Retention_Time_PrediTandem_Param_File00 Parameters for X!Tandem 2012-09-03 09:43:23.779 UTC FASTA_File00 Sequence database in FASTA format 2012-09-03 09:43:08.867 UTC Log_File00 Log file to which X!Tandem Beanshell output will be written (can be omitted if the corresponding line in the "Tandem" component is removed). 2012-09-03 09:44:19.461 UTC mzXML_File00 LC-MS/MS data in mzXML format 2012-09-03 09:40:25.17 UTC Predicted_RT_PeptidesGraphic_RetentionCoefficient_AARead_Text_Filefileurl0filecontents00 This shell reads the Tandem results to feed the XPath extractors below. 2012-08-28 13:27:15.442 UTC net.sf.taverna.t2.activitieslocalworker-activity1.4net.sf.taverna.t2.activities.localworker.LocalworkerActivity fileurl 0 'text/plain' java.lang.String true encoding 0 'text/plain' java.lang.String true filecontents 0 'text/plain' 0 workflow net.sourceforge.taverna.scuflworkers.io.TextFileReader net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeExtract_Peptidesxml_text0nodelist11 This XPath extracts the amino acid sequences of the identified peptides. 2012-08-28 13:27:37.613 UTC net.sf.taverna.t2.activitiesxpath-activity1.4net.sf.taverna.t2.activities.xpath.XPathActivity <?xml version="1.0" encoding="UTF-8"?> <?xml-stylesheet type="text/xsl" href="http://localhost:8080/ISB/data/Ecoli/interact.pep.xsl"?><msms_pipeline_analysis xmlns="http://regis-web.systemsbiology.net/pepXML" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" date="2012-01-18T19:58:42" summary_xml="c:/Inetpub/wwwroot/ISB/data/Ecoli/interact.pep.xml" xsi:schemaLocation="http://regis-web.systemsbiology.net/pepXML http://localhost/pepXML_v117.xsd"> <analysis_summary analysis="peptideprophet" time="2012-01-18T19:58:51"> <peptideprophet_summary version="PeptideProphet (TPP v4.5 RAPTURE rev 1, Build 201111221430 (MinGW))" author="AKeller@ISB" min_prob="0.05" options=" MINPROB=0.05 " est_tot_num_correct="11327.9"> <inputfile name="c:/Inetpub/wwwroot/ISB/data/Ecoli/120117.LC2.IT2.EC.scanmode_Cap_1-E,1_01_3481"/> <roc_error_data charge="all"> <roc_data_point min_prob="0.9999" sensitivity="0.0000" error="0" num_corr="0" num_incorr="0"/> <roc_data_point min_prob="0.9990" sensitivity="0.2329" error="0.0005" num_corr="2639" num_incorr="1"/> <roc_data_point min_prob="0.9900" sensitivity="0.5553" error="0.0024" num_corr="6291" num_incorr="15"/> <roc_data_point min_prob="0.9800" sensitivity="0.6320" error="0.0039" num_corr="7159" num_incorr="28"/> <roc_data_point min_prob="0.9500" sensitivity="0.7284" error="0.0077" num_corr="8252" num_incorr="64"/> <roc_data_point min_prob="0.9000" sensitivity="0.7912" error="0.0132" num_corr="8962" num_incorr="120"/> <roc_data_point min_prob="0.8500" sensitivity="0.8282" error="0.0187" num_corr="9382" num_incorr="179"/> <roc_data_point min_prob="0.8000" sensitivity="0.8528" error="0.0240" num_corr="9661" num_incorr="237"/> <roc_data_point min_prob="0.7500" sensitivity="0.8707" error="0.0291" num_corr="9864" num_incorr="295"/> <roc_data_point min_prob="0.7000" sensitivity="0.8853" error="0.0345" num_corr="10029" num_incorr="359"/> <roc_data_point min_prob="0.6500" sensitivity="0.8974" error="0.0401" num_corr="10166" num_incorr="424"/> <roc_data_point min_prob="0.6000" sensitivity="0.9078" error="0.0459" num_corr="10284" num_incorr="495"/> <roc_data_point min_prob="0.5500" sensitivity="0.9172" error="0.0523" num_corr="10390" num_incorr="574"/> <roc_data_point min_prob="0.5000" sensitivity="0.9260" error="0.0594" num_corr="10489" num_incorr="663"/> <roc_data_point min_prob="0.4500" sensitivity="0.9343" error="0.0675" num_corr="10584" num_incorr="766"/> <roc_data_point min_prob="0.4000" sensitivity="0.9416" error="0.0761" num_corr="10666" num_incorr="878"/> <roc_data_point min_prob="0.3500" sensitivity="0.9484" error="0.0858" num_corr="10743" num_incorr="1008"/> <roc_data_point min_prob="0.3000" sensitivity="0.9553" error="0.0977" num_corr="10821" num_incorr="1172"/> <roc_data_point min_prob="0.2500" sensitivity="0.9609" error="0.1096" num_corr="10885" num_incorr="1340"/> <roc_data_point min_prob="0.2000" sensitivity="0.9671" error="0.1264" num_corr="10955" num_incorr="1585"/> <roc_data_point min_prob="0.1500" sensitivity="0.9737" error="0.1495" num_corr="11030" num_incorr="1938"/> <roc_data_point min_prob="0.1000" sensitivity="0.9805" error="0.1830" num_corr="11107" num_incorr="2487"/> <roc_data_point min_prob="0.0500" sensitivity="0.9886" error="0.2474" num_corr="11198" num_incorr="3682"/> <roc_data_point min_prob="0.0000" sensitivity="1.0000" error="0.8023" num_corr="11328" num_incorr="45984"/> <error_point error="0.0000" min_prob="0.9998" num_corr="2" num_incorr="0"/> <error_point error="0.0001" min_prob="0.9998" num_corr="2" num_incorr="0"/> <error_point error="0.0002" min_prob="0.9998" num_corr="2" num_incorr="0"/> <error_point error="0.0003" min_prob="0.9996" num_corr="984" num_incorr="0"/> <error_point error="0.0004" min_prob="0.9993" num_corr="1864" num_incorr="1"/> <error_point error="0.0005" min_prob="0.9990" num_corr="2483" num_incorr="1"/> <error_point error="0.0006" min_prob="0.9987" num_corr="2960" num_incorr="2"/> <error_point error="0.0007" min_prob="0.9984" num_corr="3351" num_incorr="2"/> <error_point error="0.0008" min_prob="0.9981" num_corr="3703" num_incorr="3"/> <error_point error="0.0009" min_prob="0.9977" num_corr="4009" num_incorr="4"/> <error_point error="0.0010" min_prob="0.9973" num_corr="4276" num_incorr="4"/> <error_point error="0.0015" min_prob="0.9951" num_corr="5254" num_incorr="8"/> <error_point error="0.0020" min_prob="0.9925" num_corr="5887" num_incorr="12"/> <error_point error="0.0025" min_prob="0.9896" num_corr="6344" num_incorr="16"/> <error_point error="0.0030" min_prob="0.9864" num_corr="6695" num_incorr="20"/> <error_point error="0.0040" min_prob="0.9793" num_corr="7206" num_incorr="29"/> <error_point error="0.0050" min_prob="0.9724" num_corr="7579" num_incorr="38"/> <error_point error="0.0060" min_prob="0.9651" num_corr="7873" num_incorr="48"/> <error_point error="0.0070" min_prob="0.9558" num_corr="8109" num_incorr="57"/> <error_point error="0.0080" min_prob="0.9472" num_corr="8302" num_incorr="67"/> <error_point error="0.0090" min_prob="0.9382" num_corr="8465" num_incorr="77"/> <error_point error="0.0100" min_prob="0.9298" num_corr="8609" num_incorr="87"/> <error_point error="0.0150" min_prob="0.8822" num_corr="9124" num_incorr="139"/> <error_point error="0.0200" min_prob="0.8393" num_corr="9461" num_incorr="193"/> <error_point error="0.0250" min_prob="0.7912" num_corr="9708" num_incorr="249"/> <error_point error="0.0300" min_prob="0.7385" num_corr="9895" num_incorr="307"/> <error_point error="0.0400" min_prob="0.6501" num_corr="10165" num_incorr="424"/> <error_point error="0.0500" min_prob="0.5682" num_corr="10355" num_incorr="545"/> <error_point error="0.0750" min_prob="0.4066" num_corr="10657" num_incorr="865"/> <error_point error="0.1000" min_prob="0.2882" num_corr="10835" num_incorr="1205"/> </roc_error_data> <roc_error_data charge="1" charge_est_correct="29.1"> <roc_data_point min_prob="0.9999" sensitivity="0.0000" error="0" num_corr="0" num_incorr="0"/> <roc_data_point min_prob="0.9990" sensitivity="0.0000" error="0" num_corr="0" num_incorr="0"/> <roc_data_point min_prob="0.9900" sensitivity="0.0000" error="0" num_corr="0" num_incorr="0"/> <roc_data_point min_prob="0.9800" sensitivity="0.0337" error="0.0189" num_corr="1" num_incorr="0"/> <roc_data_point min_prob="0.9500" sensitivity="0.2990" error="0.0320" num_corr="9" num_incorr="0"/> <roc_data_point min_prob="0.9000" sensitivity="0.4899" error="0.0483" num_corr="14" num_incorr="1"/> <roc_data_point min_prob="0.8500" sensitivity="0.5206" error="0.0519" num_corr="15" num_incorr="1"/> <roc_data_point min_prob="0.8000" sensitivity="0.5786" error="0.0633" num_corr="17" num_incorr="1"/> <roc_data_point min_prob="0.7500" sensitivity="0.6060" error="0.0706" num_corr="18" num_incorr="1"/> <roc_data_point min_prob="0.7000" sensitivity="0.6566" error="0.0889" num_corr="19" num_incorr="2"/> <roc_data_point min_prob="0.6500" sensitivity="0.6804" error="0.0987" num_corr="20" num_incorr="2"/> <roc_data_point min_prob="0.6000" sensitivity="0.6804" error="0.0987" num_corr="20" num_incorr="2"/> <roc_data_point min_prob="0.5500" sensitivity="0.7582" error="0.1502" num_corr="22" num_incorr="4"/> <roc_data_point min_prob="0.5000" sensitivity="0.8132" error="0.1828" num_corr="24" num_incorr="5"/> <roc_data_point min_prob="0.4500" sensitivity="0.8464" error="0.2044" num_corr="25" num_incorr="6"/> <roc_data_point min_prob="0.4000" sensitivity="0.8760" error="0.2264" num_corr="26" num_incorr="7"/> <roc_data_point min_prob="0.3500" sensitivity="0.8760" error="0.2264" num_corr="26" num_incorr="7"/> <roc_data_point min_prob="0.3000" sensitivity="0.8982" error="0.2522" num_corr="26" num_incorr="9"/> <roc_data_point min_prob="0.2500" sensitivity="0.9076" error="0.2653" num_corr="26" num_incorr="10"/> <roc_data_point min_prob="0.2000" sensitivity="0.9230" error="0.2922" num_corr="27" num_incorr="11"/> <roc_data_point min_prob="0.1500" sensitivity="0.9230" error="0.2922" num_corr="27" num_incorr="11"/> <roc_data_point min_prob="0.1000" sensitivity="0.9489" error="0.3715" num_corr="28" num_incorr="16"/> <roc_data_point min_prob="0.0500" sensitivity="0.9682" error="0.4574" num_corr="28" num_incorr="24"/> <roc_data_point min_prob="0.0000" sensitivity="1.0000" error="0.8372" num_corr="29" num_incorr="150"/> <error_point error="0.0000" min_prob="0.9811" num_corr="2" num_incorr="0"/> <error_point error="0.0001" min_prob="0.9811" num_corr="2" num_incorr="0"/> <error_point error="0.0002" min_prob="0.9811" num_corr="2" num_incorr="0"/> <error_point error="0.0003" min_prob="0.9811" num_corr="2" num_incorr="0"/> <error_point error="0.0004" min_prob="0.9811" num_corr="2" num_incorr="0"/> <error_point error="0.0005" min_prob="0.9811" num_corr="2" num_incorr="0"/> <error_point error="0.0006" min_prob="0.9811" num_corr="2" num_incorr="0"/> <error_point error="0.0007" min_prob="0.9811" num_corr="2" num_incorr="0"/> <error_point error="0.0008" min_prob="0.9811" num_corr="2" num_incorr="0"/> <error_point error="0.0009" min_prob="0.9811" num_corr="2" num_incorr="0"/> <error_point error="0.0010" min_prob="0.9811" num_corr="2" num_incorr="0"/> <error_point error="0.0015" min_prob="0.9811" num_corr="2" num_incorr="0"/> <error_point error="0.0020" min_prob="0.9811" num_corr="2" num_incorr="0"/> <error_point error="0.0025" min_prob="0.9811" num_corr="2" num_incorr="0"/> <error_point error="0.0030" min_prob="0.9811" num_corr="2" num_incorr="0"/> <error_point error="0.0040" min_prob="0.9811" num_corr="2" num_incorr="0"/> <error_point error="0.0050" min_prob="0.9811" num_corr="2" num_incorr="0"/> <error_point error="0.0060" min_prob="0.9811" num_corr="2" num_incorr="0"/> <error_point error="0.0070" min_prob="0.9811" num_corr="2" num_incorr="0"/> <error_point error="0.0080" min_prob="0.9811" num_corr="2" num_incorr="0"/> <error_point error="0.0090" min_prob="0.9811" num_corr="2" num_incorr="0"/> <error_point error="0.0100" min_prob="0.9811" num_corr="2" num_incorr="0"/> <error_point error="0.0150" min_prob="0.9811" num_corr="2" num_incorr="0"/> <error_point error="0.0200" min_prob="0.9754" num_corr="4" num_incorr="0"/> <error_point error="0.0250" min_prob="0.9660" num_corr="6" num_incorr="0"/> <error_point error="0.0300" min_prob="0.9598" num_corr="9" num_incorr="0"/> <error_point error="0.0400" min_prob="0.9255" num_corr="13" num_incorr="1"/> <error_point error="0.0500" min_prob="0.8938" num_corr="16" num_incorr="1"/> <error_point error="0.0750" min_prob="0.7455" num_corr="19" num_incorr="2"/> <error_point error="0.1000" min_prob="0.5826" num_corr="21" num_incorr="3"/> </roc_error_data> <roc_error_data charge="2" charge_est_correct="7771.4"> <roc_data_point min_prob="0.9999" sensitivity="0.0000" error="0" num_corr="0" num_incorr="0"/> <roc_data_point min_prob="0.9990" sensitivity="0.3395" error="0.0005" num_corr="2639" num_incorr="1"/> <roc_data_point min_prob="0.9900" sensitivity="0.6803" error="0.0020" num_corr="5287" num_incorr="11"/> <roc_data_point min_prob="0.9800" sensitivity="0.7440" error="0.0031" num_corr="5782" num_incorr="18"/> <roc_data_point min_prob="0.9500" sensitivity="0.8195" error="0.0058" num_corr="6369" num_incorr="37"/> <roc_data_point min_prob="0.9000" sensitivity="0.8678" error="0.0097" num_corr="6744" num_incorr="66"/> <roc_data_point min_prob="0.8500" sensitivity="0.8921" error="0.0132" num_corr="6933" num_incorr="93"/> <roc_data_point min_prob="0.8000" sensitivity="0.9088" error="0.0167" num_corr="7063" num_incorr="120"/> <roc_data_point min_prob="0.7500" sensitivity="0.9212" error="0.0202" num_corr="7159" num_incorr="148"/> <roc_data_point min_prob="0.7000" sensitivity="0.9310" error="0.0239" num_corr="7235" num_incorr="177"/> <roc_data_point min_prob="0.6500" sensitivity="0.9385" error="0.0273" num_corr="7293" num_incorr="205"/> <roc_data_point min_prob="0.6000" sensitivity="0.9455" error="0.0313" num_corr="7348" num_incorr="238"/> <roc_data_point min_prob="0.5500" sensitivity="0.9513" error="0.0354" num_corr="7393" num_incorr="271"/> <roc_data_point min_prob="0.5000" sensitivity="0.9569" error="0.0401" num_corr="7437" num_incorr="310"/> <roc_data_point min_prob="0.4500" sensitivity="0.9614" error="0.0446" num_corr="7471" num_incorr="349"/> <roc_data_point min_prob="0.4000" sensitivity="0.9661" error="0.0503" num_corr="7508" num_incorr="397"/> <roc_data_point min_prob="0.3500" sensitivity="0.9710" error="0.0578" num_corr="7546" num_incorr="463"/> <roc_data_point min_prob="0.3000" sensitivity="0.9754" error="0.0659" num_corr="7581" num_incorr="534"/> <roc_data_point min_prob="0.2500" sensitivity="0.9787" error="0.0733" num_corr="7606" num_incorr="601"/> <roc_data_point min_prob="0.2000" sensitivity="0.9824" error="0.0842" num_corr="7635" num_incorr="701"/> <roc_data_point min_prob="0.1500" sensitivity="0.9865" error="0.1005" num_corr="7667" num_incorr="856"/> <roc_data_point min_prob="0.1000" sensitivity="0.9902" error="0.1208" num_corr="7695" num_incorr="1057"/> <roc_data_point