| Previous changeset 11:d72c96ad9a16 (2021-06-15) Next changeset 13:181bd6a5f6ce (2021-06-25) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89" |
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modified:
macros.xml maxquant.xml 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/msms.txt test-data/01/combined/txt/msmsScans.txt test-data/01/combined/txt/mzRange.txt test-data/01/combined/txt/mzTab.mzTab test-data/01/combined/txt/parameters.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/01/config.yml test-data/01/mqpar.xml test-data/02/config.yml test-data/02/mqpar.xml test-data/03/config.yml test-data/03/mqpar.xml test-data/04/config.yml test-data/04/mqpar.xml test-data/05/config.yml test-data/05/mqpar.xml test-data/06/config.yml test-data/06/mqpar.xml test-data/07/config.yml test-data/07/mqpar.xml test-data/template.xml |
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added:
test-data/07/combined/txt/report_v1.0.10_combined.pdf test-data/08/combined/txt/proteinGroups.txt test-data/08/config.yml test-data/08/mqpar.xml test-data/tmt_data.fasta test-data/tmt_data.mzXML test-data/tmt_data_16.fasta |
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removed:
test-data/07/combined/txt/report_v1.0.9_combined.pdf test-data/ptxqc.fasta test-data/ptxqc.mzXML |
| b |
| diff -r d72c96ad9a16 -r 0839f84def5e macros.xml --- a/macros.xml Tue Jun 15 07:55:59 2021 +0000 +++ b/macros.xml Sun Jun 20 16:37:41 2021 +0000 |
| [ |
| @@ -1,7 +1,8 @@ <?xml version="1.0" ?> <macros> - <token name="@VERSION@">1.6.10.43</token> - <token name="@VERSION_PTXQC@">1.0.9</token> + <token name="@VERSION@">1.6.17.0</token> + <token name="@VERSION_SUFFIX@">0</token> + <token name="@VERSION_PTXQC@">1.0.10</token> <token name="@SUBSTITUTION_RX@">[^\w\-\s\.]</token> <token name="@TMT2PLEX@"> - [TMT2plex-Lys126,TMT2plex-Nter126,0,0,0,0,True] @@ -41,6 +42,24 @@ @TMT10PLEX@ - [TMT11plex-Lys131C,TMT11plex-Nter131C,0,0,0,0,True] </token> + <token name="@TMTPRO16PLEX@"> + - [TMTpro16plex-Lys127N,TMTpro16plex-Nter127N,0,0,0,0,True] + - [TMTpro16plex-Lys127C,TMTpro16plex-Nter127C,0,0,0,0,True] + - [TMTpro16plex-Lys128N,TMTpro16plex-Nter128N,0,0,0,0,True] + - [TMTpro16plex-Lys128C,TMTpro16plex-Nter128C,0,0,0,0,True] + - [TMTpro16plex-Lys129N,TMTpro16plex-Nter129N,0,0,0,0,True] + - [TMTpro16plex-Lys129C,TMTpro16plex-Nter129C,0,0,0,0,True] + - [TMTpro16plex-Lys130N,TMTpro16plex-Nter130N,0,0,0,0,True] + - [TMTpro16plex-Lys130C,TMTpro16plex-Nter130C,0,0,0,0,True] + - [TMTpro16plex-Lys131N,TMTpro16plex-Nter131N,0,0,0,0,True] + - [TMTpro16plex-Lys131C,TMTpro16plex-Nter131C,0,0,0,0,True] + - [TMTpro16plex-Lys132N,TMTpro16plex-Nter132N,0,0,0,0,True] + - [TMTpro16plex-Lys132C,TMTpro16plex-Nter132C,0,0,0,0,True] + - [TMTpro16plex-Lys133N,TMTpro16plex-Nter133N,0,0,0,0,True] + - [TMTpro16plex-Lys133C,TMTpro16plex-Nter133C,0,0,0,0,True] + - [TMTpro16plex-Lys134N,TMTpro16plex-Nter134N,0,0,0,0,True] + - [TMTpro16plex-Lys126C,TMTpro16plex-Nter126C,0,0,0,0,True] + </token> <token name="@ITRAQ4PLEX@"> - [iTRAQ4plex-Lys114,iTRAQ4plex-Nter114,0,0,0,0,False] - [iTRAQ4plex-Lys115,iTRAQ4plex-Nter115,0,0,0,0,False] @@ -637,6 +656,10 @@ <expand macro="mod_option" value="Xle->CamCys"/> <expand macro="mod_option" value="Cysteinyl"/> <expand macro="mod_option" value="Cysteinyl - carbamidomethyl"/> + <expand macro="mod_option" value="Oxidation (MP)"/> + <expand macro="mod_option" value="Propionamide (C)"/> + <expand macro="mod_option" value="Propionamide (K)"/> + <expand macro="mod_option" value="Propionamide (N-term)"/> </xml> <xml name="label"> <expand macro="mod_option" value="Arg6"/> @@ -774,6 +797,38 @@ <expand macro="mod_option" value="iodoTMT6plex-Cys129"/> <expand macro="mod_option" value="iodoTMT6plex-Cys130"/> <expand macro="mod_option" value="iodoTMT6plex-Cys131"/> + <expand macro="mod_option" value="TMTpro16plex-Nter126C"/> + <expand macro="mod_option" value="TMTpro16plex-Nter127N"/> + <expand macro="mod_option" value="TMTpro16plex-Nter127C"/> + <expand macro="mod_option" value="TMTpro16plex-Nter128N"/> + <expand macro="mod_option" value="TMTpro16plex-Nter128C"/> + <expand macro="mod_option" value="TMTpro16plex-Nter129N"/> + <expand macro="mod_option" value="TMTpro16plex-Nter129C"/> + <expand macro="mod_option" value="TMTpro16plex-Nter130N"/> + <expand macro="mod_option" value="TMTpro16plex-Nter130C"/> + <expand macro="mod_option" value="TMTpro16plex-Nter131N"/> + <expand macro="mod_option" value="TMTpro16plex-Nter131C"/> + <expand macro="mod_option" value="TMTpro16plex-Nter132N"/> + <expand macro="mod_option" value="TMTpro16plex-Nter132C"/> + <expand macro="mod_option" value="TMTpro16plex-Nter133N"/> + <expand macro="mod_option" value="TMTpro16plex-Nter133C"/> + <expand macro="mod_option" value="TMTpro16plex-Nter134N"/> + <expand macro="mod_option" value="TMTpro16plex-Lys126C"/> + <expand macro="mod_option" value="TMTpro16plex-Lys127N"/> + <expand macro="mod_option" value="TMTpro16plex-Lys127C"/> + <expand macro="mod_option" value="TMTpro16plex-Lys128N"/> + <expand macro="mod_option" value="TMTpro16plex-Lys128C"/> + <expand macro="mod_option" value="TMTpro16plex-Lys129N"/> + <expand macro="mod_option" value="TMTpro16plex-Lys129C"/> + <expand macro="mod_option" value="TMTpro16plex-Lys130N"/> + <expand macro="mod_option" value="TMTpro16plex-Lys130C"/> + <expand macro="mod_option" value="TMTpro16plex-Lys131N"/> + <expand macro="mod_option" value="TMTpro16plex-Lys131C"/> + <expand macro="mod_option" value="TMTpro16plex-Lys132N"/> + <expand macro="mod_option" value="TMTpro16plex-Lys132C"/> + <expand macro="mod_option" value="TMTpro16plex-Lys133N"/> + <expand macro="mod_option" value="TMTpro16plex-Lys133C"/> + <expand macro="mod_option" value="TMTpro16plex-Lys134N"/> </xml> <xml name="citations"> <citations> |
| b |
| diff -r d72c96ad9a16 -r 0839f84def5e maxquant.xml --- a/maxquant.xml Tue Jun 15 07:55:59 2021 +0000 +++ b/maxquant.xml Sun Jun 20 16:37:41 2021 +0000 |
| [ |
| b'@@ -1,4 +1,4 @@\n-<tool id="maxquant" name="MaxQuant" version="@VERSION@+galaxy5">\n+<tool id="maxquant" name="MaxQuant" version="@VERSION@+galaxy@VERSION_SUFFIX@">\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@@ -16,6 +16,13 @@\n <command detect_errors="exit_code"><![CDATA[\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@@ -155,7 +162,7 @@\n #end if\n #if $pg.quant_method.select_quant_method == \'lfq\':\n lfqMode: 1\n- lfqSkipNorm: ${pg.quant_method.lfqSkipNorm}\n+ lfqNormType: ${pg.quant_method.lfqNormType}\n lfqMinEdgesPerNode: ${pg.quant_method.lfqMinEdgesPerNode}\n lfqAvEdgesPerNode: ${pg.quant_method.lfqAvEdgesPerNode}\n lfqMinRatioCount: ${pg.quant_method.lfqMinRatioCount}\n@@ -192,6 +199,9 @@\n #if $pg.quant_method.iso_labels.labeling == \'tmt11plex\':\n @TMT11PLEX@\n #end if\n+ #if $pg.quant_method.iso_labels.labeling == \'tmtpro16plex\':\n+ @TMTPRO16PLEX@\n+ #end if\n #if $pg.quant_method.iso_labels.labeling == \'itraq4plex\':\n @ITRAQ4PLEX@\n #end if\n@@ -234,6 +244,9 @@\n #if $pg.quant_method.iso_labels.labeling == \'tmt11plex\':\n @TMT11PLEX@\n #end if\n+ #if $pg.quant_method.iso_labels.labeling == \'tmtpro16plex\':\n+ @TMTPRO16PLEX@\n+ #end if\n #if $pg.quant_method.iso_labels.labeling == \'itraq4plex\':\n @ITRAQ4PLEX@\n #end if\n@@ -477,10 +490,11 @@\n <param type="integer" name="lfqAvEdgesPerNode"\n label="LFQ average number of neighbours" value="6"\n help="Defines the network to normalize the samples in the fast LFQ mode."/>\n- <param type="boolean" name="lfqSkipNorm" checked="true"\n- label="Skip normalization"\n- truevalue="True" falsevalue="False"\n- help="If checked the high-speed version of MaxLFQ is used. This is recommended for large numbers of samples (Experiments). For less than 10 samples the original MaxLFQ normalization algorithm is used."/>\n+ <param name="lfqNormType" type="select" label="Normalization type"\n+ multiple="false" help="">\n+ <option value="0">None</option>\n+ <option value="1">Classic</option>\n+ </param>\n </when>\n <when value="reporter_ion_ms2">\n <conditional name="iso_labels">\n@@ -492,6 +506,7 @@\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="itraq4plex">iTRAQ4plex</option>\n <option value="itraq8plex">iTRAQ8plex</option>\n <option value="iodotmt6plex">iodoTMT6pl'..b' <when value="tmt8plex"/>\n <when value="tmt10plex"/>\n <when value="tmt11plex"/>\n+ <when value="tmtpro16plex"/>\n <when value="itraq4plex"/>\n <when value="itraq8plex"/>\n <when value="iodotmt6plex"/>\n@@ -643,8 +661,8 @@\n <output name="mqpar" file="01/mqpar.xml" lines_diff="6"/>\n <output name="evidence" file="01/combined/txt/evidence.txt" />\n <output name="msms" file="01/combined/txt/msms.txt" />\n- <output name="mzTab" file="01/combined/txt/mzTab.mzTab" lines_diff="4"/>\n- <output name="allPeptides" file="01/combined/txt/allPeptides.txt" lines_diff="4"/>\n+ <output name="mzTab" file="01/combined/txt/mzTab.mzTab" lines_diff="34"/>\n+ <output name="allPeptides" file="01/combined/txt/allPeptides.txt" lines_diff="2"/>\n <output name="msmsScans" file="01/combined/txt/msmsScans.txt" lines_diff="8"/>\n <output name="mzRange" file="01/combined/txt/mzRange.txt" />\n <output name="parameters" file="01/combined/txt/parameters.txt" lines_diff="10"/>\n@@ -879,11 +897,11 @@\n <!-- PTXQC Test -->\n <test expect_num_outputs="3">\n <param name="ftype" value=".mzxml" />\n- <param name="fasta_files" value="ptxqc.fasta" />\n+ <param name="fasta_files" value="tmt_data.fasta" />\n <param name="identifier_parse_rule" value=">([^\\s]*)" />\n <param name="description_parse_rule" value=">(.*)" />\n <repeat name="paramGroups">\n- <param name="files" value="ptxqc.mzXML"/>\n+ <param name="files" value="tmt_data.mzXML"/>\n <param name="variableModifications" value="Oxidation (M)" />\n <param name="fixedModifications" value="" />\n <conditional name="quant_method">\n@@ -897,8 +915,32 @@\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="24" />\n- <output name="ptxqc_report" file="07/combined/txt/report_v1.0.9_combined.pdf" compare="sim_size" />\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+ </test>\n+ <!-- 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+ <param name="identifier_parse_rule" value=">([^\\s]*)" />\n+ <param name="description_parse_rule" value=">(.*)" />\n+ <repeat name="paramGroups">\n+ <param name="files" value="tmt_data.mzXML"/>\n+ <param name="variableModifications" value="Oxidation (M)" />\n+ <param name="fixedModifications" value="" />\n+ <conditional name="quant_method">\n+ <param name="select_quant_method" value="reporter_ion_ms2" />\n+ <conditional name="iso_labels">\n+ <param name="labeling" value="tmtpro16plex" />\n+ </conditional>\n+ </conditional>\n+ </repeat>\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 </tests>\n \n' |
| b |
| diff -r d72c96ad9a16 -r 0839f84def5e test-data/01/combined/txt/allPeptides.txt --- a/test-data/01/combined/txt/allPeptides.txt Tue Jun 15 07:55:59 2021 +0000 +++ b/test-data/01/combined/txt/allPeptides.txt Sun Jun 20 16:37:41 2021 +0000 |
| [ |
| b'@@ -1,167 +1,159 @@\n-Raw file\tType\tCharge\tm/z\tMass\tUncalibrated m/z\tResolution\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\r\n-BSA_min_23\tMULTI\t3\t710.69967\t2129.0772\t710.69967\tNaN\t5\t3\t2\t\t0.0771919\t0.0578164096173168\t1.08086\t711.033930698172\t0.0366\t8.26\t0\t1\t25\t\t\t-1\t\t0\t\t\t\t0\tNaN\t27555\t0;16823.720703125;10726.12109375;6644.5966796875;0\t7737.3974609375;9086.3232421875\t0\t\t\r\n-BSA_min_23\tMULTI\t3\t1567.4354\t4699.2845\t1567.4354\tNaN\t5\t3\t2\t\t0.284514\t0.0828426326752378\t7.31572\t1568.10387245715\t0.0671\t8.26\t0\t1\t25\t\t\t-1\t\t0\t\t\t\t0\tNaN\t137580\t0;23479.5932617188;59085.9194335938;20990.259765625;0\t0;0;53540.3203125;7305.36279296875\t0\t\t\r\n-BSA_min_23\tMULTI\t2\t466.26817\t930.5218\t466.26817\tNaN\t6\t4\t2\t\t0.521797\t0.0537564853223103\t1.35299\t466.26850803291\t0.107\t10.3\t0\t1\t31\t\t\t-1\t\t0\t\t\t\t0\tNaN\t33499\t0;16896.8359375;13251.4482421875;29638.681640625;21903.5859375;0\t22962.34375;6676.337890625\t0\t\t\r\n-BSA_min_23\tMULTI\t2\t835.80692\t1669.5993\t835.80692\tNaN\t7\t4\t2\t\t0.599289\t-0.208726257088529\t1.09635\t835.807035746435\t0.107\t10.3\t0\t1\t31\t\t\t-1\t\t0\t\t\t\t0\tNaN\t35250\t0;14611.8764648438;18125.6357421875;25099.0166015625;15365.583984375;0\t16483.943359375;8615.0732421875\t0\t\t\r\n-BSA_min_23\tMULTI\t2\t889.42648\t1776.8384\t889.42648\tNaN\t6\t3\t2\t\t0.838398\t-0.0189472723534436\t2.69649\t889.927320499287\t0.107\t8.26\t0\t1\t25\t\t\t-1\t\t0\t\t\t\t0\tNaN\t24592\t0;9125.99072265625;13286.1201171875;16742.716796875;0\t7208.8173828125;9533.8994140625\t0\t\t\r\n-BSA_min_23\tMULTI\t2\t378.70717\t755.39978\t378.70717\tNaN\t4\t2\t2\t\t0.399783\t0.0122990350871532\t2.65249\t378.7066995797\t0.119\t6.22\t0\t13\t31\t\t\t-1\t\t0\t\t\t\t0\tNaN\t17113\t0;15764.96875;12169.2568359375;0\t9865.826171875;5910.52587890625\t0\t\t\r\n-BSA_min_23\tMULTI\t6\t456.58136\t2733.4445\t456.58136\tNaN\t6\t5\t2\t\t0.444504\t0.14711979940148\t1.25056\t456.748107866223\t0.139\t12.6\t0\t7\t43\t\t\t-1\t\t0\t\t\t\t0\tNaN\t36582\t0;9077.5439453125;13902.0874023438;19992.689453125;13010.4306640625;0;0\t0;13844.125;6148.564453125\t1\t8\t1\r\n-BSA_min_23\tMULTI\t2\t701.87367\t1401.7328\t701.87367\tNaN\t4\t2\t2\t\t0.732779\t0.0479819779827722\t1.9101\t701.87287295525\t0.139\t6.22\t0\t13\t31\t\t\t-1\t\t0\t\t\t\t0\tNaN\t19640\t0;11736.2470703125;14934.2939453125;0\t8433.541015625;6500.7529296875\t0\t\t\r\n-BSA_min_23\tMULTI\t2\t903.84665\t1805.6788\t903.84665\tNaN\t14\t5\t3\t\t0.67875\t-0.191861895242255\t0.538046\t903.846381489202\t0.128\t12.5\t0\t1\t37\t\t\t-1\t\t0\t\t\t\t0\tNaN\t89876\t0;22660.5712890625;48080.4096679688;66770.5043945313;78759.361328125;39740.7744140625;0\t39216.41796875;30181.7421875;16944.533203125\t1\t27\t0\r\n-BSA_min_23\tMULTI\t3\t487.53462\t1459.582\t487.53462\tNaN\t16\t8\t3\t\t0.582041\t-0.129367074224319\t0.600339\t487.53461224021\t0.133\t19\t0\t1\t55\t\t\t-1\t\t0\t\t\t\t0\tNaN\t84731\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\r\n-BSA_min_23\tMULTI\t3\t583.22015\t1746.6386\t583.22015\tNaN\t7\t4\t2\t\t0.638625\t-0.204828530265331\t2.09463\t583.220239813966\t0.176\t10.5\t0\t7\t37\t\t\t-1\t\t0\t\t\t\t0\tNaN\t42292\t0;4036.83081054688;17411.11328125;19834.8046875;29221.802734375;0\t17431.560546875;11790.2421875\t0\t\t\r\n-BSA_min_23\tMULTI\t3\t635.6026\t1903.786\t635.6026\tNaN\t7\t5\t2\t\t0.785967\t-0.129774097720883\t1.11727\t635.602244079812\t0.176\t12.6\t0\t7\t43\t\t\t-1\t\t0\t\t\t\t0\tNaN\t46680\t0;4302.31201171875;12941.4526367188;23817.1057128906;30967.701171875;0;0\t17209.375;13758.326171875\t0\t\t\r\n-BSA_min_23\tMULTI\t2\t730.79903\t1459.5835\t730.79903\tNaN\t10\t6\t2\t\t0.583509\t-0.127899156014337\t0.558717\t730.799136547346\t0.151\t14.7\t0\t1\t43\t\t\t-1\t\t0\t\t\t\t0\tNaN\t77496\t0;5839.765625;27434.9599609375;42471.279296875;58278.560546875;32345.4384765625;15650.7568359375;0\t39553.00390625;19513.171875\t1\t29\t0\r\n-BSA_min_23\tMULTI\t2\t996.94429\t1991.874\t996.94429\tNaN\t15\t13\t2\t\t0.874033\t-0.0822288372489766\t0.834502\t997.4461'..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 d72c96ad9a16 -r 0839f84def5e test-data/01/combined/txt/evidence.txt --- a/test-data/01/combined/txt/evidence.txt Tue Jun 15 07:55:59 2021 +0000 +++ b/test-data/01/combined/txt/evidence.txt Sun Jun 20 16:37:41 2021 +0000 |
| [ |
| @@ -1,9 +1,7 @@ -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 Resolution 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 Reporter PIF Reporter fraction Reverse Potential contaminant id Protein group IDs Peptide ID Mod. peptide ID MS/MS IDs Best MS/MS Oxidation (M) site 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 NaN 0 0 0.54276 0.00022754 0.54276 0.00022754 419.22139467134 0.58669 0.13742 0.58669 0.46121 0.59862 0 11 4 3 0 0 0 8.9583E-05 1 96 0 0 1 768320 + 0 2 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 NaN 0.50957 1 0.50957 0.0095717 1.0096 0 0 0 0 0.010121 1 86 1.6313 1.6313 1 + 1 6 1 1 1 1 -LVTDLTK 7 Unmodified _LVTDLTK_ 0 0 CON__P02769;bsa;CON__P02768-1 CON__P02769 CON__P02769 MSMS BSA_min_23 BSA_min_23.mzXML 395.239288330078 2 395.239461 788.46437 NaN NaN NaN NaN NaN NaN NaN NaN 0.010013 1 0.010013 -0.48999 0.51001 0 0 0 0 0.005963 1 2 0 0 1 + 2 0 2 2 2 2 -QLELEKQLEK 10 Unmodified _QLELEKQLEK_ 0 1 CON__ENSEMBL:ENSBTAP00000001528 CON__ENSEMBL:ENSBTAP00000001528 CON__ENSEMBL:ENSBTAP00000001528 MULTI-MSMS BSA_min_23 BSA_min_23.mzXML 629.358581542969 2 629.356085 1256.69762 NaN 0 0 0.76901 0.00048398 0.76901 0.00048398 629.356557471474 0.3521 0.47559 0.3521 0.12303 0.59862 0 33 14 3 0 0 0 0.0003393 2 52 0 0 1 84871 + 3 1 3 3 3;4 3 -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 NaN 0 0 0.052788 2.2166E-05 0.052788 2.2166E-05 419.9067499241 0.32847 0.47559 0.32847 0.12303 0.59862 0 25 14 2 0 0 0 0.015457 1 96 0 0 1 57554 + 4 1 3 3 5 5 -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 NaN 0 0 -3.0904 -0.0014409 -3.0904 -0.0014409 466.26850803291 0.10674 0.17216 0.10674 -0.014552 0.15761 0 6 4 2 0 0 0 0.015457 1 17 0 0 1 33499 + 5 5 4 4 6 6 -SQTSHRGYSASSAR 14 Unmodified _SQTSHRGYSASSAR_ 0 1 CON__P50446 CON__P50446 CON__P50446 MULTI-MSMS BSA_min_23 BSA_min_23.mzXML 747.855651855469 2 747.855835 1493.69712 NaN 0 0 0.34543 0.00025833 0.34543 0.00025833 747.856213318885 0.29902 0.26735 0.29902 0.19386 0.46121 0 11 7 2 0 0 0 0.0091697 1 53 0 0 1 59701 + 6 4 5 5 7 7 -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 NaN 0 0 -0.28456 -0.00013026 -0.28456 -0.00013026 457.745456355006 0.4547 0.40477 0.4547 0.19386 0.59862 -5.5511E-17 18 12 2 0 0 0 0.00018307 1 72 0 0 1 61894 + 7 3 6 6 8 8 +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 d72c96ad9a16 -r 0839f84def5e test-data/01/combined/txt/modificationSpecificPeptides.txt --- a/test-data/01/combined/txt/modificationSpecificPeptides.txt Tue Jun 15 07:55:59 2021 +0000 +++ b/test-data/01/combined/txt/modificationSpecificPeptides.txt Sun Jun 20 16:37:41 2021 +0000 |
| b |
| @@ -1,8 +1,7 @@ -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 -DSFDIIK Unmodified 836.42798 0.42798405 2 CON__ENSEMBL:ENSBTAP00000016046 yes yes 0 0 1 0.58669 0.58669 2 8.9583E-05 96 BSA_min_23 0 0 + 768320 768320 0 2 0 0 0 0 1 -LLESEECR Unmodified 1034.4703 0.47025958 6 CON__Q14CN4-1;CON__Q3SY84;CON__Q9R0H5 yes no 0 0 1 0.50957 0.50957 2 0.010121 86 BSA_min_23 1.6313 1.6313 + 0 0 1 6 1 1 1 1 1 -LVTDLTK Unmodified 788.46437 0.46436956 0 CON__P02769;bsa;CON__P02768-1 yes no 0 0 1 0.010013 0.010013 2 0.005963 2 BSA_min_23 0 0 + 0 0 2 0 2 2 2 2 1 -QLELEKQLEK Unmodified 1256.6976 0.69761697 1 CON__ENSEMBL:ENSBTAP00000001528 yes yes 0 1 2 0.34029 0.34029 2;3 0.0003393 52 BSA_min_23 0 0 + 142430 142430 3 1 3 3;4 3;4;5 3 2 -SLSAIRER Unmodified 930.52468 0.52467841 5 CON__Q03247 yes yes 0 1 1 0.10674 0.10674 2 0.015457 17 BSA_min_23 0 0 + 33499 33499 4 5 4 5 6 6 0 -SQTSHRGYSASSAR Unmodified 1493.6971 0.69711648 4 CON__P50446 yes yes 0 1 1 0.29902 0.29902 2 0.0091697 53 BSA_min_23 0 0 + 59701 59701 5 4 5 6 7 7 1 -TLGPWGQR Unmodified 913.477 0.47699993 3 CON__ENSEMBL:ENSBTAP00000018574 yes yes 0 0 1 0.4547 0.4547 2 0.00018307 72 BSA_min_23 0 0 + 61894 61894 6 3 6 7 8 8 1 +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 d72c96ad9a16 -r 0839f84def5e test-data/01/combined/txt/msms.txt --- a/test-data/01/combined/txt/msms.txt Tue Jun 15 07:55:59 2021 +0000 +++ b/test-data/01/combined/txt/msms.txt Sun Jun 20 16:37:41 2021 +0000 |
