RTCalc_Retention_TimpepXML_File00 This is the input peptide identifications in pepXML format. 2014-02-06 14:28:13.757 UTC Max_Abs_Z_Score00 This is the maximum absolute Z-Score for inclusion in the Fiterered_Peptide_List. 2014-02-06 14:28:21.965 UTC 2 2014-02-06 14:25:45.17 UTC RTCalc_model This holds the trained RTCalc model. 2014-02-06 14:29:38.607 UTC RTCalc_RMSD This is the RMSD between measured and predicted ("correct") retention time in scan numbers. 2014-02-06 14:29:17.118 UTC Z_Scores_vs_Probabilities This is a PNG plot of the Z-score as a function of PeptideProphet probability, with the removed PSMs indicated in red. 2014-02-06 14:30:57.202 UTC Filtered_Peptide_List This output collects the PSMs within the Max_Abs_Z_Score in a flat file (string). 2014-02-06 14:30:14.73 UTC Read_Text_Filefileurl0filecontents00 This shell reads the X!Tandem/PeptideProphet results to feed the XPath extractors below. 2014-02-06 14:28:42.310 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" 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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! 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[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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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_Tabsin11in21training00validation_flat00 This Beanshell formats the data for RTCalc. 2014-02-06 14:27:14.706 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 training 0 0 validation_flat 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.InvokeRTCalc_Trainin10out100 This component trains the RTCalc predictor. 2014-02-06 14:27:26.634 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 /> 2e9a7c9a-6fea-4ef6-9eab-8d37c453198b c:/Inetpub/tpp-bin/RTCalc.exe TRAIN=in1 COEFF=out1 1200 1800 in1 in1 true false false windows-1252 false false false out1 out1 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.InvokeRTCalc_Predictin20in10out100 This tool applies the RTCalc predictor. 2014-02-06 14:27:39.507 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 /> 50ac6017-689c-425d-84e6-54ddc67494e4 c:/Inetpub/tpp-bin/RTCalc.exe PEPS=in1 COEFF=in2 OUTFILE=out1 1200 1800 in2 in2 true false false windows-1252 false false false in1 in1 true false false windows-1252 false false false out1 out1 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.InvokeCompare_Z_Scores_and_Probabilitiespredicted0measured0probabilities0max_abs_Z_score0rmsd200Z_scores_vs_probabilities00filtered_peptide_list00 This Rshell script calculates and plots RTCalc retention time Z-scores for all peptides in the pepXML file. There is no probability cutoff for the training of RTCalc, so for datasets with many false peptide identifications (or peptide-spectrum matches of low probability), a selection should be in the XPaths, in the Join_and_Insert_Tabs component or in an additional component at any point before the RTCalc_Train call. 2014-02-06 14:22:53.585 UTC net.sf.taverna.t2.activitiesrshell-activity1.4net.sf.taverna.t2.activities.rshell.RshellActivity measured 0 false predicted 0 false probabilities 0 false max_abs_Z_score 0 false rmsd2 0 0 Z_scores_vs_probabilities 0 0 filtered_peptide_list 0 0 false localhost 6311 false false measured STRING predicted STRING probabilities STRING max_abs_Z_score DOUBLE rmsd2 DOUBLE Z_scores_vs_probabilities PNG_FILE filtered_peptide_list 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.InvokeExtract_Probabilitiesxml_text0nodelist11 This XPath extracts the corresponding PeptideProphet probabilities for the identified peptides. 2014-02-06 14:27:05.642 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/120117.LC2.IT2.EC.scanmode_Cap_1-E,1_01_3481.tandem.interact_09997.pep.xsl"?><msms_pipeline_analysis xmlns="http://regis-web.systemsbiology.net/pepXML" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" date="2013-03-27T17:29:50" summary_xml="c:/Inetpub/wwwroot/ISB/data/Ecoli/120117.LC2.IT2.EC.scanmode_Cap_1-E,1_01_3481.tandem.interact_09997.pep.xml" xsi:schemaLocation="http://regis-web.systemsbiology.net/pepXML http://localhost/pepXML_v117.xsd"> <analysis_summary analysis="peptideprophet" time="2013-03-27T17:30:01"> <peptideprophet_summary version="PeptideProphet (TPP v4.6 OCCUPY rev 2, Build 201302140902 (MinGW))" author="AKeller@ISB" min_prob="1.00" options=" MINPROB=0.9997 " est_tot_num_correct="11350.0"> <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="0.2018" error="0.0006" num_corr="2291" num_incorr="1"/> <roc_data_point