| Next changeset 1:f444e529363d (2017-02-16) |
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Commit message:
planemo upload |
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added:
MSMS_Extractor.py MSMS_Extractor.xml test_data/Mo_Tai_iTRAQ_f1.mzml test_data/PSM_report_f1.tabular tool_dependencies.xml |
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| diff -r 000000000000 -r 093015b1b904 MSMS_Extractor.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/MSMS_Extractor.py Mon Feb 13 02:44:05 2017 -0500 |
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| @@ -0,0 +1,100 @@ +# +# Developed by Praveen Kumar +# Galaxy-P Team (Griffin's Lab) +# University of Minnesota +# +# + +def main(): + from pyteomics import mzml + import os + import sys + import shutil + import subprocess + import re + import pandas as pd + from operator import itemgetter + from itertools import groupby + if len(sys.argv) >= 5: + # Start of Reading Scans from PSM file + # Creating dictionary of PSM file: key = filename key = list of scan numbers + ScanFile = sys.argv[2] + spectrumTitleList = list(pd.read_csv(ScanFile, "\t")['Spectrum Title']) + scanFileNumber = [[".".join(each.split(".")[:-3]), int(each.split(".")[-2:-1][0])] for each in spectrumTitleList] + scanDict = {} + for each in scanFileNumber: + if scanDict.has_key(each[0]): + scanDict[each[0]].append(int(each[1])) + else: + scanDict[each[0]] = [int(each[1])] + # End of Reading Scans from PSM file + + inputPath = sys.argv[1] + ##outPath = "/".join(sys.argv[3].split("/")[:-1]) + outPath = sys.argv[3] + ##outFile = sys.argv[3].split("/")[-1] + allScanList = [] + + # Read all scan numbers using indexedmzML/indexList/index/offset tags + for k in mzml.read(inputPath).iterfind('indexedmzML/indexList/index/offset'): + if re.search("scan=(\d+)", k['idRef']): + a = re.search("scan=(\d+)", k['idRef']) + allScanList.append(int(a.group(1))) + # End of Reading mzML file + + fraction_name = sys.argv[4] + if scanDict.has_key(fraction_name): + scan2remove = scanDict[fraction_name] + else: + scan2remove = [] + scan2retain = list(set(allScanList) - set(scan2remove)) + scan2retain.sort() + scansRemoved = list(set(allScanList) - set(scan2retain)) + # scan2retain contains scans that is to be retained + + # Print Stats + print >> sys.stdout,"Total number of Scan Numbers: %d" % len(list(set(allScanList))) + print >> sys.stdout,"Number of Scans to remove: %d" % len(list(set(scan2remove))) + print >> sys.stdout,"Number of Scans retained: %d" % len(scan2retain) + print >> sys.stdout,"Number of Scans removed: %d" % len(scansRemoved) + + + # Identifying groups of continuous numbers in the scan2retain and creating scanString + scanString = "" + for a, b in groupby(enumerate(scan2retain), lambda(i,x):i-x): + x = map(itemgetter(1), b) + scanString = scanString + "["+str(x[0])+","+str(x[-1])+"] " + # end identifying + + # start create filter file + filter_file = open("filter.txt", "w") + filter_file.write("filter=scanNumber %s\n" % scanString) + filter_file.close() + # end create filter file + + # Prepare command