| [ |
| @@ -1,10 +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 0.54276 0.00022754 NaN 0.57043 8.9583E-05 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 0.010121 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 0.00309955136349784 0.00847457627118644 None Unknown 1.63126590808724;0;0 LLESEECR;LGSDMEDLR;QLNQEMEK _LLESEECR_;_LGSDMEDLR_;_QLNQEM(Oxidation (M))EK_ 1 6 1 1 1 -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 0.005963 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 52 42 QLELEKQLEK 10 1 Unmodified _QLELEKQLEK_ 0 CON__ENSEMBL:ENSBTAP00000001528 2 CID FTMS MULTI-MSMS 3 0 629.35608 1256.6976 0.76901 0.00048398 NaN 0.30417 0.0003393 0 0 NaN NaN 1 0 0 0 49 47581.3515625 1 0 0 0 0 0 None Unknown 0 QLELEKQLEK _QLELEKQLEK_ 3 1 3 3 3 -BSA_min_23 82 66 QLELEKQLEK 10 1 Unmodified _QLELEKQLEK_ 0 CON__ENSEMBL:ENSBTAP00000001528 2 CID FTMS MULTI-MSMS 1 1 629.35608 1256.6976 0.76901 0.00048398 NaN 0.48722 0.0003393 0 0 NaN NaN 1 0 0 0 81 28788.931640625 1 0 0 0 0 0 None Unknown 0 QLELEKQLEK _QLELEKQLEK_ 4 1 3 3 3 -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 0.052788 2.2166E-05 NaN 0.57043 0.015457 0 0 NaN NaN 1 0 0 0 95 346270.625 0.704625040984097 -1 0.0243583333333334 0 0 0 None Unknown 0 QLELEKQLEK _QLELEKQLEK_ 5 1 3 3 4 -BSA_min_23 17 13 SLSAIRER 8 1 Unmodified _SLSAIRER_ 0 CON__Q03247 2 CID FTMS MULTI-SECPEP 4 -1 466.26962 930.52468 -3.0904 -0.0014409 NaN 0.096553 0.015457 0 0 NaN NaN 1 0 0 0 -1 NaN NaN 0 NaN 0 0 0 None Unknown 0 SLSAIRER _SLSAIRER_ 6 5 4 4 5 -BSA_min_23 53 43 SQTSHRGYSASSAR 14 1 Unmodified _SQTSHRGYSASSAR_ 0 CON__P50446 2 CID FTMS MULTI-MSMS 4 0 747.85583 1493.6971 0.34543 0.00025833 NaN 0.30942 0.0091697 0 0 NaN NaN 1 0 0 0 49 27482.5703125 1 0 0 0 0 0 None Unknown 0;0 SQTSHRGYSASSAR;GLIDEVDQDFTSR _SQTSHRGYSASSAR_;_GLIDEVDQDFTSR_ 7 4 5 5 6 -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 -0.28456 -0.00013026 NaN 0.42593 0.00018307 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_ 8 3 6 6 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 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 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 |
| b |
| diff -r d72c96ad9a16 -r 0839f84def5e test-data/01/combined/txt/msmsScans.txt --- a/test-data/01/combined/txt/msmsScans.txt Tue Jun 15 07:55:59 2021 +0000 +++ b/test-data/01/combined/txt/msmsScans.txt Sun Jun 20 16:37:41 2021 +0000 |
| b |
| b'@@ -1,82 +1,82 @@\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\r\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\t1\tBSA_min_23.mzXML\t\t\tNaN\tNaN\tNaN\t0\t0\t0\t1\r\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\t1\tBSA_min_23.mzXML\t\t\tNaN\tNaN\tNaN\t0\t1\t0\t1\r\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\t1\tBSA_min_23.mzXML\t\t\tNaN\tNaN\tNaN\t0\t2\t0\t1\r\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\t1\tBSA_min_23.mzXML\t\t\tNaN\tNaN\tNaN\t0\t3\t0\t1\r\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\t1\tBSA_min_23.mzXML\t\t\tNaN\tNaN\tNaN\t0\t4\t0\t1\r\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\t456.581360511828\t2733.44450427137\t6\tMULTI\tCID\tFTMS\t0\t0\t0\t-1\tNaN\tNaN\t0\tNaN\t1\tUnmodified\t_TPLQYLHEFLSGILRAHVAPAVNGM_\tREV__CON__REFSEQ:XP_092267\t0\t1\tBSA_min_23.mzXML\t\t\tNaN\tNaN\tNaN\t0\t5\t1\t7\r\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\t1\tBSA_min_23.mzXML\t\t\tNaN\tNaN\tNaN\t0\t6\t1\t7\r\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\t589.203410887949\t588.196134421349\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\r\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\r\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\t1\tBSA_min_23.mzXML\t\t\tNaN\tNaN\tNaN\t0\t9\t1\t7\r\n-BSA_min_23\t14\t0.078957\t-1\t13236\t35\t0\t4982.4\t-1\t-\t\t\t-1\t \t0\t137\t883.333059829652\t1764.6515667261\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\r\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\r\n-BSA_min_23\t16\t0.090573\t-1\t12119\t35\t0\t1996\t-1\t-\t\t\t-1\t \t0\t135\t648.602725143793\t1942.78634603158\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\r\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\t1\tBSA_min_23.mzXML\t\t\tNaN\tNaN\tNaN\t0\t13\t2\t13\r\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\t605.758117675781\tNaN\t0\tPEAK\tCID\tFTMS\t0\t0\t0\t-1\tNaN\tNaN\t0\tNaN\t5\t \t \t \tNaN\tNaN\tBSA_min_23.mzXML\t\t\tNaN\tNaN\tNaN\t0\t14\t2\t13\r\n-BSA_min_23\t20\t0.11439\t-1\t65173\t3'..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 d72c96ad9a16 -r 0839f84def5e test-data/01/combined/txt/mzRange.txt --- a/test-data/01/combined/txt/mzRange.txt Tue Jun 15 07:55:59 2021 +0000 +++ b/test-data/01/combined/txt/mzRange.txt Sun Jun 20 16:37:41 2021 +0000 |
| [ |
| b'@@ -1,1881 +1,1881 @@\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 d72c96ad9a16 -r 0839f84def5e test-data/01/combined/txt/mzTab.mzTab --- a/test-data/01/combined/txt/mzTab.mzTab Tue Jun 15 07:55:59 2021 +0000 +++ b/test-data/01/combined/txt/mzTab.mzTab Sun Jun 20 16:37:41 2021 +0000 |
| [ |
| b'@@ -1,49 +1,42 @@\n-MTD\tmzTab-version\t1.0.0\r\n-MTD\tmzTab-mode\tComplete\r\n-MTD\tmzTab-type\tIdentification\r\n-MTD\ttitle\tnull\r\n-MTD\tdescription\tnull\r\n-MTD\tsoftware[1]\t[MS, MS:1001583, MaxQuant,1.6.10.43]\r\n-COM\t[, CHEMMOD:57.0214637236, Carbamidomethyl (C),]\t\r\n-MTD\tfixed_mod[1]\t[, , CHEMMOD:57.0214637236,]\r\n-MTD\tfixed_mod[1]-site\tC\r\n-MTD\tfixed_mod[1]-position\tAnywhere\r\n-COM\t[, CHEMMOD:15.9949146221, Oxidation (M),]\t\r\n-MTD\tvariable_mod[1]\t[, , CHEMMOD:15.9949146221,]\r\n-MTD\tvariable_mod[1]-site\tM\r\n-MTD\tvariable_mod[1]-position\tAnywhere\r\n-MTD\tprotein_search_engine_score[1]\t[MS, MS:1002375, protein group-level combined FDRscore, ]\r\n-MTD\tpeptide_search_engine_score[1]\t[MS, MS:1001250, local FDR, ]\r\n-MTD\tpsm_search_engine_score[1]\t[MS, MS:1002338, Andromeda:score, ]\r\n-MTD\tpsm_search_engine_score[2]\t[MS, MS:1002995, Andromeda:PEP, ]\r\n-MTD\tms_run[1]-format\t[MS, MS:1002996, Andromeda:apl file format, ]\r\n-MTD\tms_run[1]-location\tfile://d:/shared/dglaetzer/maxquant_tool/test1/combined/andromeda/allspectra.cid.ftms.secpep.sil0_0.apl\r\n-MTD\tms_run[1]-id_format\t[MS, MS:1000776, scan number only nativeID format, ]\r\n-MTD\tms_run[2]-format\t[MS, MS:1002996, Andromeda:apl file format, ]\r\n-MTD\tms_run[2]-location\tfile://d:/shared/dglaetzer/maxquant_tool/test1/combined/andromeda/allspectra.cid.ftms.iso_0.apl\r\n-MTD\tms_run[2]-id_format\t[MS, MS:1000776, scan number only nativeID format, ]\r\n-\r\n-PRH\taccession\tdescription\ttaxid\tspecies\tdatabase\tdatabase_version\tsearch_engine\tbest_search_engine_score[1]\tsearch_engine_score[1]_ms_run[1]\tsearch_engine_score[1]_ms_run[2]\tnum_psms_ms_run[1]\tnum_psms_ms_run[2]\tnum_peptides_distinct_ms_run[1]\tnum_peptides_distinct_ms_run[2]\tnum_peptides_unique_ms_run[1]\tnum_peptides_unique_ms_run[2]\tambiguity_members\tmodifications\tprotein_coverage\topt_global_cv_MS:1002217_decoy_peptide \r\n-PRT\tCON__P02769\tnull\tnull\tnull\tnull\tnull\t[MS, MS:1002337, Andromeda, 1.6.10.43]\t6.22453365714539\tnull\tnull\tnull\tnull\tnull\tnull\tnull\tnull\tCON__P02769, bsa, CON__P02768-1\tnull\t0.012\t0\r\n-PRT\tCON__ENSEMBL:ENSBTAP00000001528\tnull\tnull\tnull\tnull\tnull\t[MS, MS:1002337, Andromeda, 1.6.10.43]\t7.46941253488722\tnull\tnull\tnull\tnull\tnull\tnull\tnull\tnull\tCON__ENSEMBL:ENSBTAP00000001528\tnull\t0.008\t0\r\n-PRT\tCON__ENSEMBL:ENSBTAP00000016046\tnull\tnull\tnull\tnull\tnull\t[MS, MS:1002337, Andromeda, 1.6.10.43]\t8.04777465053044\tnull\tnull\tnull\tnull\tnull\tnull\tnull\tnull\tCON__ENSEMBL:ENSBTAP00000016046\tnull\t0.01\t0\r\n-PRT\tCON__ENSEMBL:ENSBTAP00000018574\tnull\tnull\tnull\tnull\tnull\t[MS, MS:1002337, Andromeda, 1.6.10.43]\t7.73737648138078\tnull\tnull\tnull\tnull\tnull\tnull\tnull\tnull\tCON__ENSEMBL:ENSBTAP00000018574\tnull\t0.016\t0\r\n-PRT\tCON__P50446\tnull\tnull\tnull\tnull\tnull\t[MS, MS:1002337, Andromeda, 1.6.10.43]\t6.03764269117454\tnull\tnull\tnull\tnull\tnull\tnull\tnull\tnull\tCON__P50446\tnull\t0.025\t0\r\n-PRT\tCON__Q03247\tnull\tnull\tnull\tnull\tnull\t[MS, MS:1002337, Andromeda, 1.6.10.43]\t5.81086493552667\tnull\tnull\tnull\tnull\tnull\tnull\tnull\tnull\tCON__Q03247\tnull\t0.025\t0\r\n-PRT\tCON__Q14CN4-1\tnull\tnull\tnull\tnull\tnull\t[MS, MS:1002337, Andromeda, 1.6.10.43]\t5.99478997658237\tnull\tnull\tnull\tnull\tnull\tnull\tnull\tnull\tCON__Q14CN4-1, CON__Q3SY84, CON__Q9R0H5\tnull\t0.016\t0\r\n-\r\n-PSH\tsequence\tPSM_ID\taccession\tunique\tdatabase\tdatabase_version\tsearch_engine\tsearch_engine_score[1]\tsearch_engine_score[2]\tmodifications\tretention_time\tcharge\texp_mass_to_charge\tcalc_mass_to_charge\tspectra_ref\tpre\tpost\tstart\tend\topt_global_cv_MS:1000776_scan_number_only_nativeID_format\topt_global_cv_MS:1002217_decoy_peptide \r\n-PSM\tDSFDIIK\t1\tCON__ENSEMBL:ENSBTAP00000016046\t1\tnull\tnull\t[MS, MS:1002338, Andromeda:score, 1.6.10.43]\t0\t8.95829478642414E-05\tnull\t0.570428333333333\t2\t419.22\t419.22127\tms_run[2]:index=5\tR\tR\t646\t652\t96\t0\r\n-PSM\tLLESEECR\t2\tCON__Q14CN4-1\t0\tnull\tnull\t[MS, MS:1002338, Andromeda:score, 1.6.10.43]\t1.63126590808724\t0.0101206876914345\tnull\t0.509571666666667\t2\t518.24\t518.24241\tms_run[2]:index=13\tK\tM\t430\t437\t86\t0\r\n-PSM\tLLESEECR\t2\tCON__Q3SY84\t0\tnull\tnull\t[MS, MS:1002338, Andromeda:score, 1.6.10.43]\t1.63126590808724\t0.0101206876914345\tnull\t0.5095716'..b'EMBL: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+\n+PSH\tsequence\tPSM_ID\taccession\tunique\tdatabase\tdatabase_version\tsearch_engine\tsearch_engine_score[1]\tsearch_engine_score[2]\tmodifications\tretention_time\tcharge\texp_mass_to_charge\tcalc_mass_to_charge\tspectra_ref\tpre\tpost\tstart\tend\topt_global_cv_MS:1000776_scan_number_only_nativeID_format\topt_global_cv_MS:1002217_decoy_peptide\n+PSM\tDSFDIIK\t1\tCON__ENSEMBL:ENSBTAP00000016046\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\t0.010549248059121\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/tmp9jbmb6lc/files/7/5/d/dataset_75d9a22a-c00d-4c98-b445-0f54e57ec138.dat;\tnull\t[MS, MS:1002338, Andromeda:score, 1.6.17.0]\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/tmp9jbmb6lc/files/7/5/d/dataset_75d9a22a-c00d-4c98-b445-0f54e57ec138.dat;\tnull\t[MS, MS:1002338, Andromeda:score, 1.6.17.0]\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/tmp9jbmb6lc/files/7/5/d/dataset_75d9a22a-c00d-4c98-b445-0f54e57ec138.dat;\tnull\t[MS, MS:1002338, Andromeda:score, 1.6.17.0]\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/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\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+\n' |
| b |
| diff -r d72c96ad9a16 -r 0839f84def5e test-data/01/combined/txt/parameters.txt --- a/test-data/01/combined/txt/parameters.txt Tue Jun 15 07:55:59 2021 +0000 +++ b/test-data/01/combined/txt/parameters.txt Sun Jun 20 16:37:41 2021 +0000 |
| [ |
| @@ -1,105 +1,105 @@ -Parameter Value -Version 1.6.10.43 -User name dglaetzer -Machine name FPROT-BEAST -Date of writing 02/25/2020 15:36:33 -Include contaminants True -PSM FDR 0.01 -PSM FDR Crosslink 0.01 -Protein FDR 0.01 -Site FDR 0.01 -Use Normalized Ratios For Occupancy True -Min. peptide Length 7 -Min. score for unmodified peptides 0 -Min. score for modified peptides 40 -Min. delta score for unmodified peptides 0 -Min. delta score for modified peptides 6 -Min. unique peptides 0 -Min. razor peptides 1 -Min. peptides 1 -Use only unmodified peptides and True -Modifications included in protein quantification -Peptides used for protein quantification Razor -Discard unmodified counterpart peptides False -Label min. ratio count 2 -Use delta score False -iBAQ False -iBAQ log fit False -Match between runs False -Find dependent peptides False -Fasta file D:\shared\dglaetzer\maxquant_tool\test1\bsa.fasta -Decoy mode revert -Include contaminants True -Advanced ratios True -Fixed andromeda index folder -Temporary folder -Combined folder location -Second peptides True -Stabilize large LFQ ratios True -Separate LFQ in parameter groups False -Require MS/MS for LFQ comparisons True -Calculate peak properties False -Main search max. combinations 200 -Advanced site intensities True -Write msScans table False -Write msmsScans table True -Write ms3Scans table True -Write allPeptides table True -Write mzRange table True -Write pasefMsmsScans table True -Write accumulatedPasefMsmsScans table True -Max. peptide mass [Da] 4600 -Min. peptide length for unspecific search 8 -Max. peptide length for unspecific search 25 -Razor protein FDR True -Disable MD5 False -Max mods in site table 3 -Match unidentified features False -Epsilon score for mutations -Evaluate variant peptides separately True -Variation mode None -MS/MS tol. (FTMS) 20 ppm -Top MS/MS peaks per Da interval. (FTMS) 12 -Da interval. (FTMS) 100 -MS/MS deisotoping (FTMS) True -MS/MS deisotoping tolerance (FTMS) 7 -MS/MS deisotoping tolerance unit (FTMS) ppm -MS/MS higher charges (FTMS) True -MS/MS water loss (FTMS) True -MS/MS ammonia loss (FTMS) True -MS/MS dependent losses (FTMS) True -MS/MS recalibration (FTMS) False -MS/MS tol. (ITMS) 0.5 Da -Top MS/MS peaks per Da interval. (ITMS) 8 -Da interval. (ITMS) 100 -MS/MS deisotoping (ITMS) False -MS/MS deisotoping tolerance (ITMS) 0.15 -MS/MS deisotoping tolerance unit (ITMS) Da -MS/MS higher charges (ITMS) True -MS/MS water loss (ITMS) True -MS/MS ammonia loss (ITMS) True -MS/MS dependent losses (ITMS) True -MS/MS recalibration (ITMS) False -MS/MS tol. (TOF) 40 ppm -Top MS/MS peaks per Da interval. (TOF) 10 -Da interval. (TOF) 100 -MS/MS deisotoping (TOF) True -MS/MS deisotoping tolerance (TOF) 0.01 -MS/MS deisotoping tolerance unit (TOF) Da -MS/MS higher charges (TOF) True -MS/MS water loss (TOF) True -MS/MS ammonia loss (TOF) True -MS/MS dependent losses (TOF) True -MS/MS recalibration (TOF) False -MS/MS tol. (Unknown) 20 ppm -Top MS/MS peaks per Da interval. (Unknown) 12 -Da interval. (Unknown) 100 -MS/MS deisotoping (Unknown) True -MS/MS deisotoping tolerance (Unknown) 7 -MS/MS deisotoping tolerance unit (Unknown) ppm -MS/MS higher charges (Unknown) True -MS/MS water loss (Unknown) True -MS/MS ammonia loss (Unknown) True -MS/MS dependent losses (Unknown) True -MS/MS recalibration (Unknown) False -Site tables Oxidation (M)Sites.txt +Parameter Value +Version 1.6.17.0 +User name niko +Machine name DESKTOP-I3UDKML +Date of writing 06/16/2021 16:28:26 +Include contaminants True +PSM FDR 0.01 +PSM FDR Crosslink 0.01 +Protein FDR 0.01 +Site FDR 0.01 +Use Normalized Ratios For Occupancy True +Min. peptide Length 7 +Min. score for unmodified peptides 0 +Min. score for modified peptides 40 +Min. delta score for unmodified peptides 0 +Min. delta score for modified peptides 6 +Min. unique peptides 0 +Min. razor peptides 1 +Min. peptides 1 +Use only unmodified peptides and True +Modifications included in protein quantification Oxidation (M);Acetyl (Protein N-term) +Peptides used for protein quantification Razor +Discard unmodified counterpart peptides False +Label min. ratio count 2 +Use delta score False +iBAQ False +iBAQ log fit False +Match between runs False +Find dependent peptides False +Fasta file /tmp/tmpyzym30dx/files/3/c/e/dataset_3cea3228-eaab-4e71-aba7-9ffa9900b54a.dat +Decoy mode revert +Include contaminants True +Advanced ratios True +Fixed andromeda index folder +Combined folder location +Second peptides True +Stabilize large LFQ ratios True +Separate LFQ in parameter groups False +Require MS/MS for LFQ comparisons True +Calculate peak properties False +Main search max. combinations 200 +Advanced site intensities True +Write msScans table False +Write msmsScans table True +Write ms3Scans table True +Write allPeptides table True +Write mzRange table True +Write DIA fragments table False +Write pasefMsmsScans table True +Write accumulatedPasefMsmsScans table False +Max. peptide mass [Da] 4600 +Min. peptide length for unspecific search 8 +Max. peptide length for unspecific search 25 +Razor protein FDR True +Disable MD5 False +Max mods in site table 3 +Match unidentified features False +Epsilon score for mutations +Evaluate variant peptides separately True +Variation mode None +MS/MS tol. (FTMS) 20 ppm +Top MS/MS peaks per Da interval. (FTMS) 12 +Da interval. (FTMS) 100 +MS/MS deisotoping (FTMS) True +MS/MS deisotoping tolerance (FTMS) 7 +MS/MS deisotoping tolerance unit (FTMS) ppm +MS/MS higher charges (FTMS) True +MS/MS water loss (FTMS) True +MS/MS ammonia loss (FTMS) True +MS/MS dependent losses (FTMS) True +MS/MS recalibration (FTMS) False +MS/MS tol. (ITMS) 0.5 Da +Top MS/MS peaks per Da interval. (ITMS) 8 +Da interval. (ITMS) 100 +MS/MS deisotoping (ITMS) False +MS/MS deisotoping tolerance (ITMS) 0.15 +MS/MS deisotoping tolerance unit (ITMS) Da +MS/MS higher charges (ITMS) True +MS/MS water loss (ITMS) True +MS/MS ammonia loss (ITMS) True +MS/MS dependent losses (ITMS) True +MS/MS recalibration (ITMS) False +MS/MS tol. (TOF) 40 ppm +Top MS/MS peaks per Da interval. (TOF) 10 +Da interval. (TOF) 100 +MS/MS deisotoping (TOF) True +MS/MS deisotoping tolerance (TOF) 0.01 +MS/MS deisotoping tolerance unit (TOF) Da +MS/MS higher charges (TOF) True +MS/MS water loss (TOF) True +MS/MS ammonia loss (TOF) True +MS/MS dependent losses (TOF) True +MS/MS recalibration (TOF) False +MS/MS tol. (Unknown) 20 ppm +Top MS/MS peaks per Da interval. (Unknown) 12 +Da interval. (Unknown) 100 +MS/MS deisotoping (Unknown) True +MS/MS deisotoping tolerance (Unknown) 7 +MS/MS deisotoping tolerance unit (Unknown) ppm +MS/MS higher charges (Unknown) True +MS/MS water loss (Unknown) True +MS/MS ammonia loss (Unknown) True +MS/MS dependent losses (Unknown) True +MS/MS recalibration (Unknown) False +Site tables Oxidation (M)Sites.txt |
| b |
| diff -r d72c96ad9a16 -r 0839f84def5e test-data/01/combined/txt/peptideSection.txt --- a/test-data/01/combined/txt/peptideSection.txt Tue Jun 15 07:55:59 2021 +0000 +++ b/test-data/01/combined/txt/peptideSection.txt Sun Jun 20 16:37:41 2021 +0000 |
| [ |