min_prob="0.0500" sensitivity="0.9944" error="0.1610" num_corr="7728" num_incorr="1483"/> <roc_data_point min_prob="0.0000" sensitivity="1.0000" error="0.7229" num_corr="7771" num_incorr="20271"/> <error_point error="0.0000" min_prob="0.9998" num_corr="2" num_incorr="0"/> <error_point error="0.0001" min_prob="0.9998" num_corr="2" num_incorr="0"/> <error_point error="0.0002" min_prob="0.9998" num_corr="2" num_incorr="0"/> <error_point error="0.0003" min_prob="0.9996" num_corr="984" num_incorr="0"/> <error_point error="0.0004" min_prob="0.9993" num_corr="1864" num_incorr="1"/> <error_point error="0.0005" min_prob="0.9990" num_corr="2483" num_incorr="1"/> <error_point error="0.0006" min_prob="0.9987" num_corr="2960" num_incorr="2"/> <error_point error="0.0007" min_prob="0.9983" num_corr="3340" num_incorr="2"/> <error_point error="0.0008" min_prob="0.9979" num_corr="3653" num_incorr="3"/> <error_point error="0.0009" min_prob="0.9974" num_corr="3907" num_incorr="4"/> <error_point error="0.0010" min_prob="0.9970" num_corr="4125" num_incorr="4"/> <error_point error="0.0015" min_prob="0.9940" num_corr="4848" num_incorr="7"/> <error_point error="0.0020" min_prob="0.9902" num_corr="5266" num_incorr="11"/> <error_point error="0.0025" min_prob="0.9859" num_corr="5547" num_incorr="14"/> <error_point error="0.0030" min_prob="0.9810" num_corr="5751" num_incorr="17"/> <error_point error="0.0040" min_prob="0.9716" num_corr="6045" num_incorr="24"/> <error_point error="0.0050" min_prob="0.9595" num_corr="6249" num_incorr="31"/> <error_point error="0.0060" min_prob="0.9472" num_corr="6397" num_incorr="39"/> <error_point error="0.0070" min_prob="0.9355" num_corr="6514" num_incorr="46"/> <error_point error="0.0080" min_prob="0.9220" num_corr="6611" num_incorr="53"/> <error_point error="0.0090" min_prob="0.9116" num_corr="6692" num_incorr="61"/> <error_point error="0.0100" min_prob="0.8964" num_corr="6763" num_incorr="68"/> <error_point error="0.0150" min_prob="0.8271" num_corr="7005" num_incorr="107"/> <error_point error="0.0200" min_prob="0.7540" num_corr="7156" num_incorr="146"/> <error_point error="0.0250" min_prob="0.6876" num_corr="7257" num_incorr="186"/> <error_point error="0.0300" min_prob="0.6146" num_corr="7332" num_incorr="227"/> <error_point error="0.0400" min_prob="0.5004" num_corr="7437" num_incorr="310"/> <error_point error="0.0500" min_prob="0.4039" num_corr="7507" num_incorr="396"/> <error_point error="0.0750" min_prob="0.2413" num_corr="7611" num_incorr="618"/> <error_point error="0.1000" min_prob="0.1506" num_corr="7666" num_incorr="853"/> </roc_error_data> <roc_error_data charge="3" charge_est_correct="3527.4"> <roc_data_point min_prob="0.9999" sensitivity="0.0000" error="0" num_corr="0" num_incorr="0"/> <roc_data_point min_prob="0.9990" sensitivity="0.0000" error="0" num_corr="0" num_incorr="0"/> <roc_data_point min_prob="0.9900" sensitivity="0.2845" error="0.0045" num_corr="1003" num_incorr="5"/> <roc_data_point min_prob="0.9800" sensitivity="0.3901" error="0.0072" num_corr="1376" num_incorr="10"/> <roc_data_point min_prob="0.9500" sensitivity="0.5313" error="0.0141" num_corr="1874" num_incorr="27"/> 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[ntt]"> <posmodel_distribution> <parameter name="ntt=0" value="0.000"/> <parameter name="ntt=1" value="0.000"/> <parameter name="ntt=2" value="1.000"/> </posmodel_distribution> <negmodel_distribution> <parameter name="ntt=0" value="0.000"/> <parameter name="ntt=1" value="0.000"/> <parameter name="ntt=2" value="1.000"/> </negmodel_distribution> </mixturemodel_distribution> <mixturemodel_distribution name="no. missed enz. cleavages [nmc]"> <posmodel_distribution> <parameter name="nmc=0" value="0.970"/> <parameter name="1&lt;=nmc&lt;=2" value="0.030"/> <parameter name="nmc&gt;=3" value="0.000"/> </posmodel_distribution> <negmodel_distribution> <parameter name="nmc=0" value="0.564"/> <parameter name="1&lt;=nmc&lt;=2" value="0.436"/> <parameter name="nmc&gt;=3" value="0.000"/> </negmodel_distribution> </mixturemodel_distribution> <mixturemodel_distribution name="accurate mass diff [massd] (offset: 0.500000)"> <posmodel_distribution> <parameter name="massd=-5.000000" value="0.000000000"/> <parameter name="massd=-4.000000" value="0.000000000"/> <parameter name="massd=-3.000000" value="0.000000000"/> <parameter name="massd=-2.000000" value="0.000000000"/> <parameter name="massd=-1.000000" value="0.017842901"/> <parameter name="massd=0.000000" value="0.849793029"/> <parameter name="massd=1.000000" value="0.132308840"/> <parameter name="massd=2.000000" value="0.000055130"/> <parameter name="massd=3.000000" value="0.000000100"/> <parameter name="massd=4.000000" value="0.000000000"/> <parameter name="massd=5.000000" value="0.000000000"/> </posmodel_distribution> <negmodel_distribution> <parameter name="massd=-5.000000" value="0.000000000"/> <parameter name="massd=-4.000000" value="0.000000000"/> <parameter name="massd=-3.000000" value="0.000000000"/> <parameter name="massd=-2.000000" value="0.000000000"/> <parameter name="massd=-1.000000" value="0.284651386"/> <parameter name="massd=0.000000" value="0.461161272"/> <parameter name="massd=1.000000" value="0.202549544"/> <parameter name="massd=2.000000" value="0.051637759"/> <parameter name="massd=3.000000" value="0.000000039"/> <parameter name="massd=4.000000" value="0.000000000"/> <parameter name="massd=5.000000" value="0.000000000"/> </negmodel_distribution> </mixturemodel_distribution> </mixture_model> <mixture_model precursor_ion_charge="3" comments="using training data negative distributions" prior_probability="0.122" est_tot_correct="3527.4" tot_num_spectra="29091" num_iterations="27"> <mixturemodel_distribution name="X! Tandem (k-score) discrim score [fval] negmean: -0.97"> <posmodel_distribution type="gaussian"> <parameter name="mean" value="5.08"/> <parameter name="stdev" value="2.38"/> </posmodel_distribution> <negmodel_distribution type="evd"> <parameter name="mean" value="-0.97"/> <parameter name="stdev" value="1.30"/> <parameter name="mu" value="-1.56"/> <parameter name="beta" value="1.02"/> </negmodel_distribution> </mixturemodel_distribution> <mixturemodel_distribution name="no. tolerable trypsin term. [ntt]"> <posmodel_distribution> <parameter name="ntt=0" value="0.000"/> <parameter name="ntt=1" value="0.000"/> <parameter name="ntt=2" value="1.000"/> </posmodel_distribution> <negmodel_distribution> <parameter name="ntt=0" value="0.000"/> <parameter name="ntt=1" value="0.000"/> <parameter name="ntt=2" value="1.000"/> </negmodel_distribution> </mixturemodel_distribution> <mixturemodel_distribution name="no. missed enz. cleavages [nmc]"> <posmodel_distribution> <parameter name="nmc=0" value="0.679"/> <parameter name="1&lt;=nmc&lt;=2" value="0.321"/> <parameter name="nmc&gt;=3" value="0.000"/> </posmodel_distribution> <negmodel_distribution> <parameter name="nmc=0" value="0.383"/> <parameter name="1&lt;=nmc&lt;=2" value="0.617"/> <parameter name="nmc&gt;=3" value="0.000"/> </negmodel_distribution> </mixturemodel_distribution> <mixturemodel_distribution name="accurate mass diff [massd] (offset: 1.000000)"> <posmodel_distribution> <parameter name="massd=-5.000000" value="0.000000000"/> <parameter name="massd=-4.000000" value="0.000000000"/> <parameter name="massd=-3.000000" value="0.000000000"/> <parameter name="massd=-2.000000" value="0.000000000"/> <parameter name="massd=-1.000000" value="0.036348041"/> <parameter name="massd=0.000000" value="0.556341292"/> <parameter name="massd=1.000000" value="0.405792869"/> <parameter name="massd=2.000000" value="0.001516952"/> <parameter name="massd=3.000000" value="0.000000847"/> <parameter name="massd=4.000000" value="0.000000000"/> <parameter name="massd=5.000000" value="0.000000000"/> </posmodel_distribution> <negmodel_distribution> <parameter name="massd=-5.000000" value="0.000000000"/> <parameter name="massd=-4.000000" value="0.000000000"/> <parameter name="massd=-3.000000" value="0.000000000"/> <parameter name="massd=-2.000000" value="0.000078313"/> <parameter name="massd=-1.000000" value="0.369722306"/> <parameter name="massd=0.000000" value="0.379025010"/> <parameter name="massd=1.000000" value="0.249620568"/> <parameter name="massd=2.000000" value="0.001553685"/> <parameter name="massd=3.000000" value="0.000000118"/> <parameter name="massd=4.000000" value="0.000000000"/> <parameter name="massd=5.000000" value="0.000000000"/> </negmodel_distribution> </mixturemodel_distribution> </mixture_model> <mixture_model precursor_ion_charge="4" comments="using training data negative distributions" prior_probability="0.000" est_tot_correct="0.0" tot_num_spectra="0" num_iterations="21"> <mixturemodel_distribution name="X! Tandem (k-score) discrim score [fval] negmean: -0.20"> <posmodel_distribution type="gaussian"> <parameter name="mean" value="4.01"/> <parameter name="stdev" value="2.53"/> </posmodel_distribution> <negmodel_distribution type="evd"> <parameter name="mean" value="-0.20"/> <parameter name="stdev" value="0.86"/> <parameter name="mu" value="-0.59"/> <parameter name="beta" value="0.67"/> </negmodel_distribution> </mixturemodel_distribution> <mixturemodel_distribution name="no. tolerable trypsin term. [ntt]"> <posmodel_distribution> <parameter name="ntt=0" value="0.333"/> <parameter name="ntt=1" value="0.333"/> <parameter name="ntt=2" value="0.333"/> </posmodel_distribution> <negmodel_distribution> <parameter name="ntt=0" value="0.333"/> <parameter name="ntt=1" value="0.333"/> <parameter name="ntt=2" value="0.333"/> </negmodel_distribution> </mixturemodel_distribution> <mixturemodel_distribution name="no. missed enz. cleavages [nmc]"> <posmodel_distribution> <parameter name="nmc=0" value="0.333"/> <parameter name="1&lt;=nmc&lt;=2" value="0.333"/> <parameter name="nmc&gt;=3" value="0.333"/> </posmodel_distribution> <negmodel_distribution> <parameter name="nmc=0" value="0.333"/> <parameter name="1&lt;=nmc&lt;=2" value="0.333"/> <parameter name="nmc&gt;=3" value="0.333"/> </negmodel_distribution> </mixturemodel_distribution> <mixturemodel_distribution name="accurate mass diff [massd] (offset: 0.000000)"> <posmodel_distribution> <parameter name="massd=-5.000000" value="0.090909091"/> <parameter name="massd=-4.000000" value="0.090909091"/> <parameter name="massd=-3.000000" value="0.090909091"/> <parameter name="massd=-2.000000" value="0.090909091"/> <parameter name="massd=-1.000000" value="0.090909091"/> <parameter name="massd=0.000000" value="0.090909091"/> <parameter name="massd=1.000000" value="0.090909091"/> <parameter name="massd=2.000000" value="0.090909091"/> <parameter name="massd=3.000000" value="0.090909091"/> <parameter name="massd=4.000000" value="0.090909091"/> <parameter name="massd=5.000000" value="0.090909091"/> </posmodel_distribution> <negmodel_distribution> <parameter name="massd=-5.000000" value="0.090909091"/> <parameter name="massd=-4.000000" value="0.090909091"/> <parameter name="massd=-3.000000" value="0.090909091"/> <parameter name="massd=-2.000000" value="0.090909091"/> <parameter name="massd=-1.000000" value="0.090909091"/> <parameter name="massd=0.000000" value="0.090909091"/> <parameter name="massd=1.000000" value="0.090909091"/> <parameter name="massd=2.000000" value="0.090909091"/> <parameter name="massd=3.000000" value="0.090909091"/> <parameter name="massd=4.000000" value="0.090909091"/> <parameter name="massd=5.000000" value="0.090909091"/> </negmodel_distribution> </mixturemodel_distribution> </mixture_model> <mixture_model precursor_ion_charge="5" comments="using training data negative distributions" prior_probability="0.000" est_tot_correct="0.0" tot_num_spectra="0" num_iterations="21"> <mixturemodel_distribution name="X! Tandem (k-score) discrim score [fval] negmean: -0.20"> <posmodel_distribution type="gaussian"> <parameter name="mean" value="4.01"/> <parameter name="stdev" value="2.53"/> </posmodel_distribution> <negmodel_distribution type="evd"> <parameter name="mean" value="-0.20"/> <parameter name="stdev" value="0.86"/> <parameter name="mu" value="-0.59"/> <parameter name="beta" value="0.67"/> </negmodel_distribution> </mixturemodel_distribution> <mixturemodel_distribution name="no. tolerable trypsin term. [ntt]"> <posmodel_distribution> <parameter name="ntt=0" value="0.333"/> <parameter name="ntt=1" value="0.333"/> <parameter name="ntt=2" value="0.333"/> </posmodel_distribution> <negmodel_distribution> <parameter name="ntt=0" value="0.333"/> <parameter name="ntt=1" value="0.333"/> <parameter name="ntt=2" value="0.333"/> </negmodel_distribution> </mixturemodel_distribution> <mixturemodel_distribution name="no. missed enz. cleavages [nmc]"> <posmodel_distribution> <parameter name="nmc=0" value="0.333"/> <parameter name="1&lt;=nmc&lt;=2" value="0.333"/> <parameter name="nmc&gt;=3" value="0.333"/> </posmodel_distribution> <negmodel_distribution> <parameter name="nmc=0" value="0.333"/> <parameter name="1&lt;=nmc&lt;=2" value="0.333"/> <parameter name="nmc&gt;=3" value="0.333"/> </negmodel_distribution> </mixturemodel_distribution> <mixturemodel_distribution name="accurate mass diff [massd] (offset: 0.000000)"> <posmodel_distribution> <parameter name="massd=-5.000000" value="0.090909091"/> <parameter name="massd=-4.000000" value="0.090909091"/> <parameter name="massd=-3.000000" value="0.090909091"/> <parameter name="massd=-2.000000" value="0.090909091"/> <parameter name="massd=-1.000000" value="0.090909091"/> <parameter name="massd=0.000000" value="0.090909091"/> <parameter name="massd=1.000000" value="0.090909091"/> <parameter name="massd=2.000000" value="0.090909091"/> <parameter name="massd=3.000000" value="0.090909091"/> <parameter name="massd=4.000000" value="0.090909091"/> <parameter name="massd=5.000000" value="0.090909091"/> </posmodel_distribution> <negmodel_distribution> <parameter name="massd=-5.000000" value="0.090909091"/> <parameter name="massd=-4.000000" value="0.090909091"/> <parameter name="massd=-3.000000" value="0.090909091"/> <parameter name="massd=-2.000000" value="0.090909091"/> <parameter name="massd=-1.000000" value="0.090909091"/> <parameter name="massd=0.000000" value="0.090909091"/> <parameter