for msconvert + inputFile = fraction_name+".mzML" + os.symlink(inputPath,inputFile) + outFile = "filtered_"+fraction_name+".mzML" + # msconvert_command = "msconvert " + inputFile + " --filter " + "\"scanNumber " + scanString + " \" " + " --outfile " + outFile + " --mzML --zlib" + msconvert_command = "msconvert " + inputFile + " -c filter.txt " + " --outfile " + outFile + " --mzML --zlib" + + + # Run msconvert + try: + subprocess.check_output(msconvert_command, stderr=subprocess.STDOUT, shell=True) + except subprocess.CalledProcessError as e: + sys.stderr.write( "msconvert resulted in error: %s: %s" % ( e.returncode, e.output )) + sys.exit(e.returncode) + # Copy output to + shutil.copyfile(outFile, outPath) + + else: + print "Please contact the admin. Number of inputs are not sufficient to run the program.\n" + +if __name__ == "__main__": + main() + + + + |
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| diff -r 000000000000 -r 093015b1b904 MSMS_Extractor.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/MSMS_Extractor.xml Mon Feb 13 02:44:05 2017 -0500 |
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| @@ -0,0 +1,26 @@ + +<tool id="MSMS_Extractor" name="MSMS_Extractor" version="1.0.0"> + <description>Removes identified scans from the mzML file using PSM report.</description> + <requirements> + <requirement type="package" version="3.0.9016">proteowizard</requirement> + <requirement type="package" version="3.4">pyteomics</requirement> + </requirements> + <command interpreter="python"><![CDATA[MSMS_Extractor.py $spectrumfile $psmreportfile $output ${spectrumfile.name.rsplit('.',1)[0]}]]></command> + <inputs> + <param name="spectrumfile" type="data" format="mzml"> + <label>Input mzML File</label> + </param> + <param name="psmreportfile" type="data" format="tabular"> + <label>Input PSM Report File</label> + </param> + </inputs> + + <outputs> + <data format="mzml" name="output" label="${spectrumfile.name.rsplit('.',1)[0]}.mzml" /> + </outputs> + + + <help> +Testing to run MSMS_Extractor script in Galaxy + </help> +</tool> |
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| diff -r 000000000000 -r 093015b1b904 test_data/Mo_Tai_iTRAQ_f1.mzml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test_data/Mo_Tai_iTRAQ_f1.mzml Mon Feb 13 02:44:05 2017 -0500 |
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| b'@@ -0,0 +1,723767 @@\n+<?xml version="1.0" encoding="utf-8"?>\n+<indexedmzML xmlns="http://psi.hupo.org/ms/mzml" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://psi.hupo.org/ms/mzml http://psidev.info/files/ms/mzML/xsd/mzML1.1.2_idx.xsd">\n+ <mzML xmlns="http://psi.hupo.org/ms/mzml" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://psi.hupo.org/ms/mzml http://psidev.info/files/ms/mzML/xsd/mzML1.1.0.xsd" id="Mo_Tai_iTRAQ_f1" version="1.1.0">\n+ <cvList count="2">\n+ <cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="3.65.0" URI="http://psidev.cvs.sourceforge.net/*checkout*/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo"/>\n+ <cv id="UO" fullName="Unit