| @@ -1,8 +0,0 @@ -PEH sequence accession unique database database_version search_engine best_search_engine_score[1] search_engine_score[1]_ms_run[0] modifications retention_time retention_time_window charge mass_to_charge spectra_ref peptide_abundance_study_variable[0] peptide_abundance_stdev_study_variable[0] peptide_abundance_std_error_study_variable[0] -PEP DSFDIIK null -PEP LLESEECR null -PEP LVTDLTK null -PEP QLELEKQLEK null -PEP SLSAIRER null -PEP SQTSHRGYSASSAR null -PEP TLGPWGQR null |
| b |
| diff -r d72c96ad9a16 -r 0839f84def5e test-data/01/combined/txt/peptides.txt --- a/test-data/01/combined/txt/peptides.txt Tue Jun 15 07:55:59 2021 +0000 +++ b/test-data/01/combined/txt/peptides.txt Sun Jun 20 16:37:41 2021 +0000 |
| b |
| @@ -1,8 +1,7 @@ -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 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 8.9583E-05 0 1 768320 768320 + 0 2 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 0.010121 1.6313 1 0 0 + 1 6 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 CON__P02769;bsa;CON__P02768-1 CON__P02769 257 263 yes no 2 0.005963 0 1 0 0 + 2 0 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 2;3 0.0003393 0 2 142430 142430 + 3 1 3 3;4 3;4;5 3 2 -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 0.015457 0 1 33499 33499 + 4 5 4 5 6 6 0 -SQTSHRGYSASSAR ______________________________ KSQTSHRGYSASSARVPGLNRSGFSSVSVC K S Q A R V 2 2 0 0 0 1 0 1 1 0 0 0 0 0 0 5 1 0 1 0 0 0 14 1 1493.6971 CON__P50446 CON__P50446 9 22 yes yes 2 0.0091697 0 1 59701 59701 + 5 4 5 6 7 7 1 -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 0.00018307 0 1 61894 61894 + 6 3 6 7 8 8 1 +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 d72c96ad9a16 -r 0839f84def5e test-data/01/combined/txt/proteinGroups.txt --- a/test-data/01/combined/txt/proteinGroups.txt Tue Jun 15 07:55:59 2021 +0000 +++ b/test-data/01/combined/txt/proteinGroups.txt Sun Jun 20 16:37:41 2021 +0000 |
| [ |
| @@ -1,8 +1,7 @@ -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 -CON__P02769;bsa;CON__P02768-1 CON__P02769;bsa;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 6.2245 1.2 0 0 1 + 0 2 True 2 2 2 2 -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 7.4694 0.8 142430 142430 2 + 1 3 True 3 3;4 3;4;5 3 -CON__ENSEMBL:ENSBTAP00000016046 CON__ENSEMBL:ENSBTAP00000016046 1 1 1 1 1 1 1 1 1 1 1 1 1 77.456 706 706 0 8.0478 1 768320 768320 1 + 2 0 True 0 0 0 0 -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 7.7374 1.6 61894 61894 1 + 3 6 True 6 7 8 8 -CON__P50446 CON__P50446 1 1 1 1 1 1 1 1 1 1 2.5 2.5 2.5 59.334 553 553 0 6.0376 2.5 59701 59701 1 + 4 5 True 5 6 7 7 -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 5.8109 2.5 33499 33499 0 + 5 4 True 4 5 6 6 -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 5.9948 1.6 0 0 1 + 6 1 True 1 1 1 1 +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 d72c96ad9a16 -r 0839f84def5e test-data/01/combined/txt/summary.txt --- a/test-data/01/combined/txt/summary.txt Tue Jun 15 07:55:59 2021 +0000 +++ b/test-data/01/combined/txt/summary.txt Sun Jun 20 16:37:41 2021 +0000 |
| [ |
| @@ -1,3 +1,3 @@ -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 0 111 51 0 60 7 5 0 2 6.3 9.8 0 3.3 7 1200 57 4.8 4 7 166 39 35 23 27 10 26 + 0.48635 0.52208 0.27503 0.30402 -Total 19 81 0 111 51 0 60 7 5 0 2 6.3 9.8 0 3.3 7 1200 166 39 35 23 27 10 26 0.48635 0.52208 0.27503 0.30402 +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 d72c96ad9a16 -r 0839f84def5e test-data/01/config.yml --- a/test-data/01/config.yml Tue Jun 15 07:55:59 2021 +0000 +++ b/test-data/01/config.yml Sun Jun 20 16:37:41 2021 +0000 |
| [ |
| @@ -1,5 +1,5 @@ - fastaFiles: [/tmp/tmpQsmPD9/files/7/b/e/dataset_7be42b54-5eac-4f1d-a6bb-0b85e8f1bd67.dat] + fastaFiles: [/tmp/tmpyzym30dx/files/3/c/e/dataset_3cea3228-eaab-4e71-aba7-9ffa9900b54a.dat] parseRules: identifierParseRule: '>([^\s]*)' descriptionParseRule: '>(.*)' |
| b |
| diff -r d72c96ad9a16 -r 0839f84def5e test-data/01/mqpar.xml --- a/test-data/01/mqpar.xml Tue Jun 15 07:55:59 2021 +0000 +++ b/test-data/01/mqpar.xml Sun Jun 20 16:37:41 2021 +0000 |
| [ |
| @@ -2,7 +2,7 @@ <MaxQuantParams> <fastaFiles> <FastaFileInfo> - <fastaFilePath>D:\shared\dglaetzer\maxquant_tool\test1\bsa.fasta</fastaFilePath> + <fastaFilePath>/tmp/tmpyzym30dx/files/3/c/e/dataset_3cea3228-eaab-4e71-aba7-9ffa9900b54a.dat</fastaFilePath> <identifierParseRule>>([^\s]*)</identifierParseRule> <descriptionParseRule>>(.*)</descriptionParseRule> <taxonomyParseRule/> @@ -19,8 +19,6 @@ <andromedaCacheSize>350000</andromedaCacheSize> <advancedRatios>True</advancedRatios> <pvalThres>0.005</pvalThres> - <neucodeRatioBasedQuantification>False</neucodeRatioBasedQuantification> - <neucodeStabilizeLargeRatios>False</neucodeStabilizeLargeRatios> <rtShift>False</rtShift> <separateLfq>False</separateLfq> <lfqStabilizeLargeRatios>True</lfqStabilizeLargeRatios> @@ -48,7 +46,6 @@ <dependentPeptidesWithinParameterGroup>False</dependentPeptidesWithinParameterGroup> <dependentPeptidesRestrictFractions>False</dependentPeptidesRestrictFractions> <dependentPeptidesFractionDifference>0</dependentPeptidesFractionDifference> - <msmsConnection>False</msmsConnection> <ibaq>False</ibaq> <top3>False</top3> <independentEnzymes>False</independentEnzymes> @@ -100,10 +97,11 @@ <writeMsScansTable>False</writeMsScansTable> <writeMsmsScansTable>True</writeMsmsScansTable> <writePasefMsmsScansTable>True</writePasefMsmsScansTable> - <writeAccumulatedPasefMsmsScansTable>True</writeAccumulatedPasefMsmsScansTable> + <writeAccumulatedPasefMsmsScansTable>False</writeAccumulatedPasefMsmsScansTable> <writeMs3ScansTable>True</writeMs3ScansTable> <writeAllPeptidesTable>True</writeAllPeptidesTable> <writeMzRangeTable>True</writeMzRangeTable> + <writeDiaFragmentTable>False</writeDiaFragmentTable> <writeMzTab>True</writeMzTab> <disableMd5>False</disableMd5> <cacheBinInds>True</cacheBinInds> @@ -113,11 +111,11 @@ <variationParseRule/> <variationMode>none</variationMode> <useSeriesReporters>False</useSeriesReporters> - <name>session1</name> - <maxQuantVersion>1.6.10.43</maxQuantVersion> - <tempFolder/> + <name>templateSession</name> + <maxQuantVersion>1.6.17.0</maxQuantVersion> <pluginFolder/> <numThreads>1</numThreads> + <batchSize>1</batchSize> <emailAddress/> <smtpHost/> <emailFromAddress/> @@ -130,9 +128,10 @@ <calcPeakProperties>False</calcPeakProperties> <showCentroidMassDifferences>False</showCentroidMassDifferences> <showIsotopeMassDifferences>False</showIsotopeMassDifferences> - <useDotNetCore>False</useDotNetCore> + <useDotNetCore>True</useDotNetCore> + <profilePerformance>False</profilePerformance> <filePaths> - <string>D:\shared\dglaetzer\maxquant_tool\test1\BSA_min_23.mzXML</string> + <string>/tmp/tmpyzym30dx/job_working_directory/000/3/working/BSA_min_23.mzXML</string> </filePaths> <experiments> <string>BSA_min_23.mzXML</string> @@ -151,12 +150,13 @@ </referenceChannel> <intensPred>False</intensPred> <intensPredModelReTrain>False</intensPredModelReTrain> + <lfqTopNPeptides>0</lfqTopNPeptides> <parameterGroups> <parameterGroup> <msInstrument>0</msInstrument> <maxCharge>7</maxCharge> <minPeakLen>2</minPeakLen> - <diaMinPeakLen>2</diaMinPeakLen> + <diaMinPeakLen>1</diaMinPeakLen> <useMs1Centroids>False</useMs1Centroids> <useMs2Centroids>False</useMs2Centroids> <cutPeaks>True</cutPeaks> @@ -172,14 +172,15 @@ <valleyFactor>1.4</valleyFactor> <isotopeValleyFactor>1.2</isotopeValleyFactor> <advancedPeakSplitting>False</advancedPeakSplitting> - <intensityThreshold>0</intensityThreshold> + <intensityThresholdMs1>0</intensityThresholdMs1> + <intensityThresholdMs2>0</intensityThresholdMs2> <labelMods> <string/> </labelMods> <lcmsRunType>Standard</lcmsRunType> <reQuantify>False</reQuantify> <lfqMode>0</lfqMode> - <lfqSkipNorm>False</lfqSkipNorm> + <lfqNormClusterSize>80</lfqNormClusterSize> <lfqMinEdgesPerNode>3</lfqMinEdgesPerNode> <lfqAvEdgesPerNode>6</lfqAvEdgesPerNode> <lfqMaxFeatures>100000</lfqMaxFeatures> @@ -255,7 +256,7 @@ <timsRemovePrecursor>True</timsRemovePrecursor> <timsIsobaricLabels>False</timsIsobaricLabels> <timsCollapseMsms>True</timsCollapseMsms> - <crosslinkSearch>False</crosslinkSearch> + <crossLinkingType>0</crossLinkingType> <crossLinker/> <minMatchXl>0</minMatchXl> <minPairedPepLenXl>6</minPairedPepLenXl> @@ -277,7 +278,8 @@ <isobaricSumOverWindow>True</isobaricSumOverWindow> <isobaricWeightExponent>0.75</isobaricWeightExponent> <diaLibraryType>0</diaLibraryType> - <diaLibraryPath/> + <diaLibraryPaths> + </diaLibraryPaths> <diaPeptidePaths> </diaPeptidePaths> <diaEvidencePaths> @@ -290,9 +292,37 @@ <diaPrecTolPpmFeatureClustering>2</diaPrecTolPpmFeatureClustering> <diaFragTolPpmFeatureClustering>2</diaFragTolPpmFeatureClustering> <diaScoreN>7</diaScoreN> - <diaMinScore>2.99</diaMinScore> - <diaPrecursorQuant>False</diaPrecursorQuant> - <diaDiaTopNFragmentsForQuant>3</diaDiaTopNFragmentsForQuant> + <diaMinScore>1.99</diaMinScore> + <diaXgBoostBaseScore>0.4</diaXgBoostBaseScore> + <diaXgBoostSubSample>0.9</diaXgBoostSubSample> + <centroidPosition>0</centroidPosition> + <diaQuantMethod>7</diaQuantMethod> + <diaFeatureQuantMethod>2</diaFeatureQuantMethod> + <lfqNormType>1</lfqNormType> + <diaTopNForQuant>10</diaTopNForQuant> + <diaMinMsmsIntensityForQuant>0</diaMinMsmsIntensityForQuant> + <diaTopMsmsIntensityQuantileForQuant>0.85</diaTopMsmsIntensityQuantileForQuant> + <diaPrecursorFilterType>0</diaPrecursorFilterType> + <diaMinFragmentOverlapScore>1</diaMinFragmentOverlapScore> + <diaMinPrecursorScore>0.5</diaMinPrecursorScore> + <diaMinProfileCorrelation>0</diaMinProfileCorrelation> + <diaXgBoostMinChildWeight>9</diaXgBoostMinChildWeight> + <diaXgBoostMaximumTreeDepth>12</diaXgBoostMaximumTreeDepth> + <diaXgBoostEstimators>580</diaXgBoostEstimators> + <diaXgBoostGamma>0.9</diaXgBoostGamma> + <diaXgBoostMaxDeltaStep>3</diaXgBoostMaxDeltaStep> + <diaGlobalMl>True</diaGlobalMl> + <diaAdaptiveMassAccuracy>False</diaAdaptiveMassAccuracy> + <diaMassWindowFactor>3.3</diaMassWindowFactor> + <diaRtPrediction>False</diaRtPrediction> + <diaRtPredictionSecondRound>False</diaRtPredictionSecondRound> + <diaNoMl>False</diaNoMl> + <diaPermuteRt>False</diaPermuteRt> + <diaPermuteCcs>False</diaPermuteCcs> + <diaBackgroundSubtraction>False</diaBackgroundSubtraction> + <diaBackgroundSubtractionQuantile>0.5</diaBackgroundSubtractionQuantile> + <diaBackgroundSubtractionFactor>4</diaBackgroundSubtractionFactor> + <diaLfqWeightedMedian>False</diaLfqWeightedMedian> </parameterGroup> </parameterGroups> <msmsParamsArray> |
| b |
| diff -r d72c96ad9a16 -r 0839f84def5e test-data/02/config.yml --- a/test-data/02/config.yml Tue Jun 15 07:55:59 2021 +0000 +++ b/test-data/02/config.yml Sun Jun 20 16:37:41 2021 +0000 |
| [ |
| @@ -1,5 +1,5 @@ - fastaFiles: [/tmp/tmpQsmPD9/files/7/b/e/dataset_7be42b54-5eac-4f1d-a6bb-0b85e8f1bd67.dat] + fastaFiles: [/tmp/tmpyzym30dx/files/d/3/1/dataset_d314bbcd-5f08-4e93-b285-2ad6e4739fc9.dat] parseRules: identifierParseRule: '>([^\s]*)' descriptionParseRule: '>(.*)' @@ -52,8 +52,10 @@ reporterBasePeakRatio: 0 filterPif: True isobaricLabels: + - [iTRAQ4plex-Lys114,iTRAQ4plex-Nter114,0,0,0,0,False] - [iTRAQ4plex-Lys115,iTRAQ4plex-Nter115,0,0,0,0,False] - [iTRAQ4plex-Lys116,iTRAQ4plex-Nter116,0,0,0,0,False] - [iTRAQ4plex-Lys117,iTRAQ4plex-Nter117,0,0,0,0,False] + \ No newline at end of file |
| b |
| diff -r d72c96ad9a16 -r 0839f84def5e test-data/02/mqpar.xml --- a/test-data/02/mqpar.xml Tue Jun 15 07:55:59 2021 +0000 +++ b/test-data/02/mqpar.xml Sun Jun 20 16:37:41 2021 +0000 |
| [ |
| b'@@ -2,7 +2,7 @@\n <MaxQuantParams>\n \t<fastaFiles>\n \t\t<FastaFileInfo>\n-\t\t\t<fastaFilePath>D:\\shared\\dglaetzer\\maxquant_tool\\test1\\bsa.fasta</fastaFilePath>\n+\t\t\t<fastaFilePath>/tmp/tmpyzym30dx/files/d/3/1/dataset_d314bbcd-5f08-4e93-b285-2ad6e4739fc9.dat</fastaFilePath>\n \t\t\t<identifierParseRule>>([^\\s]*)</identifierParseRule>\n \t\t\t<descriptionParseRule>>(.*)</descriptionParseRule>\n \t\t\t<taxonomyParseRule/>\n@@ -19,8 +19,6 @@\n \t<andromedaCacheSize>350000</andromedaCacheSize>\n \t<advancedRatios>True</advancedRatios>\n \t<pvalThres>0.005</pvalThres>\n-\t<neucodeRatioBasedQuantification>False</neucodeRatioBasedQuantification>\n-\t<neucodeStabilizeLargeRatios>False</neucodeStabilizeLargeRatios>\n \t<rtShift>False</rtShift>\n \t<separateLfq>False</separateLfq>\n \t<lfqStabilizeLargeRatios>True</lfqStabilizeLargeRatios>\n@@ -48,7 +46,6 @@\n \t<dependentPeptidesWithinParameterGroup>False</dependentPeptidesWithinParameterGroup>\n \t<dependentPeptidesRestrictFractions>False</dependentPeptidesRestrictFractions>\n \t<dependentPeptidesFractionDifference>0</dependentPeptidesFractionDifference>\n-\t<msmsConnection>False</msmsConnection>\n \t<ibaq>False</ibaq>\n \t<top3>False</top3>\n \t<independentEnzymes>False</independentEnzymes>\n@@ -100,10 +97,11 @@\n \t<writeMsScansTable>False</writeMsScansTable>\n \t<writeMsmsScansTable>True</writeMsmsScansTable>\n \t<writePasefMsmsScansTable>True</writePasefMsmsScansTable>\n-\t<writeAccumulatedPasefMsmsScansTable>True</writeAccumulatedPasefMsmsScansTable>\n+\t<writeAccumulatedPasefMsmsScansTable>False</writeAccumulatedPasefMsmsScansTable>\n \t<writeMs3ScansTable>True</writeMs3ScansTable>\n \t<writeAllPeptidesTable>True</writeAllPeptidesTable>\n \t<writeMzRangeTable>True</writeMzRangeTable>\n+\t<writeDiaFragmentTable>False</writeDiaFragmentTable>\n \t<writeMzTab>True</writeMzTab>\n \t<disableMd5>False</disableMd5>\n \t<cacheBinInds>True</cacheBinInds>\n@@ -113,27 +111,28 @@\n \t<variationParseRule/>\n \t<variationMode>none</variationMode>\n \t<useSeriesReporters>False</useSeriesReporters>\n-\t<name>session1</name>\n-\t<maxQuantVersion>1.6.10.43</maxQuantVersion>\n-\t<tempFolder/>\n+\t<name>templateSession</name>\n+\t<maxQuantVersion>1.6.17.0</maxQuantVersion>\n \t<pluginFolder/>\n \t<numThreads>1</numThreads>\n+\t<batchSize>1</batchSize>\n \t<emailAddress/>\n \t<smtpHost/>\n \t<emailFromAddress/>\n \t<fixedCombinedFolder/>\n-\t<fullMinMz>-1.79589544172745E+308</fullMinMz>\n-\t<fullMaxMz>1.79589544172745E+308</fullMaxMz>\n+\t<fullMinMz>-1.79769313486232E+308</fullMinMz>\n+\t<fullMaxMz>1.79769313486232E+308</fullMaxMz>\n \t<sendEmail>False</sendEmail>\n \t<ionCountIntensities>False</ionCountIntensities>\n \t<verboseColumnHeaders>False</verboseColumnHeaders>\n \t<calcPeakProperties>False</calcPeakProperties>\n \t<showCentroidMassDifferences>False</showCentroidMassDifferences>\n \t<showIsotopeMassDifferences>False</showIsotopeMassDifferences>\n-\t<useDotNetCore>False</useDotNetCore>\n+\t<useDotNetCore>True</useDotNetCore>\n+\t<profilePerformance>False</profilePerformance>\n \t<filePaths>\n-\t\t<string>D:\\shared\\dglaetzer\\maxquant_tool\\test1\\BSA_min_23.mzXML</string>\n-\t\t<string>D:\\shared\\dglaetzer\\maxquant_tool\\test2\\BSA_min_22.mzXML</string>\n+\t\t<string>/tmp/tmpyzym30dx/job_working_directory/000/7/working/BSA_min_23.mzXML</string>\n+\t\t<string>/tmp/tmpyzym30dx/job_working_directory/000/7/working/BSA_min_22.mzxml</string>\n \t</filePaths>\n \t<experiments>\n \t\t<string>BSA_min_23.mzXML</string>\n@@ -157,12 +156,13 @@\n \t</referenceChannel>\n \t<intensPred>False</intensPred>\n \t<intensPredModelReTrain>False</intensPredModelReTrain>\n+\t<lfqTopNPeptides>0</lfqTopNPeptides>\n \t<parameterGroups>\n \t\t<parameterGroup>\n \t\t\t<msInstrument>0</msInstrument>\n \t\t\t<maxCharge>7</maxCharge>\n \t\t\t<minPeakLen>2</minPeakLen>\n-\t\t\t<diaMinPeakLen>2</diaMinPeakLen>\n+\t\t\t<diaMinPeakLen>1</diaMinPeakLen>\n \t\t\t<useMs1Centroids>False</useMs1Centroids>\n \t\t\t<useMs2Centroids>False</useMs2Centroids>\n \t\t\t<cutPeaks>True</cutPeaks>\n@@ -178,14 +178,15 @@\n \t\t\t<valleyFactor>1.4</valleyFactor>\n \t\t\t<isotopeValleyFactor>1.2</isotopeValleyFactor>\n \t\t\t<advancedPeakSplitting>False</a'..b'eshold>0</intensityThreshold>\n+\t\t\t<intensityThresholdMs1>0</intensityThresholdMs1>\n+\t\t\t<intensityThresholdMs2>0</intensityThresholdMs2>\n \t\t\t<labelMods>\n \t\t\t\t<string/>\n \t\t\t</labelMods>\n \t\t\t<lcmsRunType>Reporter ion MS2</lcmsRunType>\n \t\t\t<reQuantify>False</reQuantify>\n \t\t\t<lfqMode>0</lfqMode>\n-\t\t\t<lfqSkipNorm>False</lfqSkipNorm>\n+\t\t\t<lfqNormClusterSize>80</lfqNormClusterSize>\n \t\t\t<lfqMinEdgesPerNode>3</lfqMinEdgesPerNode>\n \t\t\t<lfqAvEdgesPerNode>6</lfqAvEdgesPerNode>\n \t\t\t<lfqMaxFeatures>100000</lfqMaxFeatures>\n@@ -363,17 +393,14 @@\n \t\t\t<complementaryReporterType>0</complementaryReporterType>\n \t\t\t<reporterNormalization>0</reporterNormalization>\n \t\t\t<neucodeIntensityMode>0</neucodeIntensityMode>\n-\t\t\t<fixedModifications>\n- </fixedModifications>\n-\t\t\t<enzymes>\n- </enzymes>\n+\t\t\t<fixedModifications/>\n+\t\t\t<enzymes/>\n \t\t\t<enzymesFirstSearch>\n </enzymesFirstSearch>\n \t\t\t<enzymeModeFirstSearch>0</enzymeModeFirstSearch>\n \t\t\t<useEnzymeFirstSearch>False</useEnzymeFirstSearch>\n \t\t\t<useVariableModificationsFirstSearch>False</useVariableModificationsFirstSearch>\n-\t\t\t<variableModifications>\n- </variableModifications>\n+\t\t\t<variableModifications/>\n \t\t\t<useMultiModification>False</useMultiModification>\n \t\t\t<multiModifications>\n </multiModifications>\n@@ -453,7 +480,7 @@\n \t\t\t<timsRemovePrecursor>True</timsRemovePrecursor>\n \t\t\t<timsIsobaricLabels>False</timsIsobaricLabels>\n \t\t\t<timsCollapseMsms>True</timsCollapseMsms>\n-\t\t\t<crosslinkSearch>False</crosslinkSearch>\n+\t\t\t<crossLinkingType>0</crossLinkingType>\n \t\t\t<crossLinker/>\n \t\t\t<minMatchXl>0</minMatchXl>\n \t\t\t<minPairedPepLenXl>6</minPairedPepLenXl>\n@@ -475,7 +502,8 @@\n \t\t\t<isobaricSumOverWindow>True</isobaricSumOverWindow>\n \t\t\t<isobaricWeightExponent>0.75</isobaricWeightExponent>\n \t\t\t<diaLibraryType>0</diaLibraryType>\n-\t\t\t<diaLibraryPath/>\n+\t\t\t<diaLibraryPaths>\n+ </diaLibraryPaths>\n \t\t\t<diaPeptidePaths>\n </diaPeptidePaths>\n \t\t\t<diaEvidencePaths>\n@@ -488,9 +516,37 @@\n \t\t\t<diaPrecTolPpmFeatureClustering>2</diaPrecTolPpmFeatureClustering>\n \t\t\t<diaFragTolPpmFeatureClustering>2</diaFragTolPpmFeatureClustering>\n \t\t\t<diaScoreN>7</diaScoreN>\n-\t\t\t<diaMinScore>2.99</diaMinScore>\n-\t\t\t<diaPrecursorQuant>False</diaPrecursorQuant>\n-\t\t\t<diaDiaTopNFragmentsForQuant>3</diaDiaTopNFragmentsForQuant>\n+\t\t\t<diaMinScore>1.99</diaMinScore>\n+\t\t\t<diaXgBoostBaseScore>0.4</diaXgBoostBaseScore>\n+\t\t\t<diaXgBoostSubSample>0.9</diaXgBoostSubSample>\n+\t\t\t<centroidPosition>0</centroidPosition>\n+\t\t\t<diaQuantMethod>7</diaQuantMethod>\n+\t\t\t<diaFeatureQuantMethod>2</diaFeatureQuantMethod>\n+\t\t\t<lfqNormType>1</lfqNormType>\n+\t\t\t<diaTopNForQuant>10</diaTopNForQuant>\n+\t\t\t<diaMinMsmsIntensityForQuant>0</diaMinMsmsIntensityForQuant>\n+\t\t\t<diaTopMsmsIntensityQuantileForQuant>0.85</diaTopMsmsIntensityQuantileForQuant>\n+\t\t\t<diaPrecursorFilterType>0</diaPrecursorFilterType>\n+\t\t\t<diaMinFragmentOverlapScore>1</diaMinFragmentOverlapScore>\n+\t\t\t<diaMinPrecursorScore>0.5</diaMinPrecursorScore>\n+\t\t\t<diaMinProfileCorrelation>0</diaMinProfileCorrelation>\n+\t\t\t<diaXgBoostMinChildWeight>9</diaXgBoostMinChildWeight>\n+\t\t\t<diaXgBoostMaximumTreeDepth>12</diaXgBoostMaximumTreeDepth>\n+\t\t\t<diaXgBoostEstimators>580</diaXgBoostEstimators>\n+\t\t\t<diaXgBoostGamma>0.9</diaXgBoostGamma>\n+\t\t\t<diaXgBoostMaxDeltaStep>3</diaXgBoostMaxDeltaStep>\n+\t\t\t<diaGlobalMl>True</diaGlobalMl>\n+\t\t\t<diaAdaptiveMassAccuracy>False</diaAdaptiveMassAccuracy>\n+\t\t\t<diaMassWindowFactor>3.3</diaMassWindowFactor>\n+\t\t\t<diaRtPrediction>False</diaRtPrediction>\n+\t\t\t<diaRtPredictionSecondRound>False</diaRtPredictionSecondRound>\n+\t\t\t<diaNoMl>False</diaNoMl>\n+\t\t\t<diaPermuteRt>False</diaPermuteRt>\n+\t\t\t<diaPermuteCcs>False</diaPermuteCcs>\n+\t\t\t<diaBackgroundSubtraction>False</diaBackgroundSubtraction>\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</parameterGroup>\n \t</parameterGroups>\n \t<msmsParamsArray>\n' |
