ROC_AUC_WorkflowInteract_pepXML00 The worflow takes a pepXML file generated by PeptideProphet as input. It will never work for pepXML data that have not yet been analyzed with PeptideProphet. 2013-01-28 12:49:56.683 UTC interact.pep.xml 2013-01-28 12:50:18.8 UTC ROC_AUCExtract_Sensitivityxml_text0nodelist11 This XPath component extracts the sensitivity data from the "all charge states" ROC curve. This is the first data in the pepXML file, and can be changed by modifying the position()== criterion in the XPath. 2013-01-28 12:46:34.662 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/117.LC2.IT2.EC.scanmode_Cap_1-E,1_01_3481.tandem.interact.pep.xsl"?><msms_pipeline_analysis xmlns="http://regis-web.systemsbiology.net/pepXML" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" date="2012-10-18T11:30:56" summary_xml="c:/Taverna/data/120117.LC2.IT2.EC.scanmode_Cap_1-E,1_01_3481.tandem.interact.pep.xml" xsi:schemaLocation="http://regis-web.systemsbiology.net/pepXML http://localhost/pepXML_v117.xsd"> <analysis_summary analysis="peptideprophet" time="2012-10-18T11:31:14"> <peptideprophet_summary version="PeptideProphet (TPP v4.6 OCCUPY rev 0, Build 201208170820 (MinGW))" author="AKeller@ISB" min_prob="0.05" options=" MINPROB=0.05 " est_tot_num_correct="11375.1"> <inputfile name="C:\Taverna\data\120117.LC2.IT2.EC.scanmode_Cap_1-E,1_01_3481"/> <roc_error_data charge="all"> <roc_data_point min_prob="0.9999" sensitivity="0.0021" error="0.0001" num_corr="24" num_incorr="0"/> <roc_data_point min_prob="0.9990" sensitivity="0.2600" error="0.0005" num_corr="2958" num_incorr="1"/> <roc_data_point min_prob="0.9900" sensitivity="0.5694" error="0.0023" num_corr="6477" num_incorr="15"/> <roc_data_point min_prob="0.9800" sensitivity="0.6467" error="0.0037" num_corr="7356" num_incorr="28"/> <roc_data_point min_prob="0.9500" sensitivity="0.7365" error="0.0073" num_corr="8378" num_incorr="62"/> <roc_data_point min_prob="0.9000" sensitivity="0.7988" error="0.0127" num_corr="9087" num_incorr="117"/> <roc_data_point min_prob="0.8500" sensitivity="0.8341" error="0.0179" num_corr="9488" num_incorr="173"/> <roc_data_point min_prob="0.8000" sensitivity="0.8569" error="0.0229" num_corr="9748" num_incorr="228"/> <roc_data_point min_prob="0.7500" sensitivity="0.8736" error="0.0278" num_corr="9938" num_incorr="284"/> <roc_data_point min_prob="0.7000" sensitivity="0.8878" error="0.0331" num_corr="10099" num_incorr="345"/> <roc_data_point min_prob="0.6500" sensitivity="0.8991" error="0.0383" num_corr="10227" num_incorr="407"/> <roc_data_point min_prob="0.6000" sensitivity="0.9086" error="0.0437" num_corr="10335" num_incorr="472"/> <roc_data_point min_prob="0.5500" sensitivity="0.9182" error="0.0504" num_corr="10445" num_incorr="554"/> <roc_data_point min_prob="0.5000" sensitivity="0.9262" error="0.0569" num_corr="10536" num_incorr="635"/> <roc_data_point min_prob="0.4500" sensitivity="0.9345" error="0.0650" num_corr="10630" num_incorr="740"/> <roc_data_point min_prob="0.4000" sensitivity="0.9423" error="0.0741" num_corr="10719" num_incorr="858"/> <roc_data_point min_prob="0.3500" sensitivity="0.9492" error="0.0840" num_corr="10797" num_incorr="990"/> <roc_data_point min_prob="0.3000" sensitivity="0.9549" error="0.0939" num_corr="10862" num_incorr="1126"/> <roc_data_point min_prob="0.2500" sensitivity="0.9607" error="0.1064" num_corr="10929" num_incorr="1301"/> <roc_data_point min_prob="0.2000" sensitivity="0.9669" error="0.1232" num_corr="10999" num_incorr="1546"/> <roc_data_point min_prob="0.1500" sensitivity="0.9737" error="0.1473" num_corr="11076" num_incorr="1914"/> <roc_data_point min_prob="0.1000" sensitivity="0.9807" error="0.1816" num_corr="11155" num_incorr="2476"/> <roc_data_point min_prob="0.0500" sensitivity="0.9887" error="0.2459" num_corr="11247" num_incorr="3668"/> <roc_data_point min_prob="0.0000" sensitivity="1.0000" error="0.8015" num_corr="11375" num_incorr="45918"/> <error_point error="0.0000" min_prob="0.9999" num_corr="2" num_incorr="0"/> <error_point error="0.0001" min_prob="0.9999" num_corr="2" num_incorr="0"/> <error_point error="0.0002" min_prob="0.9998" num_corr="649" num_incorr="0"/> <error_point error="0.0003" min_prob="0.9995" num_corr="1795" num_incorr="1"/> <error_point error="0.0004" min_prob="0.9992" num_corr="2556" num_incorr="1"/> <error_point error="0.0005" min_prob="0.9989" num_corr="3103" num_incorr="2"/> <error_point error="0.0006" min_prob="0.9985" num_corr="3551" num_incorr="2"/> <error_point error="0.0007" min_prob="0.9982" num_corr="3924" num_incorr="3"/> <error_point error="0.0008" min_prob="0.9978" num_corr="4246" num_incorr="3"/> <error_point error="0.0009" min_prob="0.9974" num_corr="4524" num_incorr="4"/> <error_point error="0.0010" min_prob="0.9969" num_corr="4768" num_incorr="5"/> <error_point error="0.0015" min_prob="0.9944" num_corr="5658" num_incorr="9"/> <error_point error="0.0020" min_prob="0.9916" num_corr="6235" num_incorr="13"/> <error_point error="0.0025" min_prob="0.9885" num_corr="6654" num_incorr="17"/> <error_point error="0.0030" min_prob="0.9850" num_corr="6980" num_incorr="21"/> <error_point error="0.0040" min_prob="0.9780" num_corr="7468" num_incorr="30"/> <error_point error="0.0050" min_prob="0.9699" num_corr="7824" num_incorr="39"/> <error_point error="0.0060" min_prob="0.9618" num_corr="8094" num_incorr="49"/> <error_point error="0.0070" min_prob="0.9531" num_corr="8314" num_incorr="59"/> <error_point error="0.0080" min_prob="0.9445" num_corr="8497" num_incorr="69"/> <error_point error="0.0090" min_prob="0.9354" num_corr="8656" num_incorr="79"/> <error_point error="0.0100" min_prob="0.9261" num_corr="8793" num_incorr="89"/> <error_point error="0.0150" min_prob="0.8798" num_corr="9283" num_incorr="142"/> <error_point