</gridSpacing> + <proteinGroupingFile/> <parameterGroups> <parameterGroup> <msInstrument>0</msInstrument> @@ -258,9 +277,16 @@ <timsCollapseMsms>True</timsCollapseMsms> <crossLinkingType>0</crossLinkingType> <crossLinker/> - <minMatchXl>0</minMatchXl> + <minMatchXl>3</minMatchXl> <minPairedPepLenXl>6</minPairedPepLenXl> + <minScore_Dipeptide>40</minScore_Dipeptide> + <minScore_Monopeptide>0</minScore_Monopeptide> + <minScore_PartialCross>10</minScore_PartialCross> <crosslinkOnlyIntraProtein>False</crosslinkOnlyIntraProtein> + <crosslinkIntensityBasedPrecursor>True</crosslinkIntensityBasedPrecursor> + <isHybridPrecDetermination>False</isHybridPrecDetermination> + <topXcross>3</topXcross> + <doesSeparateInterIntraProteinCross>False</doesSeparateInterIntraProteinCross> <crosslinkMaxMonoUnsaturated>0</crosslinkMaxMonoUnsaturated> <crosslinkMaxMonoSaturated>0</crosslinkMaxMonoSaturated> <crosslinkMaxDiUnsaturated>0</crosslinkMaxDiUnsaturated> @@ -277,6 +303,7 @@ <peakRefinement>False</peakRefinement> <isobaricSumOverWindow>True</isobaricSumOverWindow> <isobaricWeightExponent>0.75</isobaricWeightExponent> + <collapseMsmsOnIsotopePatterns>False</collapseMsmsOnIsotopePatterns> <diaLibraryType>0</diaLibraryType> <diaLibraryPaths> </diaLibraryPaths> @@ -323,6 +350,12 @@ <diaBackgroundSubtractionQuantile>0.5</diaBackgroundSubtractionQuantile> <diaBackgroundSubtractionFactor>4</diaBackgroundSubtractionFactor> <diaLfqWeightedMedian>False</diaLfqWeightedMedian> + <diaTransferQvalue>0.3</diaTransferQvalue> + <diaOnlyIsosForRecal>True</diaOnlyIsosForRecal> + <diaMinPeaksForRecal>5</diaMinPeaksForRecal> + <diaUseFragIntensForMl>False</diaUseFragIntensForMl> + <diaUseFragMassesForMl>False</diaUseFragMassesForMl> + <diaMaxTrainInstances>1000000</diaMaxTrainInstances> </parameterGroup> </parameterGroups> <msmsParamsArray> @@ -332,7 +365,7 @@ <MatchToleranceInPpm>True</MatchToleranceInPpm> <DeisotopeTolerance>7</DeisotopeTolerance> <DeisotopeToleranceInPpm>True</DeisotopeToleranceInPpm> - <DeNovoTolerance>10</DeNovoTolerance> + <DeNovoTolerance>25</DeNovoTolerance> <DeNovoToleranceInPpm>True</DeNovoToleranceInPpm> <Deisotope>True</Deisotope> <Topx>12</Topx> @@ -349,7 +382,7 @@ <MatchToleranceInPpm>False</MatchToleranceInPpm> <DeisotopeTolerance>0.15</DeisotopeTolerance> <DeisotopeToleranceInPpm>False</DeisotopeToleranceInPpm> - <DeNovoTolerance>0.25</DeNovoTolerance> + <DeNovoTolerance>0.5</DeNovoTolerance> <DeNovoToleranceInPpm>False</DeNovoToleranceInPpm> <Deisotope>False</Deisotope> <Topx>8</Topx> @@ -366,8 +399,8 @@ <MatchToleranceInPpm>True</MatchToleranceInPpm> <DeisotopeTolerance>0.01</DeisotopeTolerance> <DeisotopeToleranceInPpm>False</DeisotopeToleranceInPpm> - <DeNovoTolerance>0.02</DeNovoTolerance> - <DeNovoToleranceInPpm>False</DeNovoToleranceInPpm> + <DeNovoTolerance>25</DeNovoTolerance> + <DeNovoToleranceInPpm>True</DeNovoToleranceInPpm> <Deisotope>True</Deisotope> <Topx>10</Topx> <TopxInterval>100</TopxInterval> @@ -383,7 +416,7 @@ <MatchToleranceInPpm>True</MatchToleranceInPpm> <DeisotopeTolerance>7</DeisotopeTolerance> <DeisotopeToleranceInPpm>True</DeisotopeToleranceInPpm> - <DeNovoTolerance>10</DeNovoTolerance> + <DeNovoTolerance>25</DeNovoTolerance> <DeNovoToleranceInPpm>True</DeNovoToleranceInPpm> <Deisotope>True</Deisotope> <Topx>12</Topx> |
| b |
| diff -r 837224ad1694 -r 8934bc76bb52 test-data/02/mqpar.xml --- a/test-data/02/mqpar.xml Tue Jan 31 18:14:40 2023 +0000 +++ b/test-data/02/mqpar.xml Mon Jun 19 17:02:17 2023 +0000 |
| b |
| b'@@ -23,6 +23,7 @@\n \t<separateLfq>False</separateLfq>\n \t<lfqStabilizeLargeRatios>True</lfqStabilizeLargeRatios>\n \t<lfqRequireMsms>True</lfqRequireMsms>\n+\t<lfqBayesQuant>False</lfqBayesQuant>\n \t<decoyMode>randomize</decoyMode>\n \t<boxCarMode>all</boxCarMode>\n \t<includeContaminants>False</includeContaminants>\n@@ -55,9 +56,22 @@\n \t<avalon>False</avalon>\n \t<nModColumns>3</nModColumns>\n \t<ibaqLogFit>False</ibaqLogFit>\n+\t<ibaqChargeNormalization>False</ibaqChargeNormalization>\n \t<razorProteinFdr>True</razorProteinFdr>\n \t<deNovoSequencing>False</deNovoSequencing>\n-\t<deNovoVarMods>True</deNovoVarMods>\n+\t<deNovoVarMods>False</deNovoVarMods>\n+\t<deNovoCompleteSequence>False</deNovoCompleteSequence>\n+\t<deNovoCalibratedMasses>False</deNovoCalibratedMasses>\n+\t<deNovoMaxIterations>0</deNovoMaxIterations>\n+\t<deNovoProteaseReward>0</deNovoProteaseReward>\n+\t<deNovoProteaseRewardTof>0</deNovoProteaseRewardTof>\n+\t<deNovoAgPenalty>0</deNovoAgPenalty>\n+\t<deNovoGgPenalty>0</deNovoGgPenalty>\n+\t<deNovoUseComplementScore>True</deNovoUseComplementScore>\n+\t<deNovoUseProteaseScore>True</deNovoUseProteaseScore>\n+\t<deNovoUseWaterLossScore>True</deNovoUseWaterLossScore>\n+\t<deNovoUseAmmoniaLossScore>True</deNovoUseAmmoniaLossScore>\n+\t<deNovoUseA2Score>True</deNovoUseA2Score>\n \t<massDifferenceSearch>False</massDifferenceSearch>\n \t<isotopeCalc>False</isotopeCalc>\n \t<writePeptidesForSpectrumFile/>\n@@ -97,11 +111,12 @@\n \t<writeMsScansTable>False</writeMsScansTable>\n \t<writeMsmsScansTable>True</writeMsmsScansTable>\n \t<writePasefMsmsScansTable>True</writePasefMsmsScansTable>\n-\t<writeAccumulatedPasefMsmsScansTable>False</writeAccumulatedPasefMsmsScansTable>\n+\t<writeAccumulatedMsmsScansTable>True</writeAccumulatedMsmsScansTable>\n \t<writeMs3ScansTable>True</writeMs3ScansTable>\n \t<writeAllPeptidesTable>True</writeAllPeptidesTable>\n \t<writeMzRangeTable>True</writeMzRangeTable>\n \t<writeDiaFragmentTable>False</writeDiaFragmentTable>\n+\t<writeDiaFragmentQuantTable>False</writeDiaFragmentQuantTable>\n \t<writeMzTab>True</writeMzTab>\n \t<disableMd5>False</disableMd5>\n \t<cacheBinInds>True</cacheBinInds>\n@@ -112,10 +127,9 @@\n \t<variationMode>none</variationMode>\n \t<useSeriesReporters>False</useSeriesReporters>\n \t<name>templateSession</name>\n-\t<maxQuantVersion>1.6.17.0</maxQuantVersion>\n+\t<maxQuantVersion>2.0.3.0</maxQuantVersion>\n \t<pluginFolder/>\n \t<numThreads>1</numThreads>\n-\t<batchSize>1</batchSize>\n \t<emailAddress/>\n \t<smtpHost/>\n \t<emailFromAddress/>\n@@ -157,6 +171,11 @@\n \t<intensPred>False</intensPred>\n \t<intensPredModelReTrain>False</intensPredModelReTrain>\n \t<lfqTopNPeptides>0</lfqTopNPeptides>\n+\t<diaJoinPrecChargesForLfq>False</diaJoinPrecChargesForLfq>\n+\t<diaFragChargesForQuant>1</diaFragChargesForQuant>\n+\t<timsRearrangeSpectra>False</timsRearrangeSpectra>\n+\t<gridSpacing>0.5</gridSpacing>\n+\t<proteinGroupingFile/>\n \t<parameterGroups>\n \t\t<parameterGroup>\n \t\t\t<msInstrument>0</msInstrument>\n@@ -280,9 +299,16 @@\n \t\t\t<timsCollapseMsms>True</timsCollapseMsms>\n \t\t\t<crossLinkingType>0</crossLinkingType>\n \t\t\t<crossLinker/>\n-\t\t\t<minMatchXl>0</minMatchXl>\n+\t\t\t<minMatchXl>3</minMatchXl>\n \t\t\t<minPairedPepLenXl>6</minPairedPepLenXl>\n+\t\t\t<minScore_Dipeptide>40</minScore_Dipeptide>\n+\t\t\t<minScore_Monopeptide>0</minScore_Monopeptide>\n+\t\t\t<minScore_PartialCross>10</minScore_PartialCross>\n \t\t\t<crosslinkOnlyIntraProtein>False</crosslinkOnlyIntraProtein>\n+\t\t\t<crosslinkIntensityBasedPrecursor>True</crosslinkIntensityBasedPrecursor>\n+\t\t\t<isHybridPrecDetermination>False</isHybridPrecDetermination>\n+\t\t\t<topXcross>3</topXcross>\n+\t\t\t<doesSeparateInterIntraProteinCross>False</doesSeparateInterIntraProteinCross>\n \t\t\t<crosslinkMaxMonoUnsaturated>0</crosslinkMaxMonoUnsaturated>\n \t\t\t<crosslinkMaxMonoSaturated>0</crosslinkMaxMonoSaturated>\n \t\t\t<crosslinkMaxDiUnsaturated>0</crosslinkMaxDiUnsaturated>\n@@ -299,6 +325,7 @@\n \t\t\t<peakRefinement>False</peakRefinement>\n \t\t\t<isobaricSumOverWindow>True</isobaricSumOverWindow>\n \t\t\t<isobaricWeightExponent>0.75</isobaricWeightExponent>\n+\t\t\t<collapseMsmsOnIsotopePattern'..b'actionQuantile>0.5</diaBackgroundSubtractionQuantile>\n \t\t\t<diaBackgroundSubtractionFactor>4</diaBackgroundSubtractionFactor>\n \t\t\t<diaLfqWeightedMedian>False</diaLfqWeightedMedian>\n+\t\t\t<diaTransferQvalue>0.3</diaTransferQvalue>\n+\t\t\t<diaOnlyIsosForRecal>True</diaOnlyIsosForRecal>\n+\t\t\t<diaMinPeaksForRecal>5</diaMinPeaksForRecal>\n+\t\t\t<diaUseFragIntensForMl>False</diaUseFragIntensForMl>\n+\t\t\t<diaUseFragMassesForMl>False</diaUseFragMassesForMl>\n+\t\t\t<diaMaxTrainInstances>1000000</diaMaxTrainInstances>\n \t\t</parameterGroup>\n \t\t<parameterGroup>\n \t\t\t<msInstrument>0</msInstrument>\n@@ -482,9 +515,16 @@\n \t\t\t<timsCollapseMsms>True</timsCollapseMsms>\n \t\t\t<crossLinkingType>0</crossLinkingType>\n \t\t\t<crossLinker/>\n-\t\t\t<minMatchXl>0</minMatchXl>\n+\t\t\t<minMatchXl>3</minMatchXl>\n \t\t\t<minPairedPepLenXl>6</minPairedPepLenXl>\n+\t\t\t<minScore_Dipeptide>40</minScore_Dipeptide>\n+\t\t\t<minScore_Monopeptide>0</minScore_Monopeptide>\n+\t\t\t<minScore_PartialCross>10</minScore_PartialCross>\n \t\t\t<crosslinkOnlyIntraProtein>False</crosslinkOnlyIntraProtein>\n+\t\t\t<crosslinkIntensityBasedPrecursor>True</crosslinkIntensityBasedPrecursor>\n+\t\t\t<isHybridPrecDetermination>False</isHybridPrecDetermination>\n+\t\t\t<topXcross>3</topXcross>\n+\t\t\t<doesSeparateInterIntraProteinCross>False</doesSeparateInterIntraProteinCross>\n \t\t\t<crosslinkMaxMonoUnsaturated>0</crosslinkMaxMonoUnsaturated>\n \t\t\t<crosslinkMaxMonoSaturated>0</crosslinkMaxMonoSaturated>\n \t\t\t<crosslinkMaxDiUnsaturated>0</crosslinkMaxDiUnsaturated>\n@@ -501,6 +541,7 @@\n \t\t\t<peakRefinement>False</peakRefinement>\n \t\t\t<isobaricSumOverWindow>True</isobaricSumOverWindow>\n \t\t\t<isobaricWeightExponent>0.75</isobaricWeightExponent>\n+\t\t\t<collapseMsmsOnIsotopePatterns>False</collapseMsmsOnIsotopePatterns>\n \t\t\t<diaLibraryType>0</diaLibraryType>\n \t\t\t<diaLibraryPaths>\n </diaLibraryPaths>\n@@ -547,6 +588,12 @@\n \t\t\t<diaBackgroundSubtractionQuantile>0.5</diaBackgroundSubtractionQuantile>\n \t\t\t<diaBackgroundSubtractionFactor>4</diaBackgroundSubtractionFactor>\n \t\t\t<diaLfqWeightedMedian>False</diaLfqWeightedMedian>\n+\t\t\t<diaTransferQvalue>0.3</diaTransferQvalue>\n+\t\t\t<diaOnlyIsosForRecal>True</diaOnlyIsosForRecal>\n+\t\t\t<diaMinPeaksForRecal>5</diaMinPeaksForRecal>\n+\t\t\t<diaUseFragIntensForMl>False</diaUseFragIntensForMl>\n+\t\t\t<diaUseFragMassesForMl>False</diaUseFragMassesForMl>\n+\t\t\t<diaMaxTrainInstances>1000000</diaMaxTrainInstances>\n \t\t</parameterGroup>\n \t</parameterGroups>\n \t<msmsParamsArray>\n@@ -556,7 +603,7 @@\n \t\t\t<MatchToleranceInPpm>True</MatchToleranceInPpm>\n \t\t\t<DeisotopeTolerance>7</DeisotopeTolerance>\n \t\t\t<DeisotopeToleranceInPpm>True</DeisotopeToleranceInPpm>\n-\t\t\t<DeNovoTolerance>10</DeNovoTolerance>\n+\t\t\t<DeNovoTolerance>25</DeNovoTolerance>\n \t\t\t<DeNovoToleranceInPpm>True</DeNovoToleranceInPpm>\n \t\t\t<Deisotope>True</Deisotope>\n \t\t\t<Topx>12</Topx>\n@@ -573,7 +620,7 @@\n \t\t\t<MatchToleranceInPpm>False</MatchToleranceInPpm>\n \t\t\t<DeisotopeTolerance>0.15</DeisotopeTolerance>\n \t\t\t<DeisotopeToleranceInPpm>False</DeisotopeToleranceInPpm>\n-\t\t\t<DeNovoTolerance>0.25</DeNovoTolerance>\n+\t\t\t<DeNovoTolerance>0.5</DeNovoTolerance>\n \t\t\t<DeNovoToleranceInPpm>False</DeNovoToleranceInPpm>\n \t\t\t<Deisotope>False</Deisotope>\n \t\t\t<Topx>8</Topx>\n@@ -590,8 +637,8 @@\n \t\t\t<MatchToleranceInPpm>True</MatchToleranceInPpm>\n \t\t\t<DeisotopeTolerance>0.01</DeisotopeTolerance>\n \t\t\t<DeisotopeToleranceInPpm>False</DeisotopeToleranceInPpm>\n-\t\t\t<DeNovoTolerance>0.02</DeNovoTolerance>\n-\t\t\t<DeNovoToleranceInPpm>False</DeNovoToleranceInPpm>\n+\t\t\t<DeNovoTolerance>25</DeNovoTolerance>\n+\t\t\t<DeNovoToleranceInPpm>True</DeNovoToleranceInPpm>\n \t\t\t<Deisotope>True</Deisotope>\n \t\t\t<Topx>10</Topx>\n \t\t\t<TopxInterval>100</TopxInterval>\n@@ -607,7 +654,7 @@\n \t\t\t<MatchToleranceInPpm>True</MatchToleranceInPpm>\n \t\t\t<DeisotopeTolerance>7</DeisotopeTolerance>\n \t\t\t<DeisotopeToleranceInPpm>True</DeisotopeToleranceInPpm>\n-\t\t\t<DeNovoTolerance>10</DeNovoTolerance>\n+\t\t\t<DeNovoTolerance>25</DeNovoTolerance>\n \t\t\t<DeNovoToleranceInPpm>True</DeNovoToleranceInPpm>\n \t\t\t<Deisotope>True</Deisotope>\n \t\t\t<Topx>12</Topx>\n' |
| b |
| diff -r 837224ad1694 -r 8934bc76bb52 test-data/03/mqpar.xml --- a/test-data/03/mqpar.xml Tue Jan 31 18:14:40 2023 +0000 +++ b/test-data/03/mqpar.xml Mon Jun 19 17:02:17 2023 +0000 |
| b |