| b |
| diff -r d72c96ad9a16 -r 0839f84def5e test-data/03/config.yml --- a/test-data/03/config.yml Tue Jun 15 07:55:59 2021 +0000 +++ b/test-data/03/config.yml Sun Jun 20 16:37:41 2021 +0000 |
| [ |
| @@ -33,7 +33,7 @@ enzymes: [Trypsin/P] enzymeMode: 0 lfqMode: 1 - lfqSkipNorm: True + lfqNormType: 0 lfqMinEdgesPerNode: 3 lfqAvEdgesPerNode: 6 lfqMinRatioCount: 2 |
| b |
| diff -r d72c96ad9a16 -r 0839f84def5e test-data/03/mqpar.xml --- a/test-data/03/mqpar.xml Tue Jun 15 07:55:59 2021 +0000 +++ b/test-data/03/mqpar.xml Sun Jun 20 16:37:41 2021 +0000 |
| [ |
| @@ -2,7 +2,7 @@ <MaxQuantParams> <fastaFiles> <FastaFileInfo> - <fastaFilePath>D:\shared\dglaetzer\maxquant_tool\test1\bsa.fasta</fastaFilePath> + <fastaFilePath>/tmp/tmpwu9ns_ue/files/b/7/c/dataset_b7c3a34e-122e-456d-90ed-78fe5ab2ef9a.dat</fastaFilePath> <identifierParseRule>^>.*\|(.*)\|.*$</identifierParseRule> <descriptionParseRule>^>.*\|.*\|[^ ]+ (.*) OS.*$</descriptionParseRule> <taxonomyParseRule/> @@ -19,8 +19,6 @@ <andromedaCacheSize>350000</andromedaCacheSize> <advancedRatios>True</advancedRatios> <pvalThres>0.005</pvalThres> - <neucodeRatioBasedQuantification>False</neucodeRatioBasedQuantification> - <neucodeStabilizeLargeRatios>False</neucodeStabilizeLargeRatios> <rtShift>False</rtShift> <separateLfq>False</separateLfq> <lfqStabilizeLargeRatios>True</lfqStabilizeLargeRatios> @@ -48,7 +46,6 @@ <dependentPeptidesWithinParameterGroup>False</dependentPeptidesWithinParameterGroup> <dependentPeptidesRestrictFractions>False</dependentPeptidesRestrictFractions> <dependentPeptidesFractionDifference>0</dependentPeptidesFractionDifference> - <msmsConnection>False</msmsConnection> <ibaq>True</ibaq> <top3>False</top3> <independentEnzymes>False</independentEnzymes> @@ -100,10 +97,11 @@ <writeMsScansTable>False</writeMsScansTable> <writeMsmsScansTable>True</writeMsmsScansTable> <writePasefMsmsScansTable>True</writePasefMsmsScansTable> - <writeAccumulatedPasefMsmsScansTable>True</writeAccumulatedPasefMsmsScansTable> + <writeAccumulatedPasefMsmsScansTable>False</writeAccumulatedPasefMsmsScansTable> <writeMs3ScansTable>True</writeMs3ScansTable> <writeAllPeptidesTable>True</writeAllPeptidesTable> <writeMzRangeTable>True</writeMzRangeTable> + <writeDiaFragmentTable>False</writeDiaFragmentTable> <writeMzTab>False</writeMzTab> <disableMd5>False</disableMd5> <cacheBinInds>True</cacheBinInds> @@ -113,26 +111,27 @@ <variationParseRule/> <variationMode>none</variationMode> <useSeriesReporters>False</useSeriesReporters> - <name>session1</name> - <maxQuantVersion>1.6.10.43</maxQuantVersion> - <tempFolder/> + <name>templateSession</name> + <maxQuantVersion>1.6.17.0</maxQuantVersion> <pluginFolder/> <numThreads>1</numThreads> + <batchSize>1</batchSize> <emailAddress/> <smtpHost/> <emailFromAddress/> <fixedCombinedFolder/> - <fullMinMz>-1.79589544172745E+308</fullMinMz> - <fullMaxMz>1.79589544172745E+308</fullMaxMz> + <fullMinMz>-1.79769313486232E+308</fullMinMz> + <fullMaxMz>1.79769313486232E+308</fullMaxMz> <sendEmail>False</sendEmail> <ionCountIntensities>False</ionCountIntensities> <verboseColumnHeaders>False</verboseColumnHeaders> <calcPeakProperties>False</calcPeakProperties> <showCentroidMassDifferences>False</showCentroidMassDifferences> <showIsotopeMassDifferences>False</showIsotopeMassDifferences> - <useDotNetCore>False</useDotNetCore> + <useDotNetCore>True</useDotNetCore> + <profilePerformance>False</profilePerformance> <filePaths> - <string>D:\shared\dglaetzer\maxquant_tool\test3\BSA_min_22.mzXML</string> + <string>/tmp/tmpwu9ns_ue/job_working_directory/000/6/working/BSA_min_22.mzxml</string> </filePaths> <experiments> <string>BSA_min_22.mzxml</string> @@ -151,12 +150,13 @@ </referenceChannel> <intensPred>False</intensPred> <intensPredModelReTrain>False</intensPredModelReTrain> + <lfqTopNPeptides>0</lfqTopNPeptides> <parameterGroups> <parameterGroup> <msInstrument>0</msInstrument> <maxCharge>7</maxCharge> <minPeakLen>2</minPeakLen> - <diaMinPeakLen>2</diaMinPeakLen> + <diaMinPeakLen>1</diaMinPeakLen> <useMs1Centroids>False</useMs1Centroids> <useMs2Centroids>False</useMs2Centroids> <cutPeaks>True</cutPeaks> @@ -172,14 +172,15 @@ <valleyFactor>1.4</valleyFactor> <isotopeValleyFactor>1.2</isotopeValleyFactor> <advancedPeakSplitting>False</advancedPeakSplitting> - <intensityThreshold>0</intensityThreshold> + <intensityThresholdMs1>0</intensityThresholdMs1> + <intensityThresholdMs2>0</intensityThresholdMs2> <labelMods> <string/> </labelMods> <lcmsRunType>Standard</lcmsRunType> <reQuantify>False</reQuantify> <lfqMode>1</lfqMode> - <lfqSkipNorm>True</lfqSkipNorm> + <lfqNormClusterSize>80</lfqNormClusterSize> <lfqMinEdgesPerNode>3</lfqMinEdgesPerNode> <lfqAvEdgesPerNode>6</lfqAvEdgesPerNode> <lfqMaxFeatures>100000</lfqMaxFeatures> @@ -255,7 +256,7 @@ <timsRemovePrecursor>True</timsRemovePrecursor> <timsIsobaricLabels>False</timsIsobaricLabels> <timsCollapseMsms>True</timsCollapseMsms> - <crosslinkSearch>False</crosslinkSearch> + <crossLinkingType>0</crossLinkingType> <crossLinker/> <minMatchXl>0</minMatchXl> <minPairedPepLenXl>6</minPairedPepLenXl> @@ -277,7 +278,8 @@ <isobaricSumOverWindow>True</isobaricSumOverWindow> <isobaricWeightExponent>0.75</isobaricWeightExponent> <diaLibraryType>0</diaLibraryType> - <diaLibraryPath/> + <diaLibraryPaths> + </diaLibraryPaths> <diaPeptidePaths> </diaPeptidePaths> <diaEvidencePaths> @@ -290,9 +292,37 @@ <diaPrecTolPpmFeatureClustering>2</diaPrecTolPpmFeatureClustering> <diaFragTolPpmFeatureClustering>2</diaFragTolPpmFeatureClustering> <diaScoreN>7</diaScoreN> - <diaMinScore>2.99</diaMinScore> - <diaPrecursorQuant>False</diaPrecursorQuant> - <diaDiaTopNFragmentsForQuant>3</diaDiaTopNFragmentsForQuant> + <diaMinScore>1.99</diaMinScore> + <diaXgBoostBaseScore>0.4</diaXgBoostBaseScore> + <diaXgBoostSubSample>0.9</diaXgBoostSubSample> + <centroidPosition>0</centroidPosition> + <diaQuantMethod>7</diaQuantMethod> + <diaFeatureQuantMethod>2</diaFeatureQuantMethod> + <lfqNormType>0</lfqNormType> + <diaTopNForQuant>10</diaTopNForQuant> + <diaMinMsmsIntensityForQuant>0</diaMinMsmsIntensityForQuant> + <diaTopMsmsIntensityQuantileForQuant>0.85</diaTopMsmsIntensityQuantileForQuant> + <diaPrecursorFilterType>0</diaPrecursorFilterType> + <diaMinFragmentOverlapScore>1</diaMinFragmentOverlapScore> + <diaMinPrecursorScore>0.5</diaMinPrecursorScore> + <diaMinProfileCorrelation>0</diaMinProfileCorrelation> + <diaXgBoostMinChildWeight>9</diaXgBoostMinChildWeight> + <diaXgBoostMaximumTreeDepth>12</diaXgBoostMaximumTreeDepth> + <diaXgBoostEstimators>580</diaXgBoostEstimators> + <diaXgBoostGamma>0.9</diaXgBoostGamma> + <diaXgBoostMaxDeltaStep>3</diaXgBoostMaxDeltaStep> + <diaGlobalMl>True</diaGlobalMl> + <diaAdaptiveMassAccuracy>False</diaAdaptiveMassAccuracy> + <diaMassWindowFactor>3.3</diaMassWindowFactor> + <diaRtPrediction>False</diaRtPrediction> + <diaRtPredictionSecondRound>False</diaRtPredictionSecondRound> + <diaNoMl>False</diaNoMl> + <diaPermuteRt>False</diaPermuteRt> + <diaPermuteCcs>False</diaPermuteCcs> + <diaBackgroundSubtraction>False</diaBackgroundSubtraction> + <diaBackgroundSubtractionQuantile>0.5</diaBackgroundSubtractionQuantile> + <diaBackgroundSubtractionFactor>4</diaBackgroundSubtractionFactor> + <diaLfqWeightedMedian>False</diaLfqWeightedMedian> </parameterGroup> </parameterGroups> <msmsParamsArray> |
| b |
| diff -r d72c96ad9a16 -r 0839f84def5e test-data/04/config.yml --- a/test-data/04/config.yml Tue Jun 15 07:55:59 2021 +0000 +++ b/test-data/04/config.yml Sun Jun 20 16:37:41 2021 +0000 |
| [ |
| @@ -1,5 +1,5 @@ - fastaFiles: [/home/galaxy/galaxy/database/files/000/dataset_4.dat] + fastaFiles: [/tmp/tmpyzym30dx/files/a/5/9/dataset_a592c8b5-872b-4804-9f05-abeef0fda2f1.dat] parseRules: identifierParseRule: '>([^\s]*)' descriptionParseRule: '>(.*)' |
| b |
| diff -r d72c96ad9a16 -r 0839f84def5e test-data/04/mqpar.xml --- a/test-data/04/mqpar.xml Tue Jun 15 07:55:59 2021 +0000 +++ b/test-data/04/mqpar.xml Sun Jun 20 16:37:41 2021 +0000 |
| [ |
| @@ -2,7 +2,7 @@ <MaxQuantParams> <fastaFiles> <FastaFileInfo> - <fastaFilePath>D:\shared\dglaetzer\maxquant_tool\test2\bsa.fasta</fastaFilePath> + <fastaFilePath>/tmp/tmpyzym30dx/files/a/5/9/dataset_a592c8b5-872b-4804-9f05-abeef0fda2f1.dat</fastaFilePath> <identifierParseRule>>([^\s]*)</identifierParseRule> <descriptionParseRule>>(.*)</descriptionParseRule> <taxonomyParseRule/> @@ -19,8 +19,6 @@ <andromedaCacheSize>350000</andromedaCacheSize> <advancedRatios>True</advancedRatios> <pvalThres>0.005</pvalThres> - <neucodeRatioBasedQuantification>False</neucodeRatioBasedQuantification> - <neucodeStabilizeLargeRatios>False</neucodeStabilizeLargeRatios> <rtShift>False</rtShift> <separateLfq>False</separateLfq> <lfqStabilizeLargeRatios>True</lfqStabilizeLargeRatios> @@ -48,7 +46,6 @@ <dependentPeptidesWithinParameterGroup>False</dependentPeptidesWithinParameterGroup> <dependentPeptidesRestrictFractions>False</dependentPeptidesRestrictFractions> <dependentPeptidesFractionDifference>0</dependentPeptidesFractionDifference> - <msmsConnection>False</msmsConnection> <ibaq>False</ibaq> <top3>False</top3> <independentEnzymes>False</independentEnzymes> @@ -100,10 +97,11 @@ <writeMsScansTable>False</writeMsScansTable> <writeMsmsScansTable>True</writeMsmsScansTable> <writePasefMsmsScansTable>True</writePasefMsmsScansTable> - <writeAccumulatedPasefMsmsScansTable>True</writeAccumulatedPasefMsmsScansTable> + <writeAccumulatedPasefMsmsScansTable>False</writeAccumulatedPasefMsmsScansTable> <writeMs3ScansTable>True</writeMs3ScansTable> <writeAllPeptidesTable>True</writeAllPeptidesTable> <writeMzRangeTable>True</writeMzRangeTable> + <writeDiaFragmentTable>False</writeDiaFragmentTable> <writeMzTab>False</writeMzTab> <disableMd5>False</disableMd5> <cacheBinInds>True</cacheBinInds> @@ -113,27 +111,28 @@ <variationParseRule/> <variationMode>none</variationMode> <useSeriesReporters>False</useSeriesReporters> - <name>session1</name> - <maxQuantVersion>1.6.10.43</maxQuantVersion> - <tempFolder/> + <name>templateSession</name> + <maxQuantVersion>1.6.17.0</maxQuantVersion> <pluginFolder/> <numThreads>1</numThreads> + <batchSize>1</batchSize> <emailAddress/> <smtpHost/> <emailFromAddress/> <fixedCombinedFolder/> - <fullMinMz>-1.79589544172745E+308</fullMinMz> - <fullMaxMz>1.79589544172745E+308</fullMaxMz> + <fullMinMz>-1.79769313486232E+308</fullMinMz> + <fullMaxMz>1.79769313486232E+308</fullMaxMz> <sendEmail>False</sendEmail> <ionCountIntensities>False</ionCountIntensities> <verboseColumnHeaders>False</verboseColumnHeaders> <calcPeakProperties>False</calcPeakProperties> <showCentroidMassDifferences>False</showCentroidMassDifferences> <showIsotopeMassDifferences>False</showIsotopeMassDifferences> - <useDotNetCore>False</useDotNetCore> + <useDotNetCore>True</useDotNetCore> + <profilePerformance>False</profilePerformance> <filePaths> - <string>D:\shared\dglaetzer\maxquant_tool\test2\BSA_min_22.mzXML</string> - <string>D:\shared\dglaetzer\maxquant_tool\test2\BSA_min_23.mzXML</string> + <string>/tmp/tmpyzym30dx/job_working_directory/000/22/working/BSA_min_22.mzxml</string> + <string>/tmp/tmpyzym30dx/job_working_directory/000/22/working/BSA_min_23.mzXML</string> </filePaths> <experiments> <string>e1</string> @@ -157,12 +156,13 @@ </referenceChannel> <intensPred>False</intensPred> <intensPredModelReTrain>False</intensPredModelReTrain> + <lfqTopNPeptides>0</lfqTopNPeptides> <parameterGroups> <parameterGroup> <msInstrument>0</msInstrument> <maxCharge>7</maxCharge> <minPeakLen>2</minPeakLen> - <diaMinPeakLen>2</diaMinPeakLen> + <diaMinPeakLen>1</diaMinPeakLen> <useMs1Centroids>False</useMs1Centroids> <useMs2Centroids>False</useMs2Centroids> <cutPeaks>True</cutPeaks> @@ -178,7 +178,8 @@ <valleyFactor>1.4</valleyFactor> <isotopeValleyFactor>1.2</isotopeValleyFactor> <advancedPeakSplitting>False</advancedPeakSplitting> - <intensityThreshold>0</intensityThreshold> + <intensityThresholdMs1>0</intensityThresholdMs1> + <intensityThresholdMs2>0</intensityThresholdMs2> <labelMods> <string>Arg6;Lys4</string> <string>Arg10;DimethLys8</string> @@ -186,7 +187,7 @@ <lcmsRunType>Standard</lcmsRunType> <reQuantify>False</reQuantify> <lfqMode>0</lfqMode> - <lfqSkipNorm>False</lfqSkipNorm> + <lfqNormClusterSize>80</lfqNormClusterSize> <lfqMinEdgesPerNode>3</lfqMinEdgesPerNode> <lfqAvEdgesPerNode>6</lfqAvEdgesPerNode> <lfqMaxFeatures>100000</lfqMaxFeatures> @@ -262,7 +263,7 @@ <timsRemovePrecursor>True</timsRemovePrecursor> <timsIsobaricLabels>False</timsIsobaricLabels> <timsCollapseMsms>True</timsCollapseMsms> - <crosslinkSearch>False</crosslinkSearch> + <crossLinkingType>0</crossLinkingType> <crossLinker/> <minMatchXl>0</minMatchXl> <minPairedPepLenXl>6</minPairedPepLenXl> @@ -284,7 +285,8 @@ <isobaricSumOverWindow>True</isobaricSumOverWindow> <isobaricWeightExponent>0.75</isobaricWeightExponent> <diaLibraryType>0</diaLibraryType> - <diaLibraryPath/> + <diaLibraryPaths> + </diaLibraryPaths> <diaPeptidePaths> </diaPeptidePaths> <diaEvidencePaths> @@ -297,9 +299,37 @@ <diaPrecTolPpmFeatureClustering>2</diaPrecTolPpmFeatureClustering> <diaFragTolPpmFeatureClustering>2</diaFragTolPpmFeatureClustering> <diaScoreN>7</diaScoreN> - <diaMinScore>2.99</diaMinScore> - <diaPrecursorQuant>False</diaPrecursorQuant> - <diaDiaTopNFragmentsForQuant>3</diaDiaTopNFragmentsForQuant> + <diaMinScore>1.99</diaMinScore> + <diaXgBoostBaseScore>0.4</diaXgBoostBaseScore> + <diaXgBoostSubSample>0.9</diaXgBoostSubSample> + <centroidPosition>0</centroidPosition> + <diaQuantMethod>7</diaQuantMethod> + <diaFeatureQuantMethod>2</diaFeatureQuantMethod> + <lfqNormType>1</lfqNormType> + <diaTopNForQuant>10</diaTopNForQuant> + <diaMinMsmsIntensityForQuant>0</diaMinMsmsIntensityForQuant> + <diaTopMsmsIntensityQuantileForQuant>0.85</diaTopMsmsIntensityQuantileForQuant> + <diaPrecursorFilterType>0</diaPrecursorFilterType> + <diaMinFragmentOverlapScore>1</diaMinFragmentOverlapScore> + <diaMinPrecursorScore>0.5</diaMinPrecursorScore> + <diaMinProfileCorrelation>0</diaMinProfileCorrelation> + <diaXgBoostMinChildWeight>9</diaXgBoostMinChildWeight> + <diaXgBoostMaximumTreeDepth>12</diaXgBoostMaximumTreeDepth> + <diaXgBoostEstimators>580</diaXgBoostEstimators> + <diaXgBoostGamma>0.9</diaXgBoostGamma> + <diaXgBoostMaxDeltaStep>3</diaXgBoostMaxDeltaStep> + <diaGlobalMl>True</diaGlobalMl> + <diaAdaptiveMassAccuracy>False</diaAdaptiveMassAccuracy> + <diaMassWindowFactor>3.3</diaMassWindowFactor> + <diaRtPrediction>False</diaRtPrediction> + <diaRtPredictionSecondRound>False</diaRtPredictionSecondRound> + <diaNoMl>False</diaNoMl> + <diaPermuteRt>False</diaPermuteRt> + <diaPermuteCcs>False</diaPermuteCcs> + <diaBackgroundSubtraction>False</diaBackgroundSubtraction> + <diaBackgroundSubtractionQuantile>0.5</diaBackgroundSubtractionQuantile> + <diaBackgroundSubtractionFactor>4</diaBackgroundSubtractionFactor> + <diaLfqWeightedMedian>False</diaLfqWeightedMedian> </parameterGroup> </parameterGroups> <msmsParamsArray> |
| b |
| diff -r d72c96ad9a16 -r 0839f84def5e test-data/05/config.yml --- a/test-data/05/config.yml Tue Jun 15 07:55:59 2021 +0000 +++ b/test-data/05/config.yml Sun Jun 20 16:37:41 2021 +0000 |
| [ |
| @@ -38,7 +38,7 @@ enzymes: [Trypsin/P] enzymeMode: 0 lfqMode: 1 - lfqSkipNorm: True + lfqNormType: 0 lfqMinEdgesPerNode: 3 lfqAvEdgesPerNode: 6 lfqMinRatioCount: 2 |
| b |
| diff -r d72c96ad9a16 -r 0839f84def5e test-data/05/mqpar.xml --- a/test-data/05/mqpar.xml Tue Jun 15 07:55:59 2021 +0000 +++ b/test-data/05/mqpar.xml Sun Jun 20 16:37:41 2021 +0000 |
| [ |