min_prob="0.9900" sensitivity="0.5397" error="0.0026" num_corr="6125" num_incorr="16"/> <roc_data_point min_prob="0.9800" sensitivity="0.6203" error="0.0041" num_corr="7040" num_incorr="29"/> <roc_data_point min_prob="0.9500" sensitivity="0.7183" error="0.0081" num_corr="8153" num_incorr="66"/> <roc_data_point min_prob="0.9000" sensitivity="0.7845" error="0.0138" num_corr="8905" num_incorr="124"/> <roc_data_point min_prob="0.8500" sensitivity="0.8228" error="0.0195" num_corr="9339" num_incorr="186"/> <roc_data_point min_prob="0.8000" sensitivity="0.8486" error="0.0250" num_corr="9631" num_incorr="247"/> <roc_data_point min_prob="0.7500" sensitivity="0.8668" error="0.0302" num_corr="9839" num_incorr="306"/> <roc_data_point min_prob="0.7000" sensitivity="0.8813" error="0.0355" num_corr="10003" num_incorr="368"/> <roc_data_point min_prob="0.6500" sensitivity="0.8944" error="0.0415" num_corr="10152" num_incorr="439"/> <roc_data_point min_prob="0.6000" sensitivity="0.9054" error="0.0476" num_corr="10276" num_incorr="514"/> <roc_data_point min_prob="0.5500" sensitivity="0.9150" error="0.0541" num_corr="10386" num_incorr="594"/> <roc_data_point min_prob="0.5000" sensitivity="0.9239" error="0.0613" num_corr="10486" num_incorr="685"/> <roc_data_point min_prob="0.4500" sensitivity="0.9327" error="0.0699" num_corr="10586" num_incorr="795"/> <roc_data_point min_prob="0.4000" sensitivity="0.9398" error="0.0782" num_corr="10667" num_incorr="905"/> <roc_data_point min_prob="0.3500" sensitivity="0.9468" error="0.0881" num_corr="10746" num_incorr="1038"/> <roc_data_point min_prob="0.3000" sensitivity="0.9541" error="0.1006" num_corr="10829" num_incorr="1211"/> <roc_data_point min_prob="0.2500" sensitivity="0.9599" error="0.1128" num_corr="10895" num_incorr="1385"/> <roc_data_point min_prob="0.2000" sensitivity="0.9664" error="0.1301" num_corr="10969" num_incorr="1641"/> <roc_data_point min_prob="0.1500" sensitivity="0.9731" error="0.1532" num_corr="11044" num_incorr="1999"/> <roc_data_point min_prob="0.1000" sensitivity="0.9803" error="0.1886" num_corr="11127" num_incorr="2586"/> <roc_data_point min_prob="0.0500" sensitivity="0.9884" error="0.2523" num_corr="11218" num_incorr="3785"/> <roc_data_point min_prob="0.0000" sensitivity="1.0000" error="0.8053" num_corr="11350" num_incorr="46945"/> <error_point error="0.0000" min_prob="0.9997" num_corr="2" num_incorr="0"/> <error_point error="0.0001" min_prob="0.9997" num_corr="2" num_incorr="0"/> <error_point error="0.0002" min_prob="0.9997" num_corr="2" num_incorr="0"/> <error_point error="0.0003" min_prob="0.9997" num_corr="277" num_incorr="0"/> <error_point error="0.0004" min_prob="0.9995" num_corr="1149" num_incorr="0"/> <error_point error="0.0005" min_prob="0.9992" num_corr="1852" num_incorr="1"/> <error_point error="0.0006" min_prob="0.9989" num_corr="2381" num_incorr="1"/> <error_point error="0.0007" min_prob="0.9986" num_corr="2808" num_incorr="2"/> <error_point error="0.0008" min_prob="0.9983" num_corr="3174" num_incorr="3"/> <error_point error="0.0009" min_prob="0.9980" num_corr="3506" num_incorr="3"/> <error_point error="0.0010" min_prob="0.9976" num_corr="3803" num_incorr="4"/> <error_point error="0.0015" min_prob="0.9956" num_corr="4875" num_incorr="7"/> <error_point error="0.0020" min_prob="0.9932" num_corr="5562" num_incorr="11"/> <error_point error="0.0025" min_prob="0.9904" num_corr="6059" num_incorr="15"/> <error_point error="0.0030" min_prob="0.9876" num_corr="6437" num_incorr="19"/> <error_point error="0.0040" min_prob="0.9809" num_corr="6987" num_incorr="28"/> <error_point error="0.0050" min_prob="0.9739" num_corr="7376" num_incorr="37"/> <error_point error="0.0060" min_prob="0.9670" num_corr="7686" num_incorr="46"/> <error_point error="0.0070" min_prob="0.9590" num_corr="7939" num_incorr="56"/> <error_point error="0.0080" min_prob="0.9504" num_corr="8144" num_incorr="66"/> <error_point error="0.0090" min_prob="0.9420" num_corr="8317" num_incorr="76"/> <error_point error="0.0100" min_prob="0.9337" num_corr="8468" num_incorr="86"/> <error_point error="0.0150" min_prob="0.8897" num_corr="9015" num_incorr="137"/> <error_point error="0.0200" min_prob="0.8466" num_corr="9371" num_incorr="191"/> <error_point error="0.0250" min_prob="0.7999" num_corr="9633" num_incorr="247"/> <error_point error="0.0300" min_prob="0.7528" num_corr="9833" num_incorr="304"/> <error_point error="0.0400" min_prob="0.6640" num_corr="10118" num_incorr="422"/> <error_point