name="massd=1.000000" value="0.090909091"/> <parameter name="massd=2.000000" value="0.090909091"/> <parameter name="massd=3.000000" value="0.090909091"/> <parameter name="massd=4.000000" value="0.090909091"/> <parameter name="massd=5.000000" value="0.090909091"/> </negmodel_distribution> </mixturemodel_distribution> </mixture_model> <mixture_model precursor_ion_charge="6" comments="using training data negative distributions" prior_probability="0.000" est_tot_correct="0.0" tot_num_spectra="0" num_iterations="21"> <mixturemodel_distribution name="X! Tandem (k-score) discrim score [fval] negmean: -0.20"> <posmodel_distribution type="gaussian"> <parameter name="mean" value="4.01"/> <parameter name="stdev" value="2.53"/> </posmodel_distribution> <negmodel_distribution type="evd"> <parameter name="mean" value="-0.20"/> <parameter name="stdev" value="0.86"/> <parameter name="mu" value="-0.59"/> <parameter name="beta" value="0.67"/> </negmodel_distribution> </mixturemodel_distribution> <mixturemodel_distribution name="no. tolerable trypsin term. [ntt]"> <posmodel_distribution> <parameter name="ntt=0" value="0.333"/> <parameter name="ntt=1" value="0.333"/> <parameter name="ntt=2" value="0.333"/> </posmodel_distribution> <negmodel_distribution> <parameter name="ntt=0" value="0.333"/> <parameter name="ntt=1" value="0.333"/> <parameter name="ntt=2" value="0.333"/> </negmodel_distribution> </mixturemodel_distribution> <mixturemodel_distribution name="no. missed enz. cleavages [nmc]"> <posmodel_distribution> <parameter name="nmc=0" value="0.333"/> <parameter name="1&lt;=nmc&lt;=2" value="0.333"/> <parameter name="nmc&gt;=3" value="0.333"/> </posmodel_distribution> <negmodel_distribution> <parameter name="nmc=0" value="0.333"/> <parameter name="1&lt;=nmc&lt;=2" value="0.333"/> <parameter name="nmc&gt;=3" value="0.333"/> </negmodel_distribution> </mixturemodel_distribution> <mixturemodel_distribution name="accurate mass diff [massd] (offset: 0.000000)"> <posmodel_distribution> <parameter name="massd=-5.000000" value="0.090909091"/> <parameter name="massd=-4.000000" value="0.090909091"/> <parameter name="massd=-3.000000" value="0.090909091"/> <parameter name="massd=-2.000000" value="0.090909091"/> <parameter name="massd=-1.000000" value="0.090909091"/> <parameter name="massd=0.000000" value="0.090909091"/> <parameter name="massd=1.000000" value="0.090909091"/> <parameter name="massd=2.000000" value="0.090909091"/> <parameter name="massd=3.000000" value="0.090909091"/> <parameter name="massd=4.000000" value="0.090909091"/> <parameter name="massd=5.000000" value="0.090909091"/> </posmodel_distribution> <negmodel_distribution> <parameter name="massd=-5.000000" value="0.090909091"/> <parameter name="massd=-4.000000" value="0.090909091"/> <parameter name="massd=-3.000000" value="0.090909091"/> <parameter name="massd=-2.000000" value="0.090909091"/> <parameter name="massd=-1.000000" value="0.090909091"/> <parameter name="massd=0.000000" value="0.090909091"/> <parameter name="massd=1.000000" value="0.090909091"/> <parameter name="massd=2.000000" value="0.090909091"/> <parameter name="massd=3.000000" value="0.090909091"/> <parameter name="massd=4.000000" value="0.090909091"/> <parameter name="massd=5.000000" value="0.090909091"/> </negmodel_distribution> </mixturemodel_distribution> </mixture_model> <mixture_model precursor_ion_charge="7" comments="using training data negative distributions" prior_probability="0.000" est_tot_correct="0.0" tot_num_spectra="0" num_iterations="21"> <mixturemodel_distribution name="X! Tandem (k-score) discrim score [fval] negmean: -0.20"> <posmodel_distribution type="gaussian"> <parameter name="mean" value="4.01"/> <parameter name="stdev" value="2.53"/> </posmodel_distribution> <negmodel_distribution type="evd"> <parameter name="mean" value="-0.20"/> <parameter name="stdev" value="0.86"/> <parameter name="mu" value="-0.59"/> <parameter name="beta" value="0.67"/> </negmodel_distribution> </mixturemodel_distribution> <mixturemodel_distribution name="no. tolerable trypsin term. [ntt]"> <posmodel_distribution> <parameter name="ntt=0" value="0.333"/> <parameter name="ntt=1" value="0.333"/> <parameter name="ntt=2" value="0.333"/> </posmodel_distribution> <negmodel_distribution> <parameter name="ntt=0" value="0.333"/> <parameter name="ntt=1" value="0.333"/> <parameter name="ntt=2" value="0.333"/> </negmodel_distribution> </mixturemodel_distribution> <mixturemodel_distribution name="no. missed enz. cleavages [nmc]"> <posmodel_distribution> <parameter name="nmc=0" value="0.333"/> <parameter name="1&lt;=nmc&lt;=2" value="0.333"/> <parameter name="nmc&gt;=3" value="0.333"/> </posmodel_distribution> <negmodel_distribution> <parameter name="nmc=0" value="0.333"/> <parameter name="1&lt;=nmc&lt;=2" value="0.333"/> <parameter name="nmc&gt;=3" value="0.333"/> </negmodel_distribution> </mixturemodel_distribution> <mixturemodel_distribution name="accurate mass diff [massd] (offset: 0.000000)"> <posmodel_distribution> <parameter name="massd=-5.000000" value="0.090909091"/> <parameter name="massd=-4.000000" value="0.090909091"/> <parameter name="massd=-3.000000" value="0.090909091"/> <parameter name="massd=-2.000000" value="0.090909091"/> <parameter name="massd=-1.000000" value="0.090909091"/> <parameter name="massd=0.000000" value="0.090909091"/> <parameter name="massd=1.000000" value="0.090909091"/> <parameter name="massd=2.000000" value="0.090909091"/> <parameter name="massd=3.000000" value="0.090909091"/> <parameter name="massd=4.000000" value="0.090909091"/> <parameter name="massd=5.000000" value="0.090909091"/> </posmodel_distribution> <negmodel_distribution> <parameter name="massd=-5.000000" value="0.090909091"/> <parameter name="massd=-4.000000" value="0.090909091"/> <parameter name="massd=-3.000000" value="0.090909091"/> <parameter name="massd=-2.000000" value="0.090909091"/> <parameter name="massd=-1.000000" value="0.090909091"/> <parameter name="massd=0.000000" value="0.090909091"/> <parameter name="massd=1.000000" value="0.090909091"/> <parameter name="massd=2.000000" value="0.090909091"/> <parameter name="massd=3.000000" value="0.090909091"/> <parameter name="massd=4.000000" value="0.090909091"/> <parameter name="massd=5.000000" value="0.090909091"/> </negmodel_distribution> </mixturemodel_distribution> </mixture_model> </peptideprophet_summary> </analysis_summary> <analysis_summary analysis="database_refresh" time="2012-01-18T19:58:46"/> <analysis_summary analysis="interact" time="2012-01-18T19:58:36"> <interact_summary filename="c:/Inetpub/wwwroot/ISB/data/Ecoli/interact.pep.xml" directory="c:/Inetpub/wwwroot/ISB/data/Ecoli"> <inputfile name="120117.LC2.IT2.EC.scanmode_Cap_1-E,1_01_3481.tandem.pep.xml"/> </interact_summary> </analysis_summary> <dataset_derivation generation_no="0"/> <msms_run_summary base_name="c:/Inetpub/wwwroot/ISB/data/Ecoli/120117.LC2.IT2.EC.scanmode_Cap_1-E,1_01_3481" search_engine="X! Tandem (k-score)" msManufacturer="Bruker Daltonics" msModel="esquire" msIonization="UNKNOWN" msMassAnalyzer="Quadrupole Ion Trap" msDetector="MS:1000253" raw_data_type="raw" raw_data=".mzXML"> <sample_enzyme name="trypsin"> <specificity cut="KR" no_cut="P" sense="C"/> </sample_enzyme> <search_summary base_name="c:/Inetpub/wwwroot/ISB/data/Ecoli/120117.LC2.IT2.EC.scanmode_Cap_1-E,1_01_3481" search_engine="X! Tandem (k-score)" precursor_mass_type="monoisotopic" fragment_mass_type="monoisotopic" search_id="1"> <search_database local_path="c:/Inetpub/wwwroot/ISB/data/dbase/18.E_coli_K12.fasta" type="AA"/> <enzymatic_search_constraint enzyme="trypsin" max_num_internal_cleavages="2" min_number_termini="2"/> <aminoacid_modification aminoacid="C" massdiff="57.0215" mass="160.0306" variable="N"/> <aminoacid_modification aminoacid="C" massdiff="-17.0265" mass="143.0041" variable="Y" symbol="^"/> <!--X! Tandem n-terminal AA variable modification--> <aminoacid_modification aminoacid="E" massdiff="-18.0106" mass="111.0320" variable="Y" symbol="^"/> <!--X! Tandem n-terminal AA variable modification--> <aminoacid_modification aminoacid="Q" massdiff="-17.0265" mass="111.0321" variable="Y" symbol="^"/> <!--X! Tandem n-terminal AA variable modification--> <!-- Input parameters --> <parameter name="list path, taxonomy information" value="c:/Inetpub/wwwroot/ISB/data/Ecoli/taxonomy.xml"/> <parameter name="output, histogram column width" value="30"/> <parameter name="output, histograms" value="no"/> <parameter name="output, maximum valid expectation value" value="0.1"/> <parameter name="output, message" value="1234567890"/> <parameter name="output, one sequence copy" value="no"/> <parameter name="output, parameters" value="yes"/> <parameter name="output, path" value="c:/Inetpub/wwwroot/ISB/data/Ecoli/120117.LC2.IT2.EC.scanmode_Cap_1-E,1_01_3481.tandem"/> <parameter name="output, path hashing" value="no"/> <parameter name="output, performance" value="yes"/> <parameter name="output, proteins" value="yes"/> <parameter name="output, results" value="all"/> <parameter name="output, sequences" value="no"/> <parameter name="output, sort results by" value="spectrum"/> <parameter name="output, spectra" value="yes"/> <parameter name="protein, C-terminal residue modification mass" value=""/> <parameter name="protein, N-terminal residue modification mass" value=""/> <parameter name="protein, cleavage site" value="[RK]|{P}"/> <parameter name="protein, homolog management" value="no"/> <parameter name="protein, modified residue mass file" value=""/> <parameter name="protein, taxon" value="mydatabase"/> <parameter name="refine" value="no"/> <parameter name="refine, maximum valid expectation value" value="0.1"/> <parameter name="refine, sequence path" value=""/> <parameter name="refine, spectrum synthesis" value="yes"/> <parameter name="residue, modification mass" value="57.021464@C"/> <parameter name="residue, potential modification mass" value=""/> <parameter name="residue, potential modification motif" value=""/> <parameter name="scoring, a ions" value="no"/> <parameter name="scoring, algorithm" value="k-score"/> <parameter name="scoring, b ions" value="yes"/> <parameter name="scoring, c ions" value="no"/> <parameter name="scoring, cyclic permutation" value="no"/> <parameter name="scoring, include reverse" value="no"/> <parameter name="scoring, maximum missed cleavage sites" value="2"/> <parameter name="scoring, minimum ion count" value="1"/> <parameter name="scoring, x ions" value="no"/> <parameter name="scoring, y ions" value="yes"/> <parameter name="scoring, z ions" value="no"/> <parameter name="spectrum, dynamic range" value="10000.0"/> <parameter name="spectrum, fragment mass type" value="monoisotopic"/> <parameter name="spectrum, fragment monoisotopic mass error" value="0.4"/> <parameter name="spectrum, fragment monoisotopic mass error units" value="Daltons"/> <parameter name="spectrum, maximum parent charge" value="5"/> <parameter name="spectrum, minimum fragment mz" value="125.0"/> <parameter name="spectrum, minimum parent m+h" value="600.0"/> <parameter name="spectrum, minimum peaks" value="10"/> <parameter name="spectrum, parent monoisotopic mass error minus" value="0.5"/> <parameter name="spectrum, parent monoisotopic mass error plus" value="0.5"/> <parameter name="spectrum, parent monoisotopic mass error units" value="Daltons"/> <parameter name="spectrum, parent monoisotopic mass isotope error" value="yes"/> <parameter name="spectrum, path" value="c:/Inetpub/wwwroot/ISB/data/Ecoli/120117.LC2.IT2.EC.scanmode_Cap_1-E,1_01_3481.mzXML"/> <parameter name="spectrum, sequence batch size" value="1000"/> <parameter name="spectrum, threads" value="4"/> <parameter name="spectrum, total peaks" value="400"/> <parameter name="spectrum, use conditioning" value="no"/> <parameter name="spectrum, use noise suppression" value="yes"/> <!-- Unused input parameters --> <parameter name="refine, modification mass" value=""/> <parameter name="refine, point mutations" value="no"/> <parameter name="refine, potential C-terminus modifications" value=""/> <parameter name="refine, potential N-terminus modifications" value=""/> <parameter name="refine, potential modification mass" value=""/> <parameter name="refine, potential modification motif" value=""/> <parameter name="refine, tic percent" value="10"/> <parameter name="refine, unanticipated cleavage" value="no"/> <parameter name="refine, use potential modifications for full refinement" value="no"/> <parameter name="scoring, pluggable scoring" value="yes"/> <!