| @@ -2,7 +2,7 @@ <MaxQuantParams> <fastaFiles> <FastaFileInfo> - <fastaFilePath>/tmp/tmp0wswhy4o/files/4/7/7/dataset_4770959a-66d4-405f-a5b5-48d25389063a.dat</fastaFilePath> + <fastaFilePath>/tmp/tmpwu9ns_ue/files/3/1/3/dataset_31390cc5-8f5d-4820-a5e4-e5779aca2b4b.dat</fastaFilePath> <identifierParseRule>^>.*\|(.*)\|.*$</identifierParseRule> <descriptionParseRule>^>.*\|.*\|[^ ]+ (.*) OS.*$</descriptionParseRule> <taxonomyParseRule/> @@ -19,8 +19,6 @@ <andromedaCacheSize>350000</andromedaCacheSize> <advancedRatios>True</advancedRatios> <pvalThres>0.005</pvalThres> - <neucodeRatioBasedQuantification>False</neucodeRatioBasedQuantification> - <neucodeStabilizeLargeRatios>False</neucodeStabilizeLargeRatios> <rtShift>False</rtShift> <separateLfq>False</separateLfq> <lfqStabilizeLargeRatios>True</lfqStabilizeLargeRatios> @@ -48,7 +46,6 @@ <dependentPeptidesWithinParameterGroup>False</dependentPeptidesWithinParameterGroup> <dependentPeptidesRestrictFractions>False</dependentPeptidesRestrictFractions> <dependentPeptidesFractionDifference>0</dependentPeptidesFractionDifference> - <msmsConnection>False</msmsConnection> <ibaq>True</ibaq> <top3>False</top3> <independentEnzymes>False</independentEnzymes> @@ -100,10 +97,11 @@ <writeMsScansTable>False</writeMsScansTable> <writeMsmsScansTable>True</writeMsmsScansTable> <writePasefMsmsScansTable>True</writePasefMsmsScansTable> - <writeAccumulatedPasefMsmsScansTable>True</writeAccumulatedPasefMsmsScansTable> + <writeAccumulatedPasefMsmsScansTable>False</writeAccumulatedPasefMsmsScansTable> <writeMs3ScansTable>True</writeMs3ScansTable> <writeAllPeptidesTable>True</writeAllPeptidesTable> <writeMzRangeTable>True</writeMzRangeTable> + <writeDiaFragmentTable>False</writeDiaFragmentTable> <writeMzTab>False</writeMzTab> <disableMd5>False</disableMd5> <cacheBinInds>True</cacheBinInds> @@ -114,10 +112,10 @@ <variationMode>none</variationMode> <useSeriesReporters>False</useSeriesReporters> <name>templateSession</name> - <maxQuantVersion>1.6.10.43</maxQuantVersion> - <tempFolder/> + <maxQuantVersion>1.6.17.0</maxQuantVersion> <pluginFolder/> <numThreads>1</numThreads> + <batchSize>1</batchSize> <emailAddress/> <smtpHost/> <emailFromAddress/> @@ -130,9 +128,10 @@ <calcPeakProperties>False</calcPeakProperties> <showCentroidMassDifferences>False</showCentroidMassDifferences> <showIsotopeMassDifferences>False</showIsotopeMassDifferences> - <useDotNetCore>False</useDotNetCore> + <useDotNetCore>True</useDotNetCore> + <profilePerformance>False</profilePerformance> <filePaths> - <string>/tmp/tmp0wswhy4o/job_working_directory/000/7/working/BSA_min_22.mzxml</string> + <string>/tmp/tmpwu9ns_ue/job_working_directory/000/9/working/BSA_min_22.mzxml</string> </filePaths> <experiments> <string>BSA_min_22.mzxml</string> @@ -151,12 +150,13 @@ </referenceChannel> <intensPred>False</intensPred> <intensPredModelReTrain>False</intensPredModelReTrain> + <lfqTopNPeptides>0</lfqTopNPeptides> <parameterGroups> <parameterGroup> <msInstrument>0</msInstrument> <maxCharge>7</maxCharge> <minPeakLen>2</minPeakLen> - <diaMinPeakLen>2</diaMinPeakLen> + <diaMinPeakLen>1</diaMinPeakLen> <useMs1Centroids>False</useMs1Centroids> <useMs2Centroids>False</useMs2Centroids> <cutPeaks>True</cutPeaks> @@ -172,14 +172,15 @@ <valleyFactor>1.4</valleyFactor> <isotopeValleyFactor>1.2</isotopeValleyFactor> <advancedPeakSplitting>False</advancedPeakSplitting> - <intensityThreshold>0</intensityThreshold> + <intensityThresholdMs1>0</intensityThresholdMs1> + <intensityThresholdMs2>0</intensityThresholdMs2> <labelMods> <string/> </labelMods> <lcmsRunType>Standard</lcmsRunType> <reQuantify>False</reQuantify> <lfqMode>1</lfqMode> - <lfqSkipNorm>True</lfqSkipNorm> + <lfqNormClusterSize>80</lfqNormClusterSize> <lfqMinEdgesPerNode>3</lfqMinEdgesPerNode> <lfqAvEdgesPerNode>6</lfqAvEdgesPerNode> <lfqMaxFeatures>100000</lfqMaxFeatures> @@ -255,7 +256,7 @@ <timsRemovePrecursor>True</timsRemovePrecursor> <timsIsobaricLabels>False</timsIsobaricLabels> <timsCollapseMsms>True</timsCollapseMsms> - <crosslinkSearch>False</crosslinkSearch> + <crossLinkingType>0</crossLinkingType> <crossLinker/> <minMatchXl>0</minMatchXl> <minPairedPepLenXl>6</minPairedPepLenXl> @@ -277,7 +278,8 @@ <isobaricSumOverWindow>True</isobaricSumOverWindow> <isobaricWeightExponent>0.75</isobaricWeightExponent> <diaLibraryType>0</diaLibraryType> - <diaLibraryPath/> + <diaLibraryPaths> + </diaLibraryPaths> <diaPeptidePaths> </diaPeptidePaths> <diaEvidencePaths> @@ -290,9 +292,37 @@ <diaPrecTolPpmFeatureClustering>2</diaPrecTolPpmFeatureClustering> <diaFragTolPpmFeatureClustering>2</diaFragTolPpmFeatureClustering> <diaScoreN>7</diaScoreN> - <diaMinScore>2.99</diaMinScore> - <diaPrecursorQuant>False</diaPrecursorQuant> - <diaDiaTopNFragmentsForQuant>3</diaDiaTopNFragmentsForQuant> + <diaMinScore>1.99</diaMinScore> + <diaXgBoostBaseScore>0.4</diaXgBoostBaseScore> + <diaXgBoostSubSample>0.9</diaXgBoostSubSample> + <centroidPosition>0</centroidPosition> + <diaQuantMethod>7</diaQuantMethod> + <diaFeatureQuantMethod>2</diaFeatureQuantMethod> + <lfqNormType>0</lfqNormType> + <diaTopNForQuant>10</diaTopNForQuant> + <diaMinMsmsIntensityForQuant>0</diaMinMsmsIntensityForQuant> + <diaTopMsmsIntensityQuantileForQuant>0.85</diaTopMsmsIntensityQuantileForQuant> + <diaPrecursorFilterType>0</diaPrecursorFilterType> + <diaMinFragmentOverlapScore>1</diaMinFragmentOverlapScore> + <diaMinPrecursorScore>0.5</diaMinPrecursorScore> + <diaMinProfileCorrelation>0</diaMinProfileCorrelation> + <diaXgBoostMinChildWeight>9</diaXgBoostMinChildWeight> + <diaXgBoostMaximumTreeDepth>12</diaXgBoostMaximumTreeDepth> + <diaXgBoostEstimators>580</diaXgBoostEstimators> + <diaXgBoostGamma>0.9</diaXgBoostGamma> + <diaXgBoostMaxDeltaStep>3</diaXgBoostMaxDeltaStep> + <diaGlobalMl>True</diaGlobalMl> + <diaAdaptiveMassAccuracy>False</diaAdaptiveMassAccuracy> + <diaMassWindowFactor>3.3</diaMassWindowFactor> + <diaRtPrediction>False</diaRtPrediction> + <diaRtPredictionSecondRound>False</diaRtPredictionSecondRound> + <diaNoMl>False</diaNoMl> + <diaPermuteRt>False</diaPermuteRt> + <diaPermuteCcs>False</diaPermuteCcs> + <diaBackgroundSubtraction>False</diaBackgroundSubtraction> + <diaBackgroundSubtractionQuantile>0.5</diaBackgroundSubtractionQuantile> + <diaBackgroundSubtractionFactor>4</diaBackgroundSubtractionFactor> + <diaLfqWeightedMedian>False</diaLfqWeightedMedian> </parameterGroup> </parameterGroups> <msmsParamsArray> |
| b |
| diff -r d72c96ad9a16 -r 0839f84def5e test-data/06/config.yml --- a/test-data/06/config.yml Tue Jun 15 07:55:59 2021 +0000 +++ b/test-data/06/config.yml Sun Jun 20 16:37:41 2021 +0000 |
| [ |
| @@ -1,5 +1,5 @@ - fastaFiles: [/tmp/tmp0wswhy4o/files/e/e/e/dataset_eee05aed-87d2-4635-87b0-dd7930cc43dc.dat] + fastaFiles: [/tmp/tmpyzym30dx/files/b/9/7/dataset_b97123e2-9db4-407c-bd7f-b69d65fc32cc.dat] parseRules: identifierParseRule: '>([^\s]*)' descriptionParseRule: '>(.*)' @@ -52,8 +52,10 @@ reporterBasePeakRatio: 0 filterPif: True isobaricLabels: + - [iTRAQ4plex-Lys114,iTRAQ4plex-Nter114,0,0,0,0,False] - [iTRAQ4plex-Lys115,iTRAQ4plex-Nter115,0,0,0,0,False] - [iTRAQ4plex-Lys116,iTRAQ4plex-Nter116,0,0,0,0,False] - [iTRAQ4plex-Lys117,iTRAQ4plex-Nter117,0,0,0,0,False] + \ No newline at end of file |
| b |
| diff -r d72c96ad9a16 -r 0839f84def5e test-data/06/mqpar.xml --- a/test-data/06/mqpar.xml Tue Jun 15 07:55:59 2021 +0000 +++ b/test-data/06/mqpar.xml Sun Jun 20 16:37:41 2021 +0000 |
| [ |
| b'@@ -2,7 +2,7 @@\n <MaxQuantParams>\n \t<fastaFiles>\n \t\t<FastaFileInfo>\n-\t\t\t<fastaFilePath>/tmp/tmp0wswhy4o/files/e/e/e/dataset_eee05aed-87d2-4635-87b0-dd7930cc43dc.dat</fastaFilePath>\n+\t\t\t<fastaFilePath>/tmp/tmpyzym30dx/files/b/9/7/dataset_b97123e2-9db4-407c-bd7f-b69d65fc32cc.dat</fastaFilePath>\n \t\t\t<identifierParseRule>>([^\\s]*)</identifierParseRule>\n \t\t\t<descriptionParseRule>>(.*)</descriptionParseRule>\n \t\t\t<taxonomyParseRule/>\n@@ -19,8 +19,6 @@\n \t<andromedaCacheSize>350000</andromedaCacheSize>\n \t<advancedRatios>True</advancedRatios>\n \t<pvalThres>0.005</pvalThres>\n-\t<neucodeRatioBasedQuantification>False</neucodeRatioBasedQuantification>\n-\t<neucodeStabilizeLargeRatios>False</neucodeStabilizeLargeRatios>\n \t<rtShift>False</rtShift>\n \t<separateLfq>False</separateLfq>\n \t<lfqStabilizeLargeRatios>True</lfqStabilizeLargeRatios>\n@@ -48,7 +46,6 @@\n \t<dependentPeptidesWithinParameterGroup>False</dependentPeptidesWithinParameterGroup>\n \t<dependentPeptidesRestrictFractions>False</dependentPeptidesRestrictFractions>\n \t<dependentPeptidesFractionDifference>0</dependentPeptidesFractionDifference>\n-\t<msmsConnection>False</msmsConnection>\n \t<ibaq>False</ibaq>\n \t<top3>False</top3>\n \t<independentEnzymes>False</independentEnzymes>\n@@ -100,10 +97,11 @@\n \t<writeMsScansTable>False</writeMsScansTable>\n \t<writeMsmsScansTable>True</writeMsmsScansTable>\n \t<writePasefMsmsScansTable>True</writePasefMsmsScansTable>\n-\t<writeAccumulatedPasefMsmsScansTable>True</writeAccumulatedPasefMsmsScansTable>\n+\t<writeAccumulatedPasefMsmsScansTable>False</writeAccumulatedPasefMsmsScansTable>\n \t<writeMs3ScansTable>True</writeMs3ScansTable>\n \t<writeAllPeptidesTable>True</writeAllPeptidesTable>\n \t<writeMzRangeTable>True</writeMzRangeTable>\n+\t<writeDiaFragmentTable>False</writeDiaFragmentTable>\n \t<writeMzTab>True</writeMzTab>\n \t<disableMd5>False</disableMd5>\n \t<cacheBinInds>True</cacheBinInds>\n@@ -114,10 +112,10 @@\n \t<variationMode>none</variationMode>\n \t<useSeriesReporters>False</useSeriesReporters>\n \t<name>templateSession</name>\n-\t<maxQuantVersion>1.6.10.43</maxQuantVersion>\n-\t<tempFolder/>\n+\t<maxQuantVersion>1.6.17.0</maxQuantVersion>\n \t<pluginFolder/>\n \t<numThreads>1</numThreads>\n+\t<batchSize>1</batchSize>\n \t<emailAddress/>\n \t<smtpHost/>\n \t<emailFromAddress/>\n@@ -130,10 +128,11 @@\n \t<calcPeakProperties>False</calcPeakProperties>\n \t<showCentroidMassDifferences>False</showCentroidMassDifferences>\n \t<showIsotopeMassDifferences>False</showIsotopeMassDifferences>\n-\t<useDotNetCore>False</useDotNetCore>\n+\t<useDotNetCore>True</useDotNetCore>\n+\t<profilePerformance>False</profilePerformance>\n \t<filePaths>\n-\t\t<string>/tmp/tmp0wswhy4o/job_working_directory/000/4/working/BSA_min_23.mzXML</string>\n-\t\t<string>/tmp/tmp0wswhy4o/job_working_directory/000/4/working/BSA_min_22.mzxml</string>\n+\t\t<string>/tmp/tmpyzym30dx/job_working_directory/000/11/working/BSA_min_23.mzXML</string>\n+\t\t<string>/tmp/tmpyzym30dx/job_working_directory/000/11/working/BSA_min_22.mzxml</string>\n \t</filePaths>\n \t<experiments>\n \t\t<string>BSA_min_23.mzXML</string>\n@@ -157,12 +156,13 @@\n \t</referenceChannel>\n \t<intensPred>False</intensPred>\n \t<intensPredModelReTrain>False</intensPredModelReTrain>\n+\t<lfqTopNPeptides>0</lfqTopNPeptides>\n \t<parameterGroups>\n \t\t<parameterGroup>\n \t\t\t<msInstrument>0</msInstrument>\n \t\t\t<maxCharge>7</maxCharge>\n \t\t\t<minPeakLen>2</minPeakLen>\n-\t\t\t<diaMinPeakLen>2</diaMinPeakLen>\n+\t\t\t<diaMinPeakLen>1</diaMinPeakLen>\n \t\t\t<useMs1Centroids>False</useMs1Centroids>\n \t\t\t<useMs2Centroids>False</useMs2Centroids>\n \t\t\t<cutPeaks>True</cutPeaks>\n@@ -178,14 +178,15 @@\n \t\t\t<valleyFactor>1.4</valleyFactor>\n \t\t\t<isotopeValleyFactor>1.2</isotopeValleyFactor>\n \t\t\t<advancedPeakSplitting>False</advancedPeakSplitting>\n-\t\t\t<intensityThreshold>0</intensityThreshold>\n+\t\t\t<intensityThresholdMs1>0</intensityThresholdMs1>\n+\t\t\t<intensityThresholdMs2>0</intensityThresholdMs2>\n \t\t\t<labelMods>\n \t\t\t\t<string/>\n \t\t\t</labelMods>\n \t\t\t<lcmsRunType>Reporter ion MS3</lcmsRunType>\n \t\t\t<reQuantify>False</reQuantify>\n \t\t\t<lfqMode>0'..b'iaBackgroundSubtraction>False</diaBackgroundSubtraction>\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</parameterGroup>\n \t\t<parameterGroup>\n \t\t\t<msInstrument>0</msInstrument>\n \t\t\t<maxCharge>7</maxCharge>\n \t\t\t<minPeakLen>2</minPeakLen>\n-\t\t\t<diaMinPeakLen>2</diaMinPeakLen>\n+\t\t\t<diaMinPeakLen>1</diaMinPeakLen>\n \t\t\t<useMs1Centroids>False</useMs1Centroids>\n \t\t\t<useMs2Centroids>False</useMs2Centroids>\n \t\t\t<cutPeaks>True</cutPeaks>\n@@ -336,14 +366,15 @@\n \t\t\t<valleyFactor>1.4</valleyFactor>\n \t\t\t<isotopeValleyFactor>1.2</isotopeValleyFactor>\n \t\t\t<advancedPeakSplitting>False</advancedPeakSplitting>\n-\t\t\t<intensityThreshold>0</intensityThreshold>\n+\t\t\t<intensityThresholdMs1>0</intensityThresholdMs1>\n+\t\t\t<intensityThresholdMs2>0</intensityThresholdMs2>\n \t\t\t<labelMods>\n \t\t\t\t<string/>\n \t\t\t</labelMods>\n \t\t\t<lcmsRunType>Reporter ion MS3</lcmsRunType>\n \t\t\t<reQuantify>False</reQuantify>\n \t\t\t<lfqMode>0</lfqMode>\n-\t\t\t<lfqSkipNorm>False</lfqSkipNorm>\n+\t\t\t<lfqNormClusterSize>80</lfqNormClusterSize>\n \t\t\t<lfqMinEdgesPerNode>3</lfqMinEdgesPerNode>\n \t\t\t<lfqAvEdgesPerNode>6</lfqAvEdgesPerNode>\n \t\t\t<lfqMaxFeatures>100000</lfqMaxFeatures>\n@@ -449,7 +480,7 @@\n \t\t\t<timsRemovePrecursor>True</timsRemovePrecursor>\n \t\t\t<timsIsobaricLabels>False</timsIsobaricLabels>\n \t\t\t<timsCollapseMsms>True</timsCollapseMsms>\n-\t\t\t<crosslinkSearch>False</crosslinkSearch>\n+\t\t\t<crossLinkingType>0</crossLinkingType>\n \t\t\t<crossLinker/>\n \t\t\t<minMatchXl>0</minMatchXl>\n \t\t\t<minPairedPepLenXl>6</minPairedPepLenXl>\n@@ -471,7 +502,8 @@\n \t\t\t<isobaricSumOverWindow>True</isobaricSumOverWindow>\n \t\t\t<isobaricWeightExponent>0.75</isobaricWeightExponent>\n \t\t\t<diaLibraryType>0</diaLibraryType>\n-\t\t\t<diaLibraryPath/>\n+\t\t\t<diaLibraryPaths>\n+ </diaLibraryPaths>\n \t\t\t<diaPeptidePaths>\n </diaPeptidePaths>\n \t\t\t<diaEvidencePaths>\n@@ -484,9 +516,37 @@\n \t\t\t<diaPrecTolPpmFeatureClustering>2</diaPrecTolPpmFeatureClustering>\n \t\t\t<diaFragTolPpmFeatureClustering>2</diaFragTolPpmFeatureClustering>\n \t\t\t<diaScoreN>7</diaScoreN>\n-\t\t\t<diaMinScore>2.99</diaMinScore>\n-\t\t\t<diaPrecursorQuant>False</diaPrecursorQuant>\n-\t\t\t<diaDiaTopNFragmentsForQuant>3</diaDiaTopNFragmentsForQuant>\n+\t\t\t<diaMinScore>1.99</diaMinScore>\n+\t\t\t<diaXgBoostBaseScore>0.4</diaXgBoostBaseScore>\n+\t\t\t<diaXgBoostSubSample>0.9</diaXgBoostSubSample>\n+\t\t\t<centroidPosition>0</centroidPosition>\n+\t\t\t<diaQuantMethod>7</diaQuantMethod>\n+\t\t\t<diaFeatureQuantMethod>2</diaFeatureQuantMethod>\n+\t\t\t<lfqNormType>1</lfqNormType>\n+\t\t\t<diaTopNForQuant>10</diaTopNForQuant>\n+\t\t\t<diaMinMsmsIntensityForQuant>0</diaMinMsmsIntensityForQuant>\n+\t\t\t<diaTopMsmsIntensityQuantileForQuant>0.85</diaTopMsmsIntensityQuantileForQuant>\n+\t\t\t<diaPrecursorFilterType>0</diaPrecursorFilterType>\n+\t\t\t<diaMinFragmentOverlapScore>1</diaMinFragmentOverlapScore>\n+\t\t\t<diaMinPrecursorScore>0.5</diaMinPrecursorScore>\n+\t\t\t<diaMinProfileCorrelation>0</diaMinProfileCorrelation>\n+\t\t\t<diaXgBoostMinChildWeight>9</diaXgBoostMinChildWeight>\n+\t\t\t<diaXgBoostMaximumTreeDepth>12</diaXgBoostMaximumTreeDepth>\n+\t\t\t<diaXgBoostEstimators>580</diaXgBoostEstimators>\n+\t\t\t<diaXgBoostGamma>0.9</diaXgBoostGamma>\n+\t\t\t<diaXgBoostMaxDeltaStep>3</diaXgBoostMaxDeltaStep>\n+\t\t\t<diaGlobalMl>True</diaGlobalMl>\n+\t\t\t<diaAdaptiveMassAccuracy>False</diaAdaptiveMassAccuracy>\n+\t\t\t<diaMassWindowFactor>3.3</diaMassWindowFactor>\n+\t\t\t<diaRtPrediction>False</diaRtPrediction>\n+\t\t\t<diaRtPredictionSecondRound>False</diaRtPredictionSecondRound>\n+\t\t\t<diaNoMl>False</diaNoMl>\n+\t\t\t<diaPermuteRt>False</diaPermuteRt>\n+\t\t\t<diaPermuteCcs>False</diaPermuteCcs>\n+\t\t\t<diaBackgroundSubtraction>False</diaBackgroundSubtraction>\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</parameterGroup>\n \t</parameterGroups>\n \t<msmsParamsArray>\n' |
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| diff -r d72c96ad9a16 -r 0839f84def5e test-data/07/combined/txt/report_v1.0.9_combined.pdf |
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| diff -r d72c96ad9a16 -r 0839f84def5e test-data/07/config.yml --- a/test-data/07/config.yml Tue Jun 15 07:55:59 2021 +0000 +++ b/test-data/07/config.yml Sun Jun 20 16:37:41 2021 +0000 |
| [ |
| @@ -24,7 +24,7 @@ restrictMods: [Oxidation (M),Acetyl (Protein N-term)] useCounterparts: True paramGroups: - - files: ['ptxqc.mzXML'] + - files: ['tmt_data.mzXML'] maxMissedCleavages: 2 fixedModifications: [] variableModifications: [Oxidation (M)] |
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| diff -r d72c96ad9a16 -r 0839f84def5e test-data/07/mqpar.xml --- a/test-data/07/mqpar.xml Tue Jun 15 07:55:59 2021 +0000 +++ b/test-data/07/mqpar.xml Sun Jun 20 16:37:41 2021 +0000 |
| [ |
| @@ -2,7 +2,7 @@ <MaxQuantParams> <fastaFiles> <FastaFileInfo> - <fastaFilePath>/tmp/tmpfqvn4g0u/files/5/b/8/dataset_5b803772-27b2-44fa-a4cf-8da6ee3cdfb8.dat</fastaFilePath> + <fastaFilePath>/tmp/tmpojxmxo_4/files/2/d/f/dataset_2df03e43-042c-483e-9a8a-ad29add25dbd.dat</fastaFilePath> <identifierParseRule>>([^\s]*)</identifierParseRule> <descriptionParseRule>>(.*)</descriptionParseRule> <taxonomyParseRule/> @@ -19,8 +19,6 @@ <andromedaCacheSize>350000</andromedaCacheSize> <advancedRatios>True</advancedRatios> <pvalThres>0.005</pvalThres> - <neucodeRatioBasedQuantification>False</neucodeRatioBasedQuantification> - <neucodeStabilizeLargeRatios>False</neucodeStabilizeLargeRatios> <rtShift>False</rtShift> <separateLfq>False</separateLfq> <lfqStabilizeLargeRatios>True</lfqStabilizeLargeRatios> @@ -48,7 +46,6 @@ <dependentPeptidesWithinParameterGroup>False</dependentPeptidesWithinParameterGroup> <dependentPeptidesRestrictFractions>False</dependentPeptidesRestrictFractions> <dependentPeptidesFractionDifference>0</dependentPeptidesFractionDifference> - <msmsConnection>False</msmsConnection> <ibaq>False</ibaq> <top3>False</top3> <independentEnzymes>False</independentEnzymes> @@ -100,11 +97,12 @@ <writeMsScansTable>False</writeMsScansTable> <writeMsmsScansTable>True</writeMsmsScansTable> <writePasefMsmsScansTable>True</writePasefMsmsScansTable> - <writeAccumulatedPasefMsmsScansTable>True</writeAccumulatedPasefMsmsScansTable> + <writeAccumulatedPasefMsmsScansTable>False</writeAccumulatedPasefMsmsScansTable> <writeMs3ScansTable>True</writeMs3ScansTable> <writeAllPeptidesTable>True</writeAllPeptidesTable> <writeMzRangeTable>True</writeMzRangeTable> - <writeMzTab>True</writeMzTab> + <writeDiaFragmentTable>False</writeDiaFragmentTable> + <writeMzTab>False</writeMzTab> <disableMd5>False</disableMd5> <cacheBinInds>True</cacheBinInds> <etdIncludeB>False</etdIncludeB> @@ -114,10 +112,10 @@ <variationMode>none</variationMode> <useSeriesReporters>False</useSeriesReporters> <name>templateSession</name> - <maxQuantVersion>1.6.10.43</maxQuantVersion> - <tempFolder/> + <maxQuantVersion>1.6.17.0</maxQuantVersion> <pluginFolder/> <numThreads>1</numThreads> + <batchSize>1</batchSize> <emailAddress/> <smtpHost/> <emailFromAddress/> @@ -130,12 +128,13 @@ <calcPeakProperties>False</calcPeakProperties> <showCentroidMassDifferences>False</showCentroidMassDifferences> <showIsotopeMassDifferences>False</showIsotopeMassDifferences> - <useDotNetCore>False</useDotNetCore> + <useDotNetCore>True</useDotNetCore> + <profilePerformance>False</profilePerformance> <filePaths> - <string>/tmp/tmpfqvn4g0u/job_working_directory/000/3/working/ptxqc_test3.mzXML</string> + <string>/tmp/tmpojxmxo_4/job_working_directory/000/6/working/tmt_data.mzXML</string> </filePaths> <experiments> - <string>ptxqc_test3.mzXML</string> + <string>tmt_data.mzXML</string> </experiments> <fractions> <short>32767</short> @@ -151,12 +150,13 @@ </referenceChannel> <intensPred>False</intensPred> <intensPredModelReTrain>False</intensPredModelReTrain> + <lfqTopNPeptides>0</lfqTopNPeptides> <parameterGroups> <parameterGroup> <msInstrument>0</msInstrument> <maxCharge>7</maxCharge> <minPeakLen>2</minPeakLen> - <diaMinPeakLen>2</diaMinPeakLen> + <diaMinPeakLen>1</diaMinPeakLen> <useMs1Centroids>False</useMs1Centroids> <useMs2Centroids>False</useMs2Centroids> <cutPeaks>True</cutPeaks> @@ -172,14 +172,15 @@ <valleyFactor>1.4</valleyFactor> <isotopeValleyFactor>1.2</isotopeValleyFactor> <advancedPeakSplitting>False</advancedPeakSplitting> - <intensityThreshold>0</intensityThreshold> + <intensityThresholdMs1>0</intensityThresholdMs1> + <intensityThresholdMs2>0</intensityThresholdMs2> <labelMods> <string/> </labelMods> <lcmsRunType>Reporter ion MS2</lcmsRunType> <reQuantify>False</reQuantify> <lfqMode>0</lfqMode> - <lfqSkipNorm>False</lfqSkipNorm> + <lfqNormClusterSize>80</lfqNormClusterSize> <lfqMinEdgesPerNode>3</lfqMinEdgesPerNode> <lfqAvEdgesPerNode>6</lfqAvEdgesPerNode> <lfqMaxFeatures>100000</lfqMaxFeatures> @@ -343,7 +344,7 @@ <timsRemovePrecursor>True</timsRemovePrecursor> <timsIsobaricLabels>False</timsIsobaricLabels> <timsCollapseMsms>True</timsCollapseMsms> - <crosslinkSearch>False</crosslinkSearch> + <crossLinkingType>0</crossLinkingType> <crossLinker/> <minMatchXl>0</minMatchXl> <minPairedPepLenXl>6</minPairedPepLenXl> @@ -365,7 +366,8 @@ <isobaricSumOverWindow>True</isobaricSumOverWindow> <isobaricWeightExponent>0.75</isobaricWeightExponent> <diaLibraryType>0</diaLibraryType> - <diaLibraryPath/> + <diaLibraryPaths> + </diaLibraryPaths> <diaPeptidePaths> </diaPeptidePaths> <diaEvidencePaths> @@ -378,9 +380,37 @@ <diaPrecTolPpmFeatureClustering>2</diaPrecTolPpmFeatureClustering> <diaFragTolPpmFeatureClustering>2</diaFragTolPpmFeatureClustering> <diaScoreN>7</diaScoreN> - <diaMinScore>2.99</diaMinScore> - <diaPrecursorQuant>False</diaPrecursorQuant> - <diaDiaTopNFragmentsForQuant>3</diaDiaTopNFragmentsForQuant> + <diaMinScore>1.99</diaMinScore> + <diaXgBoostBaseScore>0.4</diaXgBoostBaseScore> + <diaXgBoostSubSample>0.9</diaXgBoostSubSample> + <centroidPosition>0</centroidPosition> + <diaQuantMethod>7</diaQuantMethod> + <diaFeatureQuantMethod>2</diaFeatureQuantMethod> + <lfqNormType>1</lfqNormType> + <diaTopNForQuant>10</diaTopNForQuant> + <diaMinMsmsIntensityForQuant>0</diaMinMsmsIntensityForQuant> + <diaTopMsmsIntensityQuantileForQuant>0.85</diaTopMsmsIntensityQuantileForQuant> + <diaPrecursorFilterType>0</diaPrecursorFilterType> + <diaMinFragmentOverlapScore>1</diaMinFragmentOverlapScore> + <diaMinPrecursorScore>0.5</diaMinPrecursorScore> + <diaMinProfileCorrelation>0</diaMinProfileCorrelation> + <diaXgBoostMinChildWeight>9</diaXgBoostMinChildWeight> + <diaXgBoostMaximumTreeDepth>12</diaXgBoostMaximumTreeDepth> + <diaXgBoostEstimators>580</diaXgBoostEstimators> + <diaXgBoostGamma>0.9</diaXgBoostGamma> + <diaXgBoostMaxDeltaStep>3</diaXgBoostMaxDeltaStep> + <diaGlobalMl>True</diaGlobalMl> + <diaAdaptiveMassAccuracy>False</diaAdaptiveMassAccuracy> + <diaMassWindowFactor>3.3</diaMassWindowFactor> + <diaRtPrediction>False</diaRtPrediction> + <diaRtPredictionSecondRound>False</diaRtPredictionSecondRound> + <diaNoMl>False</diaNoMl> + <diaPermuteRt>False</diaPermuteRt> + <diaPermuteCcs>False</diaPermuteCcs> + <diaBackgroundSubtraction>False</diaBackgroundSubtraction> + <diaBackgroundSubtractionQuantile>0.5</diaBackgroundSubtractionQuantile> + <diaBackgroundSubtractionFactor>4</diaBackgroundSubtractionFactor> + <diaLfqWeightedMedian>False</diaLfqWeightedMedian> </parameterGroup> </parameterGroups> <msmsParamsArray> |