error="0.0500" min_prob="0.5816" num_corr="10320" num_incorr="544"/> <error_point error="0.0750" min_prob="0.4165" num_corr="10638" num_incorr="864"/> <error_point error="0.1000" min_prob="0.3019" num_corr="10826" num_incorr="1204"/> </roc_error_data> <roc_error_data charge="1" charge_est_correct="47.8"> <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="0.0000" error="0" num_corr="0" num_incorr="0"/> <roc_data_point min_prob="0.9500" sensitivity="0.0398" error="0.0493" num_corr="2" num_incorr="0"/> <roc_data_point min_prob="0.9000" sensitivity="0.4510" error="0.0631" num_corr="22" num_incorr="1"/> <roc_data_point min_prob="0.8500" sensitivity="0.5978" error="0.0786" num_corr="29" num_incorr="2"/> <roc_data_point min_prob="0.8000" sensitivity="0.6328" error="0.0837" num_corr="30" num_incorr="3"/> <roc_data_point min_prob="0.7500" sensitivity="0.6972" error="0.0996" num_corr="33" num_incorr="4"/> <roc_data_point min_prob="0.7000" sensitivity="0.7273" error="0.1088" num_corr="35" num_incorr="4"/> <roc_data_point min_prob="0.6500" sensitivity="0.7412" error="0.1146" num_corr="35" num_incorr="5"/> <roc_data_point min_prob="0.6000" sensitivity="0.7676" error="0.1267" num_corr="37" num_incorr="5"/> <roc_data_point min_prob="0.5500" sensitivity="0.8040" error="0.1463" num_corr="38" num_incorr="7"/> <roc_data_point min_prob="0.5000" sensitivity="0.8261" error="0.1601" num_corr="39" num_incorr="8"/> <roc_data_point min_prob="0.4500" sensitivity="0.8654" error="0.1892" num_corr="41" num_incorr="10"/> <roc_data_point min_prob="0.4000" sensitivity="0.8741" error="0.1968" num_corr="42" num_incorr="10"/> <roc_data_point min_prob="0.3500" sensitivity="0.8981" error="0.2198" num_corr="43" num_incorr="12"/> <roc_data_point min_prob="0.3000" sensitivity="0.9260" error="0.2500" num_corr="44" num_incorr="15"/> <roc_data_point min_prob="0.2500" sensitivity="0.9321" error="0.2577" num_corr="45" num_incorr="15"/> <roc_data_point min_prob="0.2000" sensitivity="0.9465" error="0.2821" num_corr="45" num_incorr="18"/> <roc_data_point min_prob="0.1500" sensitivity="0.9498" error="0.2909" num_corr="45" num_incorr="19"/> <roc_data_point min_prob="0.1000" sensitivity="0.9663" error="0.3404" num_corr="46" num_incorr="24"/> <roc_data_point min_prob="0.0500" sensitivity="0.9822" error="0.4059" num_corr="47" num_incorr="32"/> <roc_data_point min_prob="0.0000" sensitivity="1.0000" error="0.8224" num_corr="48" num_incorr="221"/> <error_point error="0.0000" min_prob="0.9510" num_corr="2" num_incorr="0"/> <error_point error="0.0001" min_prob="0.9510" num_corr="2" num_incorr="0"/> <error_point error="0.0002" min_prob="0.9510" num_corr="2" num_incorr="0"/> <error_point error="0.0003" min_prob="0.9510" num_corr="2" num_incorr="0"/> <error_point error="0.0004" min_prob="0.9510" num_corr="2" num_incorr="0"/> <error_point error="0.0005" min_prob="0.9510" num_corr="2" num_incorr="0"/> <error_point error="0.0006" min_prob="0.9510" num_corr="2" num_incorr="0"/> <error_point error="0.0007" min_prob="0.9510" num_corr="2" num_incorr="0"/> <error_point error="0.0008" min_prob="0.9510" num_corr="2" num_incorr="0"/> <error_point error="0.0009" min_prob="0.9510" num_corr="2" num_incorr="0"/> <error_point error="0.0010" min_prob="0.9510" num_corr="2" num_incorr="0"/> <error_point error="0.0015" min_prob="0.9510" num_corr="2" num_incorr="0"/> <error_point error="0.0020" min_prob="0.9510" num_corr="2" num_incorr="0"/> <error_point error="0.0025" min_prob="0.9510" num_corr="2" num_incorr="0"/> <error_point error="0.0030" min_prob="0.9510" num_corr="2" num_incorr="0"/> <error_point error="0.0040" min_prob="0.9510" num_corr="2" num_incorr="0"/> <error_point error="0.0050" min_prob="0.9510" num_corr="2" num_incorr="0"/> <error_point error="0.0060" min_prob="0.9510" num_corr="2" num_incorr="0"/> <error_point error="0.0070" min_prob="0.9510" num_corr="2" num_incorr="0"/> <error_point error="0.0080" min_prob="0.9510" num_corr="2" num_incorr="0"/> <error_point error="0.0090" min_prob="0.9510" num_corr="2" num_incorr="0"/> <error_point error="0.0100" min_prob="0.9510" num_corr="2" num_incorr="0"/> <error_point error="0.0150" min_prob="0.9510" num_corr="2" num_incorr="0"/> <error_point error="0.0200" min_prob="0.9510" num_corr="2" num_incorr="0"/> <error_point error="0.0250" min_prob="0.9510" num_corr="2" num_incorr="0"/> <error_point error="0.0300" min_prob="0.9510" num_corr="2" num_incorr="0"/> <error_point