-- Performance parameters --> <parameter name="list path, sequence source #1" value="c:/Inetpub/wwwroot/ISB/data/dbase/18.E_coli_K12.fasta"/> <parameter name="list path, sequence source description #1" value="no description"/> <parameter name="modelling, spectrum noise suppression ratio" value="0.00"/> <parameter name="modelling, total peptides used" value="16629786"/> <parameter name="modelling, total proteins used" value="4373"/> <parameter name="modelling, total spectra used" value="58618"/> <parameter name="process, start time" value="2012:01:17:17:36:54"/> <parameter name="process, version" value="x! tandem 2010.10.01.1 (LabKey, Insilicos and ISB)"/> <parameter name="quality values" value="3362 2146 1796 1705 1570 1235 919 681 398 242 123 67 34 12 10 1 3 0 0 0"/> <parameter name="refining, # input models" value="0"/> <parameter name="refining, # input spectra" value="0"/> <parameter name="refining, # partial cleavage" value="0"/> <parameter name="refining, # point mutations" value="0"/> <parameter name="refining, # potential C-terminii" value="0"/> <parameter name="refining, # potential N-terminii" value="0"/> <parameter name="refining, # unanticipated cleavage" value="0"/> <parameter name="timing, initial modelling total (sec)" value="17.97"/> <parameter name="timing, initial modelling/spectrum (sec)" value="0.000"/> <parameter name="timing, load sequence models (sec)" value="0.15"/> <parameter name="timing, refinement/spectrum (sec)" value="0.000"/> </search_summary> <analysis_timestamp analysis="peptideprophet" time="2012-01-18T19:58:51" id="1"/> <analysis_timestamp analysis="database_refresh" time="2012-01-18T19:58:46" id="1"> <database_refresh_timestamp database="c:/Inetpub/wwwroot/ISB/data/dbase/18.E_coli_K12.fasta" min_num_enz_term="2"/> </analysis_timestamp> <spectrum_query spectrum="120117.LC2.IT2.EC.scanmode_Cap_1-E,1_01_3481.00125.00125.3" start_scan="125" end_scan="125" precursor_neutral_mass="1061.4690" assumed_charge="3" index="1" retention_time_sec="25.96697600"> <search_result> <search_hit hit_rank="1" peptide="RVTGTSERR" peptide_prev_aa="K" peptide_next_aa="E" protein="sp|P0ACK2|AGAR_ECOLI" protein_descr="Putative aga operon transcriptional repressor OS=Escherichia coli (strain K12) GN=agaR" num_tot_proteins="1" num_matched_ions="11" tot_num_ions="32" calc_neutral_pep_mass="1060.5737" massdiff="0.895" num_tol_term="2" num_missed_cleavages="0" is_rejected="0"> <search_score name="hyperscore" value="338"/> <search_score name="nextscore" value="256"/> <search_score name="bscore" value="1"/> <search_score name="yscore" value="1"/> <search_score name="cscore" value="0"/> <search_score name="zscore" value="0"/> <search_score name="ascore" value="0"/> <search_score name="xscore" value="0"/> <search_score name="expect" value="1.1"/> <analysis_result analysis="peptideprophet"> <peptideprophet_result probability="0.5946" all_ntt_prob="(0.0000,0.0000,0.5946)"> <search_score_summary> <parameter name="fval" value="2.3222"/> <parameter name="ntt" value="2"/> <parameter name="nmc" value="0"/> <parameter name="massd" value="0.895"/> </search_score_summary> </peptideprophet_result> </analysis_result> </search_hit> </search_result> </spectrum_query> <spectrum_query spectrum="120117.LC2.IT2.EC.scanmode_Cap_1-E,1_01_3481.00147.00147.3" start_scan="147" end_scan="147" precursor_neutral_mass="1633.7164" assumed_charge="3" index="2" retention_time_sec="30.40096000"> <search_result> <search_hit hit_rank="1" peptide="TASGGLAGSTLSVDAAVR" peptide_prev_aa="R" peptide_next_aa="N" protein="sp|P42906|AGAA_ECOLI" protein_descr="Putative N-acetylgalactosamine-6-phosphate deacetylase OS=Escherichia coli (strain K12) GN=agaA" num_tot_proteins="1" num_matched_ions="19" tot_num_ions="68" calc_neutral_pep_mass="1631.8477" massdiff="1.869" num_tol_term="2" num_missed_cleavages="0" is_rejected="0"> <search_score name="hyperscore" value="355"/> <search_score name="nextscore" value="312"/> <search_score name="bscore" value="1"/> <search_score name="yscore" value="1"/> <search_score name="cscore" value="0"/> <search_score name="zscore" value="0"/> <search_score name="ascore" value="0"/> <search_score name="xscore" value="0"/> <search_score name="expect" value="1.9"/> <analysis_result analysis="peptideprophet"> <peptideprophet_result probability="0.0697" all_ntt_prob="(0.0000,0.0000,0.0697)"> <search_score_summary> <parameter name="fval" value="0.3691"/> <parameter name="ntt" value="2"/> <parameter name="nmc" value="0"/> <parameter name="massd" value="1.869"/> </search_score_summary> </peptideprophet_result> </analysis_result> </search_hit> </search_result> </spectrum_query> <spectrum_query spectrum="120117.LC2.IT2.EC.scanmode_Cap_1-E,1_01_3481.00197.00197.3" start_scan="197" end_scan="197" precursor_neutral_mass="1985.1253" assumed_charge="3" index="3" retention_time_sec="40.45299200"> <search_result> <search_hit hit_rank="1" peptide="EFKGDVSAEYGSWNKER" peptide_prev_aa="R" peptide_next_aa="Y" protein="sp|P16869|FHUE_ECOLI" protein_descr="FhuE receptor OS=Escherichia coli (strain K12) GN=fhuE" num_tot_proteins="1" num_matched_ions="12" tot_num_ions="64" calc_neutral_pep_mass="1982.9127" massdiff="2.213" num_tol_term="2" num_missed_cleavages="2" is_rejected="0"> <modification_info modified_peptide="E[111]FKGDVSAEYGSWNKER"> <mod_aminoacid_mass position="1" mass="111.0320"/> </modification_info> <search_score name="hyperscore" value="369"/> <search_score name="nextscore" value="310"/> <search_score name="bscore" value="0"/> <search_score name="yscore" value="1"/> <search_score name="cscore" value="0"/> <search_score name="zscore" value="0"/> <search_score name="ascore" value="0"/> <search_score name="xscore" value="0"/> <search_score name="expect" value="1.3"/> <analysis_result analysis="peptideprophet"> <peptideprophet_result probability="0.0867" all_ntt_prob="(0.0000,0.0000,0.0867)"> <search_score_summary> <parameter name="fval" value="1.2631"/> <parameter name="ntt" value="2"/> <parameter name="nmc" value="1"/> <parameter name="massd" value="2.213"/> </search_score_summary> </peptideprophet_result> </analysis_result> </search_hit> </search_result> </spectrum_query> <spectrum_query spectrum="120117.LC2.IT2.EC.scanmode_Cap_1-E,1_01_3481.00277.00277.3" start_scan="277" end_scan="277" precursor_neutral_mass="1866.1768" assumed_charge="3" index="4" retention_time_sec="56.64896000"> <search_result> <search_hit hit_rank="1" peptide="TVMPYITSQNAAITAER" peptide_prev_aa="R" peptide_next_aa="N" protein="sp|P27297|BAX_ECOLI" protein_descr="Protein bax OS=Escherichia coli (strain K12) GN=bax" num_tot_proteins="1" num_matched_ions="23" tot_num_ions="64" calc_neutral_pep_mass="1864.9357" massdiff="1.241" num_tol_term="2" num_missed_cleavages="0" is_rejected="0"> <search_score name="hyperscore" value="366"/> <search_score name="nextscore" value="323"/> <search_score name="bscore" value="1"/> <search_score name="yscore" value="1"/> <search_score name="cscore" value="0"/> <search_score name="zscore" value="0"/> <search_score name="ascore" value="0"/> <search_score name="xscore" value="0"/> <search_score name="expect" value="0.62"/> <analysis_result analysis="peptideprophet"> <peptideprophet_result probability="0.0724" all_ntt_prob="(0.0000,0.0000,0.0724)"> <search_score_summary> <parameter name="fval" value="0.4553"/> <parameter name="ntt" value="2"/> <parameter name="nmc" value="0"/> <parameter name="massd" value="1.241"/> </search_score_summary> </peptideprophet_result> </analysis_result> </search_hit> </search_result> </spectrum_query> <spectrum_query spectrum="120117.LC2.IT2.EC.scanmode_Cap_1-E,1_01_3481.00467.00467.3" start_scan="467" end_scan="467" precursor_neutral_mass="1866.0051" assumed_charge="3" index="5" retention_time_sec="94.77600000"> <search_result> <search_hit hit_rank="1" peptide="TVMPYITSQNAAITAER" peptide_prev_aa="R" peptide_next_aa="N" protein="sp|P27297|BAX_ECOLI" protein_descr="Protein bax OS=Escherichia coli (strain K12) GN=bax" num_tot_proteins="1" num_matched_ions="20" tot_num_ions="64" calc_neutral_pep_mass="1864.9357" massdiff="1.069" num_tol_term="2" num_missed_cleavages="0" is_rejected="0"> <search_score name="hyperscore" value="378"/> <search_score name="nextscore" value="337"/> <search_score name="bscore" value="1"/> <search_score name="yscore" value="1"/> <search_score name="cscore" value="0"/> <search_score name="zscore" value="0"/> <search_score name="ascore" value="0"/> <search_score name="xscore" value="0"/> <search_score name="expect" value="0.56"/> <analysis_result analysis="peptideprophet"> <peptideprophet_result probability="0.0722" all_ntt_prob="(0.0000,0.0000,0.0722)"> <search_score_summary> <parameter name="fval" value="0.4528"/> <parameter name="ntt" value="2"/> <parameter name="nmc" value="0"/> <parameter name="massd" value="1.069"/> </search_score_summary> </peptideprophet_result> </analysis_result> </search_hit> </search_result> </spectrum_query> <spectrum_query spectrum="120117.LC2.IT2.EC.scanmode_Cap_1-E,1_01_3481.00514.00514.3" start_scan="514" end_scan="514" precursor_neutral_mass="1502.0771" assumed_charge="3" index="6" retention_time_sec="104.21696000"> <search_result> <search_hit hit_rank="1" peptide="KASSTQSRPVNAGAK" peptide_prev_aa="K" peptide_next_aa="K" protein="sp|Q46861|YGIQ_ECOLI" protein_descr="UPF0313 protein ygiQ OS=Escherichia coli (strain K12) GN=ygiQ" num_tot_proteins="1" num_matched_ions="11" tot_num_ions="56" calc_neutral_pep_mass="1500.8007" massdiff="1.276" num_tol_term="2" num_missed_cleavages="0" is_rejected="0"> <search_score name="hyperscore" value="362"/> <search_score name="nextscore" value="313"/> <search_score name="bscore" value="1"/> <search_score name="yscore" value="1"/> <search_score name="cscore" value="0"/> <search_score name="zscore" value="0"/> <search_score name="ascore" value="0"/> <search_score name="xscore" value="0"/> <search_score name="expect" value="1.6"/> <analysis_result analysis="peptideprophet"> <peptideprophet_result probability="0.1086" all_ntt_prob="(0.0000,0.0000,0.1086)"> <search_score_summary> <parameter name="fval" value="0.7238"/> <parameter name="ntt" value="2"/> <parameter name="nmc" value="0"/> <parameter name="massd" value="1.276"/> </search_score_summary> </peptideprophet_result> </analysis_result> </search_hit> </search_result> </spectrum_query> <spectrum_query spectrum="120117.LC2.IT2.EC.scanmode_Cap_1-E,1_01_3481.00604.00604.3" start_scan="604" end_scan="604" precursor_neutral_mass="2295.5883" assumed_charge="3" index="7" retention_time_sec="122.30694400"> <search_result> <search_hit hit_rank="1" peptide="IAHWRGEDAAWLAATTDANVK" peptide_prev_aa="R" peptide_next_aa="T" protein="sp|P27859|TATD_ECOLI" protein_descr="Deoxyribonuclease tatD OS=Escherichia coli (strain K12) GN=tatD" num_tot_proteins="1" num_matched_ions="16" tot_num_ions="80" calc_neutral_pep_mass="2295.1397" massdiff="0.449" num_tol_term="2" num_missed_cleavages="1" is_rejected="0"> <search_score name="hyperscore" value="386"/> <search_score name="nextscore" value="297"/> <search_score name="bscore" value="1"/> <search_score name="yscore" value="1"/> <search_score name="cscore" value="0"/> <search_score name="zscore" value="0"/> <search_score name="ascore" value="0"/> <search_score name="xscore" value="0"/> <search_score name="expect" value="0.33"/> <analysis_result analysis="peptideprophet"> <peptideprophet_result probability="0.0512" all_ntt_prob="(0.0000,0.0000,0.0512)"> <search_score_summary> <parameter name="fval" value="2.7662"/> <parameter name="ntt" value="2"/> <parameter name="nmc" value="1"/> <parameter name="massd" value="0.449"/> </search_score_summary> </peptideprophet_result> </analysis_result> </search_hit> </search_result> </spectrum_query> <spectrum_query spectrum="120117.LC2.IT2.EC.scanmode_Cap_1-E,1_01_3481.00643.00643.3" start_scan="643" end_scan="643" precursor_neutral_mass="1220.2046" assumed_charge="3" index="8" retention_time_sec="130.16998400"> <search_result> <search_hit hit_rank="1" peptide="TDVELDGDNSR" peptide_prev_aa="R" peptide_next_aa="F" protein="sp|P32051|YDEK_ECOLI" protein_descr="Uncharacterized lipoprotein ydeK OS=Escherichia coli (strain K12) GN=ydeK" num_tot_proteins="1" num_matched_ions="11" tot_num_ions="40" calc_neutral_pep_mass="1219.5317" massdiff="0.673" num_tol_term="2" num_missed_cleavages="0" is_rejected="0"> <search_score name="hyperscore" value="326"/> <search_score name="nextscore" value="280"/> <search_score name="bscore" value="1"/> <search_score name="yscore" value="1"/> <search_score name="cscore" value="0"/> <search_score name="zscore" value="0"/> <search_score name="ascore" value="0"/> <search_score name="xscore" value="0"/> <search_score name="expect" value="0.71"/> <analysis_result analysis="peptideprophet"> <peptideprophet_result probability="0.0574" all_ntt_prob="(0.0000,0.0000,0.0574)"> <search_score_summary> <parameter name="fval" value="0.3058"/> <parameter name="ntt" value="2"/> <parameter name="nmc" value="0"/> <parameter name="massd" value="0.673"/> </search_score_summary> </peptideprophet_result> </analysis_result> </search_hit> </search_result> </spectrum_query> <spectrum_query spectrum="120117.LC2.IT2.EC.scanmode_Cap_1-E,1_01_3481.00682.00682.3" start_scan="682" end_scan="682" precursor_neutral_mass="1778.2794" assumed_charge="3" index="9" retention_time_sec="137.71398400"> <search_result> <search_hit hit_rank="1" peptide="GSMLPKVEAAASFARSR" peptide_prev_aa="K" peptide_next_aa="A" protein="sp|Q46807|ARCL_ECOLI" protein_descr="Carbamate kinase-like protein yqeA OS=Escherichia coli (strain K12) GN=yqeA" num_tot_proteins="1" num_matched_ions="15" tot_num_ions="64" calc_neutral_pep_mass="1776.9307" massdiff="1.349" num_tol_term="2" num_missed_cleavages="2" is_rejected="0"> <search_score name="hyperscore" value="352"/> <search_score name="nextscore" value="287"/> <search_score name="bscore" value="1"/> <search_score name="yscore" value="1"/> <search_score name="cscore" value="0"/> <search_score name="zscore" value="0"/> <search_score name="ascore" value="0"/> <search_score name="xscore" value="0"/> <search_score name="expect" value="1.3"/> <analysis_result analysis="peptideprophet"> <peptideprophet_result probability="0.1072" all_ntt_prob="(0.0000,0.0000,0.1072)"> <search_score_summary> <parameter name="fval" value="1.4761"/> <parameter name="ntt" value="2"/> <parameter name="nmc" value="1"/> <parameter name="massd" value="1.349"/> </search_score_summary> </peptideprophet_result> </analysis_result> </search_hit> </search_result> </spectrum_query> <spectrum_query spectrum="120117.LC2.IT2.EC.scanmode_Cap_1-E,1_01_3481.00856.00856.3" start_scan="856" end_scan="856" precursor_neutral_mass="2002.4584" assumed_charge="3" index="10" retention_time_sec="172.20294400"> <search_result> <search_hit hit_rank="1" peptide="ESVSHQNYPQVIKHTPR" peptide_prev_aa="K" peptide_next_aa="M" protein="sp|P71237|WCAC_ECOLI" protein_descr="Putative colanic acid biosynthesis glycosyl transferase wcaC OS=Escherichia coli (strain K12) GN=wcaC" num_tot_proteins="1" num_matched_ions="16" tot_num_ions="64" calc_neutral_pep_mass="2001.0177" massdiff="1.441" num_tol_term="2" num_missed_cleavages="1" is_rejected="0"> <modification_info modified_peptide="E[111]SVSHQNYPQVIKHTPR"> <mod_aminoacid_mass position="1" mass="111.0320"/> </modification_info> <search_score name="hyperscore" value="417"/> <search_score name="nextscore" value="327"/> <search_score name="bscore" value="1"/> <search_score name="yscore" value="1"/> <search_score name="cscore" value="0"/> <search_score name="zscore" value="0"/> <search_score name="ascore" value="0"/> <search_score name="xscore" value="0"/> <search_score name="expect" value="0.44"/> <analysis_result analysis="peptideprophet"> <peptideprophet_result