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| diff -r d72c96ad9a16 -r 0839f84def5e test-data/08/combined/txt/proteinGroups.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/08/combined/txt/proteinGroups.txt Sun Jun 20 16:37:41 2021 +0000 |
| [ |
| @@ -0,0 +1,7 @@ +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 tmt_data.mzXML Razor + unique peptides tmt_data.mzXML Unique peptides tmt_data.mzXML Sequence coverage [%] Unique + razor sequence coverage [%] Unique sequence coverage [%] Mol. weight [kDa] Sequence length Sequence lengths Q-value Score Reporter intensity corrected 1 tmt_data.mzXML Reporter intensity corrected 2 tmt_data.mzXML Reporter intensity corrected 3 tmt_data.mzXML Reporter intensity corrected 4 tmt_data.mzXML Reporter intensity corrected 5 tmt_data.mzXML Reporter intensity corrected 6 tmt_data.mzXML Reporter intensity corrected 7 tmt_data.mzXML Reporter intensity corrected 8 tmt_data.mzXML Reporter intensity corrected 9 tmt_data.mzXML Reporter intensity corrected 10 tmt_data.mzXML Reporter intensity corrected 11 tmt_data.mzXML Reporter intensity corrected 12 tmt_data.mzXML Reporter intensity corrected 13 tmt_data.mzXML Reporter intensity corrected 14 tmt_data.mzXML Reporter intensity corrected 15 tmt_data.mzXML Reporter intensity corrected 16 tmt_data.mzXML Reporter intensity 1 tmt_data.mzXML Reporter intensity 2 tmt_data.mzXML Reporter intensity 3 tmt_data.mzXML Reporter intensity 4 tmt_data.mzXML Reporter intensity 5 tmt_data.mzXML Reporter intensity 6 tmt_data.mzXML Reporter intensity 7 tmt_data.mzXML Reporter intensity 8 tmt_data.mzXML Reporter intensity 9 tmt_data.mzXML Reporter intensity 10 tmt_data.mzXML Reporter intensity 11 tmt_data.mzXML Reporter intensity 12 tmt_data.mzXML Reporter intensity 13 tmt_data.mzXML Reporter intensity 14 tmt_data.mzXML Reporter intensity 15 tmt_data.mzXML Reporter intensity 16 tmt_data.mzXML Reporter intensity count 1 tmt_data.mzXML Reporter intensity count 2 tmt_data.mzXML Reporter intensity count 3 tmt_data.mzXML Reporter intensity count 4 tmt_data.mzXML Reporter intensity count 5 tmt_data.mzXML Reporter intensity count 6 tmt_data.mzXML Reporter intensity count 7 tmt_data.mzXML Reporter intensity count 8 tmt_data.mzXML Reporter intensity count 9 tmt_data.mzXML Reporter intensity count 10 tmt_data.mzXML Reporter intensity count 11 tmt_data.mzXML Reporter intensity count 12 tmt_data.mzXML Reporter intensity count 13 tmt_data.mzXML Reporter intensity count 14 tmt_data.mzXML Reporter intensity count 15 tmt_data.mzXML Reporter intensity count 16 tmt_data.mzXML Sequence coverage tmt_data.mzXML [%] Intensity Intensity tmt_data.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 6 0 0 5121.2 220760 202180 225830 200210 259320 246570 233570 148280 4478.8 0 0 0 0 0 0 5121.2 220760 202180 225830 200210 259320 246570 233570 148280 4478.8 0 0 0 0 0 0 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0.8 99228000 99228000 1 + 0 2 True 2 2 2 2 -1 +sp|A6NKP2|D42E2_HUMAN sp|A6NKP2|D42E2_HUMAN 1 1 1 sp|A6NKP2|D42E2_HUMAN Putative short-chain dehydrogenase/reductase family 42E member 2 OS=Homo sapiens OX=9606 GN=SDR42E2 PE=3 SV=3 1 1 1 1 1 1 1 2.6 2.6 2.6 46.869 422 422 0 6 0 3941.4 4062.3 178440 117220 94899 131440 159880 91982 74974 76646 3167.4 940.58 0 0 0 0 3941.4 4062.3 178440 117220 94899 131440 159880 91982 74974 76646 3167.4 940.58 0 0 0 0 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 2.6 43797000 43797000 1 1 5 True 5 5 5 5 -1 +sp|Q32M88|PGGHG_HUMAN sp|Q32M88|PGGHG_HUMAN 1 1 1 sp|Q32M88|PGGHG_HUMAN Protein-glucosylgalactosylhydroxylysine glucosidase OS=Homo sapiens OX=9606 GN=PGGHG PE=1 SV=2 1 1 1 1 1 1 1 0.9 0.9 0.9 80.654 737 737 0 6 0 0 4057.5 92629 91851 99927 106520 117440 118770 118100 124330 3555.6 2741.6 0 0 0 0 0 4057.5 92629 91851 99927 106520 117440 118770 118100 124330 3555.6 2741.6 0 0 0 0 0 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0.9 11999000 11999000 1 2 1 True 1 1 1 1 -1 +sp|Q8IXT5|RB12B_HUMAN sp|Q8IXT5|RB12B_HUMAN 1 1 1 sp|Q8IXT5|RB12B_HUMAN RNA-binding protein 12B OS=Homo sapiens OX=9606 GN=RBM12B PE=1 SV=2 1 1 1 1 1 1 1 0.7 0.7 0.7 118.1 1001 1001 0 6 0 0 2539.1 96839 103090 105560 92520 63071 68162 70636 42876 0 0 0 0 0 0 0 2539.1 96839 103090 105560 92520 63071 68162 70636 42876 0 0 0 0 0 0 0 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0.7 53433000 53433000 1 3 0 True 0 0 0 0 -1 +sp|Q8N782|ZN525_HUMAN sp|Q8N782|ZN525_HUMAN 1 1 1 sp|Q8N782|ZN525_HUMAN Zinc finger protein 525 OS=Homo sapiens OX=9606 GN=ZNF525 PE=2 SV=2 1 1 1 1 1 1 1 4.6 4.6 4.6 23.07 197 197 0 6 0 1694.6 6271.6 277230 244210 164300 288610 344230 225420 253930 201720 11497 6283.4 0 0 0 0 1694.6 6271.6 277230 244210 164300 288610 344230 225420 253930 201720 11497 6283.4 0 0 0 0 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 4.6 365510000 365510000 1 4 4 True 4 4 4 4 -1 +sp|Q9UBQ7|GRHPR_HUMAN sp|Q9UBQ7|GRHPR_HUMAN 1 1 1 sp|Q9UBQ7|GRHPR_HUMAN Glyoxylate reductase/hydroxypyruvate reductase OS=Homo sapiens OX=9606 GN=GRHPR PE=1 SV=1 1 1 1 1 1 1 1 2.4 2.4 2.4 35.668 328 328 0 6 0 0 4516.6 233890 211220 199740 210150 244750 222310 227650 177190 5951.5 4942.8 0 0 0 0 0 4516.6 233890 211220 199740 210150 244750 222310 227650 177190 5951.5 4942.8 0 0 0 0 0 1 1 1 1 1 1 1 1 1 1 1 0 0 0 2.4 30472000 30472000 1 5 3 True 3 3 3 3 -1 |
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| diff -r d72c96ad9a16 -r 0839f84def5e test-data/08/config.yml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/08/config.yml Sun Jun 20 16:37:41 2021 +0000 |
| [ |
| @@ -0,0 +1,58 @@ + + fastaFiles: [/tmp/tmpd7w978vs/files/0/f/c/dataset_0fc77a17-694f-4046-a911-98d071f76050.dat] + parseRules: + identifierParseRule: '>([^\s]*)' + descriptionParseRule: '>(.*)' + minUniquePeptides: 0 + minPepLen: 7 + maxPeptideMass: 4600 + calcPeakProperties: False + writeMzTab: False + separateLfq: False + lfqStabilizeLargeRatios: True + lfqRequireMsms: True + advancedSiteIntensities: True + matchBetweenRuns: False + includeContaminants: True + minPeptideLengthForUnspecificSearch: 8 + maxPeptideLengthForUnspecificSearch: 25 + decoyMode: revert + peptideFdr: 0.01 + proteinFdr: 0.01 + quantMode: 1 + restrictProteinQuantification: True + restrictMods: [Oxidation (M),Acetyl (Protein N-term)] + useCounterparts: True + paramGroups: + - files: ['tmt_data.mzXML'] + maxMissedCleavages: 2 + fixedModifications: [] + variableModifications: [Oxidation (M)] + enzymes: [Trypsin/P] + enzymeMode: 0 + lcmsRunType: 'Reporter ion MS2' + reporterMassTolerance: 0.003 + reporterPif: 0 + reporterFraction: 0 + reporterBasePeakRatio: 0 + filterPif: False + isobaricLabels: + + - [TMTpro16plex-Lys127N,TMTpro16plex-Nter127N,0,0,0,0,True] + - [TMTpro16plex-Lys127C,TMTpro16plex-Nter127C,0,0,0,0,True] + - [TMTpro16plex-Lys128N,TMTpro16plex-Nter128N,0,0,0,0,True] + - [TMTpro16plex-Lys128C,TMTpro16plex-Nter128C,0,0,0,0,True] + - [TMTpro16plex-Lys129N,TMTpro16plex-Nter129N,0,0,0,0,True] + - [TMTpro16plex-Lys129C,TMTpro16plex-Nter129C,0,0,0,0,True] + - [TMTpro16plex-Lys130N,TMTpro16plex-Nter130N,0,0,0,0,True] + - [TMTpro16plex-Lys130C,TMTpro16plex-Nter130C,0,0,0,0,True] + - [TMTpro16plex-Lys131N,TMTpro16plex-Nter131N,0,0,0,0,True] + - [TMTpro16plex-Lys131C,TMTpro16plex-Nter131C,0,0,0,0,True] + - [TMTpro16plex-Lys132N,TMTpro16plex-Nter132N,0,0,0,0,True] + - [TMTpro16plex-Lys132C,TMTpro16plex-Nter132C,0,0,0,0,True] + - [TMTpro16plex-Lys133N,TMTpro16plex-Nter133N,0,0,0,0,True] + - [TMTpro16plex-Lys133C,TMTpro16plex-Nter133C,0,0,0,0,True] + - [TMTpro16plex-Lys134N,TMTpro16plex-Nter134N,0,0,0,0,True] + - [TMTpro16plex-Lys126C,TMTpro16plex-Nter126C,0,0,0,0,True] + + \ No newline at end of file |
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| diff -r d72c96ad9a16 -r 0839f84def5e test-data/08/mqpar.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/08/mqpar.xml Sun Jun 20 16:37:41 2021 +0000 |
| [ |
| b'@@ -0,0 +1,623 @@\n+<?xml version="1.0" ?>\n+<MaxQuantParams>\n+\t<fastaFiles>\n+\t\t<FastaFileInfo>\n+\t\t\t<fastaFilePath>/tmp/tmpd7w978vs/files/0/f/c/dataset_0fc77a17-694f-4046-a911-98d071f76050.dat</fastaFilePath>\n+\t\t\t<identifierParseRule>>([^\\s]*)</identifierParseRule>\n+\t\t\t<descriptionParseRule>>(.*)</descriptionParseRule>\n+\t\t\t<taxonomyParseRule/>\n+\t\t\t<variationParseRule/>\n+\t\t\t<modificationParseRule/>\n+\t\t\t<taxonomyId/>\n+\t\t</FastaFileInfo>\n+\t</fastaFiles>\n+\t<fastaFilesProteogenomics>\n+ </fastaFilesProteogenomics>\n+\t<fastaFilesFirstSearch>\n+ </fastaFilesFirstSearch>\n+\t<fixedSearchFolder/>\n+\t<andromedaCacheSize>350000</andromedaCacheSize>\n+\t<advancedRatios>True</advancedRatios>\n+\t<pvalThres>0.005</pvalThres>\n+\t<rtShift>False</rtShift>\n+\t<separateLfq>False</separateLfq>\n+\t<lfqStabilizeLargeRatios>True</lfqStabilizeLargeRatios>\n+\t<lfqRequireMsms>True</lfqRequireMsms>\n+\t<decoyMode>revert</decoyMode>\n+\t<boxCarMode>all</boxCarMode>\n+\t<includeContaminants>True</includeContaminants>\n+\t<maxPeptideMass>4600</maxPeptideMass>\n+\t<epsilonMutationScore>True</epsilonMutationScore>\n+\t<mutatedPeptidesSeparately>True</mutatedPeptidesSeparately>\n+\t<proteogenomicPeptidesSeparately>True</proteogenomicPeptidesSeparately>\n+\t<minDeltaScoreUnmodifiedPeptides>0</minDeltaScoreUnmodifiedPeptides>\n+\t<minDeltaScoreModifiedPeptides>6</minDeltaScoreModifiedPeptides>\n+\t<minScoreUnmodifiedPeptides>0</minScoreUnmodifiedPeptides>\n+\t<minScoreModifiedPeptides>40</minScoreModifiedPeptides>\n+\t<secondPeptide>True</secondPeptide>\n+\t<matchBetweenRuns>False</matchBetweenRuns>\n+\t<matchUnidentifiedFeatures>False</matchUnidentifiedFeatures>\n+\t<matchBetweenRunsFdr>False</matchBetweenRunsFdr>\n+\t<dependentPeptides>False</dependentPeptides>\n+\t<dependentPeptideFdr>0</dependentPeptideFdr>\n+\t<dependentPeptideMassBin>0</dependentPeptideMassBin>\n+\t<dependentPeptidesBetweenRuns>False</dependentPeptidesBetweenRuns>\n+\t<dependentPeptidesWithinExperiment>False</dependentPeptidesWithinExperiment>\n+\t<dependentPeptidesWithinParameterGroup>False</dependentPeptidesWithinParameterGroup>\n+\t<dependentPeptidesRestrictFractions>False</dependentPeptidesRestrictFractions>\n+\t<dependentPeptidesFractionDifference>0</dependentPeptidesFractionDifference>\n+\t<ibaq>False</ibaq>\n+\t<top3>False</top3>\n+\t<independentEnzymes>False</independentEnzymes>\n+\t<useDeltaScore>False</useDeltaScore>\n+\t<splitProteinGroupsByTaxonomy>False</splitProteinGroupsByTaxonomy>\n+\t<taxonomyLevel>Species</taxonomyLevel>\n+\t<avalon>False</avalon>\n+\t<nModColumns>3</nModColumns>\n+\t<ibaqLogFit>False</ibaqLogFit>\n+\t<razorProteinFdr>True</razorProteinFdr>\n+\t<deNovoSequencing>False</deNovoSequencing>\n+\t<deNovoVarMods>True</deNovoVarMods>\n+\t<massDifferenceSearch>False</massDifferenceSearch>\n+\t<isotopeCalc>False</isotopeCalc>\n+\t<writePeptidesForSpectrumFile/>\n+\t<intensityPredictionsFile>\n+ </intensityPredictionsFile>\n+\t<minPepLen>7</minPepLen>\n+\t<psmFdrCrosslink>0.01</psmFdrCrosslink>\n+\t<peptideFdr>0.01</peptideFdr>\n+\t<proteinFdr>0.01</proteinFdr>\n+\t<siteFdr>0.01</siteFdr>\n+\t<minPeptideLengthForUnspecificSearch>8</minPeptideLengthForUnspecificSearch>\n+\t<maxPeptideLengthForUnspecificSearch>25</maxPeptideLengthForUnspecificSearch>\n+\t<useNormRatiosForOccupancy>True</useNormRatiosForOccupancy>\n+\t<minPeptides>1</minPeptides>\n+\t<minRazorPeptides>1</minRazorPeptides>\n+\t<minUniquePeptides>0</minUniquePeptides>\n+\t<useCounterparts>True</useCounterparts>\n+\t<advancedSiteIntensities>True</advancedSiteIntensities>\n+\t<customProteinQuantification>False</customProteinQuantification>\n+\t<customProteinQuantificationFile/>\n+\t<minRatioCount>2</minRatioCount>\n+\t<restrictProteinQuantification>True</restrictProteinQuantification>\n+\t<restrictMods>\n+\t\t<string>Oxidation (M)</string>\n+\t\t<string>Acetyl (Protein N-term)</string>\n+\t</restrictMods>\n+\t<matchingTimeWindow>0</matchingTimeWindow>\n+\t<matchingIonMobilityWindow>0</matchingIonMobilityWindow>\n+\t<alignmentTimeWindow>0</alignmentTimeWindow>\n+\t<alignmentIonMobilityWindow>0</alignmentIonMobilityWindow>\n+\t<numberOfCand'..b'<IncludeWater>True</IncludeWater>\n+\t\t\t<IncludeAmmonia>True</IncludeAmmonia>\n+\t\t\t<DependentLosses>True</DependentLosses>\n+\t\t\t<Recalibration>False</Recalibration>\n+\t\t</msmsParams>\n+\t\t<msmsParams>\n+\t\t\t<Name>Unknown</Name>\n+\t\t\t<MatchTolerance>20</MatchTolerance>\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<DeNovoToleranceInPpm>True</DeNovoToleranceInPpm>\n+\t\t\t<Deisotope>True</Deisotope>\n+\t\t\t<Topx>12</Topx>\n+\t\t\t<TopxInterval>100</TopxInterval>\n+\t\t\t<HigherCharges>True</HigherCharges>\n+\t\t\t<IncludeWater>True</IncludeWater>\n+\t\t\t<IncludeAmmonia>True</IncludeAmmonia>\n+\t\t\t<DependentLosses>True</DependentLosses>\n+\t\t\t<Recalibration>False</Recalibration>\n+\t\t</msmsParams>\n+\t</msmsParamsArray>\n+\t<fragmentationParamsArray>\n+\t\t<fragmentationParams>\n+\t\t\t<Name>CID</Name>\n+\t\t\t<Connected>False</Connected>\n+\t\t\t<ConnectedScore0>1</ConnectedScore0>\n+\t\t\t<ConnectedScore1>1</ConnectedScore1>\n+\t\t\t<ConnectedScore2>1</ConnectedScore2>\n+\t\t\t<InternalFragments>False</InternalFragments>\n+\t\t\t<InternalFragmentWeight>1</InternalFragmentWeight>\n+\t\t\t<InternalFragmentAas>KRH</InternalFragmentAas>\n+\t\t</fragmentationParams>\n+\t\t<fragmentationParams>\n+\t\t\t<Name>HCD</Name>\n+\t\t\t<Connected>False</Connected>\n+\t\t\t<ConnectedScore0>1</ConnectedScore0>\n+\t\t\t<ConnectedScore1>1</ConnectedScore1>\n+\t\t\t<ConnectedScore2>1</ConnectedScore2>\n+\t\t\t<InternalFragments>False</InternalFragments>\n+\t\t\t<InternalFragmentWeight>1</InternalFragmentWeight>\n+\t\t\t<InternalFragmentAas>KRH</InternalFragmentAas>\n+\t\t</fragmentationParams>\n+\t\t<fragmentationParams>\n+\t\t\t<Name>ETD</Name>\n+\t\t\t<Connected>False</Connected>\n+\t\t\t<ConnectedScore0>1</ConnectedScore0>\n+\t\t\t<ConnectedScore1>1</ConnectedScore1>\n+\t\t\t<ConnectedScore2>1</ConnectedScore2>\n+\t\t\t<InternalFragments>False</InternalFragments>\n+\t\t\t<InternalFragmentWeight>1</InternalFragmentWeight>\n+\t\t\t<InternalFragmentAas>KRH</InternalFragmentAas>\n+\t\t</fragmentationParams>\n+\t\t<fragmentationParams>\n+\t\t\t<Name>PQD</Name>\n+\t\t\t<Connected>False</Connected>\n+\t\t\t<ConnectedScore0>1</ConnectedScore0>\n+\t\t\t<ConnectedScore1>1</ConnectedScore1>\n+\t\t\t<ConnectedScore2>1</ConnectedScore2>\n+\t\t\t<InternalFragments>False</InternalFragments>\n+\t\t\t<InternalFragmentWeight>1</InternalFragmentWeight>\n+\t\t\t<InternalFragmentAas>KRH</InternalFragmentAas>\n+\t\t</fragmentationParams>\n+\t\t<fragmentationParams>\n+\t\t\t<Name>ETHCD</Name>\n+\t\t\t<Connected>False</Connected>\n+\t\t\t<ConnectedScore0>1</ConnectedScore0>\n+\t\t\t<ConnectedScore1>1</ConnectedScore1>\n+\t\t\t<ConnectedScore2>1</ConnectedScore2>\n+\t\t\t<InternalFragments>False</InternalFragments>\n+\t\t\t<InternalFragmentWeight>1</InternalFragmentWeight>\n+\t\t\t<InternalFragmentAas>KRH</InternalFragmentAas>\n+\t\t</fragmentationParams>\n+\t\t<fragmentationParams>\n+\t\t\t<Name>ETCID</Name>\n+\t\t\t<Connected>False</Connected>\n+\t\t\t<ConnectedScore0>1</ConnectedScore0>\n+\t\t\t<ConnectedScore1>1</ConnectedScore1>\n+\t\t\t<ConnectedScore2>1</ConnectedScore2>\n+\t\t\t<InternalFragments>False</InternalFragments>\n+\t\t\t<InternalFragmentWeight>1</InternalFragmentWeight>\n+\t\t\t<InternalFragmentAas>KRH</InternalFragmentAas>\n+\t\t</fragmentationParams>\n+\t\t<fragmentationParams>\n+\t\t\t<Name>UVPD</Name>\n+\t\t\t<Connected>False</Connected>\n+\t\t\t<ConnectedScore0>1</ConnectedScore0>\n+\t\t\t<ConnectedScore1>1</ConnectedScore1>\n+\t\t\t<ConnectedScore2>1</ConnectedScore2>\n+\t\t\t<InternalFragments>False</InternalFragments>\n+\t\t\t<InternalFragmentWeight>1</InternalFragmentWeight>\n+\t\t\t<InternalFragmentAas>KRH</InternalFragmentAas>\n+\t\t</fragmentationParams>\n+\t\t<fragmentationParams>\n+\t\t\t<Name>Unknown</Name>\n+\t\t\t<Connected>False</Connected>\n+\t\t\t<ConnectedScore0>1</ConnectedScore0>\n+\t\t\t<ConnectedScore1>1</ConnectedScore1>\n+\t\t\t<ConnectedScore2>1</ConnectedScore2>\n+\t\t\t<InternalFragments>False</InternalFragments>\n+\t\t\t<InternalFragmentWeight>1</InternalFragmentWeight>\n+\t\t\t<InternalFragmentAas>KRH</InternalFragmentAas>\n+\t\t</fragmentationParams>\n+\t</fragmentationParamsArray>\n+</MaxQuantParams>\n+\n' |
| b |