Ontology" version="12:10:2011" URI="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/unit.obo"/>\n+ </cvList>\n+ <fileDescription>\n+ <fileContent>\n+ <cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" value=""/>\n+ <cvParam cvRef="MS" accession="MS:1000580" name="MSn spectrum" value=""/>\n+ </fileContent>\n+ <sourceFileList count="1">\n+ <sourceFile id="RAW1" name="Mo_Tai_iTRAQ_f1.raw" location="file:///">\n+ <cvParam cvRef="MS" accession="MS:1000768" name="Thermo nativeID format" value=""/>\n+ <cvParam cvRef="MS" accession="MS:1000563" name="Thermo RAW format" value=""/>\n+ <cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="17bd03b806e0b7b43cedc614c91144284085212b"/>\n+ </sourceFile>\n+ </sourceFileList>\n+ </fileDescription>\n+ <referenceableParamGroupList count="1">\n+ <referenceableParamGroup id="CommonInstrumentParams">\n+ <cvParam cvRef="MS" accession="MS:1001910" name="LTQ Orbitrap Elite" value=""/>\n+ <cvParam cvRef="MS" accession="MS:1000529" name="instrument serial number" value="SN05085B"/>\n+ </referenceableParamGroup>\n+ </referenceableParamGroupList>\n+ <softwareList count="2">\n+ <software id="Xcalibur" version="2.7.0">\n+ <cvParam cvRef="MS" accession="MS:1000532" name="Xcalibur" value=""/>\n+ </software>\n+ <software id="pwiz" version="3.0.6618">\n+ <cvParam cvRef="MS" accession="MS:1000615" name="ProteoWizard software" value=""/>\n+ </software>\n+ </softwareList>\n+ <instrumentConfigurationList count="2">\n+ <instrumentConfiguration id="IC1">\n+ <referenceableParamGroupRef ref="CommonInstrumentParams"/>\n+ <componentList count="3">\n+ <source order="1">\n+ <cvParam cvRef="MS" accession="MS:1000398" name="nanoelectrospray" value=""/>\n+ <cvParam cvRef="MS" accession="MS:1000485" name="nanospray inlet" value=""/>\n+ </source>\n+ <analyzer order="2">\n+ <cvParam cvRef="MS" accession="MS:1000484" name="orbitrap" value=""/>\n+ </analyzer>\n+ <detector order="3">\n+ <cvParam cvRef="MS" accession="MS:1000624" name="inductive detector" value=""/>\n+ </detector>\n+ </componentList>\n+ <softwareRef ref="Xcalibur"/>\n+ </instrumentConfiguration>\n+ <instrumentConfiguration id="IC2">\n+ <referenceableParamGroupRef ref="CommonInstrumentParams"/>\n+ <componentList count="3">\n+ <source order="1">\n+ <cvParam cvRef="MS" accession="MS:1000398" name="nanoelectrospray" value=""/>\n+ <cvParam cvRef="MS" accession="MS:1000485" name="nanospray inlet" value=""/>\n+ </source>\n+ <analyzer order="2">\n+ <cvParam cvRef="MS" accession="MS:1000083" name="radial ejection linear ion trap" value=""/>\n+ </analyzer>\n+ <detector order="3">\n+ <cvParam cvRef="MS" accession="MS:1000253" name="electron multiplier" value=""/>\n+ </detector>\n+ </componentList>\n+ <softwareRef ref="Xcalibur"/>\n+ </instrumentConfiguration>\n+ </instrumentConfigurationList>\n+ <dataProces'..b'\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=13426">275558676</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=13427">275608849</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=13428">275661463</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=13429">275712492</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=13430">275766316</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=13431">275819896</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=13432">275871606</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=13433">275923981</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=13434">275973907</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=13435">276028250</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=13436">276081329</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=13437">276134518</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=13438">276188700</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=13439">276241880</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=13440">276295544</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=13441">276349983</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=13442">276402650</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=13443">276455946</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=13444">276510041</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=13445">276564751</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=13446">276618135</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=13447">276670877</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=13448">276724798</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=13449">276779179</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=13450">276834589</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=13451">276889184</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=13452">276943250</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=13453">276999209</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=13454">277052688</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=13455">277106818</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=13456">277160152</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=13457">277214548</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=13458">277269557</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=13459">277325896</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=13460">277379958</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=13461">277434683</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=13462">277489372</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=13463">277543329</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=13464">277597845</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=13465">277651372</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=13466">277707387</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=13467">277762581</offset>\n+ </index>\n+ <index name="chromatogram">\n+ <offset idRef="TIC">277820252</offset>\n+ </index>\n+ </indexList>\n+ <indexListOffset>278036938</indexListOffset>\n+ <fileChecksum>368ae84b6a63bc91ca41d65d085b61016ee7f8e9</fileChecksum>\n+</indexedmzML>\n' |