error="0.0400" min_prob="0.9510" num_corr="2" num_incorr="0"/> <error_point error="0.0500" min_prob="0.9491" num_corr="7" num_incorr="0"/> <error_point error="0.0750" min_prob="0.8598" num_corr="29" num_incorr="2"/> <error_point error="0.1000" min_prob="0.7301" num_corr="35" num_incorr="4"/> </roc_error_data> <roc_error_data charge="2" charge_est_correct="7793.7"> <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="0.2939" error="0.0006" num_corr="2291" num_incorr="1"/> <roc_data_point min_prob="0.9900" sensitivity="0.6586" error="0.0022" num_corr="5133" num_incorr="11"/> <roc_data_point min_prob="0.9800" sensitivity="0.7279" error="0.0034" num_corr="5673" num_incorr="19"/> <roc_data_point min_prob="0.9500" sensitivity="0.8074" error="0.0062" num_corr="6292" num_incorr="40"/> <roc_data_point min_prob="0.9000" sensitivity="0.8585" error="0.0105" num_corr="6691" num_incorr="71"/> <roc_data_point min_prob="0.8500" sensitivity="0.8845" error="0.0142" num_corr="6894" num_incorr="99"/> <roc_data_point min_prob="0.8000" sensitivity="0.9031" error="0.0181" num_corr="7038" num_incorr="130"/> <roc_data_point min_prob="0.7500" sensitivity="0.9161" error="0.0218" num_corr="7140" num_incorr="159"/> <roc_data_point min_prob="0.7000" sensitivity="0.9254" error="0.0252" num_corr="7212" num_incorr="187"/> <roc_data_point min_prob="0.6500" sensitivity="0.9341" error="0.0292" num_corr="7280" num_incorr="219"/> <roc_data_point min_prob="0.6000" sensitivity="0.9417" error="0.0335" num_corr="7339" num_incorr="254"/> <roc_data_point min_prob="0.5500" sensitivity="0.9475" error="0.0375" num_corr="7385" num_incorr="288"/> <roc_data_point min_prob="0.5000" sensitivity="0.9538" error="0.0428" num_corr="7434" num_incorr="332"/> <roc_data_point 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[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="2013-03-27T17:29:54"/> <analysis_summary analysis="interact" time="2013-03-27T17:29:43"> <interact_summary filename="c:/Inetpub/wwwroot/ISB/data/Ecoli/120117.LC2.IT2.EC.scanmode_Cap_1-E,1_01_3481.tandem.interact_09997.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_MG1655.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_MG1655.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="16878952"/> <parameter name="modelling, total proteins used" value="4416"/> <parameter name="modelling, total spectra used" value="58618"/> <parameter name="process, start time" value="2012:03:30:14:26:47"/> <parameter name="process, version" value="x! tandem 2010.10.01.1 (LabKey, Insilicos and ISB)"/> <parameter name="quality values" value="3395 2151 1793 1710 1576 1214 914 682 396 246 118 76 30 15 12 3 2 1 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="17.50"/> <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="2013-03-27T17:30:01" id="1"/> <analysis_timestamp analysis="database_refresh" time="2013-03-27T17:29:54" id="1"> <database_refresh_timestamp database="c:/Inetpub/wwwroot/ISB/data/dbase/18.E_coli_MG1655.fasta" min_num_enz_term="2"/> </analysis_timestamp> <spectrum_query spectrum="120117.LC2.IT2.EC.scanmode_Cap_1-E,1_01_3481.07746.07746.2" start_scan="7746" end_scan="7746" precursor_neutral_mass="1228.2513" assumed_charge="2" index="1" retention_time_sec="1314.06099200"> <search_result> <search_hit hit_rank="1" peptide="HADNTLTFGPR" peptide_prev_aa="K" peptide_next_aa="D" protein="sp|P0AG55|RL6_ECOLI" protein_descr="50S ribosomal protein L6 OS=Escherichia coli (strain K12) GN=rplF" num_tot_proteins="1" num_matched_ions="20" tot_num_ions="20" calc_neutral_pep_mass="1227.5997" massdiff="0.652" num_tol_term="2" num_missed_cleavages="0" is_rejected="0"> <search_score name="hyperscore" value="608"/> <search_score name="nextscore" value="209"/> <search_score name="bscore" value="1"/> <search_score name="yscore" value="2"/> <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="6.8e-006"/> <analysis_result analysis="peptideprophet"> <peptideprophet_result probability="0.9997" all_ntt_prob="(0.0000,0.0000,0.9997)"> <search_score_summary> <parameter name="fval" value="9.9073"/> <parameter name="ntt" value="2"/> <parameter name="nmc" value="0"/> <parameter name="massd" value="0.652"/> </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_3481.07768.07768.2" start_scan="7768" end_scan="7768" precursor_neutral_mass="1228.1892" assumed_charge="2" index="2" retention_time_sec="1317.62400000"> <search_result> <search_hit hit_rank="1" peptide="HADNTLTFGPR" peptide_prev_aa="K" peptide_next_aa="D" protein="sp|P0AG55|RL6_ECOLI" protein_descr="50S