error="0.0200" min_prob="0.8291" num_corr="9607" num_incorr="196"/> <error_point error="0.0250" min_prob="0.7736" num_corr="9837" num_incorr="252"/> <error_point error="0.0300" min_prob="0.7264" num_corr="10010" num_incorr="310"/> <error_point error="0.0400" min_prob="0.6342" num_corr="10265" num_incorr="428"/> <error_point error="0.0500" min_prob="0.5518" num_corr="10441" num_incorr="550"/> <error_point error="0.0750" min_prob="0.3942" num_corr="10727" num_incorr="870"/> <error_point error="0.1000" min_prob="0.2711" num_corr="10897" num_incorr="1212"/> </roc_error_data> <roc_error_data charge="1" charge_est_correct="13.0"> <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="0.0000" error="0" num_corr="0" num_incorr="0"/> <roc_data_point min_prob="0.9000" sensitivity="0.0000" error="0" num_corr="0" num_incorr="0"/> <roc_data_point min_prob="0.8500" sensitivity="0.0000" error="0" num_corr="0" num_incorr="0"/> <roc_data_point min_prob="0.8000" sensitivity="0.3153" error="0.1786" num_corr="4" num_incorr="1"/> <roc_data_point min_prob="0.7500" sensitivity="0.3763" error="0.1829" num_corr="5" num_incorr="1"/> <roc_data_point min_prob="0.7000" sensitivity="0.4866" error="0.2075" num_corr="6" num_incorr="2"/> <roc_data_point min_prob="0.6500" sensitivity="0.6418" error="0.2399" num_corr="8" num_incorr="3"/> <roc_data_point min_prob="0.6000" sensitivity="0.6885" error="0.2525" num_corr="9" num_incorr="3"/> <roc_data_point min_prob="0.5500" sensitivity="0.6885" error="0.2525" num_corr="9" num_incorr="3"/> <roc_data_point min_prob="0.5000" sensitivity="0.6885" error="0.2525" num_corr="9" num_incorr="3"/> <roc_data_point min_prob="0.4500" sensitivity="0.9043" error="0.3455" num_corr="12" num_incorr="6"/> <roc_data_point min_prob="0.4000" sensitivity="0.9043" error="0.3455" num_corr="12" num_incorr="6"/> <roc_data_point min_prob="0.3500" sensitivity="0.9344" error="0.3593" num_corr="12" num_incorr="7"/> <roc_data_point min_prob="0.3000" sensitivity="0.9344" error="0.3593" num_corr="12" num_incorr="7"/> <roc_data_point min_prob="0.2500" sensitivity="0.9548" error="0.3781" num_corr="12" num_incorr="8"/> <roc_data_point min_prob="0.2000" sensitivity="0.9548" error="0.3781" num_corr="12" num_incorr="8"/> <roc_data_point min_prob="0.1500" sensitivity="0.9548" error="0.3781" num_corr="12" num_incorr="8"/> <roc_data_point min_prob="0.1000" sensitivity="0.9760" error="0.4221" num_corr="13" num_incorr="9"/> <roc_data_point min_prob="0.0500" sensitivity="0.9835" error="0.4430" num_corr="13" num_incorr="10"/> <roc_data_point min_prob="0.0000" sensitivity="1.0000" error="0.9276" num_corr="13" num_incorr="167"/> <error_point error="0.0000" min_prob="0.8300" num_corr="2" num_incorr="0"/> <error_point error="0.0001" min_prob="0.8300" num_corr="2" num_incorr="0"/> <error_point error="0.0002" min_prob="0.8300" num_corr="2" num_incorr="0"/> <error_point error="0.0003" min_prob="0.8300" num_corr="2" num_incorr="0"/> <error_point error="0.0004" min_prob="0.8300" num_corr="2" num_incorr="0"/> <error_point error="0.0005" min_prob="0.8300" num_corr="2" num_incorr="0"/> <error_point error="0.0006" min_prob="0.8300" num_corr="2" num_incorr="0"/> <error_point error="0.0007" min_prob="0.8300" num_corr="2" num_incorr="0"/> <error_point error="0.0008" min_prob="0.8300" num_corr="2" num_incorr="0"/> <error_point error="0.0009" min_prob="0.8300" num_corr="2" num_incorr="0"/> <error_point error="0.0010" min_prob="0.8300" num_corr="2" num_incorr="0"/> <error_point error="0.0015" min_prob="0.8300" num_corr="2" num_incorr="0"/> <error_point error="0.0020" min_prob="0.8300" num_corr="2" num_incorr="0"/> <error_point error="0.0025" min_prob="0.8300" num_corr="2" num_incorr="0"/> <error_point error="0.0030" min_prob="0.8300" num_corr="2" num_incorr="0"/> <error_point error="0.0040" min_prob="0.8300" num_corr="2" num_incorr="0"/> <error_point error="0.0050" min_prob="0.8300" num_corr="2" num_incorr="0"/> <error_point error="0.0060" min_prob="0.8300" num_corr="2" num_incorr="0"/> <error_point error="0.0070" min_prob="0.8300" num_corr="2" num_incorr="0"/> <error_point error="0.0080" min_prob="0.8300" num_corr="2" num_incorr="0"/> <error_point error="0.0090" min_prob="0.8300" num_corr="2" num_incorr="0"/> <error_point error="0.0100" min_prob="0.8300" num_corr="2" num_incorr="0"/> <error_point error="0.0150" min_prob="0.8300" num_corr="2" num_incorr="0"/> <error_point error="0.0200" min_prob="0.8300" num_corr="2" num_incorr="0"/> <error_point error="0.0250" min_prob="0.8300" num_corr="2" num_incorr="0"/> <error_point error="0.0300" min_prob="0.8300" num_corr="2" num_incorr="0"/> <error_point error="0.0400" min_prob="0.8300" num_corr="2" num_incorr="0"/> <error_point error="0.0500" min_prob="0.8300" num_corr="2" num_incorr="0"/> <error_point error="0.0750" min_prob="0.8300" num_corr="2" num_incorr="0"/> <error_point error="0.1000" min_prob="0.8300" num_corr="2" num_incorr="0"/> </roc_error_data> <roc_error_data charge="2" charge_est_correct="7886.1"> <roc_data_point min_prob="0.9999" sensitivity="0.0030" error="0.0001" num_corr="24" num_incorr="0"/> <roc_data_point min_prob="0.9990" sensitivity="0.3750" error="0.0005" num_corr="2958" num_incorr="1"/> <roc_data_point min_prob="0.9900" sensitivity="0.6888" error="0.0019" num_corr="5432" num_incorr="10"/> <roc_data_point min_prob="0.9800" sensitivity="0.7555" error="0.0030" num_corr="5958" num_incorr="18"/> <roc_data_point min_prob="0.9500" sensitivity="0.8255" error="0.0055" num_corr="6510" num_incorr="36"/> <roc_data_point min_prob="0.9000" sensitivity="0.8713" error="0.0092" num_corr="6871" num_incorr="64"/> <roc_data_point min_prob="0.8500" sensitivity="0.8969" error="0.0129" num_corr="7073" num_incorr="92"/> <roc_data_point min_prob="0.8000" sensitivity="0.9119" error="0.0161" num_corr="7191" num_incorr="118"/> <roc_data_point