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| diff -r 000000000000 -r 093015b1b904 test_data/PSM_report_f1.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test_data/PSM_report_f1.tabular Mon Feb 13 02:44:05 2017 -0500 |
| [ |
| b'@@ -0,0 +1,181 @@\n+\tProtein(s)\tSequence\tVariable Modifications\tFixed Modifications\tSpectrum File\tSpectrum Title\tSpectrum Scan Number\tRT\tm/z\tMeasured Charge\tIdentification Charge\tTheoretical Mass\tIsotope Number\tPrecursor m/z Error [ppm]\tLocalization Confidence\tProbabilistic PTM score\tD-score\tConfidence [%]\tValidation\n+10575\tA0A087WNL7, A0A087WNX7, A0A087WP63, A0A087WQ44, P58390, Q61670\tQPPPPPR\t\tiTRAQ 4-plex of peptide N-term(1)\tMo_Tai_iTRAQ_f1.mgf\tMo_Tai_iTRAQ_f1.10305.10305.2\t\t4652.1978\t467.2789612\t2+\t2+\t931.5361349\t1\t4.155868855\t\t\t\t93.06930693\tConfident\n+10576\tQ9D6J6, Q9D6J6-2\tGPGFGVQAGL\t\tiTRAQ 4-plex of peptide N-term(1)\tMo_Tai_iTRAQ_f1.mgf\tMo_Tai_iTRAQ_f1.8410.8410.2\t\t3878.6177\t523.791687\t2+\t2+\t1045.567829\t0\t0.947096\t\t\t\t100\tConfident\n+10577\tA0A140T8V5, P17918\tIEDEEAS\t\tiTRAQ 4-plex of peptide N-term(1)\tMo_Tai_iTRAQ_f1.mgf\tMo_Tai_iTRAQ_f1.2555.2555.2\t\t1516.3381\t468.7180481\t2+\t2+\t935.4205556\t0\t1.05361899\t\t\t\t95.04950495\tConfident\n+10578\tP10854, Q64478, Q64525, Q6ZWY9\tIAGEASR\t\tiTRAQ 4-plex of peptide N-term(1)\tMo_Tai_iTRAQ_f1.mgf\tMo_Tai_iTRAQ_f1.1505.1505.2\t\t1063.2866\t424.2417908\t2+\t2+\t846.4681149\t0\t1.076889273\t\t\t\t93.06930693\tConfident\n+10579\tQ60692\tFTIATLPPP\t\tiTRAQ 4-plex of peptide N-term(1)\tMo_Tai_iTRAQ_f1.mgf\tMo_Tai_iTRAQ_f1.10811.10811.2\t\t4869.3752\t550.828064\t2+\t2+\t1099.639931\t0\t1.492079647\t\t\t\t94.05940594\tConfident\n+10580\tQ9CXU4, Q9WTQ8\tGSLLQQSL\t\tiTRAQ 4-plex of peptide N-term(1)\tMo_Tai_iTRAQ_f1.mgf\tMo_Tai_iTRAQ_f1.8515.8515.2\t\t3922.2633\t495.291626\t2+\t2+\t988.5674946\t0\t1.215895185\t\t\t\t91.08910891\tConfident\n+10581\tA6X925, B2KF55, Q9D2M8, Q9D2M8-2\tLPQPPEGQTYNN\t\tiTRAQ 4-plex of peptide N-term(1)\tMo_Tai_iTRAQ_f1.mgf\tMo_Tai_iTRAQ_f1.5771.5771.2\t\t2795.7924\t751.3736572\t2+\t2+\t1500.733056\t0\t-0.196181326\t\t\t\t96.03960396\tConfident\n+10582\tP09411\tVLPGVDALSNV\t\tiTRAQ 4-plex of peptide N-term(1)\tMo_Tai_iTRAQ_f1.mgf\tMo_Tai_iTRAQ_f1.11153.11153.2\t\t5015.2472\t614.3571167\t2+\t2+\t1226.699237\t0\t0.360900738\t\t\t\t100\tConfident\n+10583\tP63038, P63038-2\tDPGMGAMGGMGGG\tOxidation of M(4, 10, 7)\tiTRAQ 4-plex of peptide N-term(1)\tMo_Tai_iTRAQ_f1.mgf\tMo_Tai_iTRAQ_f1.1230.1230.2\t\t936.9463\t643.7511597\t2+\t2+\t1285.485892\t0\t1.455532533\tOxidation of M (4: Very Confident, 7: Very Confident, 10: Very Confident)\tOxidation of M (4: 100.0, 7: 100.0, 10: 100.0)\tOxidation of M (4: 99.85994397759103, 7: 99.85994397759103, 10: 99.85994397759103)\t95.04950495\tConfident\n+10584\tD3Z3Z9, E9Q2Q9, F6X737, K4DI78, Q3TRP8, Q8C0D9, Q8C0D9-2, Q9DBN9, Q9JKY0, Q9WUZ7\tGIPLPPQ\t\tiTRAQ 4-plex of peptide N-term(1)\tMo_Tai_iTRAQ_f1.mgf\tMo_Tai_iTRAQ_f1.6828.6828.2\t\t3218.7408\t433.2674561\t2+\t2+\t864.5190878\t0\t1.467161264\t\t\t\t97.02970297\tConfident\n+10585\tH3BLM7, H9H9T1, Q3TGF2\tTGQEVAQAQES\t\tiTRAQ 4-plex of peptide