ribosomal protein L6 OS=Escherichia coli (strain K12) GN=rplF" num_tot_proteins="1" num_matched_ions="21" tot_num_ions="20" calc_neutral_pep_mass="1227.5997" massdiff="0.589" num_tol_term="2" num_missed_cleavages="0" is_rejected="0"> <search_score name="hyperscore" value="592"/> <search_score name="nextscore" value="203"/> <search_score name="bscore" value="1"/> <search_score name="yscore" value="2"/> <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="7.2e-005"/> <analysis_result analysis="peptideprophet"> <peptideprophet_result probability="0.9997" all_ntt_prob="(0.0000,0.0000,0.9997)"> <search_score_summary> <parameter name="fval" value="9.7855"/> <parameter name="ntt" value="2"/> <parameter name="nmc" value="0"/> <parameter name="massd" value="0.589"/> </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_3481.16047.16047.2" start_scan="16047" end_scan="16047" precursor_neutral_mass="1755.7798" assumed_charge="2" index="3" retention_time_sec="2658.12000000"> <search_result> <search_hit hit_rank="1" peptide="AVQLGGVALGTTQVINSK" peptide_prev_aa="R" peptide_next_aa="T" protein="sp|P0ABT2|DPS_ECOLI" protein_descr="DNA protection during starvation protein OS=Escherichia coli (strain K12) GN=dps" num_tot_proteins="1" num_matched_ions="24" tot_num_ions="34" calc_neutral_pep_mass="1754.9887" massdiff="0.791" num_tol_term="2" num_missed_cleavages="0" is_rejected="0"> <search_score name="hyperscore" value="676"/> <search_score name="nextscore" value="282"/> <search_score name="bscore" value="1"/> <search_score name="yscore" value="2"/> <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="0.00089"/> <analysis_result analysis="peptideprophet"> <peptideprophet_result probability="0.9997" all_ntt_prob="(0.0000,0.0000,0.9997)"> <search_score_summary> <parameter name="fval" value="9.6290"/> <parameter name="ntt" value="2"/> <parameter name="nmc" value="0"/> <parameter name="massd" value="0.791"/> </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_3481.16102.16102.2" start_scan="16102" end_scan="16102" precursor_neutral_mass="1755.8919" assumed_charge="2" index="4" retention_time_sec="2667.02995200"> <search_result> <search_hit hit_rank="1" peptide="AVQLGGVALGTTQVINSK" peptide_prev_aa="R" peptide_next_aa="T" protein="sp|P0ABT2|DPS_ECOLI" protein_descr="DNA protection during starvation protein OS=Escherichia coli (strain K12) GN=dps" num_tot_proteins="1" num_matched_ions="26" tot_num_ions="34" calc_neutral_pep_mass="1754.9887" massdiff="0.903" num_tol_term="2" num_missed_cleavages="0" is_rejected="0"> <search_score name="hyperscore" value="677"/> <search_score name="nextscore" value="260"/> <search_score name="bscore" value="1"/> <search_score name="yscore" value="2"/> <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="0.0006"/> <analysis_result analysis="peptideprophet"> <peptideprophet_result probability="0.9997" all_ntt_prob="(0.0000,0.0000,0.9997)"> <search_score_summary> <parameter name="fval" value="9.9966"/> <parameter name="ntt" value="2"/> <parameter name="nmc" value="0"/> <parameter name="massd" value="0.903"/> </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_3481.16120.16120.2" start_scan="16120" end_scan="16120" precursor_neutral_mass="1387.3917" assumed_charge="2" index="5" retention_time_sec="2670.00595200"> <search_result> <search_hit hit_rank="1" peptide="VIASCFFEASTR" peptide_prev_aa="K" peptide_next_aa="T" protein="sp|P0A786|PYRB_ECOLI" protein_descr="Aspartate carbamoyltransferase catalytic chain OS=Escherichia coli (strain K12) GN=pyrB" num_tot_proteins="1" num_matched_ions="20" tot_num_ions="22" calc_neutral_pep_mass="1386.6597" massdiff="0.732" num_tol_term="2" num_missed_cleavages="0" is_rejected="0"> <modification_info modified_peptide="VIASCFFEASTR"> <mod_aminoacid_mass position="5" mass="160.0306"/> </modification_info> <search_score name="hyperscore" value="683"/> <search_score name="nextscore" value="274"/> <search_score name="bscore" value="1"/> <search_score name="yscore" value="2"/> <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="6.3e-005"/> <analysis_result analysis="peptideprophet"> <peptideprophet_result probability="0.9997" all_ntt_prob="(0.0000,0.0000,0.9997)"> <search_score_summary> <parameter name="fval" value="9.8535"/> <parameter name="ntt" value="2"/> <parameter name="nmc" value="0"/> <parameter