| diff -r d72c96ad9a16 -r 0839f84def5e test-data/ptxqc.fasta --- a/test-data/ptxqc.fasta Tue Jun 15 07:55:59 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,998 +0,0 @@\n->sp|P16402|H13_HUMAN Histone H1.3 OS=Homo sapiens OX=9606 GN=H1-3 PE=1 SV=2\n-MSETAPLAPTIPAPAEKTPVKKKAKKAGATAGKRKASGPPVSELITKAVAASKERSGVSL\n-AALKKALAAAGYDVEKNNSRIKLGLKSLVSKGTLVQTKGTGASGSFKLNKKAASGEGKPK\n-AKKAGAAKPRKPAGAAKKPKKVAGAATPKKSIKKTPKKVKKPATAAGTKKVAKSAKKVKT\n-PQPKKAAKSPAKAKAPKPKAAKPKSGKPKVTKAKKAAPKKK\n->sp|P49736|MCM2_HUMAN DNA replication licensing factor MCM2 OS=Homo sapiens OX=9606 GN=MCM2 PE=1 SV=4\n-MAESSESFTMASSPAQRRRGNDPLTSSPGRSSRRTDALTSSPGRDLPPFEDESEGLLGTE\n-GPLEEEEDGEELIGDGMERDYRAIPELDAYEAEGLALDDEDVEELTASQREAAERAMRQR\n-DREAGRGLGRMRRGLLYDSDEEDEERPARKRRQVERATEDGEEDEEMIESIENLEDLKGH\n-SVREWVSMAGPRLEIHHRFKNFLRTHVDSHGHNVFKERISDMCKENRESLVVNYEDLAAR\n-EHVLAYFLPEAPAELLQIFDEAALEVVLAMYPKYDRITNHIHVRISHLPLVEELRSLRQL\n-HLNQLIRTSGVVTSCTGVLPQLSMVKYNCNKCNFVLGPFCQSQNQEVKPGSCPECQSAGP\n-FEVNMEETIYQNYQRIRIQESPGKVAAGRLPRSKDAILLADLVDSCKPGDEIELTGIYHN\n-NYDGSLNTANGFPVFATVILANHVAKKDNKVAVGELTDEDVKMITSLSKDQQIGEKIFAS\n-IAPSIYGHEDIKRGLALALFGGEPKNPGGKHKVRGDINVLLCGDPGTAKSQFLKYIEKVS\n-SRAIFTTGQGASAVGLTAYVQRHPVSREWTLEAGALVLADRGVCLIDEFDKMNDQDRTSI\n-HEAMEQQSISISKAGIVTSLQARCTVIAAANPIGGRYDPSLTFSENVDLTEPIISRFDIL\n-CVVRDTVDPVQDEMLARFVVGSHVRHHPSNKEEEGLANGSAAEPAMPNTYGVEPLPQEVL\n-KKYIIYAKERVHPKLNQMDQDKVAKMYSDLRKESMATGSIPITVRHIESMIRMAEAHARI\n-HLRDYVIEDDVNMAIRVMLESFIDTQKFSVMRSMRKTFARYLSFRRDNNELLLFILKQLV\n-AEQVTYQRNRFGAQQDTIEVPEKDLVDKARQINIHNLSAFYDSELFRMNKFSHDLKRKMI\n-LQQF\n->sp|P78414|IRX1_HUMAN Iroquois-class homeodomain protein IRX-1 OS=Homo sapiens OX=9606 GN=IRX1 PE=2 SV=3\n-MSFPQLGYPQYLSAAGPGAYGGERPGVLAAAAAAAAAASSGRPGAAELGGGAGAAAVTSV\n-LGMYAAAGPYAGAPNYSAFLPYAADLSLFSQMGSQYELKDNPGVHPATFAAHTAPAYYPY\n-GQFQYGDPGRPKNATRESTSTLKAWLNEHRKNPYPTKGEKIMLAIITKMTLTQVSTWFAN\n-ARRRLKKENKVTWGARSKDQEDGALFGSDTEGDPEKAEDDEEIDLESIDIDKIDEHDGDQ\n-SNEDDEDKAEAPHAPAAPSALARDQGSPLAAADVLKPQDSPLGLAKEAPEPGSTRLLSPG\n-AAAGGLQGAPHGKPKIWSLAETATSPDGAPKASPPPPAGHPGAHGPSAGAPLQHPAFLPS\n-HGLYTCHIGKFSNWTNSAFLAQGSLLNMRSFLGVGAPHAAPHGPHLPAPPPPQPPVAIAP\n-GALNGDKASVRSSPTLPERDLVPRPDSPAQQLKSPFQPVRDNSLAPQEGTPRILAALPSA\n->sp|Q8N163|CCAR2_HUMAN Cell cycle and apoptosis regulator protein 2 OS=Homo sapiens OX=9606 GN=CCAR2 PE=1 SV=2\n-MSQFKRQRINPLPGGRNFSGTASTSLLGPPPGLLTPPVATELSQNARHLQGGEKQRVFTG\n-IVTSLHDYFGVVDEEVFFQLSVVKGRLPQLGEKVLVKAAYNPGQAVPWNAVKVQTLSNQP\n-LLKSPAPPLLHVAALGQKQGILGAQPQLIFQPHRIPPLFPQKPLSLFQTSHTLHLSHLNR\n-FPARGPHGRLDQGRSDDYDSKKRKQRAGGEPWGAKKPRHDLPPYRVHLTPYTVDSPICDF\n-LELQRRYRSLLVPSDFLSVHLSWLSAFPLSQPFSLHHPSRIQVSSEKEAAPDAGAEPITA\n-DSDPAYSSKVLLLSSPGLEELYRCCMLFVDDMAEPRETPEHPLKQIKFLLGRKEEEAVLV\n-GGEWSPSLDGLDPQADPQVLVRTAIRCAQAQTGIDLSGCTKWWRFAEFQYLQPGPPRRLQ\n-TVVVYLPDVWTIMPTLEEWEALCQQKAAEAAPPTQEAQGETEPTEQAPDALEQAADTSRR\n-NAETPEATTQQETDTDLPEAPPPPLEPAVIARPGCVNLSLHGIVEDRRPKERISFEVMVL\n-AELFLEMLQRDFGYRVYKMLLSLPEKVVSPPEPEKEEAAKEEATKEEEAIKEEVVKEPKD\n-EAQNEGPATESEAPLKEDGLLPKPLSSGGEEEEKPRGEASEDLCEMALDPELLLLRDDGE\n-EEFAGAKLEDSEVRSVASNQSEMEFSSLQDMPKELDPSAVLPLDCLLAFVFFDANWCGYL\n-HRRDLERILLTLGIRLSAEQAKQLVSRVVTQNICQYRSLQYSRQEGLDGGLPEEVLFGNL\n-DLLPPPGKSTKPGAAPTEHKALVSHNGSLINVGSLLQRAEQQDSGRLYLENKIHTLELKL\n-EESHNRFSATEVTNKTLAAEMQELRVRLAEAEETARTAERQKSQLQRLLQELRRRLTPLQ\n-LEIQRVVEKADSWVEKEEPAPSN\n->sp|Q9UKA8|RCAN3_HUMAN Calcipressin-3 OS=Homo sapiens OX=9606 GN=RCAN3 PE=1 SV=1\n-MLRDTMKSWNDSQSDLCSTDQEEEEEMIFGENEDDLDEMMDLSDLPTSLFACSVHEAVFE\n-AREQKERFEALFTIYDDQVTFQLFKSFRRVRINFSKPEAAARARIELHETDFNGQKLKLY\n-FAQVQMSGEVRDKSYLLPPQPVKQFLISPPASPPVGWKQSEDAMPVINYDLLCAVSKLGP\n-GEKYELHAGTESTPSVVVHVCESETEEEEETKNPKQKIAQTRRPDPPTAALNEPQTFDCA\n-L\n->sp|Q6ZU80|CE128_HUMAN Centrosomal protein of 128 kDa OS=Homo sapiens OX=9606 GN=CEP128 PE=1 SV=2\n-MAESSSESDHFRCRDRLSPWAARSTHRGTRSLPTVEVTEKVNTITSTLQDTSRNLRQVDQ\n-MLGRYREYSNGQAGAIEHLKESLEQSIDQLRSQRLLRNSGGRSISVTSLSASDLDGGTGS\n-ELHHFPPTSPLKDYGDPQGIKRMRSRTGVRFVQETDDMTQLHGFHQSLRDLSSEQIRLGD\n-DFNRELSRRSRSDAETKRALEELTEKLNEAQKQEVVSDRVERRLQELEREMRTERELVER\n-RQDQLGLMSLQLQEALKKQEAKADEHEGAIKNKLRQTETEKNQLEQELELSRRLLNQSEG\n-SRETLLHQVEELRTQLTKAEGDRKGLQHQVSQISKQQSNYQDEQGEDWRFRRGVEREKQD\n-LEKQMSDLRVQLNFSAMASELEEVKRCMERKDKEKAHLASQVENLTRELENGEKQQLQML\n-DRLKEIQNHFDTCEAERKHADLQISELTRHAEDATKQAERYLSELQQSEALKEEAEKRRE\n-DLKLKAQESIRQWKLKHKKLERALEKQSETVDELTGKN'..b'KEPPWCDGSYCYECTARFGVTTRKHHCRHCGRLLCHKCSTK\n-EIPIIKFDLNKPVRVCNICFDVLTLGGVS\n->sp|Q9H4A4|AMPB_HUMAN Aminopeptidase B OS=Homo sapiens OX=9606 GN=RNPEP PE=1 SV=2\n-MASGEHSPGSGAARRPLHSAQAVDVASASNFRAFELLHLHLDLRAEFGPPGPGAGSRGLS\n-GTAVLDLRCLEPEGAAELRLDSHPCLEVTAAALRRERPGSEEPPAEPVSFYTQPFSHYGQ\n-ALCVSFPQPCRAAERLQVLLTYRVGEGPGVCWLAPEQTAGKKKPFVYTQGQAVLNRAFFP\n-CFDTPAVKYKYSALIEVPDGFTAVMSASTWEKRGPNKFFFQMCQPIPSYLIALAIGDLVS\n-AEVGPRSRVWAEPCLIDAAKEEYNGVIEEFLATGEKLFGPYVWGRYDLLFMPPSFPFGGM\n-ENPCLTFVTPCLLAGDRSLADVIIHEISHSWFGNLVTNANWGEFWLNEGFTMYAQRRIST\n-ILFGAAYTCLEAATGRALLRQHMDITGEENPLNKLRVKIEPGVDPDDTYNETPYEKGFCF\n-VSYLAHLVGDQDQFDSFLKAYVHEFKFRSILADDFLDFYLEYFPELKKKRVDIIPGFEFD\n-RWLNTPGWPPYLPDLSPGDSLMKPAEELAQLWAAEELDMKAIEAVAISPWKTYQLVYFLD\n-KILQKSPLPPGNVKKLGDTYPSISNARNAELRLRWGQIVLKNDHQEDFWKVKEFLHNQGK\n-QKYTLPLYHAMMGGSEVAQTLAKETFASTASQLHSNVVNYVQQIVAPKGS\n->sp|Q8TBH0|ARRD2_HUMAN Arrestin domain-containing protein 2 OS=Homo sapiens OX=9606 GN=ARRDC2 PE=1 SV=2\n-MLFDKVKAFSVQLDGATAGVEPVFSGGQAVAGRVLLELSSAARVGALRLRARGRAHVHWT\n-ESRSAGSSTAYTQSYSERVEVVSHRATLLAPDTGETTTLPPGRHEFLFSFQLPPTLVTSF\n-EGKHGSVRYCIKATLHRPWVPARRARKVFTVIEPVDINTPALLAPQAGAREKVARSWYCN\n-RGLVSLSAKIDRKGYTPGEVIPVFAEIDNGSTRPVLPRAAVVQTQTFMARGARKQKRAVV\n-ASLAGEPVGPGQRALWQGRALRIPPVGPSILHCRVLHVDYALKVCVDIPGTSKLLLELPL\n-VIGTIPLHPFGSRSSSVGSHASFLLDWRLGALPERPEAPPEYSEVVADTEEAALGQSPFP\n-LPQDPDMSLEGPFFAYIQEFRYRPPPLYSEEDPNPLLGDMRPRCMTC\n->sp|P00966|ASSY_HUMAN Argininosuccinate synthase OS=Homo sapiens OX=9606 GN=ASS1 PE=1 SV=2\n-MSSKGSVVLAYSGGLDTSCILVWLKEQGYDVIAYLANIGQKEDFEEARKKALKLGAKKVF\n-IEDVSREFVEEFIWPAIQSSALYEDRYLLGTSLARPCIARKQVEIAQREGAKYVSHGATG\n-KGNDQVRFELSCYSLAPQIKVIAPWRMPEFYNRFKGRNDLMEYAKQHGIPIPVTPKNPWS\n-MDENLMHISYEAGILENPKNQAPPGLYTKTQDPAKAPNTPDILEIEFKKGVPVKVTNVKD\n-GTTHQTSLELFMYLNEVAGKHGVGRIDIVENRFIGMKSRGIYETPAGTILYHAHLDIEAF\n-TMDREVRKIKQGLGLKFAELVYTGFWHSPECEFVRHCIAKSQERVEGKVQVSVLKGQVYI\n-LGRESPLSLYNEELVSMNVQGDYEPTDATGFININSLRLKEYHRLQSKVTAK\n->sp|Q7L266|ASGL1_HUMAN Isoaspartyl peptidase/L-asparaginase OS=Homo sapiens OX=9606 GN=ASRGL1 PE=1 SV=2\n-MNPIVVVHGGGAGPISKDRKERVHQGMVRAATVGYGILREGGSAVDAVEGAVVALEDDPE\n-FNAGCGSVLNTNGEVEMDASIMDGKDLSAGAVSAVQCIANPIKLARLVMEKTPHCFLTDQ\n-GAAQFAAAMGVPEIPGEKLVTERNKKRLEKEKHEKGAQKTDCQKNLGTVGAVALDCKGNV\n-AYATSTGGIVNKMVGRVGDSPCLGAGGYADNDIGAVSTTGHGESILKVNLARLTLFHIEQ\n-GKTVEEAADLSLGYMKSRVKGLGGLIVVSKTGDWVAKWTSTSMPWAAAKDGKLHFGIDPD\n-DTTITDLP\n->sp|P46597|ASMT_HUMAN Acetylserotonin O-methyltransferase OS=Homo sapiens OX=9606 GN=ASMT PE=1 SV=1\n-MGSSEDQAYRLLNDYANGFMVSQVLFAACELGVFDLLAEAPGPLDVAAVAAGVRASAHGT\n-ELLLDICVSLKLLKVETRGGKAFYRNTELSSDYLTTVSPTSQCSMLKYMGRTSYRCWGHL\n-ADAVREGRNQYLETFGVPAEELFTAIYRSEGERLQFMQALQEVWSVNGRSVLTAFDLSVF\n-PLMCDLGGGAGALAKECMSLYPGCKITVFDIPEVVWTAKQHFSFQEEEQIDFQEGDFFKD\n-PLPEADLYILARVLHDWADGKCSHLLERIYHTCKPGGGILVIESLLDEDRRGPLLTQLYS\n-LNMLVQTEGQERTPTHYHMLLSSAGFRDFQFKKTGAIYDAILARK\n->sp|O43683|BUB1_HUMAN Mitotic checkpoint serine/threonine-protein kinase BUB1 OS=Homo sapiens OX=9606 GN=BUB1 PE=1 SV=1\n-MDTPENVLQMLEAHMQSYKGNDPLGEWERYIQWVEENFPENKEYLITLLEHLMKEFLDKK\n-KYHNDPRFISYCLKFAEYNSDLHQFFEFLYNHGIGTLSSPLYIAWAGHLEAQGELQHASA\n-VLQRGIQNQAEPREFLQQQYRLFQTRLTETHLPAQARTSEPLHNVQVLNQMITSKSNPGN\n-NMACISKNQGSELSGVISSACDKESNMERRVITISKSEYSVHSSLASKVDVEQVVMYCKE\n-KLIRGESEFSFEELRAQKYNQRRKHEQWVNEDRHYMKRKEANAFEEQLLKQKMDELHKKL\n-HQVVETSHEDLPASQERSEVNPARMGPSVGSQQELRAPCLPVTYQQTPVNMEKNPREAPP\n-VVPPLANAISAALVSPATSQSIAPPVPLKAQTVTDSMFAVASKDAGCVNKSTHEFKPQSG\n-AEIKEGCETHKVANTSSFHTTPNTSLGMVQATPSKVQPSPTVHTKEALGFIMNMFQAPTL\n-PDISDDKDEWQSLDQNEDAFEAQFQKNVRSSGAWGVNKIISSLSSAFHVFEDGNKENYGL\n-PQPKNKPTGARTFGERSVSRLPSKPKEEVPHAEEFLDDSTVWGIRCNKTLAPSPKSPGDF\n-TSAAQLASTPFHKLPVESVHILEDKENVVAKQCTQATLDSCEENMVVPSRDGKFSPIQEK\n-SPKQALSSHMYSASLLRLSQPAAGGVLTCEAELGVEACRLTDTDAAIAEDPPDAIAGLQA\n-EWMQMSSLGTVDAPNFIVGNPWDDKLIFKLLSGLSKPVSSYPNTFEWQCKLPAIKPKTEF\n-QLGSKLVYVHHLLGEGAFAQVYEATQGDLNDAKNKQKFVLKVQKPANPWEFYIGTQLMER\n-LKPSMQHMFMKFYSAHLFQNGSVLVGELYSYGTLLNAINLYKNTPEKVMPQGLVISFAMR\n-MLYMIEQVHDCEIIHGDIKPDNFILGNGFLEQDDEDDLSAGLALIDLGQSIDMKLFPKGT\n-IFTAKCETSGFQCVEMLSNKPWNYQIDYFGVAATVYCMLFGTYMKVKNEGGECKPEGLFR\n-RLPHLDMWNEFFHVMLNIPDCHHLPSLDLLRQKLKKVFQQHYTNKIRALRNRLIVLLLEC\n-KRSRK\n' |
| b |
| diff -r d72c96ad9a16 -r 0839f84def5e test-data/ptxqc.mzXML --- a/test-data/ptxqc.mzXML Tue Jun 15 07:55:59 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| b'@@ -1,1697 +0,0 @@\n-<?xml version="1.0" encoding="ISO-8859-1"?>\n-<mzXML xmlns="http://sashimi.sourceforge.net/schema_revision/mzXML_3.1" \n- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" \n- xsi:schemaLocation="http://sashimi.sourceforge.net/schema_revision/mzXML_3.1 http://sashimi.sourceforge.net/schema_revision/mzXML_3.1/mzXML_idx_3.1.xsd">\n-\t<msRun scanCount="100" startTime="PT1000.14828S" endTime="PT1019.82204S" >\n-\t\t<parentFile fileName="FileFilter_on_data_13__out.mzML" fileType="processedData" fileSha1="70ccfd499ae5f6dcf702437f45812d8a5a1582c5"/>\n-\t\t<msInstrument>\n-\t\t\t<msManufacturer category="msManufacturer" value="Thermo Scientific"/>\n-\t\t\t<msModel category="msModel" value=""/>\n-\t\t\t<msIonisation category="msIonisation" value="NSI"/>\n-\t\t\t<msMassAnalyzer category="msMassAnalyzer" value="Quadrupole"/>\n-\t\t\t<msDetector category="msDetector" value=""/>\n-\t\t\t<software type="acquisition" name="Xcalibur" version="2.8-280502/2.8.1.2806"/>\n-\t\t\t<nameValue name="instrument serial number" value="Exactive Series slot #0012"/>\n-\t\t</msInstrument>\n-\t\t<dataProcessing deisotoped="0" chargeDeconvoluted="0" centroided="0">\n-\t\t\t<software type="processing" name="ProteoWizard software" version="3.0.20287"/>\n-\t\t</dataProcessing>\n-\t\t<dataProcessing deisotoped="0" chargeDeconvoluted="0" centroided="0">\n-\t\t\t<software type="processing" name="FileFilter" version="2.6.0-pre-exported-20201001" completionTime="2021-04-09T08:45:00"/>\n-\t\t\t<processingOperation name="parameter: in" value="in/http___ftp_pride_ebi_ac_uk_pride_data_archive_2020_05_PXD014145_MFA390_mzML.mzML"/>\n-\t\t\t<processingOperation name="parameter: in_type" value=""/>\n-\t\t\t<processingOperation name="parameter: out" value="out/output.mzML"/>\n-\t\t\t<processingOperation name="parameter: out_type" value="mzML"/>\n-\t\t\t<processingOperation name="parameter: rt" value="1000:1200"/>\n-\t\t\t<processingOperation name="parameter: mz" value=":"/>\n-\t\t\t<processingOperation name="parameter: int" value=":"/>\n-\t\t\t<processingOperation name="parameter: sort" value="false"/>\n-\t\t\t<processingOperation name="parameter: log" value="log.txt"/>\n-\t\t\t<processingOperation name="parameter: debug" value="0"/>\n-\t\t\t<processingOperation name="parameter: threads" value="1"/>\n-\t\t\t<processingOperation name="parameter: no_progress" value="true"/>\n-\t\t\t<processingOperation name="parameter: force" value="false"/>\n-\t\t\t<processingOperation name="parameter: test" value="false"/>\n-\t\t\t<processingOperation name="parameter: peak_options:sn" value="0.0"/>\n-\t\t\t<processingOperation name="parameter: peak_options:rm_pc_charge" value="[]"/>\n-\t\t\t<processingOperation name="parameter: peak_options:pc_mz_range" value=":"/>\n-\t\t\t<processingOperation name="parameter: peak_options:pc_mz_list" value="[]"/>\n-\t\t\t<processingOperation name="parameter: peak_options:level" value="[1, 2, 3]"/>\n-\t\t\t<processingOperation name="parameter: peak_options:sort_peaks" value="false"/>\n-\t\t\t<processingOperation name="parameter: peak_options:no_chromatograms" value="false"/>\n-\t\t\t<processingOperation name="parameter: peak_options:remove_chromatograms" value="false"/>\n-\t\t\t<processingOperation name="parameter: peak_options:remove_empty" value="false"/>\n-\t\t\t<processingOperation name="parameter: peak_options:mz_precision" value="64"/>\n-\t\t\t<processingOperation name="parameter: peak_options:int_precision" value="32"/>\n-\t\t\t<processingOperation name="parameter: peak_options:indexed_file" value="true"/>\n-\t\t\t<processingOperation name="parameter: peak_options:zlib_compression" value="false"/>\n-\t\t\t<processingOperation name="parameter: peak_options:numpress:masstime" value="none"/>\n-\t\t\t<processingOperation name="parameter: peak_options:numpress:lossy_mass_accuracy" value="-1.0"/>\n-\t\t\t<processingOperation name="parameter: peak_options:numpress:intensity" value="none"/>\n-\t\t\t<processingOperation name="parameter: peak_options:numpress:float_da" value="none"/>\n-\t\t\t<processingOperation name="parameter: spectra:remove_zoom" value="false"/>\n-\t\t\t<processingOperation name="parameter: spectra:remov'..b'15618668535978"/>\n-\t\t\t<nameValue name="highest observed m/z" value="2020.220186465410961"/>\n-\t\t\t<nameValue name="filter string" value="FTMS + p NSI Full ms [300.0000-2000.0000]"/>\n-\t\t\t<nameValue name="preset scan configuration" value="1"/>\n-\t\t</scan>\n-\t</msRun>\n-<index name = "scan" >\n-<offset id = "1" >10006</offset>\n-<offset id = "2" >88366</offset>\n-<offset id = "3" >166720</offset>\n-<offset id = "4" >241577</offset>\n-<offset id = "5" >245018</offset>\n-<offset id = "6" >247738</offset>\n-<offset id = "7" >325024</offset>\n-<offset id = "8" >410926</offset>\n-<offset id = "9" >488873</offset>\n-<offset id = "10" >491619</offset>\n-<offset id = "11" >494878</offset>\n-<offset id 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>1776673</offset>\n-<offset id = "66" >1779127</offset>\n-<offset id = "67" >1840486</offset>\n-<offset id = "68" >1904345</offset>\n-<offset id = "69" >1967691</offset>\n-<offset id = "70" >1971174</offset>\n-<offset id = "71" >1973916</offset>\n-<offset id = "72" >1975743</offset>\n-<offset id = "73" >2041156</offset>\n-<offset id = "74" >2100715</offset>\n-<offset id = "75" >2164211</offset>\n-<offset id = "76" >2168980</offset>\n-<offset id = "77" >2171743</offset>\n-<offset id = "78" >2174448</offset>\n-<offset id = "79" >2234985</offset>\n-<offset id = "80" >2302682</offset>\n-<offset id = "81" >2366476</offset>\n-<offset id = "82" >2368673</offset>\n-<offset id = "83" >2371135</offset>\n-<offset id = "84" >2373624</offset>\n-<offset id = "85" >2378440</offset>\n-<offset id = "86" >2382124</offset>\n-<offset id = "87" >2383959</offset>\n-<offset id = "88" >2451717</offset>\n-<offset id = "89" >2517149</offset>\n-<offset id = "90" >2587771</offset>\n-<offset id = "91" >2591002</offset>\n-<offset id = "92" >2595794</offset>\n-<offset id = "93" >2599786</offset>\n-<offset id = "94" >2602385</offset>\n-<offset id = "95" >2675470</offset>\n-<offset id = "96" >2677678</offset>\n-<offset id = "97" >2681220</offset>\n-<offset id = "98" >2683948</offset>\n-<offset id = "99" >2686473</offset>\n-<offset id = "100" >2759876</offset>\n-</index>\n-<indexOffset>2763230</indexOffset>\n-</mzXML>\n' |
| b |
| diff -r d72c96ad9a16 -r 0839f84def5e test-data/template.xml --- a/test-data/template.xml Tue Jun 15 07:55:59 2021 +0000 +++ b/test-data/template.xml Sun Jun 20 16:37:41 2021 +0000 |
| b |
| @@ -179,7 +179,7 @@ <lcmsRunType>Standard</lcmsRunType> <reQuantify>False</reQuantify> <lfqMode>0</lfqMode> - <lfqSkipNorm>False</lfqSkipNorm> + <lfqNormType>0</lfqNormType> <lfqMinEdgesPerNode>3</lfqMinEdgesPerNode> <lfqAvEdgesPerNode>6</lfqAvEdgesPerNode> <lfqMaxFeatures>100000</lfqMaxFeatures> |
| b |
| diff -r d72c96ad9a16 -r 0839f84def5e test-data/tmt_data.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tmt_data.fasta Sun Jun 20 16:37:41 2021 +0000 |
| b |
| b'@@ -0,0 +1,998 @@\n+>sp|P16402|H13_HUMAN Histone H1.3 OS=Homo sapiens OX=9606 GN=H1-3 PE=1 SV=2\n+MSETAPLAPTIPAPAEKTPVKKKAKKAGATAGKRKASGPPVSELITKAVAASKERSGVSL\n+AALKKALAAAGYDVEKNNSRIKLGLKSLVSKGTLVQTKGTGASGSFKLNKKAASGEGKPK\n+AKKAGAAKPRKPAGAAKKPKKVAGAATPKKSIKKTPKKVKKPATAAGTKKVAKSAKKVKT\n+PQPKKAAKSPAKAKAPKPKAAKPKSGKPKVTKAKKAAPKKK\n+>sp|P49736|MCM2_HUMAN DNA replication licensing factor MCM2 OS=Homo sapiens OX=9606 GN=MCM2 PE=1 SV=4\n+MAESSESFTMASSPAQRRRGNDPLTSSPGRSSRRTDALTSSPGRDLPPFEDESEGLLGTE\n+GPLEEEEDGEELIGDGMERDYRAIPELDAYEAEGLALDDEDVEELTASQREAAERAMRQR\n+DREAGRGLGRMRRGLLYDSDEEDEERPARKRRQVERATEDGEEDEEMIESIENLEDLKGH\n+SVREWVSMAGPRLEIHHRFKNFLRTHVDSHGHNVFKERISDMCKENRESLVVNYEDLAAR\n+EHVLAYFLPEAPAELLQIFDEAALEVVLAMYPKYDRITNHIHVRISHLPLVEELRSLRQL\n+HLNQLIRTSGVVTSCTGVLPQLSMVKYNCNKCNFVLGPFCQSQNQEVKPGSCPECQSAGP\n+FEVNMEETIYQNYQRIRIQESPGKVAAGRLPRSKDAILLADLVDSCKPGDEIELTGIYHN\n+NYDGSLNTANGFPVFATVILANHVAKKDNKVAVGELTDEDVKMITSLSKDQQIGEKIFAS\n+IAPSIYGHEDIKRGLALALFGGEPKNPGGKHKVRGDINVLLCGDPGTAKSQFLKYIEKVS\n+SRAIFTTGQGASAVGLTAYVQRHPVSREWTLEAGALVLADRGVCLIDEFDKMNDQDRTSI\n+HEAMEQQSISISKAGIVTSLQARCTVIAAANPIGGRYDPSLTFSENVDLTEPIISRFDIL\n+CVVRDTVDPVQDEMLARFVVGSHVRHHPSNKEEEGLANGSAAEPAMPNTYGVEPLPQEVL\n+KKYIIYAKERVHPKLNQMDQDKVAKMYSDLRKESMATGSIPITVRHIESMIRMAEAHARI\n+HLRDYVIEDDVNMAIRVMLESFIDTQKFSVMRSMRKTFARYLSFRRDNNELLLFILKQLV\n+AEQVTYQRNRFGAQQDTIEVPEKDLVDKARQINIHNLSAFYDSELFRMNKFSHDLKRKMI\n+LQQF\n+>sp|P78414|IRX1_HUMAN Iroquois-class homeodomain protein IRX-1 OS=Homo sapiens OX=9606 GN=IRX1 PE=2 SV=3\n+MSFPQLGYPQYLSAAGPGAYGGERPGVLAAAAAAAAAASSGRPGAAELGGGAGAAAVTSV\n+LGMYAAAGPYAGAPNYSAFLPYAADLSLFSQMGSQYELKDNPGVHPATFAAHTAPAYYPY\n+GQFQYGDPGRPKNATRESTSTLKAWLNEHRKNPYPTKGEKIMLAIITKMTLTQVSTWFAN\n+ARRRLKKENKVTWGARSKDQEDGALFGSDTEGDPEKAEDDEEIDLESIDIDKIDEHDGDQ\n+SNEDDEDKAEAPHAPAAPSALARDQGSPLAAADVLKPQDSPLGLAKEAPEPGSTRLLSPG\n+AAAGGLQGAPHGKPKIWSLAETATSPDGAPKASPPPPAGHPGAHGPSAGAPLQHPAFLPS\n+HGLYTCHIGKFSNWTNSAFLAQGSLLNMRSFLGVGAPHAAPHGPHLPAPPPPQPPVAIAP\n+GALNGDKASVRSSPTLPERDLVPRPDSPAQQLKSPFQPVRDNSLAPQEGTPRILAALPSA\n+>sp|Q8N163|CCAR2_HUMAN Cell cycle and apoptosis regulator protein 2 OS=Homo sapiens OX=9606 GN=CCAR2 PE=1 SV=2\n+MSQFKRQRINPLPGGRNFSGTASTSLLGPPPGLLTPPVATELSQNARHLQGGEKQRVFTG\n+IVTSLHDYFGVVDEEVFFQLSVVKGRLPQLGEKVLVKAAYNPGQAVPWNAVKVQTLSNQP\n+LLKSPAPPLLHVAALGQKQGILGAQPQLIFQPHRIPPLFPQKPLSLFQTSHTLHLSHLNR\n+FPARGPHGRLDQGRSDDYDSKKRKQRAGGEPWGAKKPRHDLPPYRVHLTPYTVDSPICDF\n+LELQRRYRSLLVPSDFLSVHLSWLSAFPLSQPFSLHHPSRIQVSSEKEAAPDAGAEPITA\n+DSDPAYSSKVLLLSSPGLEELYRCCMLFVDDMAEPRETPEHPLKQIKFLLGRKEEEAVLV\n+GGEWSPSLDGLDPQADPQVLVRTAIRCAQAQTGIDLSGCTKWWRFAEFQYLQPGPPRRLQ\n+TVVVYLPDVWTIMPTLEEWEALCQQKAAEAAPPTQEAQGETEPTEQAPDALEQAADTSRR\n+NAETPEATTQQETDTDLPEAPPPPLEPAVIARPGCVNLSLHGIVEDRRPKERISFEVMVL\n+AELFLEMLQRDFGYRVYKMLLSLPEKVVSPPEPEKEEAAKEEATKEEEAIKEEVVKEPKD\n+EAQNEGPATESEAPLKEDGLLPKPLSSGGEEEEKPRGEASEDLCEMALDPELLLLRDDGE\n+EEFAGAKLEDSEVRSVASNQSEMEFSSLQDMPKELDPSAVLPLDCLLAFVFFDANWCGYL\n+HRRDLERILLTLGIRLSAEQAKQLVSRVVTQNICQYRSLQYSRQEGLDGGLPEEVLFGNL\n+DLLPPPGKSTKPGAAPTEHKALVSHNGSLINVGSLLQRAEQQDSGRLYLENKIHTLELKL\n+EESHNRFSATEVTNKTLAAEMQELRVRLAEAEETARTAERQKSQLQRLLQELRRRLTPLQ\n+LEIQRVVEKADSWVEKEEPAPSN\n+>sp|Q9UKA8|RCAN3_HUMAN Calcipressin-3 OS=Homo sapiens OX=9606 GN=RCAN3 PE=1 SV=1\n+MLRDTMKSWNDSQSDLCSTDQEEEEEMIFGENEDDLDEMMDLSDLPTSLFACSVHEAVFE\n+AREQKERFEALFTIYDDQVTFQLFKSFRRVRINFSKPEAAARARIELHETDFNGQKLKLY\n+FAQVQMSGEVRDKSYLLPPQPVKQFLISPPASPPVGWKQSEDAMPVINYDLLCAVSKLGP\n+GEKYELHAGTESTPSVVVHVCESETEEEEETKNPKQKIAQTRRPDPPTAALNEPQTFDCA\n+L\n+>sp|Q6ZU80|CE128_HUMAN