min_prob="0.7500" sensitivity="0.9232" error="0.0194" num_corr="7280" num_incorr="144"/> <roc_data_point min_prob="0.7000" sensitivity="0.9326" error="0.0229" num_corr="7355" num_incorr="172"/> <roc_data_point min_prob="0.6500" sensitivity="0.9397" error="0.0262" num_corr="7411" num_incorr="199"/> <roc_data_point min_prob="0.6000" sensitivity="0.9462" error="0.0299" num_corr="7462" num_incorr="230"/> <roc_data_point min_prob="0.5500" sensitivity="0.9518" error="0.0338" num_corr="7506" num_incorr="263"/> <roc_data_point min_prob="0.5000" sensitivity="0.9566" error="0.0379" num_corr="7544" num_incorr="297"/> <roc_data_point min_prob="0.4500" sensitivity="0.9618" error="0.0431" num_corr="7585" num_incorr="341"/> <roc_data_point min_prob="0.4000" sensitivity="0.9666" error="0.0490" num_corr="7623" num_incorr="392"/> <roc_data_point min_prob="0.3500" sensitivity="0.9715" error="0.0563" num_corr="7661" num_incorr="457"/> <roc_data_point min_prob="0.3000" sensitivity="0.9747" error="0.0623" num_corr="7687" num_incorr="510"/> <roc_data_point min_prob="0.2500" sensitivity="0.9781" error="0.0701" num_corr="7713" num_incorr="582"/> <roc_data_point min_prob="0.2000" sensitivity="0.9823" error="0.0824" num_corr="7746" num_incorr="696"/> <roc_data_point min_prob="0.1500" sensitivity="0.9859" error="0.0968" num_corr="7775" num_incorr="833"/> <roc_data_point min_prob="0.1000" sensitivity="0.9900" error="0.1194" num_corr="7807" num_incorr="1058"/> <roc_data_point min_prob="0.0500" sensitivity="0.9942" error="0.1602" num_corr="7840" num_incorr="1496"/> <roc_data_point min_prob="0.0000" sensitivity="1.0000" error="0.7186" num_corr="7886" num_incorr="20138"/> <error_point error="0.0000" min_prob="0.9999" num_corr="2" num_incorr="0"/> <error_point error="0.0001" min_prob="0.9999" num_corr="2" num_incorr="0"/> <error_point error="0.0002" min_prob="0.9998" num_corr="649" num_incorr="0"/> <error_point error="0.0003" min_prob="0.9995" num_corr="1795" num_incorr="1"/> <error_point error="0.0004" min_prob="0.9992" num_corr="2556" num_incorr="1"/> <error_point error="0.0005" min_prob="0.9989" num_corr="3103" num_incorr="2"/> <error_point error="0.0006" min_prob="0.9984" num_corr="3528" num_incorr="2"/> <error_point error="0.0007" min_prob="0.9980" num_corr="3854" num_incorr="3"/> <error_point error="0.0008" min_prob="0.9975" num_corr="4119" num_incorr="3"/> <error_point error="0.0009" min_prob="0.9969" num_corr="4336" num_incorr="4"/> <error_point error="0.0010" min_prob="0.9964" num_corr="4522" num_incorr="5"/> <error_point error="0.0015" min_prob="0.9930" num_corr="5146" num_incorr="8"/> <error_point error="0.0020" min_prob="0.9888" num_corr="5515" num_incorr="11"/> <error_point error="0.0025" min_prob="0.9844" num_corr="5770" num_incorr="14"/> <error_point error="0.0030" min_prob="0.9798" num_corr="5965" num_incorr="18"/> <error_point error="0.0040" min_prob="0.9687" num_corr="6241" num_incorr="25"/> <error_point error="0.0050" min_prob="0.9570" num_corr="6431" num_incorr="32"/> <error_point error="0.0060" min_prob="0.9454" num_corr="6574" num_incorr="40"/> <error_point error="0.0070" min_prob="0.9327" num_corr="6689" num_incorr="47"/> <error_point error="0.0080" min_prob="0.9161" num_corr="6783" num_incorr="55"/> <error_point error="0.0090" min_prob="0.9028" num_corr="6859" num_incorr="62"/> <error_point error="0.0100" min_prob="0.8893" num_corr="6925" num_incorr="70"/> <error_point error="0.0150" min_prob="0.8151" num_corr="7157" num_incorr="109"/> <error_point error="0.0200" min_prob="0.7410" num_corr="7296" num_incorr="149"/> <error_point error="0.0250" min_prob="0.6680" num_corr="7393" num_incorr="190"/> <error_point error="0.0300" min_prob="0.5996" num_corr="7464" num_incorr="232"/> <error_point error="0.0400" min_prob="0.4809" num_corr="7562" num_incorr="316"/> <error_point error="0.0500" min_prob="0.3920" num_corr="7629" num_incorr="402"/> <error_point error="0.0750" min_prob="0.2276" num_corr="7728" num_incorr="627"/> <error_point error="0.1000" min_prob="0.1414" num_corr="7781" num_incorr="866"/> </roc_error_data> <roc_error_data charge="3" charge_est_correct="3476.0"> <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="0.3008" error="0.0044" num_corr="1045" num_incorr="5"/> <roc_data_point min_prob="0.9800" sensitivity="0.4022" error="0.0070" num_corr="1398" num_incorr="10"/> <roc_data_point min_prob="0.9500" sensitivity="0.5375" error="0.0136" num_corr="1868" num_incorr="26"/> <roc_data_point min_prob="0.9000" sensitivity="0.6374" error="0.0235" num_corr="2216" num_incorr="53"/> <roc_data_point min_prob="0.8500" sensitivity="0.6947" error="0.0325" num_corr="2415" num_incorr="81"/> <roc_data_point min_prob="0.8000" sensitivity="0.7342" error="0.0413" num_corr="2552" num_incorr="110"/> <roc_data_point min_prob="0.7500" sensitivity="0.7631" error="0.0499" num_corr="2653" num_incorr="139"/> <roc_data_point min_prob="0.7000" sensitivity="0.7875" error="0.0590" num_corr="2737" 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[ntt]"> <posmodel_distribution> <parameter name="ntt=0" value="0.000"/> <parameter name="ntt=1" value="0.008"/> <parameter name="ntt=2" value="0.992"/> </posmodel_distribution> <negmodel_distribution> <parameter name="ntt=0" value="0.000"/> <parameter name="ntt=1" value="0.053"/> <parameter name="ntt=2" value="0.947"/> </negmodel_distribution> </mixturemodel_distribution> <mixturemodel_distribution name="no. missed enz. cleavages [nmc]"> <posmodel_distribution> <parameter name="nmc=0" value="0.899"/> <parameter name="1&lt;=nmc&lt;=2" value="0.101"/> <parameter name="nmc&gt;=3" value="0.000"/> </posmodel_distribution> <negmodel_distribution> <parameter name="nmc=0" value="0.778"/> <parameter name="1&lt;=nmc&lt;=2" value="0.222"/> <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="0.000726597"/> <parameter name="massd=0.000000" value="0.664598765"/> <parameter name="massd=1.000000" value="0.334674639"/> <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="0.000065971"/> <parameter name="massd=0.000000" value="0.483068903"/> <parameter name="massd=1.000000" value="0.487178149"/> <parameter name="massd=2.000000" value="0.029686977"/> <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="0.282" est_tot_correct="7886.1" tot_num_spectra="28024" num_iterations="27"> <mixturemodel_distribution name="X! 