name="massd" value="0.732"/> </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_3481.18144.18144.2" start_scan="18144" end_scan="18144" precursor_neutral_mass="1492.6944" assumed_charge="2" index="6" retention_time_sec="2997.93996800"> <search_result> <search_hit hit_rank="1" peptide="AVAAVNGPIAQALIGK" peptide_prev_aa="K" peptide_next_aa="D" protein="sp|P0A6P9|ENO_ECOLI" protein_descr="Enolase OS=Escherichia coli (strain K12) GN=eno" num_tot_proteins="1" num_matched_ions="28" tot_num_ions="30" calc_neutral_pep_mass="1491.8777" massdiff="0.817" num_tol_term="2" num_missed_cleavages="0" is_rejected="0"> <search_score name="hyperscore" value="654"/> <search_score name="nextscore" value="255"/> <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="1.7e-005"/> <analysis_result analysis="peptideprophet"> <peptideprophet_result probability="0.9997" all_ntt_prob="(0.0000,0.0000,0.9997)"> <search_score_summary> <parameter name="fval" value="9.7631"/> <parameter name="ntt" value="2"/> <parameter name="nmc" value="0"/> <parameter name="massd" value="0.817"/> </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_3481.18155.18155.2" start_scan="18155" end_scan="18155" precursor_neutral_mass="1492.6329" 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<search_score name="xscore" value="0"/> <search_score name="expect" value="0.0014"/> <analysis_result analysis="peptideprophet"> <peptideprophet_result probability="0.9997" all_ntt_prob="(0.0000,0.0000,0.9997)"> <search_score_summary> <parameter name="fval" value="9.9100"/> <parameter name="ntt" value="2"/> <parameter name="nmc" value="0"/> <parameter name="massd" value="0.742"/> </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_3481.10562.10562.2" start_scan="10562" end_scan="10562" precursor_neutral_mass="1150.3425" assumed_charge="2" index="135" retention_time_sec="1770.48000000"> <search_result> <search_hit hit_rank="1" peptide="APVVVPAGVDVK" peptide_prev_aa="K" peptide_next_aa="L" protein="sp|P0AG55|RL6_ECOLI" protein_descr="50S ribosomal protein L6 OS=Escherichia coli (strain K12) GN=rplF" num_tot_proteins="1" num_matched_ions="20" tot_num_ions="22" 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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.InvokeMake_Tablein11probabilities00 This Beanshell formats the probabilities for the Rshell below. 2014-02-06 14:27:11.415 UTC net.sf.taverna.t2.activitiesbeanshell-activity1.4net.sf.taverna.t2.activities.beanshell.BeanshellActivity in1 1 text/plain java.lang.String true probabilities 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.InvokeRead_Text_FilefileurlpepXML_FileExtract_Peptidesxml_textRead_Text_FilefilecontentsExtract_Scan_Numbersxml_textRead_Text_FilefilecontentsJoin_and_Insert_Tabsin1Extract_PeptidesnodelistJoin_and_Insert_Tabsin2Extract_Scan_NumbersnodelistRTCalc_Trainin1Join_and_Insert_TabstrainingRTCalc_Predictin2RTCalc_Trainout1RTCalc_Predictin1Join_and_Insert_Tabsvalidation_flatCompare_Z_Scores_and_ProbabilitiespredictedRTCalc_Predictout1Compare_Z_Scores_and_ProbabilitiesmeasuredJoin_and_Insert_TabstrainingCompare_Z_Scores_and_ProbabilitiesprobabilitiesMake_TableprobabilitiesCompare_Z_Scores_and_Probabilitiesmax_abs_Z_scoreMax_Abs_Z_ScoreExtract_Probabilitiesxml_textRead_Text_FilefilecontentsMake_Tablein1Extract_ProbabilitiesnodelistRTCalc_modelRTCalc_Trainout1RTCalc_RMSDCompare_Z_Scores_and_Probabilitiesrmsd2Z_Scores_vs_ProbabilitiesCompare_Z_Scores_and_ProbabilitiesZ_scores_vs_probabilitiesFiltered_Peptide_ListCompare_Z_Scores_and_Probabilitiesfiltered_peptide_list 8aaf85b9-ca7b-48c1-8cf1-21f35a36e920 2011-12-01 12:07:14.642 UTC ed84d9b6-1a6d-4f8d-a9c7-4da8d2b03192 2011-04-06 14:28:27.542 UTC 785be58d-da6c-4d25-bbb6-6607d09e001d 2012-08-06 15:03:45.673 UTC a6e7e38d-fe52-4dfe-b98b-b43b7907d956 2014-02-05 14:54:46.95 UTC 66efbdff-1c55-4f0c-8f63-ce11bbbb2781 2012-04-16 07:22:17.235 UTC fc634334-f397-4f68-8119-a853925702b4 2011-03-29 08:02:31.511 UTC 5d42f252-597b-42d4-b9c6-16a74a8c6b70 2012-03-12 13:08:44.375 UTC 407f1b6e-00dd-4ca3-b2b3-d526d8a214d1 2012-04-16 07:30:40.669 UTC 30d5f1d6-d842-4159-9d86-dfb8cfc10256 2012-03-12 11:49:32.612 UTC aa9ca29d-28f2-45e6-87c4-3e761c1cb3d5 2012-03-12 12:26:43.930 UTC 8615d8a1-e3af-4509-b708-daefe6d0e9a2 2011-01-31 17:21:34.160 UTC eb697d2a-8528-466f-b401-dbcf77caf4d8 2014-02-06 13:31:01.600 UTC 59469ad6-71f9-40f2-9248-a8b5c7e7f64d 2014-02-05 14:48:07.969 UTC f8cce8ec-2e84-4766-ad64-8cca2aac8a55 2012-08-28 15:30:25.763 UTC 1369ea84-f32c-41a2-8a75-0a7853529f02 2014-02-05 15:14:48.254 UTC f41838e8-bf43-4c69-ba11-498fc937e6b0 