probability="0.4866" all_ntt_prob="(0.0000,0.0000,0.4866)"> <search_score_summary> <parameter name="fval" value="2.8844"/> <parameter name="ntt" value="2"/> <parameter name="nmc" value="1"/> <parameter name="massd" value="1.441"/> </search_score_summary> </peptideprophet_result> </analysis_result> </search_hit> </search_result> </spectrum_query> <spectrum_query spectrum="120117.LC2.IT2.EC.scanmode_Cap_1-E,1_01_3481.00960.00960.3" start_scan="960" end_scan="960" precursor_neutral_mass="1224.7028" assumed_charge="3" index="11" retention_time_sec="192.76499200"> <search_result> <search_hit hit_rank="1" peptide="CTEEHQAIVR" peptide_prev_aa="K" peptide_next_aa="K" protein="sp|P38521|YGGL_ECOLI" protein_descr="Uncharacterized protein yggL OS=Escherichia coli (strain K12) GN=yggL" num_tot_proteins="1" num_matched_ions="12" tot_num_ions="36" calc_neutral_pep_mass="1224.5557" massdiff="0.147" num_tol_term="2" num_missed_cleavages="0" is_rejected="0"> <modification_info modified_peptide="C[143]TEEHQAIVR"> <mod_aminoacid_mass position="1" mass="143.0041"/> </modification_info> <search_score name="hyperscore" value="316"/> <search_score name="nextscore" value="225"/> <search_score name="bscore" value="1"/> <search_score name="yscore" value="1"/> <search_score name="cscore" value="0"/> <search_score name="zscore" value="0"/> <search_score name="ascore" value="0"/> <search_score name="xscore" value="0"/> <search_score name="expect" value="0.2"/> <analysis_result analysis="peptideprophet"> <peptideprophet_result probability="0.1629" all_ntt_prob="(0.0000,0.0000,0.1629)"> <search_score_summary> <parameter name="fval" value="2.8076"/> <parameter name="ntt" value="2"/> <parameter name="nmc" value="0"/> <parameter name="massd" value="0.147"/> 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<search_score name="ascore" value="0"/> <search_score name="xscore" value="0"/> <search_score name="expect" value="0.19"/> <analysis_result analysis="peptideprophet"> <peptideprophet_result probability="0.5093" all_ntt_prob="(0.0000,0.0000,0.5093)"> <search_score_summary> <parameter name="fval" value="2.8761"/> <parameter name="ntt" value="2"/> <parameter name="nmc" value="1"/> <parameter name="massd" value="2.008"/> </search_score_summary> </peptideprophet_result> </analysis_result> </search_hit> </search_result> </spectrum_query> <spectrum_query spectrum="120117.LC2.IT2.EC.scanmode_Cap_1-E,1_01_3481.01048.01048.3" start_scan="1048" end_scan="1048" precursor_neutral_mass="1026.2627" assumed_charge="3" index="13" retention_time_sec="210.35097600"> <search_result> <search_hit hit_rank="1" peptide="DVDVLYFR" peptide_prev_aa="K" peptide_next_aa="E" protein="sp|P0A780|NUSB_ECOLI" protein_descr="N utilization substance protein B OS=Escherichia coli (strain K12) GN=nusB" num_tot_proteins="1" 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index="14879" retention_time_sec="1.68294400"> <search_result> <search_hit hit_rank="1" peptide="ALEEAGAEVEVK" peptide_prev_aa="K" peptide_next_aa="-" protein="sp|P0A7K2|RL7_ECOLI" protein_descr="50S ribosomal protein L7\L12 OS=Escherichia coli (strain K12) GN=rplL" num_tot_proteins="1" num_matched_ions="22" tot_num_ions="22" calc_neutral_pep_mass="1243.6297" massdiff="0.481" num_tol_term="2" num_missed_cleavages="0" is_rejected="0"> <search_score name="hyperscore" value="513"/> <search_score name="nextscore" value="269"/> <search_score name="bscore" value="1"/> <search_score name="yscore" value="1"/> <search_score name="cscore" value="0"/> <search_score name="zscore" value="0"/> <search_score name="ascore" value="0"/> <search_score name="xscore" value="0"/> <search_score name="expect" value="0.0013"/> <analysis_result analysis="peptideprophet"> <peptideprophet_result probability="0.9993" all_ntt_prob="(0.0000,0.0000,0.9993)"> <search_score_summary> <parameter name="fval" value="7.1076"/> <parameter name="ntt" value="2"/> <parameter name="nmc" value="0"/> <parameter name="massd" value="0.481"/> </search_score_summary> </peptideprophet_result> </analysis_result> </search_hit> </search_result> </spectrum_query> </msms_run_summary> </msms_pipeline_analysis> /default:msms_pipeline_analysis/default:msms_run_summary/default:spectrum_query/default:search_result/default:search_hit/@peptide default http://regis-web.systemsbiology.net/pepXML xsi http://www.w3.org/2001/XMLSchema-instance net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeExtract_Scan_Numbersxml_text0nodelist11 This XPath extracts the corresponding scan numbers for the identified peptides. 2012-08-28 13:28:04.3 UTC net.sf.taverna.t2.activitiesxpath-activity1.4net.sf.taverna.t2.activities.xpath.XPathActivity <?xml version="1.0" encoding="UTF-8"?> <?xml-stylesheet type="text/xsl" href="http://localhost:8080/ISB/data/Ecoli/interact.pep.xsl"?><msms_pipeline_analysis xmlns="http://regis-web.systemsbiology.net/pepXML" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" date="2012-01-18T19:58:42" summary_xml="c:/Inetpub/wwwroot/ISB/data/Ecoli/interact.pep.xml" xsi:schemaLocation="http://regis-web.systemsbiology.net/pepXML http://localhost/pepXML_v117.xsd"> <analysis_summary analysis="peptideprophet" time="2012-01-18T19:58:51"> <peptideprophet_summary version="PeptideProphet (TPP v4.5 RAPTURE rev 1, Build 201111221430 (MinGW))" author="AKeller@ISB" min_prob="0.05" options=" MINPROB=0.05 " est_tot_num_correct="11327.9"> <inputfile name="c:/Inetpub/wwwroot/ISB/data/Ecoli/120117.LC2.IT2.EC.scanmode_Cap_1-E,1_01_3481"/> <roc_error_data charge="all"> <roc_data_point min_prob="0.9999" sensitivity="0.0000" error="0" num_corr="0" num_incorr="0"/> <roc_data_point min_prob="0.9990" sensitivity="0.2329" error="0.0005" num_corr="2639" num_incorr="1"/> <roc_data_point min_prob="0.9900" sensitivity="0.5553" error="0.0024" num_corr="6291" num_incorr="15"/> <roc_data_point min_prob="0.9800" sensitivity="0.6320" error="0.0039" num_corr="7159" num_incorr="28"/> <roc_data_point min_prob="0.9500" sensitivity="0.7284" error="0.0077" num_corr="8252" num_incorr="64"/> <roc_data_point min_prob="0.9000" sensitivity="0.7912" error="0.0132" num_corr="8962" num_incorr="120"/> <roc_data_point min_prob="0.8500" sensitivity="0.8282" error="0.0187" num_corr="9382" num_incorr="179"/> <roc_data_point min_prob="0.8000" sensitivity="0.8528" error="0.0240" num_corr="9661" num_incorr="237"/> <roc_data_point min_prob="0.7500" sensitivity="0.8707" error="0.0291" num_corr="9864" num_incorr="295"/> <roc_data_point min_prob="0.7000" sensitivity="0.8853" error="0.0345" num_corr="10029" num_incorr="359"/> <roc_data_point min_prob="0.6500" sensitivity="0.8974" error="0.0401" num_corr="10166" num_incorr="424"/> <roc_data_point min_prob="0.6000" sensitivity="0.9078" error="0.0459" num_corr="10284" num_incorr="495"/> <roc_data_point min_prob="0.5500" sensitivity="0.9172" error="0.0523" num_corr="10390" num_incorr="574"/> <roc_data_point min_prob="0.5000" sensitivity="0.9260" error="0.0594" num_corr="10489" num_incorr="663"/> <roc_data_point min_prob="0.4500" sensitivity="0.9343" error="0.0675" num_corr="10584" num_incorr="766"/> <roc_data_point min_prob="0.4000" sensitivity="0.9416" error="0.0761" num_corr="10666" num_incorr="878"/> <roc_data_point min_prob="0.3500" sensitivity="0.9484" error="0.0858" num_corr="10743" num_incorr="1008"/> <roc_data_point min_prob="0.3000" sensitivity="0.9553" error="0.0977" num_corr="10821" num_incorr="1172"/> <roc_data_point min_prob="0.2500" sensitivity="0.9609" error="0.1096" num_corr="10885" num_incorr="1340"/> <roc_data_point min_prob="0.2000" sensitivity="0.9671" error="0.1264" num_corr="10955" num_incorr="1585"/> <roc_data_point min_prob="0.1500" sensitivity="0.9737" error="0.1495" num_corr="11030" num_incorr="1938"/> <roc_data_point min_prob="0.1000" sensitivity="0.9805" error="0.1830" num_corr="11107" num_incorr="2487"/> <roc_data_point min_prob="0.0500" sensitivity="0.9886" error="0.2474" num_corr="11198" num_incorr="3682"/> <roc_data_point min_prob="0.0000" sensitivity="1.0000" error="0.8023" num_corr="11328" num_incorr="45984"/> <error_point error="0.0000" min_prob="0.9998" num_corr="2" num_incorr="0"/> <error_point error="0.0001" min_prob="0.9998" num_corr="2" num_incorr="0"/> <error_point error="0.0002" min_prob="0.9998" num_corr="2" num_incorr="0"/> <error_point 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num_incorr="29"/> <error_point error="0.0050" min_prob="0.9724" num_corr="7579" num_incorr="38"/> <error_point error="0.0060" min_prob="0.9651" num_corr="7873" num_incorr="48"/> <error_point error="0.0070" min_prob="0.9558" num_corr="8109" num_incorr="57"/> <error_point error="0.0080" min_prob="0.9472" num_corr="8302" num_incorr="67"/> <error_point error="0.0090" min_prob="0.9382" num_corr="8465" num_incorr="77"/> <error_point error="0.0100" min_prob="0.9298" num_corr="8609" num_incorr="87"/> <error_point error="0.0150" min_prob="0.8822" num_corr="9124" num_incorr="139"/> <error_point error="0.0200" min_prob="0.8393" num_corr="9461" num_incorr="193"/> <error_point error="0.0250" min_prob="0.7912" num_corr="9708" num_incorr="249"/> <error_point error="0.0300" min_prob="0.7385" num_corr="9895" num_incorr="307"/> <error_point error="0.0400" min_prob="0.6501" num_corr="10165" num_incorr="424"/> <error_point error="0.0500" min_prob="0.5682" num_corr="10355" num_incorr="545"/> <error_point 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[ntt]"> <posmodel_distribution> <parameter name="ntt=0" value="0.000"/> <parameter name="ntt=1" value="0.000"/> <parameter name="ntt=2" value="1.000"/> </posmodel_distribution> <negmodel_distribution> <parameter name="ntt=0" value="0.000"/> <parameter name="ntt=1" value="0.000"/> <parameter name="ntt=2" value="1.000"/> </negmodel_distribution> </mixturemodel_distribution> <mixturemodel_distribution name="no. missed enz. cleavages [nmc]"> <posmodel_distribution> <parameter name="nmc=0" value="0.784"/> <parameter name="1&lt;=nmc&lt;=2" value="0.216"/> <parameter name="nmc&gt;=3" value="0.000"/> </posmodel_distribution> <negmodel_distribution> <parameter name="nmc=0" value="0.743"/> <parameter name="1&lt;=nmc&lt;=2" value="0.257"/> <parameter name="nmc&gt;=3" value="0.000"/> </negmodel_distribution> </mixturemodel_distribution> <mixturemodel_distribution name="accurate mass diff [massd] (offset: -0.500000)"> <posmodel_distribution> <parameter name="massd=-5.000000" value="0.000000000"/> <parameter name="massd=-4.000000" value="0.000000000"/> <parameter name="massd=-3.000000" value="0.000000000"/> <parameter name="massd=-2.000000" value="0.000000000"/> <parameter name="massd=-1.000000" value="0.000000000"/> <parameter name="massd=0.000000" value="0.577398462"/> <parameter name="massd=1.000000" value="0.422601538"/> <parameter name="massd=2.000000" value="0.000000000"/> <parameter name="massd=3.000000" value="0.000000000"/> <parameter name="massd=4.000000" value="0.000000000"/> <parameter name="massd=5.000000" value="0.000000000"/> </posmodel_distribution> <negmodel_distribution> <parameter name="massd=-5.000000" value="0.000000000"/> <parameter name="massd=-4.000000" value="0.000000000"/> <parameter name="massd=-3.000000" value="0.000000000"/> <parameter name="massd=-2.000000" value="0.000000000"/> <parameter name="massd=-1.000000" value="0.000000000"/> <parameter name="massd=0.000000" value="0.358802119"/> <parameter name="massd=1.000000" value="0.601671801"/> <parameter name="massd=2.000000" value="0.039526080"/> <parameter name="massd=3.000000" value="0.000000000"/> <parameter name="massd=4.000000" value="0.000000000"/> <parameter name="massd=5.000000" value="0.000000000"/> </negmodel_distribution> </mixturemodel_distribution> </mixture_model> <mixture_model precursor_ion_charge="2" comments="using training data negative distributions" prior_probability="0.278" est_tot_correct="7771.4" tot_num_spectra="28042" num_iterations="27"> <mixturemodel_distribution name="X! 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Tandem (k-score) discrim score [fval] negmean: -0.20"> <posmodel_distribution type="gaussian"> <parameter name="mean" value="4.01"/> <parameter name="stdev" value="2.53"/> </posmodel_distribution> <negmodel_distribution type="evd"> <parameter name="mean" value="-0.20"/> <parameter name="stdev" value="0.86"/> <parameter name="mu" value="-0.59"/> <parameter name="beta" value="0.67"/> </negmodel_distribution> </mixturemodel_distribution> <mixturemodel_distribution name="no. tolerable trypsin term. [ntt]"> <posmodel_distribution> <parameter name="ntt=0" value="0.333"/> <parameter name="ntt=1" value="0.333"/> <parameter name="ntt=2" value="0.333"/> </posmodel_distribution> <negmodel_distribution> <parameter name="ntt=0" value="0.333"/> <parameter name="ntt=1" value="0.333"/> <parameter name="ntt=2" value="0.333"/> </negmodel_distribution> </mixturemodel_distribution> <mixturemodel_distribution name="no. missed enz. cleavages [nmc]"> <posmodel_distribution> <parameter name="nmc=0" value="0.333"/> <parameter name="1&lt;=nmc&lt;=2" value="0.333"/> <parameter name="nmc&gt;=3" value="0.333"/> </posmodel_distribution> <negmodel_distribution> <parameter name="nmc=0" value="0.333"/> <parameter name="1&lt;=nmc&lt;=2" value="0.333"/> <parameter name="nmc&gt;=3" value="0.333"/> </negmodel_distribution> </mixturemodel_distribution> <mixturemodel_distribution name="accurate mass diff [massd] (offset: 0.000000)"> <posmodel_distribution> <parameter name="massd=-5.000000" value="0.090909091"/> <parameter name="massd=-4.000000" value="0.090909091"/> <parameter name="massd=-3.000000" value="0.090909091"/> <parameter name="massd=-2.000000" value="0.090909091"/> <parameter name="massd=-1.000000" value="0.090909091"/> <parameter name="massd=0.000000" value="0.090909091"/> <parameter name="massd=1.000000" value="0.090909091"/> <parameter name="massd=2.000000" value="0.090909091"/> <parameter name="massd=3.000000" value="0.090909091"/> <parameter name="massd=4.000000" value="0.090909091"/> <parameter name="massd=5.000000" value="0.090909091"/> </posmodel_distribution> <negmodel_distribution> <parameter name="massd=-5.000000" value="0.090909091"/> <parameter name="massd=-4.000000" value="0.090909091"/> <parameter