| @@ -23,6 +23,7 @@ <separateLfq>False</separateLfq> <lfqStabilizeLargeRatios>True</lfqStabilizeLargeRatios> <lfqRequireMsms>True</lfqRequireMsms> + <lfqBayesQuant>False</lfqBayesQuant> <decoyMode>revert</decoyMode> <boxCarMode>all</boxCarMode> <includeContaminants>True</includeContaminants> @@ -55,9 +56,22 @@ <avalon>False</avalon> <nModColumns>3</nModColumns> <ibaqLogFit>False</ibaqLogFit> + <ibaqChargeNormalization>False</ibaqChargeNormalization> <razorProteinFdr>True</razorProteinFdr> <deNovoSequencing>False</deNovoSequencing> - <deNovoVarMods>True</deNovoVarMods> + <deNovoVarMods>False</deNovoVarMods> + <deNovoCompleteSequence>False</deNovoCompleteSequence> + <deNovoCalibratedMasses>False</deNovoCalibratedMasses> + <deNovoMaxIterations>0</deNovoMaxIterations> + <deNovoProteaseReward>0</deNovoProteaseReward> + <deNovoProteaseRewardTof>0</deNovoProteaseRewardTof> + <deNovoAgPenalty>0</deNovoAgPenalty> + <deNovoGgPenalty>0</deNovoGgPenalty> + <deNovoUseComplementScore>True</deNovoUseComplementScore> + <deNovoUseProteaseScore>True</deNovoUseProteaseScore> + <deNovoUseWaterLossScore>True</deNovoUseWaterLossScore> + <deNovoUseAmmoniaLossScore>True</deNovoUseAmmoniaLossScore> + <deNovoUseA2Score>True</deNovoUseA2Score> <massDifferenceSearch>False</massDifferenceSearch> <isotopeCalc>False</isotopeCalc> <writePeptidesForSpectrumFile/> @@ -97,11 +111,12 @@ <writeMsScansTable>False</writeMsScansTable> <writeMsmsScansTable>True</writeMsmsScansTable> <writePasefMsmsScansTable>True</writePasefMsmsScansTable> - <writeAccumulatedPasefMsmsScansTable>False</writeAccumulatedPasefMsmsScansTable> + <writeAccumulatedMsmsScansTable>True</writeAccumulatedMsmsScansTable> <writeMs3ScansTable>True</writeMs3ScansTable> <writeAllPeptidesTable>True</writeAllPeptidesTable> <writeMzRangeTable>True</writeMzRangeTable> <writeDiaFragmentTable>False</writeDiaFragmentTable> + <writeDiaFragmentQuantTable>False</writeDiaFragmentQuantTable> <writeMzTab>False</writeMzTab> <disableMd5>False</disableMd5> <cacheBinInds>True</cacheBinInds> @@ -112,10 +127,9 @@ <variationMode>none</variationMode> <useSeriesReporters>False</useSeriesReporters> <name>templateSession</name> - <maxQuantVersion>1.6.17.0</maxQuantVersion> + <maxQuantVersion>2.0.3.0</maxQuantVersion> <pluginFolder/> - <numThreads>2</numThreads> - <batchSize>1</batchSize> + <numThreads>1</numThreads> <emailAddress/> <smtpHost/> <emailFromAddress/> @@ -151,6 +165,11 @@ <intensPred>False</intensPred> <intensPredModelReTrain>False</intensPredModelReTrain> <lfqTopNPeptides>0</lfqTopNPeptides> + <diaJoinPrecChargesForLfq>False</diaJoinPrecChargesForLfq> + <diaFragChargesForQuant>1</diaFragChargesForQuant> + <timsRearrangeSpectra>False</timsRearrangeSpectra> + <gridSpacing>0.5</gridSpacing> + <proteinGroupingFile/> <parameterGroups> <parameterGroup> <msInstrument>0</msInstrument> @@ -258,9 +277,16 @@ <timsCollapseMsms>True</timsCollapseMsms> <crossLinkingType>0</crossLinkingType> <crossLinker/> - <minMatchXl>0</minMatchXl> + <minMatchXl>3</minMatchXl> <minPairedPepLenXl>6</minPairedPepLenXl> + <minScore_Dipeptide>40</minScore_Dipeptide> + <minScore_Monopeptide>0</minScore_Monopeptide> + <minScore_PartialCross>10</minScore_PartialCross> <crosslinkOnlyIntraProtein>False</crosslinkOnlyIntraProtein> + <crosslinkIntensityBasedPrecursor>True</crosslinkIntensityBasedPrecursor> + <isHybridPrecDetermination>False</isHybridPrecDetermination> + <topXcross>3</topXcross> + <doesSeparateInterIntraProteinCross>False</doesSeparateInterIntraProteinCross> <crosslinkMaxMonoUnsaturated>0</crosslinkMaxMonoUnsaturated> <crosslinkMaxMonoSaturated>0</crosslinkMaxMonoSaturated> <crosslinkMaxDiUnsaturated>0</crosslinkMaxDiUnsaturated> @@ -277,6 +303,7 @@ <peakRefinement>False</peakRefinement> <isobaricSumOverWindow>True</isobaricSumOverWindow> <isobaricWeightExponent>0.75</isobaricWeightExponent> + <collapseMsmsOnIsotopePatterns>False</collapseMsmsOnIsotopePatterns> <diaLibraryType>0</diaLibraryType> <diaLibraryPaths> </diaLibraryPaths> @@ -298,7 +325,7 @@ <centroidPosition>0</centroidPosition> <diaQuantMethod>7</diaQuantMethod> <diaFeatureQuantMethod>2</diaFeatureQuantMethod> - <lfqNormType>0</lfqNormType> + <lfqNormType>1</lfqNormType> <diaTopNForQuant>10</diaTopNForQuant> <diaMinMsmsIntensityForQuant>0</diaMinMsmsIntensityForQuant> <diaTopMsmsIntensityQuantileForQuant>0.85</diaTopMsmsIntensityQuantileForQuant> @@ -323,6 +350,12 @@ <diaBackgroundSubtractionQuantile>0.5</diaBackgroundSubtractionQuantile> <diaBackgroundSubtractionFactor>4</diaBackgroundSubtractionFactor> <diaLfqWeightedMedian>False</diaLfqWeightedMedian> + <diaTransferQvalue>0.3</diaTransferQvalue> + <diaOnlyIsosForRecal>True</diaOnlyIsosForRecal> + <diaMinPeaksForRecal>5</diaMinPeaksForRecal> + <diaUseFragIntensForMl>False</diaUseFragIntensForMl> + <diaUseFragMassesForMl>False</diaUseFragMassesForMl> + <diaMaxTrainInstances>1000000</diaMaxTrainInstances> </parameterGroup> </parameterGroups> <msmsParamsArray> @@ -332,7 +365,7 @@ <MatchToleranceInPpm>True</MatchToleranceInPpm> <DeisotopeTolerance>7</DeisotopeTolerance> <DeisotopeToleranceInPpm>True</DeisotopeToleranceInPpm> - <DeNovoTolerance>10</DeNovoTolerance> + <DeNovoTolerance>25</DeNovoTolerance> <DeNovoToleranceInPpm>True</DeNovoToleranceInPpm> <Deisotope>True</Deisotope> <Topx>12</Topx> @@ -349,7 +382,7 @@ <MatchToleranceInPpm>False</MatchToleranceInPpm> <DeisotopeTolerance>0.15</DeisotopeTolerance> <DeisotopeToleranceInPpm>False</DeisotopeToleranceInPpm> - <DeNovoTolerance>0.25</DeNovoTolerance> + <DeNovoTolerance>0.5</DeNovoTolerance> <DeNovoToleranceInPpm>False</DeNovoToleranceInPpm> <Deisotope>False</Deisotope> <Topx>8</Topx> @@ -366,8 +399,8 @@ <MatchToleranceInPpm>True</MatchToleranceInPpm> <DeisotopeTolerance>0.01</DeisotopeTolerance> <DeisotopeToleranceInPpm>False</DeisotopeToleranceInPpm> - <DeNovoTolerance>0.02</DeNovoTolerance> - <DeNovoToleranceInPpm>False</DeNovoToleranceInPpm> + <DeNovoTolerance>25</DeNovoTolerance> + <DeNovoToleranceInPpm>True</DeNovoToleranceInPpm> <Deisotope>True</Deisotope> <Topx>10</Topx> <TopxInterval>100</TopxInterval> @@ -383,7 +416,7 @@ <MatchToleranceInPpm>True</MatchToleranceInPpm> <DeisotopeTolerance>7</DeisotopeTolerance> <DeisotopeToleranceInPpm>True</DeisotopeToleranceInPpm> - <DeNovoTolerance>10</DeNovoTolerance> + <DeNovoTolerance>25</DeNovoTolerance> <DeNovoToleranceInPpm>True</DeNovoToleranceInPpm> <Deisotope>True</Deisotope> <Topx>12</Topx> |
| b |
| diff -r 837224ad1694 -r 8934bc76bb52 test-data/04/mqpar.xml --- a/test-data/04/mqpar.xml Tue Jan 31 18:14:40 2023 +0000 +++ b/test-data/04/mqpar.xml Mon Jun 19 17:02:17 2023 +0000 |
| b |
| @@ -23,6 +23,7 @@ <separateLfq>False</separateLfq> <lfqStabilizeLargeRatios>True</lfqStabilizeLargeRatios> <lfqRequireMsms>True</lfqRequireMsms> + <lfqBayesQuant>False</lfqBayesQuant> <decoyMode>revert</decoyMode> <boxCarMode>all</boxCarMode> <includeContaminants>True</includeContaminants> @@ -55,9 +56,22 @@ <avalon>False</avalon> <nModColumns>3</nModColumns> <ibaqLogFit>False</ibaqLogFit> + <ibaqChargeNormalization>False</ibaqChargeNormalization> <razorProteinFdr>True</razorProteinFdr> <deNovoSequencing>False</deNovoSequencing> - <deNovoVarMods>True</deNovoVarMods> + <deNovoVarMods>False</deNovoVarMods> + <deNovoCompleteSequence>False</deNovoCompleteSequence> + <deNovoCalibratedMasses>False</deNovoCalibratedMasses> + <deNovoMaxIterations>0</deNovoMaxIterations> + <deNovoProteaseReward>0</deNovoProteaseReward> + <deNovoProteaseRewardTof>0</deNovoProteaseRewardTof> + <deNovoAgPenalty>0</deNovoAgPenalty> + <deNovoGgPenalty>0</deNovoGgPenalty> + <deNovoUseComplementScore>True</deNovoUseComplementScore> + <deNovoUseProteaseScore>True</deNovoUseProteaseScore> + <deNovoUseWaterLossScore>True</deNovoUseWaterLossScore> + <deNovoUseAmmoniaLossScore>True</deNovoUseAmmoniaLossScore> + <deNovoUseA2Score>True</deNovoUseA2Score> <massDifferenceSearch>False</massDifferenceSearch> <isotopeCalc>False</isotopeCalc> <writePeptidesForSpectrumFile/> @@ -97,11 +111,12 @@ <writeMsScansTable>False</writeMsScansTable> <writeMsmsScansTable>True</writeMsmsScansTable> <writePasefMsmsScansTable>True</writePasefMsmsScansTable> - <writeAccumulatedPasefMsmsScansTable>False</writeAccumulatedPasefMsmsScansTable> + <writeAccumulatedMsmsScansTable>True</writeAccumulatedMsmsScansTable> <writeMs3ScansTable>True</writeMs3ScansTable> <writeAllPeptidesTable>True</writeAllPeptidesTable> <writeMzRangeTable>True</writeMzRangeTable> <writeDiaFragmentTable>False</writeDiaFragmentTable> + <writeDiaFragmentQuantTable>False</writeDiaFragmentQuantTable> <writeMzTab>False</writeMzTab> <disableMd5>False</disableMd5> <cacheBinInds>True</cacheBinInds> @@ -112,10 +127,9 @@ <variationMode>none</variationMode> <useSeriesReporters>False</useSeriesReporters> <name>templateSession</name> - <maxQuantVersion>1.6.17.0</maxQuantVersion> + <maxQuantVersion>2.0.3.0</maxQuantVersion> <pluginFolder/> <numThreads>1</numThreads> - <batchSize>1</batchSize> <emailAddress/> <smtpHost/> <emailFromAddress/> @@ -157,6 +171,11 @@ <intensPred>False</intensPred> <intensPredModelReTrain>False</intensPredModelReTrain> <lfqTopNPeptides>0</lfqTopNPeptides> + <diaJoinPrecChargesForLfq>False</diaJoinPrecChargesForLfq> + <diaFragChargesForQuant>1</diaFragChargesForQuant> + <timsRearrangeSpectra>False</timsRearrangeSpectra> + <gridSpacing>0.5</gridSpacing> + <proteinGroupingFile/> <parameterGroups> <parameterGroup> <msInstrument>0</msInstrument> @@ -265,9 +284,16 @@ <timsCollapseMsms>True</timsCollapseMsms> <crossLinkingType>0</crossLinkingType> <crossLinker/> - <minMatchXl>0</minMatchXl> + <minMatchXl>3</minMatchXl> <minPairedPepLenXl>6</minPairedPepLenXl> + <minScore_Dipeptide>40</minScore_Dipeptide> + <minScore_Monopeptide>0</minScore_Monopeptide> + <minScore_PartialCross>10</minScore_PartialCross> <crosslinkOnlyIntraProtein>False</crosslinkOnlyIntraProtein> + <crosslinkIntensityBasedPrecursor>True</crosslinkIntensityBasedPrecursor> + <isHybridPrecDetermination>False</isHybridPrecDetermination> + <topXcross>3</topXcross> + <doesSeparateInterIntraProteinCross>False</doesSeparateInterIntraProteinCross> <crosslinkMaxMonoUnsaturated>0</crosslinkMaxMonoUnsaturated> <crosslinkMaxMonoSaturated>0</crosslinkMaxMonoSaturated> <crosslinkMaxDiUnsaturated>0</crosslinkMaxDiUnsaturated> @@ -284,6 +310,7 @@ <peakRefinement>False</peakRefinement> <isobaricSumOverWindow>True</isobaricSumOverWindow> <isobaricWeightExponent>0.75</isobaricWeightExponent> + <collapseMsmsOnIsotopePatterns>False</collapseMsmsOnIsotopePatterns> <diaLibraryType>0</diaLibraryType> <diaLibraryPaths> </diaLibraryPaths> @@ -330,6 +357,12 @@ <diaBackgroundSubtractionQuantile>0.5</diaBackgroundSubtractionQuantile> <diaBackgroundSubtractionFactor>4</diaBackgroundSubtractionFactor> <diaLfqWeightedMedian>False</diaLfqWeightedMedian> + <diaTransferQvalue>0.3</diaTransferQvalue> + <diaOnlyIsosForRecal>True</diaOnlyIsosForRecal> + <diaMinPeaksForRecal>5</diaMinPeaksForRecal> + <diaUseFragIntensForMl>False</diaUseFragIntensForMl> + <diaUseFragMassesForMl>False</diaUseFragMassesForMl> + <diaMaxTrainInstances>1000000</diaMaxTrainInstances> </parameterGroup> </parameterGroups> <msmsParamsArray> @@ -339,7 +372,7 @@ <MatchToleranceInPpm>True</MatchToleranceInPpm> <DeisotopeTolerance>7</DeisotopeTolerance> <DeisotopeToleranceInPpm>True</DeisotopeToleranceInPpm> - <DeNovoTolerance>10</DeNovoTolerance> + <DeNovoTolerance>25</DeNovoTolerance> <DeNovoToleranceInPpm>True</DeNovoToleranceInPpm> <Deisotope>True</Deisotope> <Topx>12</Topx> @@ -356,7 +389,7 @@ <MatchToleranceInPpm>False</MatchToleranceInPpm> <DeisotopeTolerance>0.15</DeisotopeTolerance> <DeisotopeToleranceInPpm>False</DeisotopeToleranceInPpm> - <DeNovoTolerance>0.25</DeNovoTolerance> + <DeNovoTolerance>0.5</DeNovoTolerance> <DeNovoToleranceInPpm>False</DeNovoToleranceInPpm> <Deisotope>False</Deisotope> <Topx>8</Topx> @@ -373,8 +406,8 @@ <MatchToleranceInPpm>True</MatchToleranceInPpm> <DeisotopeTolerance>0.01</DeisotopeTolerance> <DeisotopeToleranceInPpm>False</DeisotopeToleranceInPpm> - <DeNovoTolerance>0.02</DeNovoTolerance> - <DeNovoToleranceInPpm>False</DeNovoToleranceInPpm> + <DeNovoTolerance>25</DeNovoTolerance> + <DeNovoToleranceInPpm>True</DeNovoToleranceInPpm> <Deisotope>True</Deisotope> <Topx>10</Topx> <TopxInterval>100</TopxInterval> @@ -390,7 +423,7 @@ <MatchToleranceInPpm>True</MatchToleranceInPpm> <DeisotopeTolerance>7</DeisotopeTolerance> <DeisotopeToleranceInPpm>True</DeisotopeToleranceInPpm> - <DeNovoTolerance>10</DeNovoTolerance> + <DeNovoTolerance>25</DeNovoTolerance> <DeNovoToleranceInPpm>True</DeNovoToleranceInPpm> <Deisotope>True</Deisotope> <Topx>12</Topx> |