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[ntt]"> <posmodel_distribution> <parameter name="ntt=0" value="0.000"/> <parameter name="ntt=1" value="0.001"/> <parameter name="ntt=2" value="0.999"/> </posmodel_distribution> <negmodel_distribution> <parameter name="ntt=0" value="0.000"/> <parameter name="ntt=1" value="0.050"/> <parameter name="ntt=2" value="0.950"/> </negmodel_distribution> </mixturemodel_distribution> <mixturemodel_distribution name="no. missed enz. cleavages [nmc]"> <posmodel_distribution> <parameter name="nmc=0" value="0.972"/> <parameter name="1&lt;=nmc&lt;=2" value="0.028"/> <parameter name="nmc&gt;=3" value="0.000"/> </posmodel_distribution> <negmodel_distribution> <parameter name="nmc=0" value="0.562"/> <parameter name="1&lt;=nmc&lt;=2" value="0.438"/> <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="0.019000559"/> <parameter name="massd=0.000000" value="0.849942261"/> <parameter name="massd=1.000000" value="0.130976668"/> <parameter name="massd=2.000000" value="0.000080369"/> <parameter name="massd=3.000000" value="0.000000143"/> <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="0.284143289"/> <parameter name="massd=0.000000" value="0.458057262"/> <parameter name="massd=1.000000" value="0.205414418"/> <parameter name="massd=2.000000" value="0.052384974"/> <parameter name="massd=3.000000" value="0.000000057"/> <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="0.120" est_tot_correct="3476.0" tot_num_spectra="29089" num_iterations="27"> <mixturemodel_distribution name="X! 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[ntt]"> <posmodel_distribution> <parameter name="ntt=0" value="0.000"/> <parameter name="ntt=1" value="0.001"/> <parameter name="ntt=2" value="0.999"/> </posmodel_distribution> <negmodel_distribution> <parameter name="ntt=0" value="0.001"/> <parameter name="ntt=1" value="0.053"/> <parameter name="ntt=2" value="0.946"/> </negmodel_distribution> </mixturemodel_distribution> <mixturemodel_distribution name="no. missed enz. cleavages [nmc]"> <posmodel_distribution> <parameter name="nmc=0" value="0.673"/> <parameter name="1&lt;=nmc&lt;=2" value="0.327"/> <parameter name="nmc&gt;=3" value="0.000"/> </posmodel_distribution> <negmodel_distribution> <parameter name="nmc=0" value="0.393"/> <parameter name="1&lt;=nmc&lt;=2" value="0.607"/> <parameter name="nmc&gt;=3" value="0.000"/> </negmodel_distribution> </mixturemodel_distribution> <mixturemodel_distribution name="accurate mass diff [massd] (offset: 1.000000)"> <posmodel_distribution> <parameter name="massd=-5.000000" value="0.000000000"/> <parameter name="massd=-4.000000" value="0.000000000"/> <parameter name="massd=-3.000000" value="0.000000000"/> <parameter name="massd=-2.000000" value="0.000000000"/> <parameter name="massd=-1.000000" value="0.037308530"/> <parameter name="massd=0.000000" value="0.565219842"/> <parameter name="massd=1.000000" value="0.395975191"/> <parameter name="massd=2.000000" value="0.001495497"/> <parameter name="massd=3.000000" value="0.000000940"/> <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="0.000117506"/> <parameter name="massd=-1.000000" value="0.372591450"/> <parameter name="massd=0.000000" value="0.375890085"/> <parameter name="massd=1.000000" value="0.249687713"/> <parameter name="massd=2.000000" value="0.001713118"/> <parameter name="massd=3.000000" value="0.000000129"/> <parameter name="massd=4.000000" value="0.000000000"/> <parameter name="massd=5.000000" value="0.000000000"/> </negmodel_distribution> </mixturemodel_distribution> </mixture_model> <mixture_model precursor_ion_charge="4" comments="using 3+ positive distributions to identify candidates ('-4') above background ('0')" prior_probability="0.000" est_tot_correct="0.0" tot_num_spectra="29075" num_iterations="26"> <mixturemodel_distribution name="X! 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[ntt]"> <posmodel_distribution> <parameter name="ntt=0" value="0.000"/> <parameter name="ntt=1" value="0.001"/> <parameter name="ntt=2" value="0.999"/> </posmodel_distribution> <negmodel_distribution> <parameter name="ntt=0" value="0.001"/> <parameter name="ntt=1" value="0.053"/> <parameter name="ntt=2" value="0.946"/> </negmodel_distribution> </mixturemodel_distribution> <mixturemodel_distribution name="no. missed enz. cleavages [nmc]"> <posmodel_distribution> <parameter name="nmc=0" value="0.673"/> <parameter name="1&lt;=nmc&lt;=2" value="0.327"/> <parameter name="nmc&gt;=3" value="0.000"/> </posmodel_distribution> <negmodel_distribution> <parameter name="nmc=0" value="0.393"/> <parameter name="1&lt;=nmc&lt;=2" value="0.607"/> <parameter name="nmc&gt;=3" value="0.000"/> </negmodel_distribution> </mixturemodel_distribution> <mixturemodel_distribution name="accurate mass diff [massd] (offset: 2.000000)"> <posmodel_distribution> <parameter name="massd=-5.000000" value="0.000000000"/> <parameter name="massd=-4.000000" value="0.000000000"/> <parameter name="massd=-3.000000" value="0.000000000"/> <parameter name="massd=-2.000000" value="0.000000000"/> <parameter name="massd=-1.000000" value="0.037308530"/> <parameter name="massd=0.000000" value="0.565219842"/> <parameter name="massd=1.000000" value="0.395975191"/> <parameter