Centrosomal protein of 128 kDa OS=Homo sapiens OX=9606 GN=CEP128 PE=1 SV=2\n+MAESSSESDHFRCRDRLSPWAARSTHRGTRSLPTVEVTEKVNTITSTLQDTSRNLRQVDQ\n+MLGRYREYSNGQAGAIEHLKESLEQSIDQLRSQRLLRNSGGRSISVTSLSASDLDGGTGS\n+ELHHFPPTSPLKDYGDPQGIKRMRSRTGVRFVQETDDMTQLHGFHQSLRDLSSEQIRLGD\n+DFNRELSRRSRSDAETKRALEELTEKLNEAQKQEVVSDRVERRLQELEREMRTERELVER\n+RQDQLGLMSLQLQEALKKQEAKADEHEGAIKNKLRQTETEKNQLEQELELSRRLLNQSEG\n+SRETLLHQVEELRTQLTKAEGDRKGLQHQVSQISKQQSNYQDEQGEDWRFRRGVEREKQD\n+LEKQMSDLRVQLNFSAMASELEEVKRCMERKDKEKAHLASQVENLTRELENGEKQQLQML\n+DRLKEIQNHFDTCEAERKHADLQISELTRHAEDATKQAERYLSELQQSEALKEEAEKRRE\n+DLKLKAQESIRQWKLKHKKLERALEKQSETVDELTGKN'..b'KEPPWCDGSYCYECTARFGVTTRKHHCRHCGRLLCHKCSTK\n+EIPIIKFDLNKPVRVCNICFDVLTLGGVS\n+>sp|Q9H4A4|AMPB_HUMAN Aminopeptidase B OS=Homo sapiens OX=9606 GN=RNPEP PE=1 SV=2\n+MASGEHSPGSGAARRPLHSAQAVDVASASNFRAFELLHLHLDLRAEFGPPGPGAGSRGLS\n+GTAVLDLRCLEPEGAAELRLDSHPCLEVTAAALRRERPGSEEPPAEPVSFYTQPFSHYGQ\n+ALCVSFPQPCRAAERLQVLLTYRVGEGPGVCWLAPEQTAGKKKPFVYTQGQAVLNRAFFP\n+CFDTPAVKYKYSALIEVPDGFTAVMSASTWEKRGPNKFFFQMCQPIPSYLIALAIGDLVS\n+AEVGPRSRVWAEPCLIDAAKEEYNGVIEEFLATGEKLFGPYVWGRYDLLFMPPSFPFGGM\n+ENPCLTFVTPCLLAGDRSLADVIIHEISHSWFGNLVTNANWGEFWLNEGFTMYAQRRIST\n+ILFGAAYTCLEAATGRALLRQHMDITGEENPLNKLRVKIEPGVDPDDTYNETPYEKGFCF\n+VSYLAHLVGDQDQFDSFLKAYVHEFKFRSILADDFLDFYLEYFPELKKKRVDIIPGFEFD\n+RWLNTPGWPPYLPDLSPGDSLMKPAEELAQLWAAEELDMKAIEAVAISPWKTYQLVYFLD\n+KILQKSPLPPGNVKKLGDTYPSISNARNAELRLRWGQIVLKNDHQEDFWKVKEFLHNQGK\n+QKYTLPLYHAMMGGSEVAQTLAKETFASTASQLHSNVVNYVQQIVAPKGS\n+>sp|Q8TBH0|ARRD2_HUMAN Arrestin domain-containing protein 2 OS=Homo sapiens OX=9606 GN=ARRDC2 PE=1 SV=2\n+MLFDKVKAFSVQLDGATAGVEPVFSGGQAVAGRVLLELSSAARVGALRLRARGRAHVHWT\n+ESRSAGSSTAYTQSYSERVEVVSHRATLLAPDTGETTTLPPGRHEFLFSFQLPPTLVTSF\n+EGKHGSVRYCIKATLHRPWVPARRARKVFTVIEPVDINTPALLAPQAGAREKVARSWYCN\n+RGLVSLSAKIDRKGYTPGEVIPVFAEIDNGSTRPVLPRAAVVQTQTFMARGARKQKRAVV\n+ASLAGEPVGPGQRALWQGRALRIPPVGPSILHCRVLHVDYALKVCVDIPGTSKLLLELPL\n+VIGTIPLHPFGSRSSSVGSHASFLLDWRLGALPERPEAPPEYSEVVADTEEAALGQSPFP\n+LPQDPDMSLEGPFFAYIQEFRYRPPPLYSEEDPNPLLGDMRPRCMTC\n+>sp|P00966|ASSY_HUMAN Argininosuccinate synthase OS=Homo sapiens OX=9606 GN=ASS1 PE=1 SV=2\n+MSSKGSVVLAYSGGLDTSCILVWLKEQGYDVIAYLANIGQKEDFEEARKKALKLGAKKVF\n+IEDVSREFVEEFIWPAIQSSALYEDRYLLGTSLARPCIARKQVEIAQREGAKYVSHGATG\n+KGNDQVRFELSCYSLAPQIKVIAPWRMPEFYNRFKGRNDLMEYAKQHGIPIPVTPKNPWS\n+MDENLMHISYEAGILENPKNQAPPGLYTKTQDPAKAPNTPDILEIEFKKGVPVKVTNVKD\n+GTTHQTSLELFMYLNEVAGKHGVGRIDIVENRFIGMKSRGIYETPAGTILYHAHLDIEAF\n+TMDREVRKIKQGLGLKFAELVYTGFWHSPECEFVRHCIAKSQERVEGKVQVSVLKGQVYI\n+LGRESPLSLYNEELVSMNVQGDYEPTDATGFININSLRLKEYHRLQSKVTAK\n+>sp|Q7L266|ASGL1_HUMAN Isoaspartyl peptidase/L-asparaginase OS=Homo sapiens OX=9606 GN=ASRGL1 PE=1 SV=2\n+MNPIVVVHGGGAGPISKDRKERVHQGMVRAATVGYGILREGGSAVDAVEGAVVALEDDPE\n+FNAGCGSVLNTNGEVEMDASIMDGKDLSAGAVSAVQCIANPIKLARLVMEKTPHCFLTDQ\n+GAAQFAAAMGVPEIPGEKLVTERNKKRLEKEKHEKGAQKTDCQKNLGTVGAVALDCKGNV\n+AYATSTGGIVNKMVGRVGDSPCLGAGGYADNDIGAVSTTGHGESILKVNLARLTLFHIEQ\n+GKTVEEAADLSLGYMKSRVKGLGGLIVVSKTGDWVAKWTSTSMPWAAAKDGKLHFGIDPD\n+DTTITDLP\n+>sp|P46597|ASMT_HUMAN Acetylserotonin O-methyltransferase OS=Homo sapiens OX=9606 GN=ASMT PE=1 SV=1\n+MGSSEDQAYRLLNDYANGFMVSQVLFAACELGVFDLLAEAPGPLDVAAVAAGVRASAHGT\n+ELLLDICVSLKLLKVETRGGKAFYRNTELSSDYLTTVSPTSQCSMLKYMGRTSYRCWGHL\n+ADAVREGRNQYLETFGVPAEELFTAIYRSEGERLQFMQALQEVWSVNGRSVLTAFDLSVF\n+PLMCDLGGGAGALAKECMSLYPGCKITVFDIPEVVWTAKQHFSFQEEEQIDFQEGDFFKD\n+PLPEADLYILARVLHDWADGKCSHLLERIYHTCKPGGGILVIESLLDEDRRGPLLTQLYS\n+LNMLVQTEGQERTPTHYHMLLSSAGFRDFQFKKTGAIYDAILARK\n+>sp|O43683|BUB1_HUMAN Mitotic checkpoint serine/threonine-protein kinase BUB1 OS=Homo sapiens OX=9606 GN=BUB1 PE=1 SV=1\n+MDTPENVLQMLEAHMQSYKGNDPLGEWERYIQWVEENFPENKEYLITLLEHLMKEFLDKK\n+KYHNDPRFISYCLKFAEYNSDLHQFFEFLYNHGIGTLSSPLYIAWAGHLEAQGELQHASA\n+VLQRGIQNQAEPREFLQQQYRLFQTRLTETHLPAQARTSEPLHNVQVLNQMITSKSNPGN\n+NMACISKNQGSELSGVISSACDKESNMERRVITISKSEYSVHSSLASKVDVEQVVMYCKE\n+KLIRGESEFSFEELRAQKYNQRRKHEQWVNEDRHYMKRKEANAFEEQLLKQKMDELHKKL\n+HQVVETSHEDLPASQERSEVNPARMGPSVGSQQELRAPCLPVTYQQTPVNMEKNPREAPP\n+VVPPLANAISAALVSPATSQSIAPPVPLKAQTVTDSMFAVASKDAGCVNKSTHEFKPQSG\n+AEIKEGCETHKVANTSSFHTTPNTSLGMVQATPSKVQPSPTVHTKEALGFIMNMFQAPTL\n+PDISDDKDEWQSLDQNEDAFEAQFQKNVRSSGAWGVNKIISSLSSAFHVFEDGNKENYGL\n+PQPKNKPTGARTFGERSVSRLPSKPKEEVPHAEEFLDDSTVWGIRCNKTLAPSPKSPGDF\n+TSAAQLASTPFHKLPVESVHILEDKENVVAKQCTQATLDSCEENMVVPSRDGKFSPIQEK\n+SPKQALSSHMYSASLLRLSQPAAGGVLTCEAELGVEACRLTDTDAAIAEDPPDAIAGLQA\n+EWMQMSSLGTVDAPNFIVGNPWDDKLIFKLLSGLSKPVSSYPNTFEWQCKLPAIKPKTEF\n+QLGSKLVYVHHLLGEGAFAQVYEATQGDLNDAKNKQKFVLKVQKPANPWEFYIGTQLMER\n+LKPSMQHMFMKFYSAHLFQNGSVLVGELYSYGTLLNAINLYKNTPEKVMPQGLVISFAMR\n+MLYMIEQVHDCEIIHGDIKPDNFILGNGFLEQDDEDDLSAGLALIDLGQSIDMKLFPKGT\n+IFTAKCETSGFQCVEMLSNKPWNYQIDYFGVAATVYCMLFGTYMKVKNEGGECKPEGLFR\n+RLPHLDMWNEFFHVMLNIPDCHHLPSLDLLRQKLKKVFQQHYTNKIRALRNRLIVLLLEC\n+KRSRK\n' |
| b |
| diff -r d72c96ad9a16 -r 0839f84def5e test-data/tmt_data.mzXML --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tmt_data.mzXML Sun Jun 20 16:37:41 2021 +0000 |
| [ |
| b'@@ -0,0 +1,1697 @@\n+<?xml version="1.0" encoding="ISO-8859-1"?>\n+<mzXML xmlns="http://sashimi.sourceforge.net/schema_revision/mzXML_3.1" \n+ xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" \n+ xsi:schemaLocation="http://sashimi.sourceforge.net/schema_revision/mzXML_3.1 http://sashimi.sourceforge.net/schema_revision/mzXML_3.1/mzXML_idx_3.1.xsd">\n+\t<msRun scanCount="100" startTime="PT1000.14828S" endTime="PT1019.82204S" >\n+\t\t<parentFile fileName="FileFilter_on_data_13__out.mzML" fileType="processedData" fileSha1="70ccfd499ae5f6dcf702437f45812d8a5a1582c5"/>\n+\t\t<msInstrument>\n+\t\t\t<msManufacturer category="msManufacturer" value="Thermo Scientific"/>\n+\t\t\t<msModel category="msModel" value=""/>\n+\t\t\t<msIonisation category="msIonisation" value="NSI"/>\n+\t\t\t<msMassAnalyzer category="msMassAnalyzer" value="Quadrupole"/>\n+\t\t\t<msDetector category="msDetector" value=""/>\n+\t\t\t<software type="acquisition" name="Xcalibur" version="2.8-280502/2.8.1.2806"/>\n+\t\t\t<nameValue name="instrument serial number" value="Exactive Series slot #0012"/>\n+\t\t</msInstrument>\n+\t\t<dataProcessing deisotoped="0" chargeDeconvoluted="0" centroided="0">\n+\t\t\t<software type="processing" name="ProteoWizard software" version="3.0.20287"/>\n+\t\t</dataProcessing>\n+\t\t<dataProcessing deisotoped="0" chargeDeconvoluted="0" centroided="0">\n+\t\t\t<software type="processing" name="FileFilter" version="2.6.0-pre-exported-20201001" completionTime="2021-04-09T08:45:00"/>\n+\t\t\t<processingOperation name="parameter: in" value="in/http___ftp_pride_ebi_ac_uk_pride_data_archive_2020_05_PXD014145_MFA390_mzML.mzML"/>\n+\t\t\t<processingOperation name="parameter: in_type" value=""/>\n+\t\t\t<processingOperation name="parameter: out" value="out/output.mzML"/>\n+\t\t\t<processingOperation name="parameter: out_type" value="mzML"/>\n+\t\t\t<processingOperation name="parameter: rt" value="1000:1200"/>\n+\t\t\t<processingOperation name="parameter: mz" value=":"/>\n+\t\t\t<processingOperation name="parameter: int" value=":"/>\n+\t\t\t<processingOperation name="parameter: sort" value="false"/>\n+\t\t\t<processingOperation name="parameter: log" value="log.txt"/>\n+\t\t\t<processingOperation name="parameter: debug" value="0"/>\n+\t\t\t<processingOperation name="parameter: threads" value="1"/>\n+\t\t\t<processingOperation name="parameter: no_progress" value="true"/>\n+\t\t\t<processingOperation name="parameter: force" value="false"/>\n+\t\t\t<processingOperation name="parameter: test" value="false"/>\n+\t\t\t<processingOperation name="parameter: peak_options:sn" value="0.0"/>\n+\t\t\t<processingOperation name="parameter: peak_options:rm_pc_charge" value="[]"/>\n+\t\t\t<processingOperation name="parameter: peak_options:pc_mz_range" value=":"/>\n+\t\t\t<processingOperation name="parameter: peak_options:pc_mz_list" value="[]"/>\n+\t\t\t<processingOperation name="parameter: peak_options:level" value="[1, 2, 3]"/>\n+\t\t\t<processingOperation name="parameter: peak_options:sort_peaks" value="false"/>\n+\t\t\t<processingOperation name="parameter: peak_options:no_chromatograms" value="false"/>\n+\t\t\t<processingOperation name="parameter: peak_options:remove_chromatograms" value="false"/>\n+\t\t\t<processingOperation name="parameter: peak_options:remove_empty" value="false"/>\n+\t\t\t<processingOperation name="parameter: peak_options:mz_precision" value="64"/>\n+\t\t\t<processingOperation name="parameter: peak_options:int_precision" value="32"/>\n+\t\t\t<processingOperation name="parameter: peak_options:indexed_file" value="true"/>\n+\t\t\t<processingOperation name="parameter: peak_options:zlib_compression" value="false"/>\n+\t\t\t<processingOperation name="parameter: peak_options:numpress:masstime" value="none"/>\n+\t\t\t<processingOperation name="parameter: peak_options:numpress:lossy_mass_accuracy" value="-1.0"/>\n+\t\t\t<processingOperation name="parameter: peak_options:numpress:intensity" value="none"/>\n+\t\t\t<processingOperation name="parameter: peak_options:numpress:float_da" value="none"/>\n+\t\t\t<processingOperation name="parameter: spectra:remove_zoom" value="false"/>\n+\t\t\t<processingOperation name="parameter: spectra:remov'..b'15618668535978"/>\n+\t\t\t<nameValue name="highest observed m/z" value="2020.220186465410961"/>\n+\t\t\t<nameValue name="filter string" value="FTMS + p NSI Full ms [300.0000-2000.0000]"/>\n+\t\t\t<nameValue name="preset scan configuration" value="1"/>\n+\t\t</scan>\n+\t</msRun>\n+<index name = "scan" >\n+<offset id = "1" >10006</offset>\n+<offset id = "2" >88366</offset>\n+<offset id = "3" >166720</offset>\n+<offset id = "4" >241577</offset>\n+<offset id = "5" >245018</offset>\n+<offset id = "6" >247738</offset>\n+<offset id = "7" >325024</offset>\n+<offset id = "8" >410926</offset>\n+<offset id = "9" >488873</offset>\n+<offset id = "10" >491619</offset>\n+<offset id = "11" >494878</offset>\n+<offset id 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>2591002</offset>\n+<offset id = "92" >2595794</offset>\n+<offset id = "93" >2599786</offset>\n+<offset id = "94" >2602385</offset>\n+<offset id = "95" >2675470</offset>\n+<offset id = "96" >2677678</offset>\n+<offset id = "97" >2681220</offset>\n+<offset id = "98" >2683948</offset>\n+<offset id = "99" >2686473</offset>\n+<offset id = "100" >2759876</offset>\n+</index>\n+<indexOffset>2763230</indexOffset>\n+</mzXML>\n' |
| b |
| diff -r d72c96ad9a16 -r 0839f84def5e test-data/tmt_data_16.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tmt_data_16.fasta Sun Jun 20 16:37:41 2021 +0000 |
| b |
| b'@@ -0,0 +1,233 @@\n+>sp|A6NKP2|D42E2_HUMAN Putative short-chain dehydrogenase/reductase family 42E member 2 OS=Homo sapiens OX=9606 GN=SDR42E2 PE=3 SV=3\n+MKSNPPRSSLEACKAAGQAPQQKTQAKPTKAARQKVLVTGGGGYLGFSLGSHLAKSGTSV\n+ILLDRRRPQWELSPETKFIQADVRDEEALYRAFEGVDCVFHVASYGMSGAEKLQKEQIES\n+INVGGTKLVIDVCVRRRVPRLIYTSTVNVAFGGKPIEQGDEDSVPYFPLDEHVDHYSRTK\n+AIADQLTLMANGMPLPGGGTLRTCVLRPPGIYGPEEQRHLPRVAGHIKKRLFMFRFGDHK\n+ARMNWVHVHNLVQAHVLAAEALTTAKGYVASGQAYYINDGESVNLFEWMAPLFEKLGYSQ\n+PWIQVPTSWVYLTAAVMERLHLALRPICSLPPLLTRSEVRSVAVTHTFQIAKARAQLGYA\n+PDKFRFADAVELYVQSTTRRPRGSTARTLLRLLLRLLLFLGLLALALHFLGLQPLHAAVE\n+RL\n+>sp|Q32M88|PGGHG_HUMAN Protein-glucosylgalactosylhydroxylysine glucosidase OS=Homo sapiens OX=9606 GN=PGGHG PE=1 SV=2\n+MEDAGEDPTTFAAHSLPSDPRLLATVTNAYLGTRVFHDTLHVSGVYNGAGGDTHRAMLPS\n+PLNVRLEAPAGMGEQLTETFALDTNTGSFLHTLEGPRFRASQCIYAHRTLPHVLAFRVSI\n+ARLAPGSGPITLLLRSAFSPESPDLDLHQGPDFQGARYLYGHTLTPEQPGGPQQEVHMLW\n+TPAPPDLTLGEGEEARTWDFLTAVGGSQAEAQACLTEALQLQARGALYTAHAQAWAQLWV\n+ECGLDVVGPLQLRQALRGSLYYLLSALPQPKAPGYICHGLSPGGLSNGSREECYWGHVFW\n+DQDLWMFPSILMFHPEAARAILEYRIRTLDGALENAQNLGYQGAKFAWESADSGLEVCPE\n+DIYGVQEVHVNGAVVLAFELYYHTTQDLQLFREAGGWDVVRAVAEFWCSRVEWSPREEKY\n+HLRGVMSPDEYHSGVNNSVYTNVLVQNSLRFAAALAQDLGLPIPSQWLAVADKIKVPFDV\n+EQNFHPEFDGYEPGEVVKQADVVLLGYPVPFSLSPDVRRKNLEIYEAVTSPQGPAMTWSM\n+FAVGWMELKDAVRARGLLDRSFANMAEPFKVWTENADGSGAVNFLTGMGGFLQAVVFGCT\n+GFRVTRAGVTFDPVCLSGISRVSVSGIFYQGNKLNFSFSEDSVTVEVTARAGPWAPHLEA\n+ELWPSQSRLSLLPGHKVSFPRSAGRIQMSPPKLPGSSSSEFPGRTFSDVRDPLQSPLWVT\n+LGSSSPTESLTVDPASE\n+>sp|Q8IXT5|RB12B_HUMAN RNA-binding protein 12B OS=Homo sapiens OX=9606 GN=RBM12B PE=1 SV=2\n+MAVVIRLLGLPFIAGPVDIRHFFTGLTIPDGGVHIIGGEIGEAFIIFATDEDARRAISRS\n+GGFIKDSSVELFLSSKAEMQKTIEMKRTDRVGRGRPGSGTSGVDSLSNFIESVKEEASNS\n+GYGSSINQDAGFHTNGTGHGNLRPRKTRPLKAENPYLFLRGLPYLVNEDDVRVFFSGLCV\n+DGVIFLKHHDGRNNGDAIVKFASCVDASGGLKCHRSFMGSRFIEVMQGSEQQWIEFGGNA\n+VKEGDVLRRSEEHSPPRGINDRHFRKRSHSKSPRRTRSRSPLGFYVHLKNLSLSIDERDL\n+RNFFRGTDLTDEQIRFLYKDENRTRYAFVMFKTLKDYNTALSLHKTVLQYRPVHIDPISR\n+KQMLKFIARYEKKRSGSLERDRPGHVSQKYSQEGNSGQKLCIYIRNFPFDVTKVEVQKFF\n+ADFLLAEDDIYLLYDDKGVGLGEALVKFKSEEQAMKAERLNRRRFLGTEVLLRLISEAQI\n+QEFGVNFSVMSSEKMQARSQSRERGDHSHLFDSKDPPIYSVGAFENFRHQLEDLRQLDNF\n+KHPQRDFRQPDRHPPEDFRHSSEDFRFPPEDFRHSPEDFRRPREEDFRRPSEEDFRRPWE\n+EDFRRPPEDDFRHPREEDWRRPLEEDWRRPLEEDFRRSPTEDFRQLPEEDFRQPPEEDLR\n+WLPEEDFRRPPEEDWRRPPEEDFRRPLQGEWRRPPEDDFRRPPEEDFRHSPEEDFRQSPQ\n+EHFRRPPQEHFRRPPPEHFRRPPPEHFRRPPPEHFRRPPPEHFRRPPPEHFRRPPPEHFR\n+RPPQEHFRRPPQEHFRRSREEDFRHPPDEDFRGPPDEDFRHPPDEDFRSPQEEDFRCPSD\n+EDFRQLPEEDLREAPEEDPRLPDNFRPPGEDFRSPPDDFRSHRPFVNFGRPEGGKFDFGK\n+HNMGSFPEGRFMPDPKINCGSGRVTPIKIMNLPFKANVNEILDFFHGYRIIPDSVSIQYN\n+EQGLPTGEAIVAMINYNEAMAAIKDLNDRPVGPRKVKLTLL\n+>sp|Q8N782|ZN525_HUMAN Zinc finger protein 525 OS=Homo sapiens OX=9606 GN=ZNF525 PE=2 SV=2\n+MSSLTYHHRLHTGEKPYKCEECDKAFRHNSALQRHRRIHTGEKPHKCNECGKTFSQKSYL\n+ACHRSIHTGKKPYECEECDKAFSFKSNLESHRITHTGEKPYKCNDCGKTFSHMSTLTCHR\n+RLHTGEKPYKCEECDEAFRFKSSLERHRRIHNGEKLYKCNECGKTFSQELSLTCHCRLHS\n+GEKPCKCGECDKAYSFK\n+>sp|Q9UBQ7|GRHPR_HUMAN Glyoxylate reductase/hydroxypyruvate reductase OS=Homo sapiens OX=9606 GN=GRHPR PE=1 SV=1\n+MRPVRLMKVFVTRRIPAEGRVALARAADCEVEQWDSDEPIPAKELERGVAGAHGLLCLLS\n+DHVDKRILDAAGANLKVISTMSVGIDHLALDEIKKRGIRVGYTPDVLTDTTAELAVSLLL\n+TTCRRLPEAIEEVKNGGWTSWKPLWLCGYGLTQSTVGIIGLGRIGQAIARRLKPFGVQRF\n+LYTGRQPRPEEAAEFQAEFVSTPELAAQSDFIVVACSLTPATEGLCNKDFFQKMKETAVF\n+INISRGDVVNQDDLYQALASGKIAAAGLDVTSPEPLPTNHPLLTLKNCVILPHIGSATHR\n+TRNTMSLLAANNLLAGLRGEPMPSELKL\n+>sp|Q03181|PPARD_HUMAN Peroxisome proliferator-activated receptor delta OS=Homo sapiens OX=9606 GN=PPARD PE=1 SV=1\n+MEQPQEEAPEVREEEEKEEVAEAEGAPELNGGPQHALPSSSYTDLSRSSSPPSLLDQLQM\n+GCDGASCGSLNMECRVCGDKASGFHYGVHACEGCKGFFRRTIRMKLEYEKCERSCKIQKK\n+NRNKCQYCRFQKCLALGMSHNAIRFGRMPEAEKRKLVAGLTANEGSQYNPQVADLKAFSK\n+HIYNAYLKNFNMTKKKARSILTGKASHTAPFVIHDIETLWQAEKGLVWKQLVNGLPPYKE\n+ISVHVFYRCQCTTVETVRELTEFAKSIPSFSSLFLNDQVTLLKYGVHEAIFAMLASIVNK\n+DGLLVANGSGFVTREFLRSLRKPFSDIIEPKFEFAVKFNALELDDSDLALFIAAIILCGD\n+RPGLMNVPRVEAIQDTILRALEFHLQANHPDAQYLFPKLLQKMADLRQLVTEHAQMMQRI\n+KKTETETSLHPLLQEIYKDMY\n+>sp|P78424|PO6F2_HUMAN POU domain, class 6, transcription factor 2 OS=Homo '..b'CFGMLRGFLMTLPQKRKSFQSKSFVRLKDVTAY\n+MWEKVLTFLRLETPKLEEAEMVENHNYYLDEFANLLDELLMKINGLSDSLQLPLLEKTSN\n+NTGEARTEESPLVDISSYQAAEPADIKDF\n+>sp|Q7Z3K3|POGZ_HUMAN Pogo transposable element with ZNF domain OS=Homo sapiens OX=9606 GN=POGZ PE=1 SV=2\n+MADTDLFMECEEEELEPWQKISDVIEDSVVEDYNSVDKTTTVSVSQQPVSAPVPIAAHAS\n+VAGHLSTSTTVSSSGAQNSDSTKKTLVTLIANNNAGNPLVQQGGQPLILTQNPAPGLGTM\n+VTQPVLRPVQVMQNANHVTSSPVASQPIFITTQGFPVRNVRPVQNAMNQVGIVLNVQQGQ\n+TVRPITLVPAPGTQFVKPTVGVPQVFSQMTPVRPGSTMPVRPTTNTFTTVIPATLTIRST\n+VPQSQSQQTKSTPSTSTTPTATQPTSLGQLAVQSPGQSNQTTNPKLAPSFPSPPAVSIAS\n+FVTVKRPGVTGENSNEVAKLVNTLNTIPSLGQSPGPVVVSNNSSAHGSQRTSGPESSMKV\n+TSSIPVFDLQDGGRKICPRCNAQFRVTEALRGHMCYCCPEMVEYQKKGKSLDSEPSVPSA\n+AKPPSPEKTAPVASTPSSTPIPALSPPTKVPEPNENVGDAVQTKLIMLVDDFYYGRDGGK\n+VAQLTNFPKVATSFRCPHCTKRLKNNIRFMNHMKHHVELDQQNGEVDGHTICQHCYRQFS\n+TPFQLQCHLENVHSPYESTTKCKICEWAFESEPLFLQHMKDTHKPGEMPYVCQVCQYRSS\n+LYSEVDVHFRMIHEDTRHLLCPYCLKVFKNGNAFQQHYMRHQKRNVYHCNKCRLQFLFAK\n+DKIEHKLQHHKTFRKPKQLEGLKPGTKVTIRASRGQPRTVPVSSNDTPPSALQEAAPLTS\n+SMDPLPVFLYPPVQRSIQKRAVRKMSVMGRQTCLECSFEIPDFPNHFPTYVHCSLCRYST\n+CCSRAYANHMINNHVPRKSPKYLALFKNSVSGIKLACTSCTFVTSVGDAMAKHLVFNPSH\n+RSSSILPRGLTWIAHSRHGQTRDRVHDRNVKNMYPPPSFPTNKAATVKSAGATPAEPEEL\n+LTPLAPALPSPASTATPPPTPTHPQALALPPLATEGAECLNVDDQDEGSPVTQEPELASG\n+GGGSGGVGKKEQLSVKKLRVVLFALCCNTEQAAEHFRNPQRRIRRWLRRFQASQGENLEG\n+KYLSFEAEEKLAEWVLTQREQQLPVNEETLFQKATKIGRSLEGGFKISYEWAVRFMLRHH\n+LTPHARRAVAHTLPKDVAENAGLFIDFVQRQIHNQDLPLSMIVAIDEISLFLDTEVLSSD\n+DRKENALQTVGTGEPWCDVVLAILADGTVLPTLVFYRGQMDQPANMPDSILLEAKESGYS\n+DDEIMELWSTRVWQKHTACQRSKGMLVMDCHRTHLSEEVLAMLSASSTLPAVVPAGCSSK\n+IQPLDVCIKRTVKNFLHKKWKEQAREMADTACDSDVLLQLVLVWLGEVLGVIGDCPELVQ\n+RSFLVASVLPGPDGNINSPTRNADMQEELIASLEEQLKLSGEHSESSTPRPRSSPEETIE\n+PESLHQLFEGESETESFYGFEEADLDLMEI\n+>sp|Q9WJR5|POK19_HUMAN Endogenous retrovirus group K member 19 Pol protein OS=Homo sapiens OX=9606 GN=ERVK-19 PE=2 SV=2\n+NKSKKRRNRVSFLGAATVEPPKPIPLTWKTEKPVWVNQWPLPKQKLEALHLLANEQLEKG\n+HIEPSFSPWNSPVFVIQKKSGKWRMLTDLRAVNAVNAVIQPMGPLQPGLPSLAMIPKDWP\n+LIIIDLKDCFFTIPLAEQDCEKFAFTIPAINNKEPATRFQWKVLPQGMLNSPTICQTFVG\n+RALQPVREKFSDCYIIHYIDDILCAAEMKDKLIDCYTFLQAEVANAGLAIASDKIQTSTP\n+FHYLEMQIENRKIKPPKIEIRKDTLKTLNDFQKLLGDINWIRPTLGIPTYAMSNLFSILR\n+GDSDLNSKRMLTPEATKEIKLVEEKIQSAQINRIDPLAPLQLLIFATAHSPTGIIIQNTD\n+LVEWSFLPHSTVKTFTLYLDQMATLIGQTRLRIIKLCGNDPDKIVVPLTKEQVRQAFINS\n+GAWQIGLANFVGIIDNHYPKTKIFQFLKMTTWILPKITRREPLENALTVFTDGSSNGKAA\n+YTGPKERVIKTQYQSAQRAELVAVITVLQDFDQPINIISDSAYVVQATRDVETALIKYSM\n+DDQLNQLFNLLQQTVRKRNFPFYITHIRAHTNLPGPLTKANEQADLLVSSALIKAQELHA\n+LTHVNVAGLKNKFDVTWKQAKDIVQHCTQCQVLHLPTQEAGVNPRGLCPNALWQMDVTHV\n+SSFGRLSYIHVTVDTYSHFIWATCQTGESTSHVKKHLLSCFAVMGVPEKIKTDNGPGYCS\n+KAFQKFLSQWKISHTTGIPYNSQGQAIVERTNRTLKTQLVKQKEGGDSKECTTPQMQLNL\n+ALYTLNFLNIYRNQTTTSAEQHLTGKKNSPHEGKLIWWKDNKNKTWEIGKVITWGRGFAC\n+VSPGENQLPVWIPTRHLKFYNEPIGDAKKSTSAETETPQSSTVDSQDEQNGDVRRTDEVA\n+IHQESRAADLGTTKEADAVSYKISREHKGDTNPREYAACGLDDCINGGKSPYACRSSCS\n+>sp|A0A1W2PS18|PMIS2_HUMAN Transmembrane protein PMIS2 OS=Homo sapiens OX=9606 GN=PMIS2 PE=3 SV=1\n+MALKPPSATQPAPNAPATPDAPPTTGDPGASAAPGSPTTTGGPGAPAEVPQEPQEPTQTP\n+EELAFYAPNYLCLTIFAILLFPPFGLAALYFSYEGSWTQKPTSMLPPLQTMKANQNSEWE\n+EAYINSGRTGWFGAFVVMIGLGIIYGLVLY\n+>sp|Q96AD5|PLPL2_HUMAN Patatin-like phospholipase domain-containing protein 2 OS=Homo sapiens OX=9606 GN=PNPLA2 PE=1 SV=1\n+MFPREKTWNISFAGCGFLGVYYVGVASCLREHAPFLVANATHIYGASAGALTATALVTGV\n+CLGEAGAKFIEVSKEARKRFLGPLHPSFNLVKIIRSFLLKVLPADSHEHASGRLGISLTR\n+VSDGENVIISHFNSKDELIQANVCSGFIPVYCGLIPPSLQGVRYVDGGISDNLPLYELKN\n+TITVSPFSGESDICPQDSSTNIHELRVTNTSIQFNLRNLYRLSKALFPPEPLVLREMCKQ\n+GYRDGLRFLQRNGLLNRPNPLLALPPARPHGPEDKDQAVESAQAEDYSQLPGEDHILEHL\n+PARLNEALLEACVEPTDLLTTLSNMLPVRLATAMMVPYTLPLESALSFTIRLLEWLPDVP\n+EDIRWMKEQTGSICQYLVMRAKRKLGRHLPSRLPEQVELRRVQSLPSVPLSCAAYREALP\n+GWMRNNLSLGDALAKWEECQRQLLLGLFCTNVAFPPEALRMRAPADPAPAPADPASPQHQ\n+LAGPAPLLSTPAPEARPVIGALGL\n+>sp|Q9Y342|PLLP_HUMAN Plasmolipin OS=Homo sapiens OX=9606 GN=PLLP PE=1 SV=1\n+MAEFPSKVSTRTSSPAQGAEASVSALRPDLGFVRSRLGALMLLQLVLGLLVWALIADTPY\n+HLYPAYGWVMFVAVFLWLVTIVLFNLYLFQLHMKLYMVPWPLVLMIFNISATVLYITAFI\n+ACSAAVDLTSLRGTRPYNQRAAASFFACLVMIAYGVSAFFSYQAWRGVGSNAATSQMAGG\n+YA\n\\ No newline at end of file\n' |