| b |
| diff -r 837224ad1694 -r 8934bc76bb52 test-data/05/mqpar.xml --- a/test-data/05/mqpar.xml Tue Jan 31 18:14:40 2023 +0000 +++ b/test-data/05/mqpar.xml Mon Jun 19 17:02:17 2023 +0000 |
| b |
| @@ -23,6 +23,7 @@ <separateLfq>False</separateLfq> <lfqStabilizeLargeRatios>True</lfqStabilizeLargeRatios> <lfqRequireMsms>True</lfqRequireMsms> + <lfqBayesQuant>False</lfqBayesQuant> <decoyMode>revert</decoyMode> <boxCarMode>all</boxCarMode> <includeContaminants>True</includeContaminants> @@ -55,9 +56,22 @@ <avalon>False</avalon> <nModColumns>3</nModColumns> <ibaqLogFit>False</ibaqLogFit> + <ibaqChargeNormalization>False</ibaqChargeNormalization> <razorProteinFdr>True</razorProteinFdr> <deNovoSequencing>False</deNovoSequencing> - <deNovoVarMods>True</deNovoVarMods> + <deNovoVarMods>False</deNovoVarMods> + <deNovoCompleteSequence>False</deNovoCompleteSequence> + <deNovoCalibratedMasses>False</deNovoCalibratedMasses> + <deNovoMaxIterations>0</deNovoMaxIterations> + <deNovoProteaseReward>0</deNovoProteaseReward> + <deNovoProteaseRewardTof>0</deNovoProteaseRewardTof> + <deNovoAgPenalty>0</deNovoAgPenalty> + <deNovoGgPenalty>0</deNovoGgPenalty> + <deNovoUseComplementScore>True</deNovoUseComplementScore> + <deNovoUseProteaseScore>True</deNovoUseProteaseScore> + <deNovoUseWaterLossScore>True</deNovoUseWaterLossScore> + <deNovoUseAmmoniaLossScore>True</deNovoUseAmmoniaLossScore> + <deNovoUseA2Score>True</deNovoUseA2Score> <massDifferenceSearch>False</massDifferenceSearch> <isotopeCalc>False</isotopeCalc> <writePeptidesForSpectrumFile/> @@ -97,11 +111,12 @@ <writeMsScansTable>False</writeMsScansTable> <writeMsmsScansTable>True</writeMsmsScansTable> <writePasefMsmsScansTable>True</writePasefMsmsScansTable> - <writeAccumulatedPasefMsmsScansTable>False</writeAccumulatedPasefMsmsScansTable> + <writeAccumulatedMsmsScansTable>True</writeAccumulatedMsmsScansTable> <writeMs3ScansTable>True</writeMs3ScansTable> <writeAllPeptidesTable>True</writeAllPeptidesTable> <writeMzRangeTable>True</writeMzRangeTable> <writeDiaFragmentTable>False</writeDiaFragmentTable> + <writeDiaFragmentQuantTable>False</writeDiaFragmentQuantTable> <writeMzTab>False</writeMzTab> <disableMd5>False</disableMd5> <cacheBinInds>True</cacheBinInds> @@ -112,10 +127,9 @@ <variationMode>none</variationMode> <useSeriesReporters>False</useSeriesReporters> <name>templateSession</name> - <maxQuantVersion>1.6.17.0</maxQuantVersion> + <maxQuantVersion>2.0.3.0</maxQuantVersion> <pluginFolder/> - <numThreads>2</numThreads> - <batchSize>1</batchSize> + <numThreads>1</numThreads> <emailAddress/> <smtpHost/> <emailFromAddress/> @@ -151,6 +165,11 @@ <intensPred>False</intensPred> <intensPredModelReTrain>False</intensPredModelReTrain> <lfqTopNPeptides>0</lfqTopNPeptides> + <diaJoinPrecChargesForLfq>False</diaJoinPrecChargesForLfq> + <diaFragChargesForQuant>1</diaFragChargesForQuant> + <timsRearrangeSpectra>False</timsRearrangeSpectra> + <gridSpacing>0.5</gridSpacing> + <proteinGroupingFile/> <parameterGroups> <parameterGroup> <msInstrument>0</msInstrument> @@ -258,9 +277,16 @@ <timsCollapseMsms>True</timsCollapseMsms> <crossLinkingType>0</crossLinkingType> <crossLinker/> - <minMatchXl>0</minMatchXl> + <minMatchXl>3</minMatchXl> <minPairedPepLenXl>6</minPairedPepLenXl> + <minScore_Dipeptide>40</minScore_Dipeptide> + <minScore_Monopeptide>0</minScore_Monopeptide> + <minScore_PartialCross>10</minScore_PartialCross> <crosslinkOnlyIntraProtein>False</crosslinkOnlyIntraProtein> + <crosslinkIntensityBasedPrecursor>True</crosslinkIntensityBasedPrecursor> + <isHybridPrecDetermination>False</isHybridPrecDetermination> + <topXcross>3</topXcross> + <doesSeparateInterIntraProteinCross>False</doesSeparateInterIntraProteinCross> <crosslinkMaxMonoUnsaturated>0</crosslinkMaxMonoUnsaturated> <crosslinkMaxMonoSaturated>0</crosslinkMaxMonoSaturated> <crosslinkMaxDiUnsaturated>0</crosslinkMaxDiUnsaturated> @@ -277,6 +303,7 @@ <peakRefinement>False</peakRefinement> <isobaricSumOverWindow>True</isobaricSumOverWindow> <isobaricWeightExponent>0.75</isobaricWeightExponent> + <collapseMsmsOnIsotopePatterns>False</collapseMsmsOnIsotopePatterns> <diaLibraryType>0</diaLibraryType> <diaLibraryPaths> </diaLibraryPaths> @@ -323,6 +350,12 @@ <diaBackgroundSubtractionQuantile>0.5</diaBackgroundSubtractionQuantile> <diaBackgroundSubtractionFactor>4</diaBackgroundSubtractionFactor> <diaLfqWeightedMedian>False</diaLfqWeightedMedian> + <diaTransferQvalue>0.3</diaTransferQvalue> + <diaOnlyIsosForRecal>True</diaOnlyIsosForRecal> + <diaMinPeaksForRecal>5</diaMinPeaksForRecal> + <diaUseFragIntensForMl>False</diaUseFragIntensForMl> + <diaUseFragMassesForMl>False</diaUseFragMassesForMl> + <diaMaxTrainInstances>1000000</diaMaxTrainInstances> </parameterGroup> </parameterGroups> <msmsParamsArray> @@ -332,7 +365,7 @@ <MatchToleranceInPpm>True</MatchToleranceInPpm> <DeisotopeTolerance>7</DeisotopeTolerance> <DeisotopeToleranceInPpm>True</DeisotopeToleranceInPpm> - <DeNovoTolerance>10</DeNovoTolerance> + <DeNovoTolerance>25</DeNovoTolerance> <DeNovoToleranceInPpm>True</DeNovoToleranceInPpm> <Deisotope>True</Deisotope> <Topx>12</Topx> @@ -349,7 +382,7 @@ <MatchToleranceInPpm>False</MatchToleranceInPpm> <DeisotopeTolerance>0.15</DeisotopeTolerance> <DeisotopeToleranceInPpm>False</DeisotopeToleranceInPpm> - <DeNovoTolerance>0.25</DeNovoTolerance> + <DeNovoTolerance>0.5</DeNovoTolerance> <DeNovoToleranceInPpm>False</DeNovoToleranceInPpm> <Deisotope>False</Deisotope> <Topx>8</Topx> @@ -366,8 +399,8 @@ <MatchToleranceInPpm>True</MatchToleranceInPpm> <DeisotopeTolerance>0.01</DeisotopeTolerance> <DeisotopeToleranceInPpm>False</DeisotopeToleranceInPpm> - <DeNovoTolerance>0.02</DeNovoTolerance> - <DeNovoToleranceInPpm>False</DeNovoToleranceInPpm> + <DeNovoTolerance>25</DeNovoTolerance> + <DeNovoToleranceInPpm>True</DeNovoToleranceInPpm> <Deisotope>True</Deisotope> <Topx>10</Topx> <TopxInterval>100</TopxInterval> @@ -383,7 +416,7 @@ <MatchToleranceInPpm>True</MatchToleranceInPpm> <DeisotopeTolerance>7</DeisotopeTolerance> <DeisotopeToleranceInPpm>True</DeisotopeToleranceInPpm> - <DeNovoTolerance>10</DeNovoTolerance> + <DeNovoTolerance>25</DeNovoTolerance> <DeNovoToleranceInPpm>True</DeNovoToleranceInPpm> <Deisotope>True</Deisotope> <Topx>12</Topx> |
| b |
| diff -r 837224ad1694 -r 8934bc76bb52 test-data/06/mqpar.xml --- a/test-data/06/mqpar.xml Tue Jan 31 18:14:40 2023 +0000 +++ b/test-data/06/mqpar.xml Mon Jun 19 17:02:17 2023 +0000 |
| b |
| b'@@ -23,6 +23,7 @@\n \t<separateLfq>False</separateLfq>\n \t<lfqStabilizeLargeRatios>True</lfqStabilizeLargeRatios>\n \t<lfqRequireMsms>True</lfqRequireMsms>\n+\t<lfqBayesQuant>False</lfqBayesQuant>\n \t<decoyMode>randomize</decoyMode>\n \t<boxCarMode>all</boxCarMode>\n \t<includeContaminants>False</includeContaminants>\n@@ -55,9 +56,22 @@\n \t<avalon>False</avalon>\n \t<nModColumns>3</nModColumns>\n \t<ibaqLogFit>False</ibaqLogFit>\n+\t<ibaqChargeNormalization>False</ibaqChargeNormalization>\n \t<razorProteinFdr>True</razorProteinFdr>\n \t<deNovoSequencing>False</deNovoSequencing>\n-\t<deNovoVarMods>True</deNovoVarMods>\n+\t<deNovoVarMods>False</deNovoVarMods>\n+\t<deNovoCompleteSequence>False</deNovoCompleteSequence>\n+\t<deNovoCalibratedMasses>False</deNovoCalibratedMasses>\n+\t<deNovoMaxIterations>0</deNovoMaxIterations>\n+\t<deNovoProteaseReward>0</deNovoProteaseReward>\n+\t<deNovoProteaseRewardTof>0</deNovoProteaseRewardTof>\n+\t<deNovoAgPenalty>0</deNovoAgPenalty>\n+\t<deNovoGgPenalty>0</deNovoGgPenalty>\n+\t<deNovoUseComplementScore>True</deNovoUseComplementScore>\n+\t<deNovoUseProteaseScore>True</deNovoUseProteaseScore>\n+\t<deNovoUseWaterLossScore>True</deNovoUseWaterLossScore>\n+\t<deNovoUseAmmoniaLossScore>True</deNovoUseAmmoniaLossScore>\n+\t<deNovoUseA2Score>True</deNovoUseA2Score>\n \t<massDifferenceSearch>False</massDifferenceSearch>\n \t<isotopeCalc>False</isotopeCalc>\n \t<writePeptidesForSpectrumFile/>\n@@ -97,11 +111,12 @@\n \t<writeMsScansTable>False</writeMsScansTable>\n \t<writeMsmsScansTable>True</writeMsmsScansTable>\n \t<writePasefMsmsScansTable>True</writePasefMsmsScansTable>\n-\t<writeAccumulatedPasefMsmsScansTable>False</writeAccumulatedPasefMsmsScansTable>\n+\t<writeAccumulatedMsmsScansTable>True</writeAccumulatedMsmsScansTable>\n \t<writeMs3ScansTable>True</writeMs3ScansTable>\n \t<writeAllPeptidesTable>True</writeAllPeptidesTable>\n \t<writeMzRangeTable>True</writeMzRangeTable>\n \t<writeDiaFragmentTable>False</writeDiaFragmentTable>\n+\t<writeDiaFragmentQuantTable>False</writeDiaFragmentQuantTable>\n \t<writeMzTab>True</writeMzTab>\n \t<disableMd5>False</disableMd5>\n \t<cacheBinInds>True</cacheBinInds>\n@@ -112,10 +127,9 @@\n \t<variationMode>none</variationMode>\n \t<useSeriesReporters>False</useSeriesReporters>\n \t<name>templateSession</name>\n-\t<maxQuantVersion>1.6.17.0</maxQuantVersion>\n+\t<maxQuantVersion>2.0.3.0</maxQuantVersion>\n \t<pluginFolder/>\n-\t<numThreads>2</numThreads>\n-\t<batchSize>1</batchSize>\n+\t<numThreads>1</numThreads>\n \t<emailAddress/>\n \t<smtpHost/>\n \t<emailFromAddress/>\n@@ -157,6 +171,11 @@\n \t<intensPred>False</intensPred>\n \t<intensPredModelReTrain>False</intensPredModelReTrain>\n \t<lfqTopNPeptides>0</lfqTopNPeptides>\n+\t<diaJoinPrecChargesForLfq>False</diaJoinPrecChargesForLfq>\n+\t<diaFragChargesForQuant>1</diaFragChargesForQuant>\n+\t<timsRearrangeSpectra>False</timsRearrangeSpectra>\n+\t<gridSpacing>0.5</gridSpacing>\n+\t<proteinGroupingFile/>\n \t<parameterGroups>\n \t\t<parameterGroup>\n \t\t\t<msInstrument>0</msInstrument>\n@@ -280,9 +299,16 @@\n \t\t\t<timsCollapseMsms>True</timsCollapseMsms>\n \t\t\t<crossLinkingType>0</crossLinkingType>\n \t\t\t<crossLinker/>\n-\t\t\t<minMatchXl>0</minMatchXl>\n+\t\t\t<minMatchXl>3</minMatchXl>\n \t\t\t<minPairedPepLenXl>6</minPairedPepLenXl>\n+\t\t\t<minScore_Dipeptide>40</minScore_Dipeptide>\n+\t\t\t<minScore_Monopeptide>0</minScore_Monopeptide>\n+\t\t\t<minScore_PartialCross>10</minScore_PartialCross>\n \t\t\t<crosslinkOnlyIntraProtein>False</crosslinkOnlyIntraProtein>\n+\t\t\t<crosslinkIntensityBasedPrecursor>True</crosslinkIntensityBasedPrecursor>\n+\t\t\t<isHybridPrecDetermination>False</isHybridPrecDetermination>\n+\t\t\t<topXcross>3</topXcross>\n+\t\t\t<doesSeparateInterIntraProteinCross>False</doesSeparateInterIntraProteinCross>\n \t\t\t<crosslinkMaxMonoUnsaturated>0</crosslinkMaxMonoUnsaturated>\n \t\t\t<crosslinkMaxMonoSaturated>0</crosslinkMaxMonoSaturated>\n \t\t\t<crosslinkMaxDiUnsaturated>0</crosslinkMaxDiUnsaturated>\n@@ -299,6 +325,7 @@\n \t\t\t<peakRefinement>False</peakRefinement>\n \t\t\t<isobaricSumOverWindow>True</isobaricSumOverWindow>\n \t\t\t<isobaricWeightExponent>0.75</isobaricWeightExponent>\n+\t\t\t'..b'actionQuantile>0.5</diaBackgroundSubtractionQuantile>\n \t\t\t<diaBackgroundSubtractionFactor>4</diaBackgroundSubtractionFactor>\n \t\t\t<diaLfqWeightedMedian>False</diaLfqWeightedMedian>\n+\t\t\t<diaTransferQvalue>0.3</diaTransferQvalue>\n+\t\t\t<diaOnlyIsosForRecal>True</diaOnlyIsosForRecal>\n+\t\t\t<diaMinPeaksForRecal>5</diaMinPeaksForRecal>\n+\t\t\t<diaUseFragIntensForMl>False</diaUseFragIntensForMl>\n+\t\t\t<diaUseFragMassesForMl>False</diaUseFragMassesForMl>\n+\t\t\t<diaMaxTrainInstances>1000000</diaMaxTrainInstances>\n \t\t</parameterGroup>\n \t\t<parameterGroup>\n \t\t\t<msInstrument>0</msInstrument>\n@@ -482,9 +515,16 @@\n \t\t\t<timsCollapseMsms>True</timsCollapseMsms>\n \t\t\t<crossLinkingType>0</crossLinkingType>\n \t\t\t<crossLinker/>\n-\t\t\t<minMatchXl>0</minMatchXl>\n+\t\t\t<minMatchXl>3</minMatchXl>\n \t\t\t<minPairedPepLenXl>6</minPairedPepLenXl>\n+\t\t\t<minScore_Dipeptide>40</minScore_Dipeptide>\n+\t\t\t<minScore_Monopeptide>0</minScore_Monopeptide>\n+\t\t\t<minScore_PartialCross>10</minScore_PartialCross>\n \t\t\t<crosslinkOnlyIntraProtein>False</crosslinkOnlyIntraProtein>\n+\t\t\t<crosslinkIntensityBasedPrecursor>True</crosslinkIntensityBasedPrecursor>\n+\t\t\t<isHybridPrecDetermination>False</isHybridPrecDetermination>\n+\t\t\t<topXcross>3</topXcross>\n+\t\t\t<doesSeparateInterIntraProteinCross>False</doesSeparateInterIntraProteinCross>\n \t\t\t<crosslinkMaxMonoUnsaturated>0</crosslinkMaxMonoUnsaturated>\n \t\t\t<crosslinkMaxMonoSaturated>0</crosslinkMaxMonoSaturated>\n \t\t\t<crosslinkMaxDiUnsaturated>0</crosslinkMaxDiUnsaturated>\n@@ -501,6 +541,7 @@\n \t\t\t<peakRefinement>False</peakRefinement>\n \t\t\t<isobaricSumOverWindow>True</isobaricSumOverWindow>\n \t\t\t<isobaricWeightExponent>0.75</isobaricWeightExponent>\n+\t\t\t<collapseMsmsOnIsotopePatterns>False</collapseMsmsOnIsotopePatterns>\n \t\t\t<diaLibraryType>0</diaLibraryType>\n \t\t\t<diaLibraryPaths>\n </diaLibraryPaths>\n@@ -547,6 +588,12 @@\n \t\t\t<diaBackgroundSubtractionQuantile>0.5</diaBackgroundSubtractionQuantile>\n \t\t\t<diaBackgroundSubtractionFactor>4</diaBackgroundSubtractionFactor>\n \t\t\t<diaLfqWeightedMedian>False</diaLfqWeightedMedian>\n+\t\t\t<diaTransferQvalue>0.3</diaTransferQvalue>\n+\t\t\t<diaOnlyIsosForRecal>True</diaOnlyIsosForRecal>\n+\t\t\t<diaMinPeaksForRecal>5</diaMinPeaksForRecal>\n+\t\t\t<diaUseFragIntensForMl>False</diaUseFragIntensForMl>\n+\t\t\t<diaUseFragMassesForMl>False</diaUseFragMassesForMl>\n+\t\t\t<diaMaxTrainInstances>1000000</diaMaxTrainInstances>\n \t\t</parameterGroup>\n \t</parameterGroups>\n \t<msmsParamsArray>\n@@ -556,7 +603,7 @@\n \t\t\t<MatchToleranceInPpm>True</MatchToleranceInPpm>\n \t\t\t<DeisotopeTolerance>7</DeisotopeTolerance>\n \t\t\t<DeisotopeToleranceInPpm>True</DeisotopeToleranceInPpm>\n-\t\t\t<DeNovoTolerance>10</DeNovoTolerance>\n+\t\t\t<DeNovoTolerance>25</DeNovoTolerance>\n \t\t\t<DeNovoToleranceInPpm>True</DeNovoToleranceInPpm>\n \t\t\t<Deisotope>True</Deisotope>\n \t\t\t<Topx>12</Topx>\n@@ -573,7 +620,7 @@\n \t\t\t<MatchToleranceInPpm>False</MatchToleranceInPpm>\n \t\t\t<DeisotopeTolerance>0.15</DeisotopeTolerance>\n \t\t\t<DeisotopeToleranceInPpm>False</DeisotopeToleranceInPpm>\n-\t\t\t<DeNovoTolerance>0.25</DeNovoTolerance>\n+\t\t\t<DeNovoTolerance>0.5</DeNovoTolerance>\n \t\t\t<DeNovoToleranceInPpm>False</DeNovoToleranceInPpm>\n \t\t\t<Deisotope>False</Deisotope>\n \t\t\t<Topx>8</Topx>\n@@ -590,8 +637,8 @@\n \t\t\t<MatchToleranceInPpm>True</MatchToleranceInPpm>\n \t\t\t<DeisotopeTolerance>0.01</DeisotopeTolerance>\n \t\t\t<DeisotopeToleranceInPpm>False</DeisotopeToleranceInPpm>\n-\t\t\t<DeNovoTolerance>0.02</DeNovoTolerance>\n-\t\t\t<DeNovoToleranceInPpm>False</DeNovoToleranceInPpm>\n+\t\t\t<DeNovoTolerance>25</DeNovoTolerance>\n+\t\t\t<DeNovoToleranceInPpm>True</DeNovoToleranceInPpm>\n \t\t\t<Deisotope>True</Deisotope>\n \t\t\t<Topx>10</Topx>\n \t\t\t<TopxInterval>100</TopxInterval>\n@@ -607,7 +654,7 @@\n \t\t\t<MatchToleranceInPpm>True</MatchToleranceInPpm>\n \t\t\t<DeisotopeTolerance>7</DeisotopeTolerance>\n \t\t\t<DeisotopeToleranceInPpm>True</DeisotopeToleranceInPpm>\n-\t\t\t<DeNovoTolerance>10</DeNovoTolerance>\n+\t\t\t<DeNovoTolerance>25</DeNovoTolerance>\n \t\t\t<DeNovoToleranceInPpm>True</DeNovoToleranceInPpm>\n \t\t\t<Deisotope>True</Deisotope>\n \t\t\t<Topx>12</Topx>\n' |
| b |
| diff -r 837224ad1694 -r 8934bc76bb52 test-data/07/combined/txt/report_v1.0.10_combined.pdf |
| b |
| Binary file test-data/07/combined/txt/report_v1.0.10_combined.pdf has changed |
| b |
| diff -r 837224ad1694 -r 8934bc76bb52 test-data/07/mqpar.xml --- a/test-data/07/mqpar.xml Tue Jan 31 18:14:40 2023 +0000 +++ b/test-data/07/mqpar.xml Mon Jun 19 17:02:17 2023 +0000 |
| b |
| @@ -23,6 +23,7 @@ <separateLfq>False</separateLfq> <lfqStabilizeLargeRatios>True</lfqStabilizeLargeRatios> <lfqRequireMsms>True</lfqRequireMsms> + <lfqBayesQuant>False</lfqBayesQuant> <decoyMode>revert</decoyMode> <boxCarMode>all</boxCarMode> <includeContaminants>True</includeContaminants> @@ -55,9 +56,22 @@ <avalon>False</avalon> <nModColumns>3</nModColumns> <ibaqLogFit>False</ibaqLogFit> + <ibaqChargeNormalization>False</ibaqChargeNormalization> <razorProteinFdr>True</razorProteinFdr> <deNovoSequencing>False</deNovoSequencing> - <deNovoVarMods>True</deNovoVarMods> + <deNovoVarMods>False</deNovoVarMods> + <deNovoCompleteSequence>False</deNovoCompleteSequence> + <deNovoCalibratedMasses>False</deNovoCalibratedMasses> + <deNovoMaxIterations>0</deNovoMaxIterations> + <deNovoProteaseReward>0</deNovoProteaseReward> + <deNovoProteaseRewardTof>0</deNovoProteaseRewardTof> + <deNovoAgPenalty>0</deNovoAgPenalty> + <deNovoGgPenalty>0</deNovoGgPenalty> + <deNovoUseComplementScore>True</deNovoUseComplementScore> + <deNovoUseProteaseScore>True</deNovoUseProteaseScore> + <deNovoUseWaterLossScore>True</deNovoUseWaterLossScore> + <deNovoUseAmmoniaLossScore>True</deNovoUseAmmoniaLossScore> + <deNovoUseA2Score>True</deNovoUseA2Score> <massDifferenceSearch>False</massDifferenceSearch> <isotopeCalc>False</isotopeCalc> <writePeptidesForSpectrumFile/> @@ -97,11 +111,12 @@ <writeMsScansTable>False</writeMsScansTable> <writeMsmsScansTable>True</writeMsmsScansTable> <writePasefMsmsScansTable>True</writePasefMsmsScansTable> - <writeAccumulatedPasefMsmsScansTable>False</writeAccumulatedPasefMsmsScansTable> + <writeAccumulatedMsmsScansTable>True</writeAccumulatedMsmsScansTable> <writeMs3ScansTable>True</writeMs3ScansTable> <writeAllPeptidesTable>True</writeAllPeptidesTable> <writeMzRangeTable>True</writeMzRangeTable> <writeDiaFragmentTable>False</writeDiaFragmentTable> + <writeDiaFragmentQuantTable>False</writeDiaFragmentQuantTable> <writeMzTab>False</writeMzTab> <disableMd5>False</disableMd5> <cacheBinInds>True</cacheBinInds> @@ -112,10 +127,9 @@ <variationMode>none</variationMode> <useSeriesReporters>False</useSeriesReporters> <name>templateSession</name> - <maxQuantVersion>1.6.17.0</maxQuantVersion> + <maxQuantVersion>2.0.3.0</maxQuantVersion> <pluginFolder/> - <numThreads>2</numThreads> - <batchSize>1</batchSize> + <numThreads>1</numThreads> <emailAddress/> <smtpHost/> <emailFromAddress/> @@ -151,6 +165,11 @@ <intensPred>False</intensPred> <intensPredModelReTrain>False</intensPredModelReTrain> <lfqTopNPeptides>0</lfqTopNPeptides> + <diaJoinPrecChargesForLfq>False</diaJoinPrecChargesForLfq> + <diaFragChargesForQuant>1</diaFragChargesForQuant> + <timsRearrangeSpectra>False</timsRearrangeSpectra> + <gridSpacing>0.5</gridSpacing> + <proteinGroupingFile/> <parameterGroups> <parameterGroup> <msInstrument>0</msInstrument> @@ -346,9 +365,16 @@ <timsCollapseMsms>True</timsCollapseMsms> <crossLinkingType>0</crossLinkingType> <crossLinker/> - <minMatchXl>0</minMatchXl> + <minMatchXl>3</minMatchXl> <minPairedPepLenXl>6</minPairedPepLenXl> + <minScore_Dipeptide>40</minScore_Dipeptide> + <minScore_Monopeptide>0</minScore_Monopeptide> + <minScore_PartialCross>10</minScore_PartialCross> <crosslinkOnlyIntraProtein>False</crosslinkOnlyIntraProtein> + <crosslinkIntensityBasedPrecursor>True</crosslinkIntensityBasedPrecursor> + <isHybridPrecDetermination>False</isHybridPrecDetermination> + <topXcross>3</topXcross> + <doesSeparateInterIntraProteinCross>False</doesSeparateInterIntraProteinCross> <crosslinkMaxMonoUnsaturated>0</crosslinkMaxMonoUnsaturated> <crosslinkMaxMonoSaturated>0</crosslinkMaxMonoSaturated> <crosslinkMaxDiUnsaturated>0</crosslinkMaxDiUnsaturated> @@ -365,6 +391,7 @@ <peakRefinement>False</peakRefinement> <isobaricSumOverWindow>True</isobaricSumOverWindow> <isobaricWeightExponent>0.75</isobaricWeightExponent> + <collapseMsmsOnIsotopePatterns>False</collapseMsmsOnIsotopePatterns> <diaLibraryType>0</diaLibraryType> <diaLibraryPaths> </diaLibraryPaths> @@ -411,6 +438,12 @@ <diaBackgroundSubtractionQuantile>0.5</diaBackgroundSubtractionQuantile> <diaBackgroundSubtractionFactor>4</diaBackgroundSubtractionFactor> <diaLfqWeightedMedian>False</diaLfqWeightedMedian> + <diaTransferQvalue>0.3</diaTransferQvalue> + <diaOnlyIsosForRecal>True</diaOnlyIsosForRecal> + <diaMinPeaksForRecal>5</diaMinPeaksForRecal> + <diaUseFragIntensForMl>False</diaUseFragIntensForMl> + <diaUseFragMassesForMl>False</diaUseFragMassesForMl> + <diaMaxTrainInstances>1000000</diaMaxTrainInstances> </parameterGroup> </parameterGroups> <msmsParamsArray> @@ -420,7 +453,7 @@ <MatchToleranceInPpm>True</MatchToleranceInPpm> <DeisotopeTolerance>7</DeisotopeTolerance> <DeisotopeToleranceInPpm>True</DeisotopeToleranceInPpm> - <DeNovoTolerance>10</DeNovoTolerance> + <DeNovoTolerance>25</DeNovoTolerance> <DeNovoToleranceInPpm>True</DeNovoToleranceInPpm> <Deisotope>True</Deisotope> <Topx>12</Topx> @@ -437,7 +470,7 @@ <MatchToleranceInPpm>False</MatchToleranceInPpm> <DeisotopeTolerance>0.15</DeisotopeTolerance> <DeisotopeToleranceInPpm>False</DeisotopeToleranceInPpm> - <DeNovoTolerance>0.25</DeNovoTolerance> + <DeNovoTolerance>0.5</DeNovoTolerance> <DeNovoToleranceInPpm>False</DeNovoToleranceInPpm> <Deisotope>False</Deisotope> <Topx>8</Topx> @@ -454,8 +487,8 @@ <MatchToleranceInPpm>True</MatchToleranceInPpm> <DeisotopeTolerance>0.01</DeisotopeTolerance> <DeisotopeToleranceInPpm>False</DeisotopeToleranceInPpm> - <DeNovoTolerance>0.02</DeNovoTolerance> - <DeNovoToleranceInPpm>False</DeNovoToleranceInPpm> + <DeNovoTolerance>25</DeNovoTolerance> + <DeNovoToleranceInPpm>True</DeNovoToleranceInPpm> <Deisotope>True</Deisotope> <Topx>10</Topx> <TopxInterval>100</TopxInterval> @@ -471,7 +504,7 @@ <MatchToleranceInPpm>True</MatchToleranceInPpm> <DeisotopeTolerance>7</DeisotopeTolerance> <DeisotopeToleranceInPpm>True</DeisotopeToleranceInPpm> - <DeNovoTolerance>10</DeNovoTolerance> + <DeNovoTolerance>25</DeNovoTolerance> <DeNovoToleranceInPpm>True</DeNovoToleranceInPpm> <Deisotope>True</Deisotope> <Topx>12</Topx> |
| b |
| diff -r 837224ad1694 -r 8934bc76bb52 test-data/08/combined/txt/proteinGroups.txt --- a/test-data/08/combined/txt/proteinGroups.txt Tue Jan 31 18:14:40 2023 +0000 +++ b/test-data/08/combined/txt/proteinGroups.txt Mon Jun 19 17:02:17 2023 +0000 |
| [ |
| b'@@ -1,7 +1,7 @@\n-Protein IDs\tMajority protein IDs\tPeptide counts (all)\tPeptide counts (razor+unique)\tPeptide counts (unique)\tFasta headers\tNumber of proteins\tPeptides\tRazor + unique peptides\tUnique peptides\tPeptides tmt_data.mzXML\tRazor + unique peptides tmt_data.mzXML\tUnique peptides tmt_data.mzXML\tSequence coverage [%]\tUnique + razor sequence coverage [%]\tUnique sequence coverage [%]\tMol. weight [kDa]\tSequence length\tSequence lengths\tQ-value\tScore\tReporter intensity corrected 1 tmt_data.mzXML\tReporter intensity corrected 2 tmt_data.mzXML\tReporter intensity corrected 3 tmt_data.mzXML\tReporter intensity corrected 4 tmt_data.mzXML\tReporter intensity corrected 5 tmt_data.mzXML\tReporter intensity corrected 6 tmt_data.mzXML\tReporter intensity corrected 7 tmt_data.mzXML\tReporter intensity corrected 8 tmt_data.mzXML\tReporter intensity corrected 9 tmt_data.mzXML\tReporter intensity corrected 10 tmt_data.mzXML\tReporter intensity corrected 11 tmt_data.mzXML\tReporter intensity corrected 12 tmt_data.mzXML\tReporter intensity corrected 13 tmt_data.mzXML\tReporter intensity corrected 14 tmt_data.mzXML\tReporter intensity corrected 15 tmt_data.mzXML\tReporter intensity corrected 16 tmt_data.mzXML\tReporter intensity 1 tmt_data.mzXML\tReporter intensity 2 tmt_data.mzXML\tReporter intensity 3 tmt_data.mzXML\tReporter intensity 4 tmt_data.mzXML\tReporter intensity 5 tmt_data.mzXML\tReporter intensity 6 tmt_data.mzXML\tReporter intensity 7 tmt_data.mzXML\tReporter intensity 8 tmt_data.mzXML\tReporter intensity 9 tmt_data.mzXML\tReporter intensity 10 tmt_data.mzXML\tReporter intensity 11 tmt_data.mzXML\tReporter intensity 12 tmt_data.mzXML\tReporter intensity 13 tmt_data.mzXML\tReporter intensity 14 tmt_data.mzXML\tReporter intensity 15 tmt_data.mzXML\tReporter intensity 16 tmt_data.mzXML\tReporter intensity count 1 tmt_data.mzXML\tReporter intensity count 2 tmt_data.mzXML\tReporter intensity count 3 tmt_data.mzXML\tReporter intensity count 4 tmt_data.mzXML\tReporter intensity count 5 tmt_data.mzXML\tReporter intensity count 6 tmt_data.mzXML\tReporter intensity count 7 tmt_data.mzXML\tReporter intensity count 8 tmt_data.mzXML\tReporter intensity count 9 tmt_data.mzXML\tReporter intensity count 10 tmt_data.mzXML\tReporter intensity count 11 tmt_data.mzXML\tReporter intensity count 12 tmt_data.mzXML\tReporter intensity count 13 tmt_data.mzXML\tReporter intensity count 14 tmt_data.mzXML\tReporter intensity count 15 tmt_data.mzXML\tReporter intensity count 16 tmt_data.mzXML\tSequence coverage tmt_data.mzXML [%]\tIntensity\tIntensity tmt_data.mzXML\tMS/MS count\tOnly identified by site\tReverse\tPotential contaminant\tid\tPeptide IDs\tPeptide is razor\tMod. peptide IDs\tEvidence IDs\tMS/MS IDs\tBest MS/MS\tOxidation (M) site IDs\tOxidation (M) site positions\tTaxonomy