name="massd=-3.000000" value="0.090909091"/> <parameter name="massd=-2.000000" value="0.090909091"/> <parameter name="massd=-1.000000" value="0.090909091"/> <parameter name="massd=0.000000" value="0.090909091"/> <parameter name="massd=1.000000" value="0.090909091"/> <parameter name="massd=2.000000" value="0.090909091"/> <parameter name="massd=3.000000" value="0.090909091"/> <parameter name="massd=4.000000" value="0.090909091"/> <parameter name="massd=5.000000" value="0.090909091"/> </negmodel_distribution> </mixturemodel_distribution> </mixture_model> <mixture_model precursor_ion_charge="7" comments="using training data negative distributions" prior_probability="0.000" est_tot_correct="0.0" tot_num_spectra="0" num_iterations="21"> <mixturemodel_distribution name="X! Tandem (k-score) discrim score [fval] negmean: -0.20"> <posmodel_distribution type="gaussian"> <parameter name="mean" value="4.01"/> <parameter name="stdev" value="2.53"/> </posmodel_distribution> <negmodel_distribution type="evd"> <parameter name="mean" value="-0.20"/> <parameter name="stdev" value="0.86"/> <parameter name="mu" value="-0.59"/> <parameter name="beta" value="0.67"/> </negmodel_distribution> </mixturemodel_distribution> <mixturemodel_distribution name="no. tolerable trypsin term. [ntt]"> <posmodel_distribution> <parameter name="ntt=0" value="0.333"/> <parameter name="ntt=1" value="0.333"/> <parameter name="ntt=2" value="0.333"/> </posmodel_distribution> <negmodel_distribution> <parameter name="ntt=0" value="0.333"/> <parameter name="ntt=1" value="0.333"/> <parameter name="ntt=2" value="0.333"/> </negmodel_distribution> </mixturemodel_distribution> <mixturemodel_distribution name="no. missed enz. cleavages [nmc]"> <posmodel_distribution> <parameter name="nmc=0" value="0.333"/> <parameter name="1&lt;=nmc&lt;=2" value="0.333"/> <parameter name="nmc&gt;=3" value="0.333"/> </posmodel_distribution> <negmodel_distribution> <parameter name="nmc=0" value="0.333"/> <parameter name="1&lt;=nmc&lt;=2" value="0.333"/> <parameter name="nmc&gt;=3" value="0.333"/> </negmodel_distribution> </mixturemodel_distribution> <mixturemodel_distribution name="accurate mass diff [massd] (offset: 0.000000)"> <posmodel_distribution> <parameter name="massd=-5.000000" value="0.090909091"/> <parameter name="massd=-4.000000" value="0.090909091"/> <parameter name="massd=-3.000000" value="0.090909091"/> <parameter name="massd=-2.000000" value="0.090909091"/> <parameter name="massd=-1.000000" value="0.090909091"/> <parameter name="massd=0.000000" value="0.090909091"/> <parameter name="massd=1.000000" value="0.090909091"/> <parameter name="massd=2.000000" value="0.090909091"/> <parameter name="massd=3.000000" value="0.090909091"/> <parameter name="massd=4.000000" value="0.090909091"/> <parameter name="massd=5.000000" value="0.090909091"/> </posmodel_distribution> <negmodel_distribution> <parameter name="massd=-5.000000" value="0.090909091"/> <parameter name="massd=-4.000000" value="0.090909091"/> <parameter name="massd=-3.000000" value="0.090909091"/> <parameter name="massd=-2.000000" value="0.090909091"/> <parameter name="massd=-1.000000" value="0.090909091"/> <parameter name="massd=0.000000" value="0.090909091"/> <parameter name="massd=1.000000" value="0.090909091"/> <parameter name="massd=2.000000" value="0.090909091"/> <parameter name="massd=3.000000" value="0.090909091"/> <parameter name="massd=4.000000" value="0.090909091"/> <parameter name="massd=5.000000" value="0.090909091"/> </negmodel_distribution> </mixturemodel_distribution> </mixture_model> </peptideprophet_summary> </analysis_summary> <analysis_summary analysis="database_refresh" time="2012-01-18T19:58:46"/> <analysis_summary analysis="interact" time="2012-01-18T19:58:36"> <interact_summary filename="c:/Inetpub/wwwroot/ISB/data/Ecoli/interact.pep.xml" directory="c:/Inetpub/wwwroot/ISB/data/Ecoli"> <inputfile name="120117.LC2.IT2.EC.scanmode_Cap_1-E,1_01_3481.tandem.pep.xml"/> </interact_summary> </analysis_summary> <dataset_derivation generation_no="0"/> <msms_run_summary base_name="c:/Inetpub/wwwroot/ISB/data/Ecoli/120117.LC2.IT2.EC.scanmode_Cap_1-E,1_01_3481" search_engine="X! Tandem (k-score)" msManufacturer="Bruker Daltonics" msModel="esquire" msIonization="UNKNOWN" msMassAnalyzer="Quadrupole Ion Trap" msDetector="MS:1000253" raw_data_type="raw" raw_data=".mzXML"> <sample_enzyme name="trypsin"> <specificity cut="KR" no_cut="P" sense="C"/> </sample_enzyme> <search_summary base_name="c:/Inetpub/wwwroot/ISB/data/Ecoli/120117.LC2.IT2.EC.scanmode_Cap_1-E,1_01_3481" search_engine="X! Tandem (k-score)" precursor_mass_type="monoisotopic" fragment_mass_type="monoisotopic" search_id="1"> <search_database local_path="c:/Inetpub/wwwroot/ISB/data/dbase/18.E_coli_K12.fasta" type="AA"/> <enzymatic_search_constraint enzyme="trypsin" max_num_internal_cleavages="2" min_number_termini="2"/> <aminoacid_modification aminoacid="C" massdiff="57.0215" mass="160.0306" variable="N"/> <aminoacid_modification aminoacid="C" massdiff="-17.0265" mass="143.0041" variable="Y" symbol="^"/> <!--X! Tandem n-terminal AA variable modification--> <aminoacid_modification aminoacid="E" massdiff="-18.0106" mass="111.0320" variable="Y" symbol="^"/> <!--X! Tandem n-terminal AA variable modification--> <aminoacid_modification aminoacid="Q" massdiff="-17.0265" mass="111.0321" variable="Y" symbol="^"/> <!--X! Tandem n-terminal AA variable modification--> <!-- Input parameters --> <parameter name="list path, taxonomy information" value="c:/Inetpub/wwwroot/ISB/data/Ecoli/taxonomy.xml"/> <parameter name="output, histogram column width" value="30"/> <parameter name="output, histograms" value="no"/> <parameter name="output, maximum valid expectation value" value="0.1"/> <parameter name="output, message" value="1234567890"/> <parameter name="output, one sequence copy" value="no"/> <parameter name="output, parameters" value="yes"/> <parameter name="output, path" value="c:/Inetpub/wwwroot/ISB/data/Ecoli/120117.LC2.IT2.EC.scanmode_Cap_1-E,1_01_3481.tandem"/> <parameter name="output, path hashing" value="no"/> <parameter name="output, performance" value="yes"/> <parameter name="output, proteins" value="yes"/> <parameter name="output, results" value="all"/> <parameter name="output, sequences" value="no"/> <parameter name="output, sort results by" value="spectrum"/> <parameter name="output, spectra" value="yes"/> <parameter name="protein, C-terminal residue modification mass" value=""/> <parameter name="protein, N-terminal residue modification mass" value=""/> <parameter name="protein, cleavage site" value="[RK]|{P}"/> <parameter name="protein, homolog management" value="no"/> <parameter name="protein, modified residue mass file" value=""/> <parameter name="protein, taxon" value="mydatabase"/> <parameter name="refine" value="no"/> <parameter name="refine, maximum valid expectation value" value="0.1"/> <parameter name="refine, sequence path" value=""/> <parameter name="refine, spectrum synthesis" value="yes"/> <parameter name="residue, modification mass" value="57.021464@C"/> <parameter name="residue, potential modification mass" value=""/> <parameter name="residue, potential modification motif" value=""/> <parameter name="scoring, a ions" value="no"/> <parameter name="scoring, algorithm" value="k-score"/> <parameter name="scoring, b ions" value="yes"/> <parameter name="scoring, c ions" value="no"/> <parameter name="scoring, cyclic permutation" value="no"/> <parameter name="scoring, include reverse" value="no"/> <parameter name="scoring, maximum missed cleavage sites" value="2"/> <parameter name="scoring, minimum ion count" value="1"/> <parameter name="scoring, x ions" value="no"/> <parameter name="scoring, y ions" value="yes"/> <parameter name="scoring, z ions" value="no"/> <parameter name="spectrum, dynamic range" value="10000.0"/> <parameter name="spectrum, fragment mass type" value="monoisotopic"/> <parameter name="spectrum, fragment monoisotopic mass error" value="0.4"/> <parameter name="spectrum, fragment monoisotopic mass error units" value="Daltons"/> <parameter name="spectrum, maximum parent charge" value="5"/> <parameter name="spectrum, minimum fragment mz" value="125.0"/> <parameter name="spectrum, minimum parent m+h" value="600.0"/> <parameter name="spectrum, minimum peaks" value="10"/> <parameter name="spectrum, parent monoisotopic mass error minus" value="0.5"/> <parameter name="spectrum, parent monoisotopic mass error plus" value="0.5"/> <parameter name="spectrum, parent monoisotopic mass error units" value="Daltons"/> <parameter name="spectrum, parent monoisotopic mass isotope error" value="yes"/> <parameter name="spectrum, path" value="c:/Inetpub/wwwroot/ISB/data/Ecoli/120117.LC2.IT2.EC.scanmode_Cap_1-E,1_01_3481.mzXML"/> <parameter name="spectrum, sequence batch size" value="1000"/> <parameter name="spectrum, threads" value="4"/> <parameter name="spectrum, total peaks" value="400"/> <parameter name="spectrum, use conditioning" value="no"/> <parameter name="spectrum, use noise suppression" value="yes"/> <!-- Unused input parameters --> <parameter name="refine, modification mass" value=""/> <parameter name="refine, point mutations" value="no"/> <parameter name="refine, potential C-terminus modifications" value=""/> <parameter name="refine, potential N-terminus modifications" value=""/> <parameter name="refine, potential modification mass" value=""/> <parameter name="refine, potential modification motif" value=""/> <parameter name="refine, tic percent" value="10"/> <parameter name="refine, unanticipated cleavage" value="no"/> <parameter name="refine, use potential modifications for full refinement" value="no"/> <parameter name="scoring, pluggable scoring" value="yes"/> <!-- Performance parameters --> <parameter name="list path, sequence source #1" value="c:/Inetpub/wwwroot/ISB/data/dbase/18.E_coli_K12.fasta"/> <parameter name="list path, sequence source description #1" value="no description"/> <parameter name="modelling, spectrum noise suppression ratio" value="0.00"/> <parameter name="modelling, total peptides used" value="16629786"/> <parameter name="modelling, total proteins used" value="4373"/> <parameter name="modelling, total spectra used" value="58618"/> <parameter name="process, start time" value="2012:01:17:17:36:54"/> <parameter name="process, version" value="x! tandem 2010.10.01.1 (LabKey, Insilicos and ISB)"/> <parameter name="quality values" value="3362 2146 1796 1705 1570 1235 919 681 398 242 123 67 34 12 10 1 3 0 0 0"/> <parameter name="refining, # input models" value="0"/> <parameter name="refining, # input spectra" value="0"/> <parameter name="refining, # partial cleavage" value="0"/> <parameter name="refining, # point mutations" value="0"/> <parameter name="refining, # potential C-terminii" value="0"/> <parameter name="refining, # potential N-terminii" value="0"/> <parameter name="refining, # unanticipated cleavage" value="0"/> <parameter name="timing, initial modelling total (sec)" value="17.97"/> <parameter name="timing, initial modelling/spectrum (sec)" value="0.000"/> <parameter name="timing, load sequence models (sec)" value="0.15"/> <parameter name="timing, refinement/spectrum (sec)" value="0.000"/> </search_summary> <analysis_timestamp analysis="peptideprophet" time="2012-01-18T19:58:51" id="1"/> <analysis_timestamp analysis="database_refresh" time="2012-01-18T19:58:46" id="1"> <database_refresh_timestamp database="c:/Inetpub/wwwroot/ISB/data/dbase/18.E_coli_K12.fasta" min_num_enz_term="2"/> </analysis_timestamp> <spectrum_query spectrum="120117.LC2.IT2.EC.scanmode_Cap_1-E,1_01_3481.00125.00125.3" start_scan="125" end_scan="125" precursor_neutral_mass="1061.4690" assumed_charge="3" index="1" retention_time_sec="25.96697600"> <search_result> <search_hit hit_rank="1" peptide="RVTGTSERR" peptide_prev_aa="K" peptide_next_aa="E" protein="sp|P0ACK2|AGAR_ECOLI" protein_descr="Putative aga operon transcriptional repressor OS=Escherichia coli (strain K12) GN=agaR" num_tot_proteins="1" num_matched_ions="11" tot_num_ions="32" calc_neutral_pep_mass="1060.5737" massdiff="0.895" num_tol_term="2" num_missed_cleavages="0" is_rejected="0"> <search_score name="hyperscore" value="338"/> <search_score name="nextscore" value="256"/> <search_score name="bscore" value="1"/> <search_score name="yscore" value="1"/> <search_score name="cscore" value="0"/> <search_score name="zscore" value="0"/> <search_score name="ascore" value="0"/> <search_score name="xscore" value="0"/> <search_score name="expect" value="1.1"/> <analysis_result analysis="peptideprophet"> <peptideprophet_result probability="0.5946" all_ntt_prob="(0.0000,0.0000,0.5946)"> <search_score_summary> <parameter name="fval" value="2.3222"/> <parameter name="ntt" value="2"/> <parameter name="nmc" value="0"/> <parameter name="massd" value="0.895"/> </search_score_summary> </peptideprophet_result> </analysis_result> </search_hit> </search_result> </spectrum_query> <spectrum_query spectrum="120117.LC2.IT2.EC.scanmode_Cap_1-E,1_01_3481.00147.00147.3" start_scan="147" end_scan="147" precursor_neutral_mass="1633.7164" assumed_charge="3" index="2" retention_time_sec="30.40096000"> <search_result> <search_hit hit_rank="1" peptide="TASGGLAGSTLSVDAAVR" peptide_prev_aa="R" peptide_next_aa="N" protein="sp|P42906|AGAA_ECOLI" protein_descr="Putative N-acetylgalactosamine-6-phosphate deacetylase OS=Escherichia coli (strain K12) GN=agaA" num_tot_proteins="1" num_matched_ions="19" tot_num_ions="68" calc_neutral_pep_mass="1631.8477" massdiff="1.869" num_tol_term="2" num_missed_cleavages="0" is_rejected="0"> <search_score name="hyperscore" value="355"/> <search_score name="nextscore" value="312"/> <search_score name="bscore" value="1"/> <search_score name="yscore" value="1"/> <search_score name="cscore" value="0"/> <search_score name="zscore" value="0"/> <search_score name="ascore" value="0"/> <search_score name="xscore" value="0"/> <search_score name="expect" value="1.9"/> <analysis_result analysis="peptideprophet"> <peptideprophet_result probability="0.0697" all_ntt_prob="(0.0000,0.0000,0.0697)"> <search_score_summary> <parameter name="fval" value="0.3691"/> <parameter