2012-04-11 13:11:36.976 UTC f86b1828-bb50-417b-a33c-10213d0a577b 2013-03-24 13:56:21.629 UTC 541df59b-37a5-4515-92b9-1b58254e54f5 2012-03-12 10:40:27.65 UTC 8e0e9b2d-6420-4411-9f61-e7841aae2563 2011-04-07 12:25:11.816 UTC f7de5cac-1926-4ec2-9838-47a53f5c04fd 2011-04-12 14:43:35.130 UTC Magnus Palmblad (n.m.palmblad@lumc.nl) Sonja Holl 2014-02-06 14:23:21.114 UTC de095acc-94a9-4a65-b33e-692126a25bb1 2012-04-19 11:26:47.518 UTC 624593fc-452f-470c-adf7-4d7d8b6d6f0c 2011-03-30 08:59:22.85 UTC 2c8faf07-5e70-4073-a637-95ce0add9658 2012-08-09 13:31:49.710 UTC 6d3d8308-b6e9-4f79-b040-57c0baeb1db7 2012-04-11 10:01:10.121 UTC 5081f9c2-a817-4aa4-9b46-0a55dbfc638d 2013-03-27 14:42:55.499 UTC 7d356e09-ab0f-49a0-b8b2-e04c79b4831c 2011-03-01 10:43:55.657 UTC 32b1eaa4-480c-4b41-a3c4-75afae4968e5 2013-03-24 13:21:18.549 UTC c1c4ae2b-7726-486e-b6e0-57d45b2d51e4 2013-03-27 15:53:43.979 UTC 6ddebe57-9b8c-4942-9664-d50ce8de5d81 2012-08-06 16:16:55.296 UTC 0a265c18-2489-4cb7-b167-073f7484a770 2012-09-03 09:44:21.557 UTC 540ac1af-179a-4eb2-91e5-1484e9b674b8 2012-03-09 09:24:49.38 UTC 7f209aab-88b3-45c0-a496-6455464ac4c3 2013-03-27 11:52:10.991 UTC 81118a85-86a2-40d0-b01f-c197d17ed374 2013-03-27 14:40:35.755 UTC 17d00fe8-f32c-46dc-9889-3527199ccc5f 2014-02-06 13:52:00.849 UTC d4430f80-5827-4fa3-83f3-0c58410ffc92 2011-01-31 17:35:12.220 UTC 57bd932e-3ca7-4b4f-91f9-bcddd29c1572 2013-03-27 16:19:10.384 UTC 2dc4297c-e078-4ae9-89cf-957b7a9de818 2011-12-01 11:54:35.986 UTC ee54123b-6086-4e07-82b2-b49ce31abfa3 2012-04-11 10:40:39.711 UTC 37ef858f-1292-49e6-8d05-84b590c50ca8 2013-03-27 16:11:47.578 UTC 92b17ca3-8100-4ce0-9139-7f923538c574 2013-03-27 12:11:50.90 UTC bb167c46-673d-43b0-a863-4d87f887c263 2012-08-09 12:46:45.433 UTC dfa67b08-6a4e-4ded-9894-deb6063e6099 2014-02-05 12:37:27.824 UTC b9c0d7f1-fd39-469c-8de5-0078e96ad5c4 2013-03-27 15:44:11.689 UTC ebe93854-8931-41b0-bbd1-8af675d22239 2012-04-12 15:55:28.605 UTC afbf984e-fcf1-4396-b711-e48f7bbc08a5 2014-02-05 14:51:33.551 UTC b42fbfb4-9c9a-4b1f-ad25-2f7fa6210f2e 2014-02-06 13:12:04.847 UTC 6de94bc9-1d49-4b13-bfcd-354d24130bce 2013-03-27 11:28:37.839 UTC 97e13731-a9eb-42cf-a1ce-2e9c76d91ea4 2014-02-05 12:37:10.319 UTC This workflow trains a retention time predictor using the RTCalc algorithm supplied by the Trans- Proteomic Pipeline. The Rshell component calculates and plots RTCalc retention time Z-scores for all peptides in the pepXML file. There is no probability cutoff for the training of RTCalc, so for datasets with many false peptide identifications (or peptide-spectrum matches of low probability), a selection should be in the XPaths, in the Join_and_Insert_Tabs component or in an additional component at any point before the RTCalc_Train call. 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.). 2014-02-06 14:25:14.798 UTC 9dea1a41-65e7-4709-bdfe-a0a0f18a68d9 2012-08-06 16:45:23.271 UTC 5bada5bc-e95c-423a-b248-1bcdb6fd81a9 2012-04-16 07:44:32.880 UTC c0ac18f3-1922-45b5-8ac9-9e1931e312c7 2012-01-11 13:41:48.789 UTC d0c718fc-3264-47a7-934b-1458130b65e5 2014-02-06 13:28:04.82 UTC bef6fa28-1bbf-4d4a-bd34-32120cc97d1f 2012-03-12 10:45:32.953 UTC 42e2f42b-9001-4e9e-9c0b-dcec46712b2a 2012-04-11 11:06:41.585 UTC 956c597b-e5c8-4d7d-82a2-b1d5e1efcc8b 2014-02-05 13:46:17.975 UTC 30d69e84-a4f1-46fa-ab51-bdfb4270ee4c 2013-03-24 13:20:55.928 UTC 8672ad15-eebb-4220-9bd9-30b4c4ca0dfa 2013-03-27 18:04:52.110 UTC 1182c10a-b0ba-472c-9283-ac71e1650d63 2013-03-27 12:49:05.479 UTC 3ce3f027-e65e-4f23-8993-d50d45a0d198 2011-01-31 09:56:42.353 UTC 56d89322-2864-4bee-b71b-535a74078068 2011-04-06 13:54:29.498 UTC 7d8af289-0d34-4ac7-9478-e62f4f418c0d 2012-08-09 09:14:21.663 UTC 5d6ba88b-b3b6-45bb-bfca-9823451e4388 2011-03-30 09:25:11.740 UTC 14822062-cd7b-4327-af45-aab107e71127 2013-03-27 14:47:54.147 UTC 4528c554-8d6f-4cb1-a004-fcba1b71f94f 2014-02-05 15:10:06.581 UTC fc505117-909d-449e-8de6-d4c24090d665 2012-08-08 10:49:39.176 UTC 880f1df3-9831-44bb-9705-bbc47103ac98 2012-04-12 15:35:20.839 UTC e3325237-0fd9-456a-9ef7-b53618da8f4f 2014-02-06 13:26:24.246 UTC 1b672318-d3ad-4db8-82a0-27e6abd171a7 2012-08-28 14:47:19.905 UTC 4d07676a-6393-4df0-997f-f57da1f74def 2012-08-09 13:17:03.226 UTC ae929373-53c9-4f13-871f-5108b2585bcd 2013-03-27 16:01:56.107 UTC adb99e1f-570f-4d59-b7ad-7567bf8ac99a 2014-02-05 13:28:40.940 UTC 6d1beb57-abe2-45dc-926e-3b4f1c07cc7a 2013-03-27 11:48:13.425 UTC 04d83187-2364-4930-ba2d-1eee4d3d5e6f 2011-03-22 12:27:25.556 UTC 4ba626e0-3073-49b4-88e4-c7821b4616dd 2014-02-05 