name="massd=2.000000" value="0.001495497"/> <parameter name="massd=3.000000" value="0.000000940"/> <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="0.000117506"/> <parameter name="massd=-1.000000" value="0.372591450"/> <parameter name="massd=0.000000" value="0.375890085"/> <parameter name="massd=1.000000" value="0.249687713"/> <parameter name="massd=2.000000" value="0.001713118"/> <parameter name="massd=3.000000" value="0.000000129"/> <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="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="2012-10-18T11:31:04"/> <analysis_summary analysis="interact" time="2012-10-18T11:30:47"> <interact_summary filename="c:/Taverna/data/120117.LC2.IT2.EC.scanmode_Cap_1-E,1_01_3481.tandem.interact.pep.xml" directory=""> <inputfile name="C:\Taverna\data\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:\Taverna\data\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:\Taverna\data\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:\Taverna\data\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="M" massdiff="15.9949" mass="147.0354" variable="Y"/> <aminoacid_modification aminoacid="Q" massdiff="-17.0265" mass="111.0321" variable="Y" symbol="^"/> <!--X! Tandem n-terminal AA variable modification--> <terminal_modification terminus="n" massdiff="42.0106" mass="43.0184" protein_terminus="N" variable="Y" symbol="^"/> <!--X! Tandem n-terminal AA variable modification--> <!-- Input parameters --> <parameter name="list path, taxonomy information" value="C:\Taverna\data\120117.LC2.IT2.EC.scanmode_Cap_1-E,1_01_3481.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:\Taverna\data\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="+15.994915@M"/> <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="0.5"/> <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:\Taverna\data\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="protein, use minimal annotations" value="yes"/> <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:\Taverna\data\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="43884539"/> <parameter name="modelling, total proteins used" value="4416"/> <parameter name="modelling, total spectra used" value="87722"/> <parameter name="process, start time" value="2012:10:18:11:24:28"/> <parameter name="process, version" value="x! tandem CYCLONE TPP (2011.12.01.1 - LabKey, Insilicos, ISB) "/> <parameter name="quality values" value="5032 2580 1994 1820 1575 1233 899 658 424 222 101 52 28 8 4 1 1 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="63.67"/> <parameter name="timing, initial modelling/spectrum (sec)" value="0.0007"/> <parameter name="timing, load sequence models (sec)" value="0.02"/> <parameter name="timing, refinement/spectrum (sec)" value="0.0000"/> </search_summary> <analysis_timestamp analysis="peptideprophet" time="2012-10-18T11:31:14" id="1"/> <analysis_timestamp analysis="database_refresh" time="2012-10-18T11:31:04" id="1"> <database_refresh_timestamp database="c:/Taverna/data/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_3481.03336.03336.2" start_scan="3336" end_scan="3336" precursor_neutral_mass="693.4211" assumed_charge="2" index="1" retention_time_sec="597.50"> <search_result> <search_hit hit_rank="1" peptide="GDSAGCK" peptide_prev_aa="R" peptide_next_aa="N" protein="sp|P77337|YDIS_ECOLI" protein_descr="Probable electron transfer flavoprotein-quinone oxidoreductase ydiS OS=Escherichia coli (strain K12) GN=ydiS" num_tot_proteins="1" num_matched_ions="6" tot_num_ions="12" calc_neutral_pep_mass="693.2747" massdiff="0.146" num_tol_term="2" num_missed_cleavages="0" is_rejected="0"> <modification_info modified_peptide="GDSAGCK"> <mod_aminoacid_mass position="6" mass="160.0306"/> </modification_info> <search_score name="hyperscore" value="196"/> <search_score name="nextscore" value="141"/> <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="54"/> <analysis_result analysis="peptideprophet"> <peptideprophet_result probability="0.1277" all_ntt_prob="(0.0000,0.0028,0.1277)"> <search_score_summary> <parameter name="fval" value="0.2612"/> <parameter name="ntt" value="2"/> <parameter name="nmc" value="0"/> <parameter name="massd" value="0.146"/> </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_3481.04760.04760.2" start_scan="4760" end_scan="4760" precursor_neutral_mass="712.7950" assumed_charge="2" index="2" retention_time_sec="829.68"> <search_result> <search_hit hit_rank="1" peptide="SLGLPVK" peptide_prev_aa="K" peptide_next_aa="R" protein="sp|P00934|THRC_ECOLI" protein_descr="Threonine synthase OS=Escherichia coli (strain K12) GN=thrC" num_tot_proteins="1" num_matched_ions="7" tot_num_ions="12" calc_neutral_pep_mass="712.4487" massdiff="0.346" num_tol_term="2" num_missed_cleavages="0" is_rejected="0"> <search_score name="hyperscore" value="246"/> <search_score name="nextscore" value="204"/> <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="19"/> <analysis_result analysis="peptideprophet"> <peptideprophet_result probability="0.1111" all_ntt_prob="(0.0000,0.0024,0.1111)"> <search_score_summary> <parameter name="fval" value="0.1811"/> <parameter name="ntt" value="2"/> <parameter name="nmc" value="0"/> <parameter name="massd" value="0.346"/> </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_3481.04454.04454.2" start_scan="4454" end_scan="4454" precursor_neutral_mass="718.4573" assumed_charge="2" index="3" retention_time_sec="779.83"> <search_result> <search_hit hit_rank="1" peptide="ITGLTSK" peptide_prev_aa="K" peptide_next_aa="A" protein="sp|P0A9G4|CUER_ECOLI" protein_descr="HTH-type transcriptional regulator cueR OS=Escherichia coli (strain K12) GN=cueR" num_tot_proteins="1" num_matched_ions="11" tot_num_ions="12" calc_neutral_pep_mass="718.4227" massdiff="0.035" num_tol_term="2" num_missed_cleavages="0" is_rejected="0"> <search_score