name="ntt" value="2"/> <parameter name="nmc" value="0"/> <parameter name="massd" value="1.869"/> </search_score_summary> </peptideprophet_result> </analysis_result> </search_hit> </search_result> </spectrum_query> <spectrum_query spectrum="120117.LC2.IT2.EC.scanmode_Cap_1-E,1_01_3481.00197.00197.3" start_scan="197" end_scan="197" precursor_neutral_mass="1985.1253" assumed_charge="3" index="3" retention_time_sec="40.45299200"> <search_result> <search_hit hit_rank="1" peptide="EFKGDVSAEYGSWNKER" peptide_prev_aa="R" peptide_next_aa="Y" protein="sp|P16869|FHUE_ECOLI" protein_descr="FhuE receptor OS=Escherichia coli (strain K12) GN=fhuE" num_tot_proteins="1" num_matched_ions="12" tot_num_ions="64" calc_neutral_pep_mass="1982.9127" massdiff="2.213" num_tol_term="2" num_missed_cleavages="2" is_rejected="0"> <modification_info modified_peptide="E[111]FKGDVSAEYGSWNKER"> <mod_aminoacid_mass position="1" mass="111.0320"/> </modification_info> <search_score name="hyperscore" value="369"/> <search_score name="nextscore" value="310"/> <search_score name="bscore" value="0"/> <search_score name="yscore" value="1"/> <search_score name="cscore" value="0"/> <search_score name="zscore" value="0"/> <search_score name="ascore" value="0"/> <search_score name="xscore" value="0"/> <search_score name="expect" value="1.3"/> <analysis_result analysis="peptideprophet"> <peptideprophet_result probability="0.0867" all_ntt_prob="(0.0000,0.0000,0.0867)"> <search_score_summary> <parameter name="fval" value="1.2631"/> <parameter name="ntt" value="2"/> <parameter name="nmc" value="1"/> <parameter name="massd" value="2.213"/> </search_score_summary> </peptideprophet_result> </analysis_result> </search_hit> </search_result> </spectrum_query> <spectrum_query spectrum="120117.LC2.IT2.EC.scanmode_Cap_1-E,1_01_3481.00277.00277.3" start_scan="277" end_scan="277" precursor_neutral_mass="1866.1768" assumed_charge="3" index="4" retention_time_sec="56.64896000"> <search_result> <search_hit hit_rank="1" peptide="TVMPYITSQNAAITAER" peptide_prev_aa="R" peptide_next_aa="N" protein="sp|P27297|BAX_ECOLI" protein_descr="Protein bax OS=Escherichia coli (strain K12) GN=bax" num_tot_proteins="1" num_matched_ions="23" tot_num_ions="64" calc_neutral_pep_mass="1864.9357" massdiff="1.241" num_tol_term="2" num_missed_cleavages="0" is_rejected="0"> <search_score name="hyperscore" value="366"/> <search_score name="nextscore" value="323"/> <search_score name="bscore" value="1"/> <search_score name="yscore" value="1"/> <search_score name="cscore" value="0"/> <search_score name="zscore" value="0"/> <search_score name="ascore" value="0"/> <search_score name="xscore" value="0"/> <search_score name="expect" value="0.62"/> <analysis_result analysis="peptideprophet"> <peptideprophet_result probability="0.0724" all_ntt_prob="(0.0000,0.0000,0.0724)"> <search_score_summary> <parameter name="fval" value="0.4553"/> <parameter name="ntt" value="2"/> <parameter name="nmc" value="0"/> <parameter name="massd" value="1.241"/> </search_score_summary> </peptideprophet_result> </analysis_result> </search_hit> </search_result> </spectrum_query> <spectrum_query spectrum="120117.LC2.IT2.EC.scanmode_Cap_1-E,1_01_3481.00467.00467.3" start_scan="467" end_scan="467" precursor_neutral_mass="1866.0051" assumed_charge="3" index="5" retention_time_sec="94.77600000"> <search_result> <search_hit hit_rank="1" peptide="TVMPYITSQNAAITAER" peptide_prev_aa="R" peptide_next_aa="N" protein="sp|P27297|BAX_ECOLI" protein_descr="Protein bax OS=Escherichia coli (strain K12) GN=bax" num_tot_proteins="1" num_matched_ions="20" tot_num_ions="64" calc_neutral_pep_mass="1864.9357" massdiff="1.069" num_tol_term="2" num_missed_cleavages="0" is_rejected="0"> <search_score name="hyperscore" value="378"/> <search_score name="nextscore" value="337"/> <search_score name="bscore" value="1"/> <search_score name="yscore" value="1"/> <search_score name="cscore" value="0"/> <search_score name="zscore" value="0"/> <search_score name="ascore" value="0"/> <search_score name="xscore" value="0"/> <search_score name="expect" value="0.56"/> <analysis_result analysis="peptideprophet"> <peptideprophet_result probability="0.0722" all_ntt_prob="(0.0000,0.0000,0.0722)"> <search_score_summary> <parameter name="fval" value="0.4528"/> <parameter name="ntt" value="2"/> <parameter name="nmc" value="0"/> <parameter name="massd" value="1.069"/> </search_score_summary> </peptideprophet_result> </analysis_result> </search_hit> </search_result> </spectrum_query> <spectrum_query spectrum="120117.LC2.IT2.EC.scanmode_Cap_1-E,1_01_3481.00514.00514.3" start_scan="514" end_scan="514" precursor_neutral_mass="1502.0771" assumed_charge="3" index="6" retention_time_sec="104.21696000"> <search_result> <search_hit hit_rank="1" peptide="KASSTQSRPVNAGAK" peptide_prev_aa="K" peptide_next_aa="K" protein="sp|Q46861|YGIQ_ECOLI" protein_descr="UPF0313 protein ygiQ OS=Escherichia coli (strain K12) GN=ygiQ" num_tot_proteins="1" num_matched_ions="11" tot_num_ions="56" calc_neutral_pep_mass="1500.8007" massdiff="1.276" num_tol_term="2" num_missed_cleavages="0" is_rejected="0"> <search_score name="hyperscore" value="362"/> <search_score name="nextscore" value="313"/> <search_score name="bscore" value="1"/> <search_score name="yscore" value="1"/> <search_score name="cscore" value="0"/> <search_score name="zscore" value="0"/> <search_score name="ascore" value="0"/> <search_score name="xscore" value="0"/> <search_score name="expect" value="1.6"/> <analysis_result analysis="peptideprophet"> <peptideprophet_result probability="0.1086" all_ntt_prob="(0.0000,0.0000,0.1086)"> <search_score_summary> <parameter name="fval" value="0.7238"/> <parameter name="ntt" value="2"/> <parameter name="nmc" value="0"/> <parameter name="massd" value="1.276"/> </search_score_summary> </peptideprophet_result> </analysis_result> </search_hit> </search_result> </spectrum_query> <spectrum_query spectrum="120117.LC2.IT2.EC.scanmode_Cap_1-E,1_01_3481.00604.00604.3" start_scan="604" end_scan="604" precursor_neutral_mass="2295.5883" assumed_charge="3" index="7" retention_time_sec="122.30694400"> <search_result> <search_hit hit_rank="1" peptide="IAHWRGEDAAWLAATTDANVK" peptide_prev_aa="R" peptide_next_aa="T" protein="sp|P27859|TATD_ECOLI" protein_descr="Deoxyribonuclease tatD OS=Escherichia coli (strain K12) GN=tatD" num_tot_proteins="1" num_matched_ions="16" tot_num_ions="80" calc_neutral_pep_mass="2295.1397" massdiff="0.449" num_tol_term="2" num_missed_cleavages="1" is_rejected="0"> <search_score name="hyperscore" value="386"/> <search_score name="nextscore" value="297"/> <search_score name="bscore" value="1"/> <search_score name="yscore" value="1"/> <search_score name="cscore" value="0"/> <search_score name="zscore" value="0"/> <search_score name="ascore" value="0"/> <search_score name="xscore" value="0"/> <search_score name="expect" value="0.33"/> <analysis_result analysis="peptideprophet"> <peptideprophet_result probability="0.0512" all_ntt_prob="(0.0000,0.0000,0.0512)"> <search_score_summary> <parameter name="fval" value="2.7662"/> <parameter name="ntt" value="2"/> <parameter name="nmc" value="1"/> <parameter name="massd" value="0.449"/> </search_score_summary> </peptideprophet_result> </analysis_result> </search_hit> </search_result> </spectrum_query> <spectrum_query spectrum="120117.LC2.IT2.EC.scanmode_Cap_1-E,1_01_3481.00643.00643.3" start_scan="643" end_scan="643" precursor_neutral_mass="1220.2046" assumed_charge="3" index="8" retention_time_sec="130.16998400"> <search_result> <search_hit hit_rank="1" peptide="TDVELDGDNSR" peptide_prev_aa="R" peptide_next_aa="F" protein="sp|P32051|YDEK_ECOLI" protein_descr="Uncharacterized lipoprotein ydeK OS=Escherichia coli (strain K12) GN=ydeK" num_tot_proteins="1" num_matched_ions="11" tot_num_ions="40" calc_neutral_pep_mass="1219.5317" massdiff="0.673" num_tol_term="2" num_missed_cleavages="0" is_rejected="0"> <search_score name="hyperscore" value="326"/> <search_score name="nextscore" value="280"/> <search_score name="bscore" value="1"/> <search_score name="yscore" value="1"/> <search_score name="cscore" value="0"/> <search_score name="zscore" value="0"/> <search_score name="ascore" value="0"/> <search_score name="xscore" value="0"/> <search_score name="expect" value="0.71"/> <analysis_result analysis="peptideprophet"> <peptideprophet_result probability="0.0574" all_ntt_prob="(0.0000,0.0000,0.0574)"> <search_score_summary> <parameter name="fval" value="0.3058"/> <parameter name="ntt" value="2"/> <parameter name="nmc" value="0"/> <parameter name="massd" value="0.673"/> </search_score_summary> </peptideprophet_result> </analysis_result> </search_hit> </search_result> </spectrum_query> <spectrum_query spectrum="120117.LC2.IT2.EC.scanmode_Cap_1-E,1_01_3481.00682.00682.3" start_scan="682" end_scan="682" precursor_neutral_mass="1778.2794" assumed_charge="3" index="9" retention_time_sec="137.71398400"> <search_result> <search_hit hit_rank="1" peptide="GSMLPKVEAAASFARSR" peptide_prev_aa="K" peptide_next_aa="A" protein="sp|Q46807|ARCL_ECOLI" protein_descr="Carbamate kinase-like protein yqeA OS=Escherichia coli (strain K12) GN=yqeA" num_tot_proteins="1" num_matched_ions="15" tot_num_ions="64" calc_neutral_pep_mass="1776.9307" massdiff="1.349" num_tol_term="2" num_missed_cleavages="2" is_rejected="0"> <search_score name="hyperscore" value="352"/> <search_score name="nextscore" value="287"/> <search_score name="bscore" value="1"/> <search_score name="yscore" value="1"/> <search_score name="cscore" value="0"/> <search_score name="zscore" value="0"/> <search_score name="ascore" value="0"/> <search_score name="xscore" value="0"/> <search_score name="expect" value="1.3"/> <analysis_result analysis="peptideprophet"> <peptideprophet_result probability="0.1072" all_ntt_prob="(0.0000,0.0000,0.1072)"> <search_score_summary> <parameter name="fval" value="1.4761"/> <parameter name="ntt" value="2"/> <parameter name="nmc" value="1"/> <parameter name="massd" value="1.349"/> </search_score_summary> </peptideprophet_result> </analysis_result> </search_hit> </search_result> </spectrum_query> <spectrum_query spectrum="120117.LC2.IT2.EC.scanmode_Cap_1-E,1_01_3481.00856.00856.3" start_scan="856" end_scan="856" precursor_neutral_mass="2002.4584" assumed_charge="3" index="10" retention_time_sec="172.20294400"> <search_result> <search_hit hit_rank="1" peptide="ESVSHQNYPQVIKHTPR" peptide_prev_aa="K" peptide_next_aa="M" protein="sp|P71237|WCAC_ECOLI" protein_descr="Putative colanic acid biosynthesis glycosyl transferase wcaC OS=Escherichia coli (strain K12) GN=wcaC" num_tot_proteins="1" num_matched_ions="16" tot_num_ions="64" calc_neutral_pep_mass="2001.0177" massdiff="1.441" num_tol_term="2" num_missed_cleavages="1" is_rejected="0"> <modification_info modified_peptide="E[111]SVSHQNYPQVIKHTPR"> <mod_aminoacid_mass position="1" mass="111.0320"/> </modification_info> <search_score name="hyperscore" value="417"/> <search_score name="nextscore" value="327"/> <search_score name="bscore" value="1"/> <search_score name="yscore" value="1"/> <search_score name="cscore" value="0"/> <search_score name="zscore" value="0"/> <search_score name="ascore" value="0"/> <search_score name="xscore" value="0"/> <search_score name="expect" value="0.44"/> <analysis_result analysis="peptideprophet"> <peptideprophet_result probability="0.4866" all_ntt_prob="(0.0000,0.0000,0.4866)"> <search_score_summary> <parameter name="fval" value="2.8844"/> <parameter name="ntt" value="2"/> <parameter name="nmc" value="1"/> <parameter name="massd" value="1.441"/> </search_score_summary> </peptideprophet_result> </analysis_result> </search_hit> </search_result> </spectrum_query> <spectrum_query spectrum="120117.LC2.IT2.EC.scanmode_Cap_1-E,1_01_3481.00960.00960.3" start_scan="960" end_scan="960" precursor_neutral_mass="1224.7028" assumed_charge="3" index="11" retention_time_sec="192.76499200"> <search_result> <search_hit hit_rank="1" peptide="CTEEHQAIVR" peptide_prev_aa="K" peptide_next_aa="K" protein="sp|P38521|YGGL_ECOLI" protein_descr="Uncharacterized protein yggL OS=Escherichia coli (strain K12) GN=yggL" num_tot_proteins="1" num_matched_ions="12" tot_num_ions="36" calc_neutral_pep_mass="1224.5557" massdiff="0.147" num_tol_term="2" num_missed_cleavages="0" is_rejected="0"> <modification_info modified_peptide="C[143]TEEHQAIVR"> <mod_aminoacid_mass position="1" mass="143.0041"/> </modification_info> <search_score name="hyperscore" value="316"/> <search_score name="nextscore" value="225"/> <search_score name="bscore" value="1"/> <search_score name="yscore" value="1"/> <search_score name="cscore" value="0"/> <search_score name="zscore" value="0"/> <search_score name="ascore" value="0"/> <search_score name="xscore" value="0"/> <search_score name="expect" value="0.2"/> <analysis_result analysis="peptideprophet"> <peptideprophet_result probability="0.1629" all_ntt_prob="(0.0000,0.0000,0.1629)"> <search_score_summary> <parameter name="fval" value="2.8076"/> <parameter name="ntt" value="2"/> <parameter name="nmc" value="0"/> <parameter name="massd" value="0.147"/> 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<search_score name="ascore" value="0"/> <search_score name="xscore" value="0"/> <search_score name="expect" value="0.19"/> <analysis_result analysis="peptideprophet"> <peptideprophet_result probability="0.5093" all_ntt_prob="(0.0000,0.0000,0.5093)"> <search_score_summary> <parameter name="fval" value="2.8761"/> <parameter name="ntt" value="2"/> <parameter name="nmc" value="1"/> <parameter name="massd" value="2.008"/> </search_score_summary> </peptideprophet_result> </analysis_result> </search_hit> </search_result> </spectrum_query> <spectrum_query spectrum="120117.LC2.IT2.EC.scanmode_Cap_1-E,1_01_3481.01048.01048.3" start_scan="1048" end_scan="1048" precursor_neutral_mass="1026.2627" assumed_charge="3" index="13" retention_time_sec="210.35097600"> <search_result> <search_hit hit_rank="1" peptide="DVDVLYFR" peptide_prev_aa="K" peptide_next_aa="E" protein="sp|P0A780|NUSB_ECOLI" protein_descr="N utilization substance protein B OS=Escherichia coli (strain K12) GN=nusB" num_tot_proteins="1" 