IDs\n-CON__ENSEMBL:ENSBTAP00000001528\tCON__ENSEMBL:ENSBTAP00000001528\t1\t1\t1\t\t1\t1\t1\t1\t1\t1\t1\t0.8\t0.8\t0.8\t137.98\t1222\t1222\t0\t6\t0\t0\t5121.2\t220760\t202180\t225830\t200210\t259320\t246570\t233570\t148280\t4478.8\t0\t0\t0\t0\t0\t0\t5121.2\t220760\t202180\t225830\t200210\t259320\t246570\t233570\t148280\t4478.8\t0\t0\t0\t0\t0\t0\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t0\t0\t0\t0\t0.8\t99228000\t99228000\t1\t\t\t+\t0\t2\tTrue\t2\t2\t2\t2\t\t\t-1\n-sp|A6NKP2|D42E2_HUMAN\tsp|A6NKP2|D42E2_HUMAN\t1\t1\t1\tsp|A6NKP2|D42E2_HUMAN Putative short-chain dehydrogenase/reductase family 42E member 2 OS=Homo sapiens OX=9606 GN=SDR42E2 PE=3 SV=3\t1\t1\t1\t1\t1\t1\t1\t2.6\t2.6\t2.6\t46.869\t422\t422\t0\t6\t0\t3941.4\t4062.3\t178440\t117220\t94899\t131440\t159880\t91982\t74974\t76646\t3167.4\t940.58\t0\t0\t0\t0\t3941.4\t4062.3\t178440\t117220\t94899\t131440\t159880\t91982\t74974\t76646\t3167.4\t940.58\t0\t0\t0\t0\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t0\t0\t0\t2.6\t43797000\t43797000\t1\t\t\t\t1\t5\tTrue\t5\t5\t5\t5\t\t\t-1\n-sp|Q32M88|PGGHG_HUMAN\tsp|Q32M88|PGGHG_HUMAN\t1\t1\t1\tsp|Q32M88|PGGHG_HUMAN Protein-glucosylgalactosylhydroxylysine glucosidase OS=Homo sapiens OX=9606 GN=PGGHG PE=1 SV=2\t1\t1\t1\t1\t1\t1\t1\t0.9\t0.9\t0.9\t80.654\t737\t737\t0\t6\t0\t0\t4057.5\t92629\t91851\t99927\t106520\t117440\t118770\t118100\t124330\t3555.6\t2741.6\t0\t0\t0\t0\t0\t4057.5\t92629\t91851\t99927\t106520\t117440\t118770\t118100\t124330\t3555.6\t2741.6\t0\t0\t0\t0\t0\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1'..b' intensity 8 tmt_data.mzXML\tReporter intensity 9 tmt_data.mzXML\tReporter intensity 10 tmt_data.mzXML\tReporter intensity 11 tmt_data.mzXML\tReporter intensity 12 tmt_data.mzXML\tReporter intensity 13 tmt_data.mzXML\tReporter intensity 14 tmt_data.mzXML\tReporter intensity 15 tmt_data.mzXML\tReporter intensity 16 tmt_data.mzXML\tReporter intensity count 1 tmt_data.mzXML\tReporter intensity count 2 tmt_data.mzXML\tReporter intensity count 3 tmt_data.mzXML\tReporter intensity count 4 tmt_data.mzXML\tReporter intensity count 5 tmt_data.mzXML\tReporter intensity count 6 tmt_data.mzXML\tReporter intensity count 7 tmt_data.mzXML\tReporter intensity count 8 tmt_data.mzXML\tReporter intensity count 9 tmt_data.mzXML\tReporter intensity count 10 tmt_data.mzXML\tReporter intensity count 11 tmt_data.mzXML\tReporter intensity count 12 tmt_data.mzXML\tReporter intensity count 13 tmt_data.mzXML\tReporter intensity count 14 tmt_data.mzXML\tReporter intensity count 15 tmt_data.mzXML\tReporter intensity count 16 tmt_data.mzXML\tSequence coverage tmt_data.mzXML [%]\tIntensity\tIntensity tmt_data.mzXML\tMS/MS count\tPeptide sequences\tOnly identified by site\tReverse\tPotential contaminant\tid\tPeptide IDs\tPeptide is razor\tMod. peptide IDs\tEvidence IDs\tMS/MS IDs\tBest MS/MS\tOxidation (M) site IDs\tOxidation (M) site positions\tTaxonomy IDs\n+CON__ENSEMBL:ENSBTAP00000001528\tCON__ENSEMBL:ENSBTAP00000001528\t1\t1\t1\t\t1\t1\t1\t1\t1\t1\t1\t0.8\t0.8\t0.8\t137.98\t1222\t1222\t0\t6\t0\t0\t5121.2\t220760\t202180\t225830\t200210\t259320\t246570\t233570\t148280\t4478.8\t0\t0\t0\t0\t0\t0\t5121.2\t220760\t202180\t225830\t200210\t259320\t246570\t233570\t148280\t4478.8\t0\t0\t0\t0\t0\t0\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t0\t0\t0\t0\t0.8\t99228000\t99228000\t1\tDSEGSGTAGK\t\t\t+\t0\t2\tTrue\t2\t2\t2\t2\t\t\t-1\n+sp|A6NKP2|D42E2_HUMAN\tsp|A6NKP2|D42E2_HUMAN\t1\t1\t1\tsp|A6NKP2|D42E2_HUMAN Putative short-chain dehydrogenase/reductase family 42E member 2 OS=Homo sapiens OX=9606 GN=SDR42E2 PE=3 SV=3\t1\t1\t1\t1\t1\t1\t1\t2.6\t2.6\t2.6\t46.869\t422\t422\t0\t6\t0\t3941.4\t4062.3\t178440\t117220\t94899\t131440\t159880\t91982\t74974\t76646\t3167.4\t940.58\t0\t0\t0\t0\t3941.4\t4062.3\t178440\t117220\t94899\t131440\t159880\t91982\t74974\t76646\t3167.4\t940.58\t0\t0\t0\t0\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t0\t0\t0\t2.6\t43797000\t43797000\t1\tPRGSTARTLLR\t\t\t\t1\t5\tTrue\t5\t5\t5\t5\t\t\t-1\n+sp|Q32M88|PGGHG_HUMAN\tsp|Q32M88|PGGHG_HUMAN\t1\t1\t1\tsp|Q32M88|PGGHG_HUMAN Protein-glucosylgalactosylhydroxylysine glucosidase OS=Homo sapiens OX=9606 GN=PGGHG PE=1 SV=2\t1\t1\t1\t1\t1\t1\t1\t0.9\t0.9\t0.9\t80.654\t737\t737\t0\t6\t0\t0\t4057.5\t92629\t91851\t99927\t106520\t117440\t118770\t118100\t124330\t3555.6\t2741.6\t0\t0\t0\t0\t0\t4057.5\t92629\t91851\t99927\t106520\t117440\t118770\t118100\t124330\t3555.6\t2741.6\t0\t0\t0\t0\t0\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t0\t0\t0\t0.9\t11999000\t11999000\t1\tARGLLDR\t\t\t\t2\t1\tTrue\t1\t1\t1\t1\t\t\t-1\n+sp|Q8IXT5|RB12B_HUMAN\tsp|Q8IXT5|RB12B_HUMAN\t1\t1\t1\tsp|Q8IXT5|RB12B_HUMAN RNA-binding protein 12B OS=Homo sapiens OX=9606 GN=RBM12B PE=1 SV=2\t1\t1\t1\t1\t1\t1\t1\t0.7\t0.7\t0.7\t118.1\t1001\t1001\t0\t6\t0\t0\t2539.1\t96839\t103090\t105560\t92520\t63071\t68162\t70636\t42876\t0\t0\t0\t0\t0\t0\t0\t2539.1\t96839\t103090\t105560\t92520\t63071\t68162\t70636\t42876\t0\t0\t0\t0\t0\t0\t0\t1\t1\t1\t1\t1\t1\t1\t1\t1\t0\t0\t0\t0\t0\t0.7\t53433000\t53433000\t1\tAERLNRR\t\t\t\t3\t0\tTrue\t0\t0\t0\t0\t\t\t-1\n+sp|Q8N782|ZN525_HUMAN\tsp|Q8N782|ZN525_HUMAN\t1\t1\t1\tsp|Q8N782|ZN525_HUMAN Zinc finger protein 525 OS=Homo sapiens OX=9606 GN=ZNF525 PE=2 SV=2\t1\t1\t1\t1\t1\t1\t1\t4.6\t4.6\t4.6\t23.07\t197\t197\t0\t6\t0\t1694.6\t6271.6\t277230\t244210\t164300\t288610\t344230\t225420\t253930\t201720\t11497\t6283.4\t0\t0\t0\t0\t1694.6\t6271.6\t277230\t244210\t164300\t288610\t344230\t225420\t253930\t201720\t11497\t6283.4\t0\t0\t0\t0\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t0\t0\t0\t4.6\t365510000\t365510000\t1\tLHSGEKPCK\t\t\t\t4\t4\tTrue\t4\t4\t4\t4\t\t\t-1\n+sp|Q9UBQ7|GRHPR_HUMAN\tsp|Q9UBQ7|GRHPR_HUMAN\t1\t1\t1\tsp|Q9UBQ7|GRHPR_HUMAN Glyoxylate reductase/hydroxypyruvate reductase OS=Homo sapiens OX=9606 GN=GRHPR PE=1 SV=1\t1\t1\t1\t1\t1\t1\t1\t2.4\t2.4\t2.4\t35.668\t328\t328\t0\t6\t0\t0\t4516.6\t233890\t211220\t199740\t210150\t244750\t222310\t227650\t177190\t5951.5\t4942.8\t0\t0\t0\t0\t0\t4516.6\t233890\t211220\t199740\t210150\t244750\t222310\t227650\t177190\t5951.5\t4942.8\t0\t0\t0\t0\t0\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t0\t0\t0\t2.4\t30472000\t30472000\t1\tIGQAIARR\t\t\t\t5\t3\tTrue\t3\t3\t3\t3\t\t\t-1\n' |
| b |
| diff -r 837224ad1694 -r 8934bc76bb52 test-data/08/mqpar.xml --- a/test-data/08/mqpar.xml Tue Jan 31 18:14:40 2023 +0000 +++ b/test-data/08/mqpar.xml Mon Jun 19 17:02:17 2023 +0000 |
| b |
| @@ -23,6 +23,7 @@ <separateLfq>False</separateLfq> <lfqStabilizeLargeRatios>True</lfqStabilizeLargeRatios> <lfqRequireMsms>True</lfqRequireMsms> + <lfqBayesQuant>False</lfqBayesQuant> <decoyMode>revert</decoyMode> <boxCarMode>all</boxCarMode> <includeContaminants>True</includeContaminants> @@ -55,9 +56,22 @@ <avalon>False</avalon> <nModColumns>3</nModColumns> <ibaqLogFit>False</ibaqLogFit> + <ibaqChargeNormalization>False</ibaqChargeNormalization> <razorProteinFdr>True</razorProteinFdr> <deNovoSequencing>False</deNovoSequencing> - <deNovoVarMods>True</deNovoVarMods> + <deNovoVarMods>False</deNovoVarMods> + <deNovoCompleteSequence>False</deNovoCompleteSequence> + <deNovoCalibratedMasses>False</deNovoCalibratedMasses> + <deNovoMaxIterations>0</deNovoMaxIterations> + <deNovoProteaseReward>0</deNovoProteaseReward> + <deNovoProteaseRewardTof>0</deNovoProteaseRewardTof> + <deNovoAgPenalty>0</deNovoAgPenalty> + <deNovoGgPenalty>0</deNovoGgPenalty> + <deNovoUseComplementScore>True</deNovoUseComplementScore> + <deNovoUseProteaseScore>True</deNovoUseProteaseScore> + <deNovoUseWaterLossScore>True</deNovoUseWaterLossScore> + <deNovoUseAmmoniaLossScore>True</deNovoUseAmmoniaLossScore> + <deNovoUseA2Score>True</deNovoUseA2Score> <massDifferenceSearch>False</massDifferenceSearch> <isotopeCalc>False</isotopeCalc> <writePeptidesForSpectrumFile/> @@ -97,11 +111,12 @@ <writeMsScansTable>False</writeMsScansTable> <writeMsmsScansTable>True</writeMsmsScansTable> <writePasefMsmsScansTable>True</writePasefMsmsScansTable> - <writeAccumulatedPasefMsmsScansTable>False</writeAccumulatedPasefMsmsScansTable> + <writeAccumulatedMsmsScansTable>True</writeAccumulatedMsmsScansTable> <writeMs3ScansTable>True</writeMs3ScansTable> <writeAllPeptidesTable>True</writeAllPeptidesTable> <writeMzRangeTable>True</writeMzRangeTable> <writeDiaFragmentTable>False</writeDiaFragmentTable> + <writeDiaFragmentQuantTable>False</writeDiaFragmentQuantTable> <writeMzTab>False</writeMzTab> <disableMd5>False</disableMd5> <cacheBinInds>True</cacheBinInds> @@ -112,10 +127,9 @@ <variationMode>none</variationMode> <useSeriesReporters>False</useSeriesReporters> <name>templateSession</name> - <maxQuantVersion>1.6.17.0</maxQuantVersion> + <maxQuantVersion>2.0.3.0</maxQuantVersion> <pluginFolder/> <numThreads>1</numThreads> - <batchSize>1</batchSize> <emailAddress/> <smtpHost/> <emailFromAddress/> @@ -134,7 +148,7 @@ <string>/tmp/tmpd7w978vs/job_working_directory/000/3/working/tmt16_ori.mzXML</string> </filePaths> <experiments> - <string>tmt16_ori.mzXML</string> + <string>tmt_data.mzXML</string> </experiments> <fractions> <short>32767</short> @@ -151,6 +165,11 @@ <intensPred>False</intensPred> <intensPredModelReTrain>False</intensPredModelReTrain> <lfqTopNPeptides>0</lfqTopNPeptides> + <diaJoinPrecChargesForLfq>False</diaJoinPrecChargesForLfq> + <diaFragChargesForQuant>1</diaFragChargesForQuant> + <timsRearrangeSpectra>False</timsRearrangeSpectra> + <gridSpacing>0.5</gridSpacing> + <proteinGroupingFile/> <parameterGroups> <parameterGroup> <msInstrument>0</msInstrument> @@ -400,9 +419,16 @@ <timsCollapseMsms>True</timsCollapseMsms> <crossLinkingType>0</crossLinkingType> <crossLinker/> - <minMatchXl>0</minMatchXl> + <minMatchXl>3</minMatchXl> <minPairedPepLenXl>6</minPairedPepLenXl> + <minScore_Dipeptide>40</minScore_Dipeptide> + <minScore_Monopeptide>0</minScore_Monopeptide> + <minScore_PartialCross>10</minScore_PartialCross> <crosslinkOnlyIntraProtein>False</crosslinkOnlyIntraProtein> + <crosslinkIntensityBasedPrecursor>True</crosslinkIntensityBasedPrecursor> + <isHybridPrecDetermination>False</isHybridPrecDetermination> + <topXcross>3</topXcross> + <doesSeparateInterIntraProteinCross>False</doesSeparateInterIntraProteinCross> <crosslinkMaxMonoUnsaturated>0</crosslinkMaxMonoUnsaturated> <crosslinkMaxMonoSaturated>0</crosslinkMaxMonoSaturated> <crosslinkMaxDiUnsaturated>0</crosslinkMaxDiUnsaturated> @@ -419,6 +445,7 @@ <peakRefinement>False</peakRefinement> <isobaricSumOverWindow>True</isobaricSumOverWindow> <isobaricWeightExponent>0.75</isobaricWeightExponent> + <collapseMsmsOnIsotopePatterns>False</collapseMsmsOnIsotopePatterns> <diaLibraryType>0</diaLibraryType> <diaLibraryPaths> </diaLibraryPaths> @@ -465,6 +492,12 @@ <diaBackgroundSubtractionQuantile>0.5</diaBackgroundSubtractionQuantile> <diaBackgroundSubtractionFactor>4</diaBackgroundSubtractionFactor> <diaLfqWeightedMedian>False</diaLfqWeightedMedian> + <diaTransferQvalue>0.3</diaTransferQvalue> + <diaOnlyIsosForRecal>True</diaOnlyIsosForRecal> + <diaMinPeaksForRecal>5</diaMinPeaksForRecal> + <diaUseFragIntensForMl>False</diaUseFragIntensForMl> + <diaUseFragMassesForMl>False</diaUseFragMassesForMl> + <diaMaxTrainInstances>1000000</diaMaxTrainInstances> </parameterGroup> </parameterGroups> <msmsParamsArray> @@ -474,7 +507,7 @@ <MatchToleranceInPpm>True</MatchToleranceInPpm> <DeisotopeTolerance>7</DeisotopeTolerance> <DeisotopeToleranceInPpm>True</DeisotopeToleranceInPpm> - <DeNovoTolerance>10</DeNovoTolerance> + <DeNovoTolerance>25</DeNovoTolerance> <DeNovoToleranceInPpm>True</DeNovoToleranceInPpm> <Deisotope>True</Deisotope> <Topx>12</Topx> @@ -491,7 +524,7 @@ <MatchToleranceInPpm>False</MatchToleranceInPpm> <DeisotopeTolerance>0.15</DeisotopeTolerance> <DeisotopeToleranceInPpm>False</DeisotopeToleranceInPpm> - <DeNovoTolerance>0.25</DeNovoTolerance> + <DeNovoTolerance>0.5</DeNovoTolerance> <DeNovoToleranceInPpm>False</DeNovoToleranceInPpm> <Deisotope>False</Deisotope> <Topx>8</Topx> @@ -508,8 +541,8 @@ <MatchToleranceInPpm>True</MatchToleranceInPpm> <DeisotopeTolerance>0.01</DeisotopeTolerance> <DeisotopeToleranceInPpm>False</DeisotopeToleranceInPpm> - <DeNovoTolerance>0.02</DeNovoTolerance> - <DeNovoToleranceInPpm>False</DeNovoToleranceInPpm> + <DeNovoTolerance>25</DeNovoTolerance> + <DeNovoToleranceInPpm>True</DeNovoToleranceInPpm> <Deisotope>True</Deisotope> <Topx>10</Topx> <TopxInterval>100</TopxInterval> @@ -525,7 +558,7 @@ <MatchToleranceInPpm>True</MatchToleranceInPpm> <DeisotopeTolerance>7</DeisotopeTolerance> <DeisotopeToleranceInPpm>True</DeisotopeToleranceInPpm> - <DeNovoTolerance>10</DeNovoTolerance> + <DeNovoTolerance>25</DeNovoTolerance> <DeNovoToleranceInPpm>True</DeNovoToleranceInPpm> <Deisotope>True</Deisotope> <Topx>12</Topx> |