name="hyperscore" value="250"/> <search_score name="nextscore" value="212"/> <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="18"/> <analysis_result analysis="peptideprophet"> <peptideprophet_result probability="0.0888" all_ntt_prob="(0.0000,0.0019,0.0888)"> <search_score_summary> <parameter name="fval" value="0.0564"/> <parameter name="ntt" value="2"/> <parameter name="nmc" value="0"/> <parameter name="massd" value="0.035"/> </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_3481.06268.06268.2" start_scan="6268" end_scan="6268" precursor_neutral_mass="726.6274" assumed_charge="2" index="4" retention_time_sec="1074.60"> <search_result> <search_hit hit_rank="1" peptide="VGFGYGK" peptide_prev_aa="R" peptide_next_aa="A" protein="sp|P0A7W1|RS5_ECOLI" protein_descr="30S ribosomal protein S5 OS=Escherichia coli (strain K12) GN=rpsE" num_tot_proteins="1" num_matched_ions="8" tot_num_ions="12" calc_neutral_pep_mass="726.3697" massdiff="0.258" num_tol_term="2" num_missed_cleavages="0" is_rejected="0"> <search_score name="hyperscore" value="366"/> <search_score name="nextscore" value="257"/> <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="1.6"/> <analysis_result analysis="peptideprophet"> <peptideprophet_result probability="0.9759" all_ntt_prob="(0.0076,0.4372,0.9759)"> <search_score_summary> <parameter name="fval" value="3.5147"/> <parameter name="ntt" value="2"/> <parameter name="nmc" value="0"/> <parameter name="massd" value="0.258"/> </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_3481.06291.06291.2" start_scan="6291" end_scan="6291" precursor_neutral_mass="726.7963" assumed_charge="2" index="5" retention_time_sec="1078.31"> <search_result> <search_hit hit_rank="1" peptide="VGFGYGK" peptide_prev_aa="R" peptide_next_aa="A" protein="sp|P0A7W1|RS5_ECOLI" protein_descr="30S ribosomal protein S5 OS=Escherichia coli (strain K12) GN=rpsE" num_tot_proteins="1" num_matched_ions="9" tot_num_ions="12" calc_neutral_pep_mass="726.3697" massdiff="0.427" num_tol_term="2" num_missed_cleavages="0" is_rejected="0"> <search_score name="hyperscore" value="352"/> <search_score name="nextscore" value="255"/> <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="2.2"/> <analysis_result analysis="peptideprophet"> <peptideprophet_result probability="0.9553" all_ntt_prob="(0.0040,0.2909,0.9553)"> <search_score_summary> <parameter name="fval" value="3.0812"/> <parameter name="ntt" value="2"/> <parameter name="nmc" value="0"/> <parameter name="massd" value="0.427"/> </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_3481.08495.08495.2" start_scan="8495" end_scan="8495" precursor_neutral_mass="732.8326" assumed_charge="2" index="6" retention_time_sec="1435.69"> <search_result> <search_hit hit_rank="1" peptide="SIEGTAR" peptide_prev_aa="R" peptide_next_aa="S" protein="sp|P0A7J7|RL11_ECOLI" protein_descr="50S ribosomal protein L11 OS=Escherichia coli (strain K12) GN=rplK" num_tot_proteins="1" num_matched_ions="10" tot_num_ions="12" calc_neutral_pep_mass="732.3767" massdiff="0.456" num_tol_term="2" num_missed_cleavages="0" is_rejected="0"> <search_score name="hyperscore" value="366"/> <search_score name="nextscore" value="343"/> <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="0.3"/> <analysis_result analysis="peptideprophet"> <peptideprophet_result probability="0.3609" all_ntt_prob="(0.0001,0.0107,0.3609)"> <search_score_summary> <parameter name="fval" value="0.9578"/> <parameter name="ntt" value="2"/> <parameter name="nmc" value="0"/> <parameter name="massd" value="0.456"/> </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_3481.02780.02780.2" start_scan="2780" end_scan="2780" precursor_neutral_mass="740.8819" assumed_charge="2" index="7" retention_time_sec="506.46"> <search_result> <search_hit hit_rank="1" peptide="VLAGEPR" peptide_prev_aa="R" peptide_next_aa="L" protein="sp|P05055|PNP_ECOLI" protein_descr="Polyribonucleotide nucleotidyltransferase OS=Escherichia coli (strain K12) GN=pnp" num_tot_proteins="1" num_matched_ions="11" tot_num_ions="12" calc_neutral_pep_mass="740.4177" massdiff="0.464" num_tol_term="2" num_missed_cleavages="0" is_rejected="0"> <search_score name="hyperscore" value="206"/> <search_score name="nextscore" value="160"/> <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="45"/> <analysis_result analysis="peptideprophet"> <peptideprophet_result probability="0.0644" all_ntt_prob="(0.0000,0.0013,0.0644)"> <search_score_summary> <parameter name="fval" value="-0.1182"/> <parameter name="ntt" value="2"/> <parameter name="nmc" value="0"/> <parameter name="massd" value="0.464"/> </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_3481.08131.08131.2" start_scan="8131" end_scan="8131" precursor_neutral_mass="744.8465" assumed_charge="2" index="8" retention_time_sec="1376.57"> <search_result> <search_hit hit_rank="1" peptide="AISLSVR" peptide_prev_aa="R" peptide_next_aa="A" protein="sp|P0AG67|RS1_ECOLI" protein_descr="30S ribosomal protein S1 OS=Escherichia coli (strain K12) GN=rpsA" num_tot_proteins="1" num_matched_ions="12" tot_num_ions="12" calc_neutral_pep_mass="744.4497" massdiff="0.397" num_tol_term="2" num_missed_cleavages="0" is_rejected="0"> <search_score name="hyperscore" value="409"/> <search_score name="nextscore" value="338"/> <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="0.31"/> <analysis_result analysis="peptideprophet"> <peptideprophet_result probability="0.9230" all_ntt_prob="(0.0022,0.1871,0.9230)"> <search_score_summary> <parameter name="fval" value="2.7084"/> <parameter name="ntt" value="2"/> <parameter name="nmc" value="0"/> <parameter