13:41:22.814 UTC 83dd948d-a363-412c-8a69-9583b9318ba6 2012-01-04 10:22:28.854 UTC 9ba4212c-ea24-426e-9832-1a26a4a214e6 2012-04-12 15:38:42.44 UTC 76745d08-c285-4987-a70c-872e38f1bdbe 2013-03-27 17:55:05.25 UTC 2adf8556-7541-4a44-a59d-61db0f854656 2014-02-06 14:02:16.751 UTC bde0f9e9-0d5f-4fa6-b783-b15479f24a6d 2012-08-09 13:11:04.325 UTC 80756480-76ec-4d56-9f5f-63a04fc1fd5b 2013-03-27 15:54:09.321 UTC 1520eabd-565d-4a01-a68d-0ac96f73ddf9 2011-03-30 08:59:48.925 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 e6b54f0b-7514-473e-9920-aa8d1391ae26 2012-08-06 10:57:37.883 UTC fb20da80-0512-4a84-8b73-5e7983b157a0 2014-02-06 14:31:00.909 UTC fe700c84-7071-4433-8a63-6429e5038b5e 2014-02-05 15:06:15.542 UTC fcde5c53-f349-4d82-b38c-98be9ebd0837 2012-08-28 13:43:19.743 UTC ece5d70f-8799-4855-8d30-686bed7ddc4c 2014-02-06 13:56:43.227 UTC 71a48acb-d549-4ac2-a166-20e753b95b93 2014-02-05 15:12:41.621 UTC 08175c13-4377-408f-9f1e-b20a417eba2a 2014-02-06 14:36:19.449 UTC d40ac8e4-dcef-4c1a-b2d4-2831b775edba 2014-02-06 12:54:36.57 UTC e5693140-26f8-401d-918e-815d0a7e3150 2013-03-27 18:00:43.99 UTC c68d4688-4ccf-4c5e-88be-b6ffcf4dca48 2012-03-09 09:12:38.299 UTC 0f69acfa-32e7-4a1c-ad7f-d5778a7e2751 2014-02-05 13:38:30.952 UTC de000ea1-cff6-4679-b42e-9d315fa1db23 2011-04-07 14:36:51.860 UTC 45926357-0432-4509-ab95-c710a93c1a0e 2012-08-28 13:29:42.104 UTC d8f357be-7c2e-45a0-8d37-499dee5c6529 2012-03-22 13:09:25.231 UTC acd3a31e-8c1f-4e97-a991-5b1dda63a8dd 2012-03-12 13:02:36.280 UTC 2b495a11-3c0a-43c2-8ce0-14b79f6c1777 2013-03-28 11:51:55.933 UTC 5236d1de-a266-4003-b22e-6f9d640c282e 2014-02-06 13:11:12.470 UTC 550c6775-13db-4058-ba84-15bb0351701d 2014-02-06 14:16:02.173 UTC fad53bf0-f8a4-4998-8bbd-3ca1e7356d27 2012-04-16 10:11:05.67 UTC 4840599a-0b97-449e-9757-c2b3276c79a4 2012-04-11 11:31:50.303 UTC 1630eb6c-0c41-48d3-8cbc-cd70c95be2af 2012-03-09 09:30:53.119 UTC a96c95d7-4e7b-45ce-9a76-b9fd9ed2a2b0 2013-03-27 11:33:21.54 UTC 7eeffbe6-b48b-4fcb-ab4d-2651561607fc 2012-04-15 13:24:22.140 UTC c1d60e14-a0df-4749-87a4-80adad360923 2012-04-16 07:54:33.780 UTC f0403ba3-c249-462f-a162-0a84eb56ef6a 2012-08-09 13:33:50.160 UTC 1877c16f-627a-4ba7-9b78-7ca51d45b843 2014-02-05 12:56:09.1 UTC 72d49499-cea8-494b-8d6f-ca288ea62ac4 2013-03-27 15:34:58.119 UTC 8599f9ea-baa0-4abf-860e-18a36914ea8b 2014-02-05 15:06:00.335 UTC 471566c3-6f4e-48d1-bd0c-9cf6b92d86f9 2012-08-06 10:49:56.669 UTC 13409438-46da-4786-88bb-a4dbb3732076 2012-04-11 08:38:40.884 UTC 08d9da29-7537-4ba1-9957-00773616dec1 2013-03-27 14:39:18.153 UTC e4bbbe00-ff98-4187-85be-66b1bf4d2da8 2012-04-16 08:03:41.409 UTC ceca149e-012a-4abb-82ad-ea66289e1796 2013-03-27 12:38:49.785 UTC ce45dc51-de9a-45a6-9d4d-3ca389bd6601 2011-04-06 14:31:57.156 UTC 262783b0-845f-4bc0-9310-b1617db7c047 2012-08-06 16:44:22.629 UTC e1f1fc32-22c6-4ec7-bc9f-5129b0d20c8c 2012-08-10 08:21:54.204 UTC ad160db0-a2c6-4689-bc01-29eeb7fbb684 2012-08-28 15:06:04.261 UTC 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d5b5088c-cb5b-46d6-aabf-f68e2e43158e 2013-03-27 12:34:37.749 UTC 99560d91-04bf-41c3-8379-162f7313ddd7 2012-08-08 13:37:16.6 UTC 9836fe58-8e93-4a05-af76-8e63166fee0a 2014-02-05 14:51:05.686 UTC f66e38ef-e19b-43ca-9488-2e91382c9668 2012-04-19 11:22:35.370 UTC 28a0fde9-5d43-4dd5-93df-16b3ecdff418 2014-02-05 13:48:22.517 UTC c956f727-c4c7-4922-8be9-4dbd7146a52d 2013-03-27 10:38:27.727 UTC 0be1586d-8caa-45af-bbbc-158431f8136b 2014-02-06 13:36:09.824 UTC 24d6537e-c64c-42d2-96be-14d4906f61cf 2014-02-06 13:18:22.965 UTC 82e01409-1114-4a6e-a1c9-e09144055c3e 2012-03-12 12:01:54.533 UTC 2f559381-0f32-4c21-bae0-4819eadbafe8 2013-03-27 16:06:52.433 UTC 67965542-b33d-4636-8520-b2ea6076c703 2014-02-06 13:42:35.965 UTC 023e9115-05b5-420c-8db1-f324d40570cb 2012-04-16 12:14:07.669 UTC RTCalc Retention Time Prediction and Outlier Removal 2014-02-06 14:24:01.540 UTC 20178567-0598-484e-87f8-16b85b59f5fc 2012-08-08 10:49:24.101 UTC 53317b78-d33f-40cd-bc8f-f26ecee69bd6 2012-08-09 13:27:49.698 UTC 835b5558-a1ec-4354-b6dc-cce5e440409b 2013-03-27 17:57:29.998 UTC 51340b18-2b4b-43c7-ab77-ec15cdf0a6e5 2013-03-27 16:16:32.768 UTC d7132444-69af-45bd-8423-2da00722619c 2014-02-05 14:55:45.298 UTC 8b3fb14f-31ab-4170-99d5-0952c97d1f45 2012-08-28 15:19:31.4 UTC eb132715-6579-46e9-9ea2-e71a38d7143d 2012-04-19 11:29:12.583 UTC 3ef4e457-2b05-4c55-be04-e669c669db8b 2013-03-27 12:10:15.141 UTC b8bbef6f-374c-4d93-8033-29053e70f518 2011-04-06 16:18:12.291 UTC e7f3c287-196f-4e4c-b36f-bb96df3aab33 2012-03-09 08:58:57.490 UTC