| b |
| diff -r 837224ad1694 -r 8934bc76bb52 test-data/09/combined/txt/msmsScans.txt --- a/test-data/09/combined/txt/msmsScans.txt Tue Jan 31 18:14:40 2023 +0000 +++ b/test-data/09/combined/txt/msmsScans.txt Mon Jun 19 17:02:17 2023 +0000 |
| b |
| @@ -1,9 +1,9 @@ Raw file Scan number Retention time Ion injection time Total ion current Collision energy Summations Base peak intensity Elapsed time Identified Matched Reverse MS/MS IDs Sequence Length Filtered peaks m/z Mass Charge Type Fragmentation Mass analyzer Parent intensity fraction Fraction of total spectrum Base peak fraction Precursor full scan number Precursor intensity Precursor apex fraction Precursor apex offset Precursor apex offset time Scan event number Modifications Modified sequence Proteins Score PEP Experiment Reporter intensity corrected 1 Reporter intensity corrected 2 Reporter intensity corrected 3 Reporter intensity corrected 4 Reporter intensity corrected 5 Reporter intensity corrected 6 Reporter intensity corrected 7 Reporter intensity corrected 8 Reporter intensity corrected 9 Reporter intensity corrected 10 Reporter intensity corrected 11 Reporter intensity corrected 12 Reporter intensity corrected 13 Reporter intensity corrected 14 Reporter intensity corrected 15 Reporter intensity corrected 16 Reporter intensity corrected 17 Reporter intensity corrected 18 Reporter intensity 1 Reporter intensity 2 Reporter intensity 3 Reporter intensity 4 Reporter intensity 5 Reporter intensity 6 Reporter intensity 7 Reporter intensity 8 Reporter intensity 9 Reporter intensity 10 Reporter intensity 11 Reporter intensity 12 Reporter intensity 13 Reporter intensity 14 Reporter intensity 15 Reporter intensity 16 Reporter intensity 17 Reporter intensity 18 Reporter PIF Reporter fraction Intens Comp Factor CTCD Comp RawOvFtT AGC Fill Scan index MS scan index MS scan number -tmt_data_18 4 0.022647 -1 1555.1 35 0 429.62 -1 - -1 0 19 496.5587 NaN 0 PEAK CID ITMS NaN NaN NaN -1 NaN NaN 0 NaN 1 NaN NaN tmt_data_18.mzXML 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 NaN NaN NaN 0 0 2 3 -tmt_data_18 6 0.028164 -1 306.22 35 0 210 -1 - -1 0 3 562.254 NaN 0 PEAK CID ITMS NaN NaN NaN -1 NaN NaN 0 NaN 1 NaN NaN tmt_data_18.mzXML 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 NaN NaN NaN 0 1 3 5 -tmt_data_18 7 0.030756 -1 76712 0 0 6269.6 -1 - -1 0 84 1 NaN 0 PEAK CID FTMS NaN NaN NaN -1 NaN NaN 0 NaN 2 NaN NaN tmt_data_18.mzXML 437.7 465.76 538.68 473.42 0 662.1 803.52 0 1148.3 592.81 894.98 1139.6 977.11 1107.6 934.33 696.59 576.46 1213.5 437.7 465.76 538.68 473.42 0 662.1 803.52 0 1148.3 592.81 894.98 1139.6 977.11 1107.6 934.33 696.59 576.46 1213.5 NaN NaN NaN 0 2 3 5 -tmt_data_18 10 0.043625 -1 374.34 35 0 119.96 -1 - + -1 GANDSMMM 8 7 604.7506 NaN 0 PEAK CID ITMS NaN NaN NaN -1 NaN NaN 0 NaN 1 3 Oxidation (M) _GANDSM(Oxidation (M))M(Oxidation (M))M(Oxidation (M))_ REV__sp|Q8N7M0|DYLT5_HUMAN 0 0.01 tmt_data_18.mzXML 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 NaN NaN NaN 0 3 5 9 -tmt_data_18 14 0.05893 -1 417.62 35 0 66.299 -1 - -1 0 10 553.2144 NaN 0 PEAK CID ITMS NaN NaN NaN -1 NaN NaN 0 NaN 1 NaN NaN tmt_data_18.mzXML 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 NaN NaN NaN 0 4 8 13 -tmt_data_18 39 0.17826 -1 136.05 35 0 61.009 -1 - + -1 QEMEPTR 7 3 404.2059 NaN 0 PEAK CID ITMS NaN NaN NaN -1 NaN NaN 0 NaN 1 Oxidation (M) _QEM(Oxidation (M))EPTR_ REV__sp|O15457|MSH4_HUMAN 4.59465663460819 0.01 tmt_data_18.mzXML 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 NaN NaN NaN 0 5 32 38 -tmt_data_18 155 0.75055 -1 211.81 35 0 69.087 -1 - -1 PGTSGWDSCR 10 6 457.2214 NaN 0 PEAK CID ITMS NaN NaN NaN -1 NaN NaN 0 NaN 1 Unmodified _PGTSGWDSCR_ CON__Q6KB66-1 0 0.01 tmt_data_18.mzXML 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 NaN NaN NaN 0 6 147 154 -tmt_data_18 162 0.781 -1 239.53 35 0 62.874 -1 - + -1 MRLQIEQR 8 6 459.9375 NaN 0 PEAK CID ITMS NaN NaN NaN -1 NaN NaN 0 NaN 1 Unmodified _MRLQIEQR_ REV__sp|Q8ND30|LIPB2_HUMAN 4.96526132859811 0.01 tmt_data_18.mzXML 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 NaN NaN NaN 0 7 153 161 +tmt_data_18 4 0.022647 -1 1555.1 35 0 429.62 -1 -1 0 19 496.5587 NaN 0 PEAK CID ITMS NaN NaN NaN -1 NaN NaN 0 NaN 1 NaN NaN tmt_data_18.mzXML 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 NaN NaN NaN 0 0 2 3 +tmt_data_18 6 0.028164 -1 306.22 35 0 210 -1 -1 0 3 562.254 NaN 0 PEAK CID ITMS NaN NaN NaN -1 NaN NaN 0 NaN 1 NaN NaN tmt_data_18.mzXML 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 NaN NaN NaN 0 1 3 5 +tmt_data_18 7 0.030756 -1 76712 0 0 6269.6 -1 -1 0 84 1 NaN 0 PEAK CID FTMS NaN NaN NaN -1 NaN NaN 0 NaN 2 NaN NaN tmt_data_18.mzXML 437.7 465.76 538.68 473.42 0 662.1 803.52 0 1148.3 592.81 894.98 1139.6 977.11 1107.6 934.33 696.59 576.46 1213.5 437.7 465.76 538.68 473.42 0 662.1 803.52 0 1148.3 592.81 894.98 1139.6 977.11 1107.6 934.33 696.59 576.46 1213.5 NaN NaN NaN 0 2 3 5 +tmt_data_18 10 0.043625 -1 374.34 35 0 119.96 -1 + -1 GANDSMMM 8 7 604.7506 NaN 0 PEAK CID ITMS NaN NaN NaN -1 NaN NaN 0 NaN 1 3 Oxidation (M) _GANDSM(Oxidation (M))M(Oxidation (M))M(Oxidation (M))_ REV__sp|Q8N7M0|DYLT5_HUMAN 0 0.01 tmt_data_18.mzXML 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 NaN NaN NaN 0 3 5 9 +tmt_data_18 14 0.05893 -1 417.62 35 0 66.299 -1 -1 0 10 553.2144 NaN 0 PEAK CID ITMS NaN NaN NaN -1 NaN NaN 0 NaN 1 NaN NaN tmt_data_18.mzXML 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 NaN NaN NaN 0 4 8 13 +tmt_data_18 39 0.17826 -1 136.05 35 0 61.009 -1 + -1 QEMEPTR 7 3 404.2059 NaN 0 PEAK CID ITMS NaN NaN NaN -1 NaN NaN 0 NaN 1 Oxidation (M) _QEM(Oxidation (M))EPTR_ REV__sp|O15457|MSH4_HUMAN 4.59465663460819 0.01 tmt_data_18.mzXML 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 NaN NaN NaN 0 5 32 38 +tmt_data_18 155 0.75055 -1 211.81 35 0 69.087 -1 -1 PGTSGWDSCR 10 6 457.2214 NaN 0 PEAK CID ITMS NaN NaN NaN -1 NaN NaN 0 NaN 1 Unmodified _PGTSGWDSCR_ CON__Q6KB66-1 0 0.01 tmt_data_18.mzXML 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 NaN NaN NaN 0 6 147 154 +tmt_data_18 162 0.781 -1 239.53 35 0 62.874 -1 + -1 MRLQIEQR 8 6 459.9375 NaN 0 PEAK CID ITMS NaN NaN NaN -1 NaN NaN 0 NaN 1 Unmodified _MRLQIEQR_ REV__sp|Q8ND30|LIPB2_HUMAN 4.96526132859811 0.01 tmt_data_18.mzXML 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 NaN NaN NaN 0 7 153 161 |
| b |
| diff -r 837224ad1694 -r 8934bc76bb52 test-data/10/mqpar.xml --- a/test-data/10/mqpar.xml Tue Jan 31 18:14:40 2023 +0000 +++ b/test-data/10/mqpar.xml Mon Jun 19 17:02:17 2023 +0000 |
| b |
| @@ -23,6 +23,7 @@ <separateLfq>False</separateLfq> <lfqStabilizeLargeRatios>True</lfqStabilizeLargeRatios> <lfqRequireMsms>True</lfqRequireMsms> + <lfqBayesQuant>False</lfqBayesQuant> <decoyMode>revert</decoyMode> <boxCarMode>all</boxCarMode> <includeContaminants>True</includeContaminants> @@ -55,9 +56,22 @@ <avalon>False</avalon> <nModColumns>3</nModColumns> <ibaqLogFit>False</ibaqLogFit> + <ibaqChargeNormalization>False</ibaqChargeNormalization> <razorProteinFdr>True</razorProteinFdr> <deNovoSequencing>False</deNovoSequencing> - <deNovoVarMods>True</deNovoVarMods> + <deNovoVarMods>False</deNovoVarMods> + <deNovoCompleteSequence>False</deNovoCompleteSequence> + <deNovoCalibratedMasses>False</deNovoCalibratedMasses> + <deNovoMaxIterations>0</deNovoMaxIterations> + <deNovoProteaseReward>0</deNovoProteaseReward> + <deNovoProteaseRewardTof>0</deNovoProteaseRewardTof> + <deNovoAgPenalty>0</deNovoAgPenalty> + <deNovoGgPenalty>0</deNovoGgPenalty> + <deNovoUseComplementScore>True</deNovoUseComplementScore> + <deNovoUseProteaseScore>True</deNovoUseProteaseScore> + <deNovoUseWaterLossScore>True</deNovoUseWaterLossScore> + <deNovoUseAmmoniaLossScore>True</deNovoUseAmmoniaLossScore> + <deNovoUseA2Score>True</deNovoUseA2Score> <massDifferenceSearch>False</massDifferenceSearch> <isotopeCalc>False</isotopeCalc> <writePeptidesForSpectrumFile/> @@ -97,11 +111,12 @@ <writeMsScansTable>False</writeMsScansTable> <writeMsmsScansTable>True</writeMsmsScansTable> <writePasefMsmsScansTable>True</writePasefMsmsScansTable> - <writeAccumulatedPasefMsmsScansTable>False</writeAccumulatedPasefMsmsScansTable> + <writeAccumulatedMsmsScansTable>True</writeAccumulatedMsmsScansTable> <writeMs3ScansTable>True</writeMs3ScansTable> <writeAllPeptidesTable>True</writeAllPeptidesTable> <writeMzRangeTable>True</writeMzRangeTable> <writeDiaFragmentTable>False</writeDiaFragmentTable> + <writeDiaFragmentQuantTable>False</writeDiaFragmentQuantTable> <writeMzTab>False</writeMzTab> <disableMd5>False</disableMd5> <cacheBinInds>True</cacheBinInds> @@ -112,10 +127,9 @@ <variationMode>none</variationMode> <useSeriesReporters>False</useSeriesReporters> <name>templateSession</name> - <maxQuantVersion>1.6.17.0</maxQuantVersion> + <maxQuantVersion>2.0.3.0</maxQuantVersion> <pluginFolder/> <numThreads>1</numThreads> - <batchSize>1</batchSize> <emailAddress/> <smtpHost/> <emailFromAddress/> @@ -151,6 +165,11 @@ <intensPred>False</intensPred> <intensPredModelReTrain>False</intensPredModelReTrain> <lfqTopNPeptides>0</lfqTopNPeptides> + <diaJoinPrecChargesForLfq>False</diaJoinPrecChargesForLfq> + <diaFragChargesForQuant>1</diaFragChargesForQuant> + <timsRearrangeSpectra>False</timsRearrangeSpectra> + <gridSpacing>0.5</gridSpacing> + <proteinGroupingFile/> <parameterGroups> <parameterGroup> <msInstrument>0</msInstrument> @@ -258,9 +277,16 @@ <timsCollapseMsms>True</timsCollapseMsms> <crossLinkingType>0</crossLinkingType> <crossLinker/> - <minMatchXl>0</minMatchXl> + <minMatchXl>3</minMatchXl> <minPairedPepLenXl>6</minPairedPepLenXl> + <minScore_Dipeptide>40</minScore_Dipeptide> + <minScore_Monopeptide>0</minScore_Monopeptide> + <minScore_PartialCross>10</minScore_PartialCross> <crosslinkOnlyIntraProtein>False</crosslinkOnlyIntraProtein> + <crosslinkIntensityBasedPrecursor>True</crosslinkIntensityBasedPrecursor> + <isHybridPrecDetermination>False</isHybridPrecDetermination> + <topXcross>3</topXcross> + <doesSeparateInterIntraProteinCross>False</doesSeparateInterIntraProteinCross> <crosslinkMaxMonoUnsaturated>0</crosslinkMaxMonoUnsaturated> <crosslinkMaxMonoSaturated>0</crosslinkMaxMonoSaturated> <crosslinkMaxDiUnsaturated>0</crosslinkMaxDiUnsaturated> @@ -277,6 +303,7 @@ <peakRefinement>False</peakRefinement> <isobaricSumOverWindow>True</isobaricSumOverWindow> <isobaricWeightExponent>0.75</isobaricWeightExponent> + <collapseMsmsOnIsotopePatterns>False</collapseMsmsOnIsotopePatterns> <diaLibraryType>0</diaLibraryType> <diaLibraryPaths> </diaLibraryPaths> @@ -323,6 +350,12 @@ <diaBackgroundSubtractionQuantile>0.5</diaBackgroundSubtractionQuantile> <diaBackgroundSubtractionFactor>4</diaBackgroundSubtractionFactor> <diaLfqWeightedMedian>False</diaLfqWeightedMedian> + <diaTransferQvalue>0.3</diaTransferQvalue> + <diaOnlyIsosForRecal>True</diaOnlyIsosForRecal> + <diaMinPeaksForRecal>5</diaMinPeaksForRecal> + <diaUseFragIntensForMl>False</diaUseFragIntensForMl> + <diaUseFragMassesForMl>False</diaUseFragMassesForMl> + <diaMaxTrainInstances>1000000</diaMaxTrainInstances> </parameterGroup> </parameterGroups> <msmsParamsArray> @@ -332,7 +365,7 @@ <MatchToleranceInPpm>True</MatchToleranceInPpm> <DeisotopeTolerance>7</DeisotopeTolerance> <DeisotopeToleranceInPpm>True</DeisotopeToleranceInPpm> - <DeNovoTolerance>10</DeNovoTolerance> + <DeNovoTolerance>25</DeNovoTolerance> <DeNovoToleranceInPpm>True</DeNovoToleranceInPpm> <Deisotope>True</Deisotope> <Topx>12</Topx> @@ -349,7 +382,7 @@ <MatchToleranceInPpm>False</MatchToleranceInPpm> <DeisotopeTolerance>0.15</DeisotopeTolerance> <DeisotopeToleranceInPpm>False</DeisotopeToleranceInPpm> - <DeNovoTolerance>0.25</DeNovoTolerance> + <DeNovoTolerance>0.5</DeNovoTolerance> <DeNovoToleranceInPpm>False</DeNovoToleranceInPpm> <Deisotope>False</Deisotope> <Topx>8</Topx> @@ -366,8 +399,8 @@ <MatchToleranceInPpm>True</MatchToleranceInPpm> <DeisotopeTolerance>0.01</DeisotopeTolerance> <DeisotopeToleranceInPpm>False</DeisotopeToleranceInPpm> - <DeNovoTolerance>0.02</DeNovoTolerance> - <DeNovoToleranceInPpm>False</DeNovoToleranceInPpm> + <DeNovoTolerance>25</DeNovoTolerance> + <DeNovoToleranceInPpm>True</DeNovoToleranceInPpm> <Deisotope>True</Deisotope> <Topx>10</Topx> <TopxInterval>100</TopxInterval> @@ -383,7 +416,7 @@ <MatchToleranceInPpm>True</MatchToleranceInPpm> <DeisotopeTolerance>7</DeisotopeTolerance> <DeisotopeToleranceInPpm>True</DeisotopeToleranceInPpm> - <DeNovoTolerance>10</DeNovoTolerance> + <DeNovoTolerance>25</DeNovoTolerance> <DeNovoToleranceInPpm>True</DeNovoToleranceInPpm> <Deisotope>True</Deisotope> <Topx>12</Topx> |