N-term(1)\tMo_Tai_iTRAQ_f1.mgf\tMo_Tai_iTRAQ_f1.1968.1968.2\t\t1266.375\t646.3167114\t2+\t2+\t1290.617358\t0\t1.169742125\t\t\t\t96.03960396\tConfident\n+10586\tE9Q3W4, Q9QXS1, Q9QXS1-10, Q9QXS1-11, Q9QXS1-12, Q9QXS1-13, Q9QXS1-14, Q9QXS1-15, Q9QXS1-16, Q9QXS1-2, Q9QXS1-3, Q9QXS1-4, Q9QXS1-5, Q9QXS1-6, Q9QXS1-7, Q9QXS1-8, Q9QXS1-9\tYASGPSASLGGPESAVA\t\tiTRAQ 4-plex of peptide N-term(1)\tMo_Tai_iTRAQ_f1.mgf\tMo_Tai_iTRAQ_f1.6943.6943.2\t\t3266.5296\t832.9186401\t2+\t2+\t1663.817514\t0\t3.1294327\t\t\t\t100\tConfident\n+10587\tQ8BGD8\tFEAGGFQSSQSTENS\t\tiTRAQ 4-plex of peptide N-term(1)\tMo_Tai_iTRAQ_f1.mgf\tMo_Tai_iTRAQ_f1.5795.5795.2\t\t2804.2182\t860.8845215\t2+\t2+\t1718.750557\t1\t0.336087629\t\t\t\t97.02970297\tConfident\n+10588\tA0A087WQS2, Q9CQC6\tNAEEESESEAEEGD\t\tiTRAQ 4-plex of peptide N-term(1)\tMo_Tai_iTRAQ_f1.mgf\tMo_Tai_iTRAQ_f1.2725.2725.2\t\t1584.4306\t834.8273315\t2+\t2+\t1667.640397\t0\t-0.171970548\t\t\t\t100\tConfident\n+10589\tQ99L27\tVTQQVNPIFSNSQ\t\tiTRAQ 4-plex of peptide N-term(1)\tMo_Tai_iTRAQ_f1.mgf\tMo_Tai_iTRAQ_f1.7612.7612.2\t\t3547.5953\t803.92\t2+\t2+\t1604.828019\t1\t-3.688672461\t\t\t\t90.0990099\tConfident\n+10590\tH3BLM7, H9H9T1, Q3TGF2\tTGQEVAQAQES\t\tiTRAQ 4-plex of peptide N-term(1)\tMo_Tai_iTRAQ_f1.mgf\tMo_Tai_iTRAQ_f1.2044.2044.2\t\t1298.5425\t646.3157959\t2+\t2+\t1290.617358\t0\t-0.246790046\t\t\t\t99.00990099\tConfident\n+10591\tD3Z2H9, E9Q5J9, P21107-2\tMLDQTLLDLNEM\tO'..b'0, 5: 100.0, 8: 100.0, 12: 100.0, 16: 100.0)\t100\tConfident\n+10740\tP63038, P63038-2\tGMGAMGGMGGGMGGGMF\tOxidation of M(2, 5, 8, 12, 16)\tiTRAQ 4-plex of peptide N-term(1)\tMo_Tai_iTRAQ_f1.mgf\tMo_Tai_iTRAQ_f1.3249.3249.2\t\t1801.9408\t843.8135376\t2+\t2+\t1685.60979\t0\t1.619193898\tOxidation of M (2: Very Confident, 5: Very Confident, 8: Very Confident, 12: Very Confident, 16: Very Confident)\tOxidation of M (2: 100.0, 5: 100.0, 8: 100.0, 12: 100.0, 16: 100.0)\tOxidation of M (2: 99.86249570299071, 5: 99.86249570299071, 8: 99.86249570299071, 12: 99.86249570299071, 16: 99.86249570299071)\t95.04950495\tConfident\n+10741\tQ9DCG9\tGIPNMLLNDEETET\tOxidation of M(5)\tiTRAQ 4-plex of peptide N-term(1)\tMo_Tai_iTRAQ_f1.mgf\tMo_Tai_iTRAQ_f1.8609.8609.2\t\t3956.7595\t868.4111938\t2+\t2+\t1734.81038\t0\t-1.465595619\tOxidation of M (5: Very Confident)\tOxidation of M (5: 100.0)\tOxidation of M (5: 100.0)\t100\tConfident\n+10742\tA2ADA5, A2ADA5-2\tSVLYDNFGPTS\t\tiTRAQ 4-plex of peptide N-term(1)\tMo_Tai_iTRAQ_f1.mgf\tMo_Tai_iTRAQ_f1.9033.9033.2\t\t4130.0547\t672.3346558\t2+\t2+\t1342.652681\t0\t1.545243508\t\t\t\t93.06930693\tConfident\n+10743\tE9Q7D8, P57722, P57722-2, P60335, Q61990, Q61990-2, Q61990-3\tESTGAQVQVAGDMLPN\tOxidation of M(13)\tiTRAQ 4-plex of peptide N-term(1)\tMo_Tai_iTRAQ_f1.mgf\tMo_Tai_iTRAQ_f1.5929.5929.2\t\t2856.3233\t888.9321289\t2+\t2+\t1775.848163\t0\t0.867414065\tOxidation of M (13: Very Confident)\tOxidation of M (13: 100.0)\tOxidation of M (13: 99.54640614096301)\t91.08910891\tConfident\n+10744\tQ6ZWN5\tGQGGAGAGDDEEED\t\tiTRAQ 4-plex of peptide