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<analysis_result analysis="peptideprophet"> <peptideprophet_result probability="0.0816" all_ntt_prob="(0.0000,0.0000,0.0816)"> <search_score_summary> <parameter name="fval" value="0.1116"/> <parameter name="ntt" value="2"/> <parameter name="nmc" value="0"/> <parameter name="massd" value="0.196"/> </search_score_summary> </peptideprophet_result> </analysis_result> </search_hit> </search_result> </spectrum_query> <spectrum_query spectrum="120117.LC2.IT2.EC.scanmode_Cap_1-E,1_01_3481.00014.00014.2" start_scan="14" end_scan="14" precursor_neutral_mass="1244.0564" assumed_charge="2" index="14878" retention_time_sec="3.86099200"> <search_result> <search_hit hit_rank="1" peptide="ALEEAGAEVEVK" peptide_prev_aa="K" peptide_next_aa="-" protein="sp|P0A7K2|RL7_ECOLI" protein_descr="50S ribosomal protein L7\L12 OS=Escherichia coli (strain K12) GN=rplL" num_tot_proteins="1" num_matched_ions="20" tot_num_ions="22" calc_neutral_pep_mass="1243.6297" massdiff="0.427" num_tol_term="2" 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index="14879" retention_time_sec="1.68294400"> <search_result> <search_hit hit_rank="1" peptide="ALEEAGAEVEVK" peptide_prev_aa="K" peptide_next_aa="-" protein="sp|P0A7K2|RL7_ECOLI" protein_descr="50S ribosomal protein L7\L12 OS=Escherichia coli (strain K12) GN=rplL" num_tot_proteins="1" num_matched_ions="22" tot_num_ions="22" calc_neutral_pep_mass="1243.6297" massdiff="0.481" num_tol_term="2" num_missed_cleavages="0" is_rejected="0"> <search_score name="hyperscore" value="513"/> <search_score name="nextscore" value="269"/> <search_score name="bscore" value="1"/> <search_score name="yscore" value="1"/> <search_score name="cscore" value="0"/> <search_score name="zscore" value="0"/> <search_score name="ascore" value="0"/> <search_score name="xscore" value="0"/> <search_score name="expect" value="0.0013"/> <analysis_result analysis="peptideprophet"> <peptideprophet_result probability="0.9993" all_ntt_prob="(0.0000,0.0000,0.9993)"> <search_score_summary> <parameter name="fval" value="7.1076"/> <parameter name="ntt" value="2"/> <parameter name="nmc" value="0"/> <parameter name="massd" value="0.481"/> </search_score_summary> </peptideprophet_result> </analysis_result> </search_hit> </search_result> </spectrum_query> </msms_run_summary> </msms_pipeline_analysis> /default:msms_pipeline_analysis/default:msms_run_summary/default:spectrum_query/@start_scan default http://regis-web.systemsbiology.net/pepXML xsi http://www.w3.org/2001/XMLSchema-instance net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Loop net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeJoin_and_Insert_Tabsin11in21out100 This Beanshell formats the data for rt. 2012-08-28 13:28:17.213 UTC net.sf.taverna.t2.activitiesbeanshell-activity1.4net.sf.taverna.t2.activities.beanshell.BeanshellActivity in1 1 text/plain java.lang.String true in2 1 text/plain java.lang.String true out1 0 0 workflow net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokertin10STDOUT00 This tool calls a local installation of rt - here rt 3.0. 2012-08-28 13:28:54.353 UTC net.sf.taverna.t2.activitiesexternal-tool-activity1.4net.sf.taverna.t2.activities.externaltool.ExternalToolActivity 789663B8-DA91-428A-9F7D-B3F3DA185FD4 default local <?xml version="1.0" encoding="UTF-8"?> <localInvocation /> f558263a-838b-43ab-af65-3a61ad86b1e6 C:\Taverna\programs\rt3.exe -i in1 -f tab 1200 1800 in1 in1 true false false windows-1252 false false false false true true 0 false net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokePlot_Predicted_vs_Measured_RTin20in10in30output_file_name00 This Rshell script plots predicted versus measured retention time for the identified peptides. 2012-08-28 13:29:18.114 UTC net.sf.taverna.t2.activitiesrshell-activity1.4net.sf.taverna.t2.activities.rshell.RshellActivity in1 0 false in2 0 false in3 0 false output_file_name 0 0 false localhost 6311 false false in1 STRING in2 STRING in3 STRING output_file_name STRING net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokePlot_Retention_Coefficientsin10in20output_file_name00 This Rshell script plots the retention coefficients for the different amino acids. 2012-08-28 13:29:42.4 UTC net.sf.taverna.t2.activitiesrshell-activity1.4net.sf.taverna.t2.activities.rshell.RshellActivity in1 0 false in2 0 false output_file_name 0 0 false localhost 6311 false false in1 STRING in2 STRING output_file_name STRING net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeTandemfasta_file0mzxml_file0log_file0parameter_file0tandem_file00pepxml_file00interact_file00 This Beanshell sets up and runs X!Tandem with the provided FASTA file and LC-MS/MS data in mzXML. 2012-08-28 13:25:03.691 UTC net.sf.taverna.t2.activitiesbeanshell-activity1.4net.sf.taverna.t2.activities.beanshell.BeanshellActivity mzxml_file 0 text/plain java.lang.String true fasta_file 0 text/plain java.lang.String true parameter_file 0 text/plain java.lang.String true log_file 0 text/plain java.lang.String true tandem_file 0 0 pepxml_file 0 0 interact_file 0 0 workflow net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeTandem2XMLin10in20 This tool calls the Tandem2XML converter for transforming X!Tandem results to pepXML. 2012-08-28 13:25:31.671 UTC net.sf.taverna.t2.activitiesexternal-tool-activity1.4net.sf.taverna.t2.activities.externaltool.ExternalToolActivity 789663B8-DA91-428A-9F7D-B3F3DA185FD4 default local <?xml version="1.0" encoding="UTF-8"?> <localInvocation /> 97209d29-53d0-4771-9abf-123f6d2a9f05 C:\Inetpub\tpp-bin\Tandem2XML "%%in1%%" "%%in2%%" 1200 1800 in1 in2 in2 in2 false false false windows-1252 false false false in1 in1 false false false windows-1252 false false false false true true 0 false net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokePeptideProphet_Tandemin10in20 The PeptideProphet_Tandem tool runs PeptideProphet (in its default location after a standard installation of the Trans-Proteomic Pipeline). 2012-08-28 13:26:42.812 UTC net.sf.taverna.t2.activitiesexternal-tool-activity1.4net.sf.taverna.t2.activities.externaltool.ExternalToolActivity 789663B8-DA91-428A-9F7D-B3F3DA185FD4 default local <?xml version="1.0" encoding="UTF-8"?> <localInvocation /> 0d2eda5e-7889-4b15-bc14-9613cdf73440 C:\Inetpub\tpp-bin\xinteract.exe -N"%%in2%%" -p0.99 -l7 "%%in1%%" 1200 1800 in1 in2 in2 in2 false false false windows-1252 false false false in1 in1 false false false windows-1252 false false false false false false 0 false net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeRead_Text_FilefileurlTandeminteract_fileExtract_Peptidesxml_textRead_Text_FilefilecontentsExtract_Scan_Numbersxml_textRead_Text_FilefilecontentsJoin_and_Insert_Tabsin1Extract_PeptidesnodelistJoin_and_Insert_Tabsin2Extract_Scan_Numbersnodelistrtin1Join_and_Insert_Tabsout1Plot_Predicted_vs_Measured_RTin2rtSTDOUTPlot_Predicted_vs_Measured_RTin1Join_and_Insert_Tabsout1Plot_Predicted_vs_Measured_RTin3Tandeminteract_filePlot_Retention_Coefficientsin1rtSTDOUTPlot_Retention_Coefficientsin2Tandeminteract_fileTandemfasta_fileFASTA_FileTandemmzxml_filemzXML_FileTandemlog_fileLog_FileTandemparameter_fileTandem_Param_FileTandem2XMLin1Tandemtandem_fileTandem2XMLin2Tandempepxml_filePeptideProphet_Tandemin1Tandempepxml_filePeptideProphet_Tandemin2Tandeminteract_filePredicted_RT_PeptidesPlot_Predicted_vs_Measured_RToutput_file_nameGraphic_RetentionCoefficient_AAPlot_Retention_Coefficientsoutput_file_name Jeroen de Bruin Yassene Mohammed Wendy Plugge Alex Henneman Magnus Palmblad (n.m.palmblad@lumc.nl) 2012-08-28 13:24:11.10 UTC 20178567-0598-484e-87f8-16b85b59f5fc 2012-08-08 10:49:24.101 UTC 05ea30e7-2776-4795-8aed-0df2a2c8c512 2011-04-07 14:39:21.195 UTC 6d3d8308-b6e9-4f79-b040-57c0baeb1db7 2012-04-11 10:01:10.121 UTC 4840599a-0b97-449e-9757-c2b3276c79a4 2012-04-11 11:31:50.303 UTC b8bbef6f-374c-4d93-8033-29053e70f518 2011-04-06 16:18:12.291 UTC e6bbc783-b24d-461c-9928-c78596f56d54 2012-03-12 12:09:14.102 UTC f8cce8ec-2e84-4766-ad64-8cca2aac8a55 2012-08-28 15:30:25.763 UTC c1d60e14-a0df-4749-87a4-80adad360923 2012-04-16 07:54:33.780 UTC e1f1fc32-22c6-4ec7-bc9f-5129b0d20c8c 2012-08-10 08:21:54.204 UTC e6b54f0b-7514-473e-9920-aa8d1391ae26 2012-08-06 10:57:37.883 UTC 82e01409-1114-4a6e-a1c9-e09144055c3e 2012-03-12 12:01:54.533 UTC 13409438-46da-4786-88bb-a4dbb3732076 2012-04-11 08:38:40.884 UTC fc634334-f397-4f68-8119-a853925702b4 2011-03-29 08:02:31.511 UTC 262783b0-845f-4bc0-9310-b1617db7c047 2012-08-06 16:44:22.629 UTC 624593fc-452f-470c-adf7-4d7d8b6d6f0c 2011-03-30 08:59:22.85 UTC 42e2f42b-9001-4e9e-9c0b-dcec46712b2a 2012-04-11 11:06:41.585 UTC 541df59b-37a5-4515-92b9-1b58254e54f5 2012-03-12 10:40:27.65 UTC 407f1b6e-00dd-4ca3-b2b3-d526d8a214d1 2012-04-16 07:30:40.669 UTC c0ac18f3-1922-45b5-8ac9-9e1931e312c7 2012-01-11 13:41:48.789 UTC d4430f80-5827-4fa3-83f3-0c58410ffc92 2011-01-31 17:35:12.220 UTC 53317b78-d33f-40cd-bc8f-f26ecee69bd6 2012-08-09 13:27:49.698 UTC d8f357be-7c2e-45a0-8d37-499dee5c6529 2012-03-22 13:09:25.231 UTC 7d356e09-ab0f-49a0-b8b2-e04c79b4831c 2011-03-01 10:43:55.657 UTC fcde5c53-f349-4d82-b38c-98be9ebd0837 2012-08-28 13:43:19.743 UTC 5bada5bc-e95c-423a-b248-1bcdb6fd81a9 2012-04-16 07:44:32.880 UTC de095acc-94a9-4a65-b33e-692126a25bb1 2012-04-19 11:26:47.518 UTC 2c8faf07-5e70-4073-a637-95ce0add9658 2012-08-09 13:31:49.710 UTC 3ce3f027-e65e-4f23-8993-d50d45a0d198 2011-01-31 09:56:42.353 UTC 83dd948d-a363-412c-8a69-9583b9318ba6 2012-01-04 10:22:28.854 UTC fad53bf0-f8a4-4998-8bbd-3ca1e7356d27 2012-04-16 10:11:05.67 UTC 66efbdff-1c55-4f0c-8f63-ce11bbbb2781 2012-04-16 07:22:17.235 UTC c2b3ecbf-3400-4610-ba06-2ca1f25109e3 2012-08-28 16:12:37.18 UTC 6ddebe57-9b8c-4942-9664-d50ce8de5d81 2012-08-06 16:16:55.296 UTC e4bbbe00-ff98-4187-85be-66b1bf4d2da8 2012-04-16 08:03:41.409 UTC 56d89322-2864-4bee-b71b-535a74078068 2011-04-06 13:54:29.498 UTC f41838e8-bf43-4c69-ba11-498fc937e6b0 2012-04-11 13:11:36.976 UTC 36491e21-c712-4a5a-b562-241807763ed9 2011-01-31 10:02:11.569 UTC de000ea1-cff6-4679-b42e-9d315fa1db23 2011-04-07 14:36:51.860 UTC 2dc4297c-e078-4ae9-89cf-957b7a9de818 2011-12-01 11:54:35.986 UTC 04d83187-2364-4930-ba2d-1eee4d3d5e6f 2011-03-22 12:27:25.556 UTC 8b3fb14f-31ab-4170-99d5-0952c97d1f45 2012-08-28 15:19:31.4 UTC bee38ae2-d96f-48d0-80e8-367349f4b8e1 2011-03-02 14:12:56.636 UTC 4d07676a-6393-4df0-997f-f57da1f74def 2012-08-09 13:17:03.226 UTC 8615d8a1-e3af-4509-b708-daefe6d0e9a2 2011-01-31 17:21:34.160 UTC 9dea1a41-65e7-4709-bdfe-a0a0f18a68d9 2012-08-06 16:45:23.271 UTC ed84d9b6-1a6d-4f8d-a9c7-4da8d2b03192 2011-04-06 14:28:27.542 UTC 7d8af289-0d34-4ac7-9478-e62f4f418c0d 2012-08-09 09:14:21.663 UTC 1b672318-d3ad-4db8-82a0-27e6abd171a7 2012-08-28 14:47:19.905 UTC f0403ba3-c249-462f-a162-0a84eb56ef6a 2012-08-09 13:33:50.160 UTC 785be58d-da6c-4d25-bbb6-6607d09e001d 2012-08-06 15:03:45.673 UTC e7f3c287-196f-4e4c-b36f-bb96df3aab33 2012-03-09 08:58:57.490 UTC Retention Time Prediction with X!Tandem 2012-08-09 13:12:41.569 UTC 4e920b38-61dd-472d-a4e2-e35cce026a1f 2012-08-28 14:20:01.148 UTC f9a6f95b-b792-4915-9d29-c01310e6a268 2012-03-12 13:03:11.420 UTC c68d4688-4ccf-4c5e-88be-b6ffcf4dca48 2012-03-09 09:12:38.299 UTC 0a265c18-2489-4cb7-b167-073f7484a770 2012-09-03 09:44:21.557 UTC f7de5cac-1926-4ec2-9838-47a53f5c04fd 2011-04-12 14:43:35.130 UTC 880f1df3-9831-44bb-9705-bbc47103ac98 2012-04-12 15:35:20.839 UTC bde0f9e9-0d5f-4fa6-b783-b15479f24a6d 2012-08-09 13:11:04.325 UTC f66e38ef-e19b-43ca-9488-2e91382c9668 2012-04-19 11:22:35.370 UTC 7e000430-8739-465b-8377-569c8f95246c 2012-04-19 11:21:43.503 UTC 3507c9f5-f5f2-4033-9f7c-2db5f50d88f1 2011-01-31 10:07:39.185 UTC 8aaf85b9-ca7b-48c1-8cf1-21f35a36e920 2011-12-01 12:07:14.642 UTC f4bfe0fd-4074-42f5-81fa-acf3cf08b695 2012-04-16 08:32:24.707 UTC fdd1d11b-9b5b-4b01-83f6-b9c3095fcd11 2012-08-28 14:23:52.402 UTC bb167c46-673d-43b0-a863-4d87f887c263 2012-08-09 12:46:45.433 UTC 45926357-0432-4509-ab95-c710a93c1a0e 2012-08-28 13:29:42.104 UTC 99560d91-04bf-41c3-8379-162f7313ddd7 2012-08-08 13:37:16.6 UTC 023e9115-05b5-420c-8db1-f324d40570cb 2012-04-16 12:14:07.669 UTC 9ba4212c-ea24-426e-9832-1a26a4a214e6 2012-04-12 15:38:42.44 UTC This workflow identifies peptides from tandem mass spectra using X!Tandem as in a standard installation of the Trans-Proteomic Pipeline (TPP, version 4.6, but earlier versions should also work). The peptide-spectrum matches are validates using PeptideProphet (also from a standard installation of TPP) and peptides with at least a probability 0.95 are used to train a linear retention time predictor (Palmblad et al., 2002), whereby retention coefficients are also derived. These indirectly provide information on the chromatographic stationary and mobile phase (composition and pH) and the gradient. The two Rshell scrips visualize the prediction versus measured retention times and amino acid coefficients colored by physico-chemical properties (basic/acidic/polar etc.). 2012-08-09 13:27:48.398 UTC aa9ca29d-28f2-45e6-87c4-3e761c1cb3d5 2012-03-12 12:26:43.930 UTC 5d6ba88b-b3b6-45bb-bfca-9823451e4388 2011-03-30 09:25:11.740 UTC bef6fa28-1bbf-4d4a-bd34-32120cc97d1f 2012-03-12 10:45:32.953 UTC 5d42f252-597b-42d4-b9c6-16a74a8c6b70 2012-03-12 13:08:44.375 UTC ebe93854-8931-41b0-bbd1-8af675d22239 2012-04-12 15:55:28.605 UTC ce45dc51-de9a-45a6-9d4d-3ca389bd6601 2011-04-06 14:31:57.156 UTC 30d5f1d6-d842-4159-9d86-dfb8cfc10256 2012-03-12 11:49:32.612 UTC eb132715-6579-46e9-9ea2-e71a38d7143d 2012-04-19 11:29:12.583 UTC ee54123b-6086-4e07-82b2-b49ce31abfa3 2012-04-11 10:40:39.711 UTC acd3a31e-8c1f-4e97-a991-5b1dda63a8dd 2012-03-12 13:02:36.280 UTC fc505117-909d-449e-8de6-d4c24090d665 2012-08-08 10:49:39.176 UTC 8e0e9b2d-6420-4411-9f61-e7841aae2563 2011-04-07 12:25:11.816 UTC 1630eb6c-0c41-48d3-8cbc-cd70c95be2af 2012-03-09 09:30:53.119 UTC 540ac1af-179a-4eb2-91e5-1484e9b674b8 2012-03-09 09:24:49.38 UTC f3300eee-4266-4559-8506-f6c0c66a828d 2012-08-28 14:20:22.19 UTC 7eeffbe6-b48b-4fcb-ab4d-2651561607fc 2012-04-15 13:24:22.140 UTC ad160db0-a2c6-4689-bc01-29eeb7fbb684 2012-08-28 15:06:04.261 UTC 1520eabd-565d-4a01-a68d-0ac96f73ddf9 2011-03-30 08:59:48.925 UTC 471566c3-6f4e-48d1-bd0c-9cf6b92d86f9 2012-08-06 10:49:56.669 UTC