| b |
| diff -r 837224ad1694 -r 8934bc76bb52 test-data/mqpar/mqpar.xml --- a/test-data/mqpar/mqpar.xml Tue Jan 31 18:14:40 2023 +0000 +++ b/test-data/mqpar/mqpar.xml Mon Jun 19 17:02:17 2023 +0000 |
| b |
| @@ -112,10 +112,9 @@ <variationMode>none</variationMode> <useSeriesReporters>False</useSeriesReporters> <name>session1</name> - <maxQuantVersion>1.6.17.0</maxQuantVersion> + <maxQuantVersion>2.0.3.0</maxQuantVersion> <pluginFolder/> <numThreads>1</numThreads> - <batchSize>1</batchSize> <emailAddress/> <smtpHost/> <emailFromAddress/> |
| b |
| diff -r 837224ad1694 -r 8934bc76bb52 test-data/mqpar/txt/allPeptides.txt --- a/test-data/mqpar/txt/allPeptides.txt Tue Jan 31 18:14:40 2023 +0000 +++ b/test-data/mqpar/txt/allPeptides.txt Mon Jun 19 17:02:17 2023 +0000 |
| [ |
| b'@@ -1,116 +1,116 @@\n Raw file\tType\tCharge\tm/z\tMass\tUncalibrated m/z\tNumber of data points\tNumber of scans\tNumber of isotopic peaks\tPIF\tMass fractional part\tMass deficit\tMass precision [ppm]\tMax intensity m/z 0\tRetention time\tRetention length\tRetention length (FWHM)\tMin scan number\tMax scan number\tIdentified\tReverse\tMS/MS IDs\tSequence\tLength\tModifications\tModified sequence\tProteins\tScore\tPEP\tIntensity\tIntensities\tIsotope pattern\tMS/MS Count\tMSMS Scan Numbers\tMSMS Isotope Indices\n BSA_min_21\tMULTI\t2\t752.78847\t1503.5624\t752.78847\t8\t4\t2\t\t0.562384\t-0.16925473367246\t0.775183\t752.788732084711\t0.0728\t10.5\t0\t1\t31\t\t\t-1\t\t0\t\t\t\t0\tNaN\t29581\t0;10127.0834960938;21733.4140625;15751.8271484375;11119.455078125;0\t12711.455078125;9021.958984375\t0\t\t\n BSA_min_21\tMULTI\t2\t485.29192\t968.5693\t485.29192\t22\t13\t3\t\t0.569296\t0.0837541655223504\t0.713993\t485.291493836352\t0.158\t29.2\t0\t1\t84\t\t\t-1\t\t0\t\t\t\t0\tNaN\t35127\t0;6617.423828125;22640.4897460938;31257.1982421875;34228.8039550781;35066.3161621094;22591.3203125;25334.1130371094;10954.4208984375;10387.701171875;5409.716796875;5679.3515625;3629.8916015625;3413.14501953125;0\t22239.669921875;10595.8701171875;3631.79956054688\t0\t\t\n-BSA_min_21\tMULTI\t1\t609.34313\t608.33585\t609.34313\t15\t10\t2\t\t0.335855\t0.0160203484621206\t0.653578\t609.343255068747\t0.14\t22.8\t0\t1\t66\t\t\t-1\t\t0\t\t\t\t0\tNaN\t16988\t0;9840.98266601562;11124.4873046875;15963.8212890625;11129.7348632812;11067.9287109375;5360.87646484375;5169.17236328125;5964.7109375;5728.80078125;4231.7958984375;0\t9241.0615234375;7473.39013671875\t0\t\t\n+BSA_min_21\tMULTI\t1\t609.34313\t608.33585\t609.34313\t15\t10\t2\t\t0.335855\t0.0160203484621206\t0.653578\t609.343255068747\t0.14\t22.8\t0\t1\t66\t\t\t-1\t\t0\t\t\t\t0\tNaN\t16988\t0;9840.98266601563;11124.4873046875;15963.8212890625;11129.7348632813;11067.9287109375;5360.87646484375;5169.17236328125;5964.7109375;5728.80078125;4231.7958984375;0\t9241.0615234375;7473.39013671875\t0\t\t\n BSA_min_21\tMULTI\t2\t752.31297\t1502.6114\t752.31297\t9\t6\t2\t\t0.611386\t-0.119815223783917\t0.685468\t752.312709646655\t0.121\t14.7\t0\t1\t43\t\t\t-1\t\t0\t\t\t\t0\tNaN\t40064\t0;4285.77001953125;11859.416015625;29434.9091796875;28467.7021484375;21782.734375;7783.14453125;0\t22226.8125;12791.9208984375\t1\t36\t0\n-BSA_min_21\tMULTI\t4\t835.11285\t3336.4223\t835.11285\t18\t7\t3\t\t0.422302\t-0.152452077995349\t0.513615\t835.363566648992\t0.151\t16.7\t0\t1\t48\t\t\t-1\t\t0\t\t\t\t0\tNaN\t63787\t0;17149.9038085938;25055.0866699219;28565.6630859375;44055.3051757812;40159.6279296875;23483.638671875;9918.11328125;0\t0;20459.83203125;17639.462890625;9406.8017578125\t1\t41\t2\n-BSA_min_21\tMULTI\t1\t1129.4643\t1128.457\t1129.4643\t7\t4\t2\t\t0.456986\t-0.102104602059853\t1.36127\t1129.46329424631\t0.127\t10.5\t0\t7\t37\t\t\t-1\t\t0\t\t\t\t0\tNaN\t16468\t0;7075.529296875;14889.8579101562;13879.3891601562;10506.4604492188;0\t8219.6025390625;7768.6494140625\t0\t\t\n+BSA_min_21\tMULTI\t4\t835.11285\t3336.4223\t835.11285\t18\t7\t3\t\t0.422302\t-0.152452077995349\t0.513615\t835.363566648992\t0.151\t16.7\t0\t1\t48\t\t\t-1\t\t0\t\t\t\t0\tNaN\t63787\t0;17149.9038085938;25055.0866699219;28565.6630859375;44055.3051757813;40159.6279296875;23483.638671875;9918.11328125;0\t0;20459.83203125;17639.462890625;9406.8017578125\t1\t41\t2\n+BSA_min_21\tMULTI\t1\t1129.4643\t1128.457\t1129.4643\t7\t4\t2\t\t0.456986\t-0.102104602059853\t1.36127\t1129.46329424631\t0.127\t10.5\t0\t7\t37\t\t\t-1\t\t0\t\t\t\t0\tNaN\t16468\t0;7075.529296875;14889.8579101563;13879.3891601563;10506.4604492188;0\t8219.6025390625;7768.6494140625\t0\t\t\n BSA_min_21\tMULTI\t2\t529.23526\t1056.456\t529.23526\t11\t6\t2\t\t0.455969\t-0.0700012324659838\t0.57417\t529.23524702789\t0.144\t14.6\t0\t7\t48\t\t\t-1\t\t0\t\t\t\t0\tNaN\t40276\t0;20066.6826171875;28887.369140625;34706.0693359375;23093.0561523438;20422.7763671875;4860.98779296875;0\t20563.033203125;14143.0361328125\t1\t30\t0\n BSA_min_21\tMULTI\t2\t558.2828\t1114.551\t558.2828\t4\t2\t2\t\t0.55104\t-0.00165384098022514\t1.21174\t558.28243824793\t0.199\t6.41\t0\t25\t43\t\t\t-1\t\t0\t\t\t\t0\tNaN\t10557\t0;6792.45678710938;8991.09375;0\t4918.08203125;4216.0205078125\t0\t\t\n BSA_min_21\tMULTI\t2\t637.83382\t1273.6531\t637.83382\t8\t4\t2\t\t0.653089\t0.0272087376192758\t1.19726\t637.833851166233\t0.144\t10.6\t0\t13\t43\t\t\t-1\t\t0\t\t\t\t0\tNaN\t23966\t0;12504.616699'..b'076.1640625;1087181.0390625;1083330.80859375;1064600.79492188;967271.58203125;760838.3828125;712827.775390625;711122.657226563;657815.7890625;639986.428710938;568138.3671875;498523.453125;0\t816282.4375;246289.265625;56386.8359375\t0\t\t\n+BSA_min_22\tMULTI\t2\t687.86486\t1373.7152\t687.86486\t34\t19\t2\t\t0.715162\t0.0432531900291906\t0.361393\t687.864771258339\t0.45\t30.4\t0\t19\t97\t\t\t-1\t\t0\t\t\t\t0\tNaN\t154530\t0;17070.9765625;15239.01953125;37858.7900390625;49730.232421875;83999.640625;108620.02734375;78961.19921875;68455.525390625;103047.68359375;76193.4423828125;60915.087890625;103987.82421875;80639.453125;96846.3671875;59798.15625;50967.80859375;118319.59375;92429.69140625;0;0\t80212.90625;56705.4921875\t1\t81\t0\n+BSA_min_22\tMULTI\t2\t691.87178\t1381.729\t691.87178\t27\t17\t2\t\t0.72901\t0.0534145086980971\t0.619773\t691.872041785377\t0.504\t26.2\t0\t31\t97\t\t\t-1\t\t0\t\t\t\t0\tNaN\t89847\t0;31056.8515625;24916.55859375;42320.4921875;33702.22265625;30072.40234375;54384.478515625;39607.3984375;67881.76171875;70223.21484375;56608.279296875;67995.814453125;48903.1484375;61068.0712890625;78135.9296875;60122.98046875;34629.55859375;20974.099609375;0\t45579.89453125;44678.484375\t0\t\t\n+BSA_min_22\tMULTI\t2\t760.30996\t1518.6054\t760.30996\t38\t21\t2\t\t0.605366\t-0.133192149836077\t0.498546\t760.310131649569\t0.405\t34.5\t0\t7\t97\t\t\t-1\t\t0\t\t\t\t0\tNaN\t208680\t0;36578.73828125;35192.98046875;64308.9140625;105542.3984375;139310.45703125;114743.15234375;104284.55078125;173741.90625;124384.26171875;122811.6171875;118852.75390625;119179.0390625;95637.0078125;153314.75390625;109609.643554688;90966.337890625;97841.005859375;109332.62109375;95516.654296875;67384.787109375;43305.8515625;0\t130571.7890625;63446.5625\t0\t\t\n+BSA_min_22\tMULTI\t2\t771.36091\t1540.7073\t771.36091\t4\t2\t2\t\t0.707267\t-0.0414584089676282\t1.00387\t771.862096841899\t0.582\t3.25\t0\t94\t97\t\t\t-1\t\t0\t\t\t\t0\tNaN\t91241\t0;51686.912109375;66223.453125;0\t30713.21875;35510.234375\t0\t\t\n+BSA_min_22\tMULTI\t1\t784.34691\t783.33964\t784.34691\t30\t15\t2\t\t0.339636\t-0.0607003816246561\t2.30826\t784.349756464299\t0.383\t22\t0\t43\t97\t\t\t-1\t\t0\t\t\t\t0\tNaN\t260350\t0;70757.70703125;189261.94140625;222351.78515625;199627.3203125;236004.41796875;230515.21875;190031.2265625;175600.515625;145150.48046875;144838.58203125;131776.0390625;109370.369140625;100637.03515625;105928.84375;90421.66015625;0\t176021.15625;68246.65625\t0\t\t\n+BSA_min_22\tMULTI\t1\t794.64688\t793.63961\t794.64688\t30\t15\t2\t\t0.639608\t0.234533860482884\t2.05185\t794.643543730692\t0.384\t22\t0\t43\t97\t\t\t-1\t\t0\t\t\t\t0\tNaN\t239190\t0;75799.166015625;182819.57421875;205794.7265625;190388.55078125;216829.5625;232016.9453125;192153.88671875;159977.91015625;138327.91796875;133145.87890625;134100.47265625;98902.771484375;91682.572265625;94544.208984375;90000.30859375;0\t154234.703125;77830.1171875\t0\t\t\n+BSA_min_22\tMULTI\t2\t882.35364\t1762.6927\t882.35364\t37\t10\t4\t\t0.692729\t-0.158109462239054\t0.263604\t882.3537934524\t0.506\t13.3\t0\t66\t97\t\t\t-1\t\t0\t\t\t\t0\tNaN\t590530\t0;124034.1953125;163759.890625;282199.0859375;462152.302734375;567479.9140625;517910.6875;574728.921875;462919.96484375;487479.03125;390846.802734375;0\t260553.25;218559.125;96019.7890625;50340.6796875\t2\t79;76\t0;1\n+BSA_min_22\tMULTI\t1\t885.46037\t884.4531\t885.46037\t30\t15\t2\t\t0.453097\t0.00624859595677663\t0.225017\t885.460184927629\t0.523\t22\t0\t43\t97\t\t\t-1\t\t0\t\t\t\t0\tNaN\t462900\t0;113598.3125;268971.296875;273512.21875;327821.2734375;293932.546875;284912.0546875;317776.6875;276913.546875;282582.9375;309678.84375;315305.8359375;341380.8984375;412443.2890625;350983.1953125;333208.1015625;0\t311737.5;106428.734375\t0\t\t\n+BSA_min_22\tMULTI\t2\t891.32977\t1780.645\t891.32977\t7\t4\t3\t\t0.644994\t-0.214102799046941\t1.64694\t891.330602133011\t0.564\t5.37\t0\t88\t97\t\t\t-1\t\t0\t\t\t\t0\tNaN\t108770\t0;18189.900390625;36413.9580078125;95086.095703125;33709.892578125;0\t54638.015625;26095.5859375;17093.90234375\t0\t\t\n+BSA_min_22\tMULTI\t1\t998.47572\t997.46845\t998.47572\t8\t5\t2\t\t0.468446\t-0.0303893371509503\t0.899083\t998.476134677568\t0.575\t6.3\t0\t86\t97\t\t\t-1\t\t0\t\t\t\t0\tNaN\t69512\t0;24384.458984375;29209.26171875;59130.58984375;43881.052734375;60372.1484375;0\t43851.453125;18626.490234375\t0\t\t\n' |
| b |
| diff -r 837224ad1694 -r 8934bc76bb52 test-data/mqpar/txt/mqpar.xml --- a/test-data/mqpar/txt/mqpar.xml Tue Jan 31 18:14:40 2023 +0000 +++ b/test-data/mqpar/txt/mqpar.xml Mon Jun 19 17:02:17 2023 +0000 |
| b |
| @@ -112,10 +112,9 @@ <variationMode>none</variationMode> <useSeriesReporters>False</useSeriesReporters> <name>session1</name> - <maxQuantVersion>1.6.17.0</maxQuantVersion> + <maxQuantVersion>2.0.3.0</maxQuantVersion> <pluginFolder/> <numThreads>1</numThreads> - <batchSize>1</batchSize> <emailAddress/> <smtpHost/> <emailFromAddress/> |
| b |
| diff -r 837224ad1694 -r 8934bc76bb52 test-data/mqpar/txt/mzRange.txt --- a/test-data/mqpar/txt/mzRange.txt Tue Jan 31 18:14:40 2023 +0000 +++ b/test-data/mqpar/txt/mzRange.txt Mon Jun 19 17:02:17 2023 +0000 |
| b |