name="massd" value="0.397"/> </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_3481.08077.08077.2" start_scan="8077" end_scan="8077" precursor_neutral_mass="744.9336" assumed_charge="2" index="9" retention_time_sec="1367.80"> <search_result> <search_hit hit_rank="1" peptide="AISLSVR" peptide_prev_aa="R" peptide_next_aa="A" protein="sp|P0AG67|RS1_ECOLI" protein_descr="30S ribosomal protein S1 OS=Escherichia coli (strain K12) GN=rpsA" num_tot_proteins="1" num_matched_ions="9" tot_num_ions="12" calc_neutral_pep_mass="744.4497" massdiff="0.484" num_tol_term="2" num_missed_cleavages="0" is_rejected="0"> <search_score name="hyperscore" value="372"/> <search_score name="nextscore" value="341"/> <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="0.82"/> <analysis_result analysis="peptideprophet"> <peptideprophet_result probability="0.4986" all_ntt_prob="(0.0002,0.0187,0.4986)"> <search_score_summary> <parameter name="fval" value="1.2606"/> <parameter name="ntt" value="2"/> <parameter name="nmc" value="0"/> <parameter name="massd" value="0.484"/> </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_3481.06827.06827.2" start_scan="6827" end_scan="6827" precursor_neutral_mass="757.5373" assumed_charge="2" index="10" retention_time_sec="1165.10"> <search_result> <search_hit hit_rank="1" peptide="TVGQLLK" peptide_prev_aa="K" peptide_next_aa="E" protein="sp|P0A6P1|EFTS_ECOLI" protein_descr="Elongation factor Ts OS=Escherichia coli (strain K12) GN=tsf" num_tot_proteins="1" num_matched_ions="11" tot_num_ions="12" calc_neutral_pep_mass="757.4697" massdiff="0.068" num_tol_term="2" num_missed_cleavages="0" is_rejected="0"> <search_score name="hyperscore" value="268"/> <search_score name="nextscore" value="224"/> <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="0.65"/> <analysis_result analysis="peptideprophet"> <peptideprophet_result probability="0.1989" all_ntt_prob="(0.0000,0.0047,0.1989)"> <search_score_summary> <parameter name="fval" value="0.5303"/> <parameter name="ntt" value="2"/> <parameter name="nmc" value="0"/> <parameter name="massd" value="0.068"/> </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_3481.05614.05614.2" start_scan="5614" end_scan="5614" precursor_neutral_mass="758.7279" assumed_charge="2" index="11" retention_time_sec="968.48"> <search_result> <search_hit hit_rank="1" peptide="VTVDGLR" peptide_prev_aa="K" peptide_next_aa="A" protein="sp|P23721|SERC_ECOLI" protein_descr="Phosphoserine aminotransferase OS=Escherichia coli (strain K12) GN=serC" num_tot_proteins="1" num_matched_ions="10" tot_num_ions="12" calc_neutral_pep_mass="758.4287" massdiff="0.299" num_tol_term="2" num_missed_cleavages="0" is_rejected="0"> <search_score name="hyperscore" value="380"/> <search_score name="nextscore" value="232"/> <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="0.12"/> <analysis_result analysis="peptideprophet"> <peptideprophet_result probability="0.9948" all_ntt_prob="(0.0347,0.7859,0.9948)"> <search_score_summary> <parameter name="fval" value="4.6965"/> <parameter name="ntt" value="2"/> <parameter name="nmc" value="0"/> <parameter name="massd" value="0.299"/> </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_3481.05604.05604.2" start_scan="5604" end_scan="5604" precursor_neutral_mass="758.7866" assumed_charge="2" index="12" retention_time_sec="966.84"> <search_result> <search_hit hit_rank="1" peptide="VTVDGLR" peptide_prev_aa="K" peptide_next_aa="A" protein="sp|P23721|SERC_ECOLI" protein_descr="Phosphoserine aminotransferase OS=Escherichia coli (strain K12) GN=serC" num_tot_proteins="1" num_matched_ions="9" tot_num_ions="12" calc_neutral_pep_mass="758.4287" massdiff="0.358" num_tol_term="2" num_missed_cleavages="0" is_rejected="0"> <search_score name="hyperscore" value="346"/> <search_score name="nextscore" value="285"/> <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"/> <analysis_result analysis="peptideprophet"> <peptideprophet_result probability="0.7630" all_ntt_prob="(0.0006,0.0582,0.7630)"> <search_score_summary> <parameter name="fval" value="1.9165"/> <parameter name="ntt" value="2"/> <parameter name="nmc" value="0"/> <parameter name="massd" value="0.358"/> </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_3481.05640.05640.2" start_scan="5640" end_scan="5640" precursor_neutral_mass="758.9121" assumed_charge="2" index="13" retention_time_sec="972.65"> <search_result> <search_hit hit_rank="1" peptide="VTVDGLR" peptide_prev_aa="K" peptide_next_aa="A" protein="sp|P23721|SERC_ECOLI" protein_descr="Phosphoserine aminotransferase OS=Escherichia coli (strain K12) GN=serC" num_tot_proteins="1" num_matched_ions="12" tot_num_ions="12" calc_neutral_pep_mass="758.4287" massdiff="0.483" num_tol_term="2" num_missed_cleavages="0" is_rejected="0"> <search_score name="hyperscore" value="363"/> <search_score name="nextscore" value="269"/> <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="0.13"/> <analysis_result analysis="peptideprophet"> <peptideprophet_result probability="0.9533" all_ntt_prob="(0.0038,0.2817,0.9533)"> <search_score_summary> <parameter name="fval" value="3.0514"/> <parameter name="ntt" value="2"/> <parameter name="nmc" value="0"/> <parameter name="massd" value="0.483"/> </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_3481.06627.06627.2" start_scan="6627" end_scan="6627" precursor_neutral_mass="767.7979" assumed_charge="2" index="14" retention_time_sec="1132.80"> <search_result> <search_hit hit_rank="1" peptide="LPNGVLR" peptide_prev_aa="R" peptide_next_aa="T" protein="sp|P0A7R1|RL9_ECOLI" protein_descr="50S ribosomal protein L9 OS=Escherichia coli (strain K12) GN=rplI" num_tot_proteins="1" num_matched_ions="10" tot_num_ions="12" calc_neutral_pep_mass="767.4657" massdiff="0.332" num_tol_term="2" num_missed_cleavages="0" is_rejected="0"> <search_score name="hyperscore" value="421"/> <search_score