N-term(1)\tMo_Tai_iTRAQ_f1.mgf\tMo_Tai_iTRAQ_f1.1378.1378.2\t\t1005.3149\t725.7890015\t2+\t2+\t1449.561359\t0\t1.440419751\t\t\t\t100\tConfident\n+10745\tQ91WK2\tLFMAQALQEYNN\tOxidation of M(3)\tiTRAQ 4-plex of peptide N-term(1)\tMo_Tai_iTRAQ_f1.mgf\tMo_Tai_iTRAQ_f1.9233.9233.2\t\t4211.1222\t801.3913574\t2+\t2+\t1600.767728\t0\t0.270980688\tOxidation of M (3: Very Confident)\tOxidation of M (3: 100.0)\tOxidation of M (3: 98.64583333333333)\t97.02970297\tConfident\n+10746\tQ9CR61\tVAQGQGEGEVGPEVAL\t\tiTRAQ 4-plex of peptide N-term(1)\tMo_Tai_iTRAQ_f1.mgf\tMo_Tai_iTRAQ_f1.8029.8029.2\t\t3723.6095\t842.4378662\t2+\t2+\t1682.859713\t0\t0.870149578\t\t\t\t100\tConfident\n+10747\tQ923B1\tNQAIYAAVDDGDASAE\t\tiTRAQ 4-plex of peptide N-term(1)\tMo_Tai_iTRAQ_f1.mgf\tMo_Tai_iTRAQ_f1.6933.6933.2\t\t3262.1197\t877.4032593\t2+\t2+\t1752.792422\t0\t-0.259892047\t\t\t\t92.07920792\tConfident\n+10748\tQ8BJ71, Q8BJ71-2\tLVQMEVLMN\tOxidation of M(4, 8)\tiTRAQ 4-plex of peptide N-term(1)\tMo_Tai_iTRAQ_f1.mgf\tMo_Tai_iTRAQ_f1.6453.6453.2\t\t3068.9498\t626.8238525\t2+\t2+\t1251.63248\t0\t0.536163891\tOxidation of M (4: Very Confident, 8: Very Confident)\tOxidation of M (4: 100.0, 8: 100.0)\tOxidation of M (4: 100.0, 8: 100.0)\t100\tConfident\n+10749\tQ8R2P8, Q99MN1\tETAATTETPESTEASPSV\t\tiTRAQ 4-plex of peptide N-term(1)\tMo_Tai_iTRAQ_f1.mgf\tMo_Tai_iTRAQ_f1.4630.4630.2\t\t2352.1831\t976.4592896\t2+\t2+\t1950.90276\t0\t0.648359185\t\t\t\t100\tConfident\n+10750\tA0A0R4J259, G3UXJ6, G3UY67, G3UYK7, G3UZ48, G3UZI2, Q7TMK9-2\tGVEAGPDLLQ\t\tiTRAQ 4-plex of peptide N-term(1)\tMo_Tai_iTRAQ_f1.mgf\tMo_Tai_iTRAQ_f1.7903.7903.2\t\t3672.2559\t571.8132324\t2+\t2+\t1141.610088\t0\t1.595144535\t\t\t\t100\tConfident\n+10751\tP62806\tTLYGFGG\t\tiTRAQ 4-plex of peptide N-term(1)\tMo_Tai_iTRAQ_f1.mgf\tMo_Tai_iTRAQ_f1.8779.8779.2\t\t4023.7802\t429.727356\t2+\t2+\t857.4405032\t0\t-0.400459395\t\t\t\t95.04950495\tConfident\n+10752\tQ6ZQ38\tDSSSTNLESMDTS\tOxidation of M(10)\tiTRAQ 4-plex of peptide N-term(1)\tMo_Tai_iTRAQ_f1.mgf\tMo_Tai_iTRAQ_f1.2507.2507.2\t\t1496.0082\t767.3215332\t2+\t2+\t1532.626996\t0\t0.988715252\tOxidation of M (10: Very Confident)\tOxidation of M (10: 100.0)\tOxidation of M (10: 100.0)\t100\tConfident\n+10753\tP62305\tGDNITLLQSVSN\t\tiTRAQ 4-plex of peptide N-term(1)\tMo_Tai_iTRAQ_f1.mgf\tMo_Tai_iTRAQ_f1.8956.8956.2\t\t4098.3567\t702.8768921\t2+\t2+\t1403.737807\t0\t1.012901215\t\t\t\t100\tConfident\n+10754\tP10853, P10854, P70696, Q64475, Q64478, Q64525, Q6ZWY9, Q8CBB6, Q8CGP1, Q8CGP2, Q8CGP2-2\tEIQTAVR\t\tiTRAQ 4-plex of peptide N-term(1)\tMo_Tai_iTRAQ_f1.mgf\tMo_Tai_iTRAQ_f1.2492.2492.2\t\t1489.6677\t480.7835083\t2+\t2+\t959.5521789\t0\t0.296186773\t\t\t\t92.07920792\tConfident\n' |
| b |
| diff -r 000000000000 -r 093015b1b904 tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Mon Feb 13 02:44:05 2017 -0500 |
| b |
| @@ -0,0 +1,6 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="proteowizard" version="3.0.9016"> + <repository changeset_revision="e9ae8f0be737" name="package_proteowizard_3_0_9016" owner="galaxyp" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> +</tool_dependency> |