| b'@@ -171,166 +171,166 @@\n BSA_min_21\t287.061454772949\t0\t0\t0\t0\t0\t0\tNaN\t0\t0\t\n BSA_min_21\t288.061454772949\t0\t0\t0\t0\t0\t0\tNaN\t0\t0\t\n BSA_min_21\t289.061454772949\t0\t0\t0\t0\t0\t0\tNaN\t0\t0\t\n-BSA_min_21\t290.061454772949\t0.01844\t0.000834\t0.0008779\t0\t4.39E-05\t0\t0\t2.195E-05\t0\t0\n-BSA_min_21\t291.061454772949\t0.3184\t0.01441\t0.01516\t0\t0.0007582\t0\t0\t0.0003791\t0\t0\n-BSA_min_21\t292.061454772949\t0.6184\t0.02798\t0.02945\t0\t0.001472\t0\t0\t0.0007362\t0\t0\n-BSA_min_21\t293.061454772949\t0.9184\t0.04155\t0.04374\t0\t0.002187\t0\t0\t0.001093\t0\t0\n-BSA_min_21\t294.061454772949\t1.218\t0.05512\t0.05802\t0\t0.002901\t0\t0\t0.001451\t0\t0\n-BSA_min_21\t295.061454772949\t1.518\t0.06869\t0.07231\t0\t0.003615\t0\t0\t0.001808\t0\t0\n-BSA_min_21\t296.061454772949\t1.818\t0.08226\t0.08659\t0\t0.00433\t0\t0\t0.002165\t0\t0\n-BSA_min_21\t297.061454772949\t2.118\t0.09583\t0.1009\t0\t0.005044\t0\t0\t0.002522\t0\t0\n-BSA_min_21\t298.061454772949\t2.418\t0.1094\t0.1152\t0\t0.005758\t0\t0\t0.002879\t0\t0\n-BSA_min_21\t299.061454772949\t2.718\t0.123\t0.1294\t0\t0.006472\t0\t0\t0.003236\t0\t0\n-BSA_min_21\t300.061454772949\t3.018\t0.1365\t0.1437\t0\t0.007187\t0\t0\t0.003593\t0\t0\n-BSA_min_21\t301.061454772949\t3.318\t0.1501\t0.158\t0\t0.007901\t0\t0\t0.003951\t0\t0\n-BSA_min_21\t302.061454772949\t3.618\t0.1637\t0.1723\t0\t0.008615\t0\t0\t0.004308\t0\t0\n-BSA_min_21\t303.061454772949\t3.918\t0.1773\t0.1866\t0\t0.00933\t0\t0\t0.004665\t0\t0\n-BSA_min_21\t304.061454772949\t4.218\t0.1908\t0.2009\t0\t0.01004\t0\t0\t0.005022\t0\t0\n-BSA_min_21\t305.061454772949\t4.518\t0.2044\t0.2152\t0\t0.01076\t0\t0\t0.005379\t0\t0\n-BSA_min_21\t306.061454772949\t4.818\t0.218\t0.2294\t0\t0.01147\t0\t0\t0.005736\t0\t0\n-BSA_min_21\t307.061454772949\t5.118\t0.2315\t0.2437\t0\t0.01219\t0\t0\t0.006093\t0\t0\n-BSA_min_21\t308.061454772949\t5.418\t0.2451\t0.258\t0\t0.0129\t0\t0\t0.006451\t0\t0\n-BSA_min_21\t309.061454772949\t5.718\t0.2587\t0.2723\t0\t0.01362\t0\t0\t0.006808\t0\t0\n-BSA_min_21\t310.061454772949\t6.019\t0.2724\t0.2857\t0\t0.01429\t0\t0\t0.007143\t0\t0\n-BSA_min_21\t311.061454772949\t6.326\t0.2877\t0.2857\t0\t0.01429\t0\t0\t0.007143\t0\t0\n-BSA_min_21\t312.061454772949\t6.633\t0.3031\t0.2857\t0\t0.01429\t0\t0\t0.007143\t0\t0\n-BSA_min_21\t313.061454772949\t6.94\t0.3184\t0.2857\t0\t0.01429\t0\t0\t0.007143\t0\t0\n-BSA_min_21\t314.061454772949\t7.247\t0.3338\t0.2857\t0\t0.01429\t0\t0\t0.007143\t0\t0\n-BSA_min_21\t315.061454772949\t7.555\t0.3492\t0.2857\t0\t0.01429\t0\t0\t0.007143\t0\t0\n-BSA_min_21\t316.061454772949\t7.862\t0.3645\t0.2857\t0\t0.01429\t0\t0\t0.007143\t0\t0\n-BSA_min_21\t317.061454772949\t8.169\t0.3799\t0.2857\t0\t0.01429\t0\t0\t0.007143\t0\t0\n-BSA_min_21\t318.061454772949\t8.476\t0.3952\t0.2857\t0\t0.01429\t0\t0\t0.007143\t0\t0\n-BSA_min_21\t319.061454772949\t8.783\t0.4106\t0.2857\t0\t0.01429\t0\t0\t0.007143\t0\t0\n-BSA_min_21\t320.061454772949\t9.09\t0.4259\t0.2857\t0\t0.01429\t0\t0\t0.007143\t0\t0\n-BSA_min_21\t321.061454772949\t9.397\t0.4413\t0.2857\t0\t0.01429\t0\t0\t0.007143\t0\t0\n-BSA_min_21\t322.061454772949\t9.705\t0.4567\t0.2857\t0\t0.01429\t0\t0\t0.007143\t0\t0\n-BSA_min_21\t323.061454772949\t10.01\t0.472\t0.2857\t0\t0.01429\t0\t0\t0.007143\t0\t0\n-BSA_min_21\t324.061454772949\t10.32\t0.4874\t0.2857\t0\t0.01429\t0\t0\t0.007143\t0\t0\n-BSA_min_21\t325.061454772949\t10.63\t0.5027\t0.2857\t0\t0.01429\t0\t0\t0.007143\t0\t0\n-BSA_min_21\t326.061454772949\t10.93\t0.5181\t0.2857\t0\t0.01429\t0\t0\t0.007143\t0\t0\n-BSA_min_21\t327.061454772949\t11.24\t0.5334\t0.2857\t0\t0.01429\t0\t0\t0.007143\t0\t0\n-BSA_min_21\t328.061454772949\t11.55\t0.5488\t0.2857\t0\t0.01429\t0\t0\t0.007143\t0\t0\n-BSA_min_21\t329.061454772949\t11.85\t0.5642\t0.2857\t0\t0.01429\t0\t0\t0.007143\t0\t0\n-BSA_min_21\t330.061454772949\t12.17\t0.5799\t0.2866\t0\t0.01433\t0\t0\t0.007143\t0\t0\n-BSA_min_21\t331.061454772949\t12.64\t0.6017\t0.3009\t0\t0.01504\t0\t0\t0.007143\t0\t0\n-BSA_min_21\t332.061454772949\t13.1\t0.6235\t0.3152\t0\t0.01576\t0\t0\t0.007143\t0\t0\n-BSA_min_21\t333.061454772949\t13.56\t0.6453\t0.3294\t0\t0.01647\t0\t0\t0.007143\t0\t0\n-BSA_min_21\t334.061454772949\t14.03\t0.6671\t0.3437\t0\t0.01719\t0\t0\t0.007143\t0\t0\n-BSA_min_21\t335.061454772949\t14.49\t0.6888\t0.358\t0\t0.0179\t0\t0\t0.007143\t0\t0\n-BSA_min_21\t336.061454772949\t14.96\t0.7106\t0.3723\t0\t0.01862\t0\t0\t0.007143\t0\t0\n-BSA_min_21\t337.061454772949\t15.42\t0.7324\t0.3866\t0\t0.01933\t0\t0\t0.007143\t0\t0\n-BSA_min_21\t338.061454772949\t15.89\t0.7542\t0.4009\t0\t0.02004\t0\t0\t0.007143\t0\t0\n-BSA_min_21\t339.061454772949\t16.35\t0.776\t0.4152\t0\t0.02076\t0\t0\t0.007143\t0\t'..b'in_22\t1650.18692779541\t2.838\t0.1206\t0.1415\t0\t0.007076\t0\t0\t0\t0\t\n+BSA_min_22\t1651.18692779541\t2.738\t0.1159\t0.1344\t0\t0.006719\t0\t0\t0\t0\t\n+BSA_min_22\t1652.18692779541\t2.638\t0.1113\t0.1272\t0\t0.006362\t0\t0\t0\t0\t\n+BSA_min_22\t1653.18692779541\t2.538\t0.1066\t0.1201\t0\t0.006005\t0\t0\t0\t0\t\n+BSA_min_22\t1654.18692779541\t2.438\t0.102\t0.113\t0\t0.005648\t0\t0\t0\t0\t\n+BSA_min_22\t1655.18692779541\t2.338\t0.09735\t0.1058\t0\t0.00529\t0\t0\t0\t0\t\n+BSA_min_22\t1656.18692779541\t2.238\t0.0927\t0.09866\t0\t0.004933\t0\t0\t0\t0\t\n+BSA_min_22\t1657.18692779541\t2.138\t0.08806\t0.09152\t0\t0.004576\t0\t0\t0\t0\t\n+BSA_min_22\t1658.18692779541\t2.038\t0.08342\t0.08438\t0\t0.004219\t0\t0\t0\t0\t\n+BSA_min_22\t1659.18692779541\t1.938\t0.07877\t0.07724\t0\t0.003862\t0\t0\t0\t0\t\n+BSA_min_22\t1660.18692779541\t1.838\t0.07413\t0.07009\t0\t0.003505\t0\t0\t0\t0\t\n+BSA_min_22\t1661.18692779541\t1.738\t0.06949\t0.06295\t0\t0.003148\t0\t0\t0\t0\t\n+BSA_min_22\t1662.18692779541\t1.638\t0.06485\t0.05581\t0\t0.00279\t0\t0\t0\t0\t\n+BSA_min_22\t1663.18692779541\t1.538\t0.0602\t0.04866\t0\t0.002433\t0\t0\t0\t0\t\n+BSA_min_22\t1664.18692779541\t1.438\t0.05556\t0.04152\t0\t0.002076\t0\t0\t0\t0\t\n+BSA_min_22\t1665.18692779541\t1.338\t0.05092\t0.03438\t0\t0.001719\t0\t0\t0\t0\t\n+BSA_min_22\t1666.18692779541\t1.238\t0.04627\t0.02724\t0\t0.001362\t0\t0\t0\t0\t\n+BSA_min_22\t1667.18692779541\t1.138\t0.04163\t0.02009\t0\t0.001005\t0\t0\t0\t0\t\n+BSA_min_22\t1668.18692779541\t1.038\t0.03699\t0.01295\t0\t0.0006475\t0\t0\t0\t0\t\n+BSA_min_22\t1669.18692779541\t0.9385\t0.03235\t0.005808\t0\t0.0002904\t0\t0\t0\t0\t\n+BSA_min_22\t1670.18692779541\t0.8538\t0.02854\t0\t0\t0\t0\tNaN\t0\t0\t\n+BSA_min_22\t1671.18692779541\t0.8359\t0.02836\t0\t0\t0\t0\tNaN\t0\t0\t\n+BSA_min_22\t1672.18692779541\t0.8181\t0.02818\t0\t0\t0\t0\tNaN\t0\t0\t\n+BSA_min_22\t1673.18692779541\t0.8002\t0.028\t0\t0\t0\t0\tNaN\t0\t0\t\n+BSA_min_22\t1674.18692779541\t0.7824\t0.02782\t0\t0\t0\t0\tNaN\t0\t0\t\n+BSA_min_22\t1675.18692779541\t0.7645\t0.02765\t0\t0\t0\t0\tNaN\t0\t0\t\n+BSA_min_22\t1676.18692779541\t0.7467\t0.02747\t0\t0\t0\t0\tNaN\t0\t0\t\n+BSA_min_22\t1677.18692779541\t0.7288\t0.02729\t0\t0\t0\t0\tNaN\t0\t0\t\n+BSA_min_22\t1678.18692779541\t0.7109\t0.02711\t0\t0\t0\t0\tNaN\t0\t0\t\n+BSA_min_22\t1679.18692779541\t0.6931\t0.02693\t0\t0\t0\t0\tNaN\t0\t0\t\n+BSA_min_22\t1680.18692779541\t0.6752\t0.02675\t0\t0\t0\t0\tNaN\t0\t0\t\n+BSA_min_22\t1681.18692779541\t0.6574\t0.02657\t0\t0\t0\t0\tNaN\t0\t0\t\n+BSA_min_22\t1682.18692779541\t0.6395\t0.0264\t0\t0\t0\t0\tNaN\t0\t0\t\n+BSA_min_22\t1683.18692779541\t0.6217\t0.02622\t0\t0\t0\t0\tNaN\t0\t0\t\n+BSA_min_22\t1684.18692779541\t0.6038\t0.02604\t0\t0\t0\t0\tNaN\t0\t0\t\n+BSA_min_22\t1685.18692779541\t0.5859\t0.02586\t0\t0\t0\t0\tNaN\t0\t0\t\n+BSA_min_22\t1686.18692779541\t0.5681\t0.02568\t0\t0\t0\t0\tNaN\t0\t0\t\n+BSA_min_22\t1687.18692779541\t0.5502\t0.0255\t0\t0\t0\t0\tNaN\t0\t0\t\n+BSA_min_22\t1688.18692779541\t0.5324\t0.02532\t0\t0\t0\t0\tNaN\t0\t0\t\n+BSA_min_22\t1689.18692779541\t0.5145\t0.02515\t0\t0\t0\t0\tNaN\t0\t0\t\n+BSA_min_22\t1690.18692779541\t0.4953\t0.02477\t0\t0\t0\t0\tNaN\t0\t0\t\n+BSA_min_22\t1691.18692779541\t0.4703\t0.02352\t0\t0\t0\t0\tNaN\t0\t0\t\n+BSA_min_22\t1692.18692779541\t0.4453\t0.02227\t0\t0\t0\t0\tNaN\t0\t0\t\n+BSA_min_22\t1693.18692779541\t0.4203\t0.02102\t0\t0\t0\t0\tNaN\t0\t0\t\n+BSA_min_22\t1694.18692779541\t0.3953\t0.01977\t0\t0\t0\t0\tNaN\t0\t0\t\n+BSA_min_22\t1695.18692779541\t0.3703\t0.01852\t0\t0\t0\t0\tNaN\t0\t0\t\n+BSA_min_22\t1696.18692779541\t0.3453\t0.01727\t0\t0\t0\t0\tNaN\t0\t0\t\n+BSA_min_22\t1697.18692779541\t0.3203\t0.01602\t0\t0\t0\t0\tNaN\t0\t0\t\n+BSA_min_22\t1698.18692779541\t0.2953\t0.01477\t0\t0\t0\t0\tNaN\t0\t0\t\n+BSA_min_22\t1699.18692779541\t0.2703\t0.01352\t0\t0\t0\t0\tNaN\t0\t0\t\n+BSA_min_22\t1700.18692779541\t0.2453\t0.01227\t0\t0\t0\t0\tNaN\t0\t0\t\n+BSA_min_22\t1701.18692779541\t0.2203\t0.01102\t0\t0\t0\t0\tNaN\t0\t0\t\n+BSA_min_22\t1702.18692779541\t0.1953\t0.009766\t0\t0\t0\t0\tNaN\t0\t0\t\n+BSA_min_22\t1703.18692779541\t0.1703\t0.008516\t0\t0\t0\t0\tNaN\t0\t0\t\n+BSA_min_22\t1704.18692779541\t0.1453\t0.007266\t0\t0\t0\t0\tNaN\t0\t0\t\n+BSA_min_22\t1705.18692779541\t0.1203\t0.006016\t0\t0\t0\t0\tNaN\t0\t0\t\n+BSA_min_22\t1706.18692779541\t0.09533\t0.004766\t0\t0\t0\t0\tNaN\t0\t0\t\n+BSA_min_22\t1707.18692779541\t0.07033\t0.003516\t0\t0\t0\t0\tNaN\t0\t0\t\n+BSA_min_22\t1708.18692779541\t0.04533\t0.002266\t0\t0\t0\t0\tNaN\t0\t0\t\n+BSA_min_22\t1709.18692779541\t0.02033\t0.001016\t0\t0\t0\t0\tNaN\t0\t0\t\n BSA_min_22\t1710.18692779541\t0\t0\t0\t0\t0\t0\tNaN\t0\t0\t\n BSA_min_22\t1711.18692779541\t0\t0\t0\t0\t0\t0\tNaN\t0\t0\t\n BSA_min_22\t1712.18692779541\t0\t0\t0\t0\t0\t0\tNaN\t0\t0\t\n' |
| b |
| diff -r 837224ad1694 -r 8934bc76bb52 test-data/mqpar/txt/parameters.txt --- a/test-data/mqpar/txt/parameters.txt Tue Jan 31 18:14:40 2023 +0000 +++ b/test-data/mqpar/txt/parameters.txt Mon Jun 19 17:02:17 2023 +0000 |
| [ |
| @@ -1,5 +1,5 @@ Parameter Value -Version 1.6.17.0 +Version 2.0.3.0 User name niko Machine name DESKTOP-I3UDKML Date of writing 08/05/2021 17:10:11 @@ -46,8 +46,9 @@ Write allPeptides table True Write mzRange table True Write DIA fragments table False +Write DIA fragments quant table False Write pasefMsmsScans table True -Write accumulatedPasefMsmsScans table True +Write accumulatedMsmsScans table True Max. peptide mass [Da] 4600 Min. peptide length for unspecific search 8 Max. peptide length for unspecific search 25 |
| b |
| diff -r 837224ad1694 -r 8934bc76bb52 test-data/mqpar/txt/summary.txt --- a/test-data/mqpar/txt/summary.txt Tue Jan 31 18:14:40 2023 +0000 +++ b/test-data/mqpar/txt/summary.txt Mon Jun 19 17:02:17 2023 +0000 |
| [ |
| @@ -1,4 +1,4 @@ -Raw file Enzyme Enzyme mode Enzyme first search Enzyme mode first search Use enzyme first search Variable modifications Fixed modifications Multi modifications Variable modifications first search Use variable modifications first search Requantify Multiplicity Max. missed cleavages Labels0 LC-MS run type Time-dependent recalibration MS MS/MS MS3 MS/MS Submitted MS/MS Submitted (SIL) MS/MS Submitted (ISO) MS/MS Submitted (PEAK) MS/MS Identified MS/MS Identified (SIL) MS/MS Identified (ISO) MS/MS Identified (PEAK) MS/MS Identified [%] MS/MS Identified (SIL) [%] MS/MS Identified (ISO) [%] MS/MS Identified (PEAK) [%] Peptide Sequences Identified Peaks Peaks Sequenced Peaks Sequenced [%] Peaks Repeatedly Sequenced Peaks Repeatedly Sequenced [%] Isotope Patterns Isotope Patterns Sequenced Isotope Patterns Sequenced (z>1) Isotope Patterns Sequenced [%] Isotope Patterns Sequenced (z>1) [%] Isotope Patterns Repeatedly Sequenced Isotope Patterns Repeatedly Sequenced [%] Recalibrated Av. Absolute Mass Deviation [ppm] Mass Standard Deviation [ppm] Av. Absolute Mass Deviation [mDa] Mass Standard Deviation [mDa] -BSA_min_21 Trypsin/P Specific False Oxidation (M);Acetyl (Protein N-term) Carbamidomethyl (C) False False 1 0 Standard 18 82 0 124 40 0 84 10 6 0 4 8.1 15 0 4.8 10 1031 56 5.4 1 1.8 110 34 33 31 36 6 18 + 0.89167 1.1143 0.66988 0.8615 -BSA_min_22 Trypsin/P Specific False Oxidation (M);Acetyl (Protein N-term) Carbamidomethyl (C) False False 1 0 Standard 23 77 0 101 53 0 48 3 3 0 0 3 5.7 0 0 1 1675 61 3.6 1 1.6 294 43 41 15 15 10 23 + 0.73592 0.87072 0.46838 0.52262 -Total 41 159 0 225 93 0 132 13 9 0 4 5.8 9.7 0 3 11 2706 404 77 74 19 21 16 21 0.84717 1.0505 0.61231 0.77985 +Raw file Enzyme Enzyme mode Enzyme first search Enzyme mode first search Use enzyme first search Variable modifications Fixed modifications Multi modifications Variable modifications first search Use variable modifications first search Requantify Multiplicity Max. missed cleavages Labels0 LC-MS run type Time-dependent recalibration MS MS/MS MS3 MS/MS submitted MS/MS submitted (SIL) MS/MS submitted (ISO) MS/MS submitted (PEAK) MS/MS identified MS/MS identified (SIL) MS/MS identified (ISO) MS/MS identified (PEAK) MS/MS identified [%] MS/MS identified (SIL) [%] MS/MS identified (ISO) [%] MS/MS identified (PEAK) [%] Peptide sequences identified Peaks Peaks sequenced Peaks sequenced [%] Peaks repeatedly sequenced Peaks repeatedly sequenced [%] Isotope patterns Isotope patterns sequenced Isotope patterns sequenced (z>1) Isotope patterns sequenced [%] Isotope patterns sequenced (z>1) [%] Isotope patterns repeatedly sequenced Isotope patterns repeatedly sequenced [%] Recalibrated Av. absolute mass deviation [ppm] Mass standard deviation [ppm] Av. absolute mass deviation [mDa] Mass standard deviation [mDa] +BSA_min_21 Trypsin/P Specific False Oxidation (M);Acetyl (Protein N-term) Carbamidomethyl (C) False False 1 0 Standard 18 82 0 124 40 0 84 10 6 0 4 8.1 15 0 4.8 10 1028 56 5.4 1 1.8 110 34 33 31 36 6 18 + 0.89167 1.1143 0.66988 0.8615 +BSA_min_22 Trypsin/P Specific False Oxidation (M);Acetyl (Protein N-term) Carbamidomethyl (C) False False 1 0 Standard 23 77 0 101 53 0 48 3 3 0 0 3 5.7 0 0 2 1675 61 3.6 1 1.6 293 43 41 15 15 10 23 + 0.73592 0.87072 0.46838 0.52262 +Total 41 159 0 225 93 0 132 13 9 0 4 5.8 9.7 0 3 12 2703 403 77 74 19 21 16 21 0.84717 1.0505 0.61231 0.77985 |