name="nextscore" value="371"/> <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="0.51"/> <analysis_result analysis="peptideprophet"> <peptideprophet_result probability="0.8511" all_ntt_prob="(0.0011,0.0989,0.8511)"> <search_score_summary> <parameter name="fval" value="2.2537"/> <parameter name="ntt" value="2"/> <parameter name="nmc" value="0"/> <parameter name="massd" value="0.332"/> </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_3481.06582.06582.2" start_scan="6582" end_scan="6582" precursor_neutral_mass="767.8856" assumed_charge="2" index="15" retention_time_sec="1125.53"> <search_result> <search_hit hit_rank="1" peptide="LPNGVLR" peptide_prev_aa="R" peptide_next_aa="T" protein="sp|P0A7R1|RL9_ECOLI" protein_descr="50S ribosomal protein L9 OS=Escherichia coli (strain K12) GN=rplI" num_tot_proteins="1" num_matched_ions="11" tot_num_ions="12" calc_neutral_pep_mass="767.4657" massdiff="0.420" num_tol_term="2" num_missed_cleavages="0" is_rejected="0"> <search_score name="hyperscore" value="429"/> <search_score name="nextscore" value="380"/> <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="0.44"/> <analysis_result analysis="peptideprophet"> <peptideprophet_result probability="0.8600" all_ntt_prob="(0.0012,0.1055,0.8600)"> <search_score_summary> <parameter name="fval" value="2.2967"/> <parameter name="ntt" value="2"/> <parameter name="nmc" value="0"/> <parameter name="massd" value="0.420"/> </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_3481.06604.06604.2" start_scan="6604" end_scan="6604" precursor_neutral_mass="767.9272" assumed_charge="2" index="16" retention_time_sec="1129.10"> <search_result> <search_hit hit_rank="1" peptide="LPNGVLR" peptide_prev_aa="R" peptide_next_aa="T" protein="sp|P0A7R1|RL9_ECOLI" protein_descr="50S ribosomal protein L9 OS=Escherichia coli (strain K12) GN=rplI" num_tot_proteins="1" num_matched_ions="11" tot_num_ions="12" calc_neutral_pep_mass="767.4657" massdiff="0.461" num_tol_term="2" num_missed_cleavages="0" is_rejected="0"> <search_score name="hyperscore" value="424"/> <search_score name="nextscore" value="368"/> <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="0.48"/> <analysis_result analysis="peptideprophet"> <peptideprophet_result probability="0.8850" all_ntt_prob="(0.0014,0.1287,0.8850)"> <search_score_summary> <parameter name="fval" value="2.4334"/> <parameter name="ntt" value="2"/> <parameter name="nmc" value="0"/> <parameter name="massd" value="0.461"/> </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_3481.07836.07836.2" start_scan="7836" end_scan="7836" precursor_neutral_mass="769.8944" assumed_charge="2" index="17" retention_time_sec="1328.63"> <search_result> <search_hit hit_rank="1" peptide="IGVLVAAK" peptide_prev_aa="R" peptide_next_aa="G" protein="sp|P0A6P1|EFTS_ECOLI" protein_descr="Elongation factor Ts OS=Escherichia coli (strain K12) GN=tsf" num_tot_proteins="1" num_matched_ions="12" tot_num_ions="14" calc_neutral_pep_mass="769.5057" massdiff="0.389" num_tol_term="2" num_missed_cleavages="0" is_rejected="0"> <search_score name="hyperscore" value="425"/> <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="0.47"/> <analysis_result analysis="peptideprophet"> <peptideprophet_result probability="0.9964" all_ntt_prob="(0.0488,0.8398,0.9964)"> <search_score_summary> <parameter name="fval" value="5.0021"/> <parameter name="ntt" value="2"/> <parameter name="nmc" value="0"/> <parameter name="massd" value="0.389"/> </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_3481.07869.07869.2" start_scan="7869" end_scan="7869" precursor_neutral_mass="769.9968" assumed_charge="2" index="18" retention_time_sec="1333.98"> <search_result> <search_hit hit_rank="1" peptide="IGVLVAAK" peptide_prev_aa="R" peptide_next_aa="G" protein="sp|P0A6P1|EFTS_ECOLI" protein_descr="Elongation factor Ts OS=Escherichia coli (strain K12) GN=tsf" num_tot_proteins="1" num_matched_ions="12" tot_num_ions="14" calc_neutral_pep_mass="769.5057" massdiff="0.491" num_tol_term="2" num_missed_cleavages="0" is_rejected="0"> <search_score name="hyperscore" value="379"/> <search_score name="nextscore" value="259"/> <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="0.084"/> <analysis_result analysis="peptideprophet"> <peptideprophet_result probability="0.9856" all_ntt_prob="(0.0127,0.5675,0.9856)"> <search_score_summary> <parameter name="fval" value="3.8908"/> <parameter name="ntt" value="2"/> <parameter name="nmc" value="0"/> <parameter name="massd" value="0.491"/> </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_3481.08641.08641.2" start_scan="8641" end_scan="8641" precursor_neutral_mass="770.7958" assumed_charge="2" index="19" retention_time_sec="1459.25"> <search_result> <search_hit hit_rank="1" peptide="IAGIQAAK" peptide_prev_aa="R" peptide_next_aa="R" protein="sp|P0A738|MOAC_ECOLI" protein_descr="Molybdenum cofactor biosynthesis protein C OS=Escherichia coli (strain K12) GN=moaC" num_tot_proteins="1" num_matched_ions="7" tot_num_ions="14" calc_neutral_pep_mass="770.4647" massdiff="0.331" num_tol_term="2" num_missed_cleavages="0" is_rejected="0"> <search_score name="hyperscore" value="280"/> <search_score name="nextscore" value="254"/> <search_score name="bscore" value="1"/> <search_score name="yscore" value="0"/> <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="6.1"/> <analysis_result analysis="peptideprophet"> <peptideprophet_result probability="0.0757" all_ntt_prob="(0.0000,0.0016,0.0757)"> <search_score_summary> <parameter name="fval" value="-0.0307"/> <parameter name="ntt" value="2"/> <parameter name="nmc" value="0"/> <parameter name="massd" value="0.331"/> </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_3481.08439.08439.2" start_scan="8439" end_scan="8439" precursor_neutral_mass="770.8462" assumed_charge="2" index="20" retention_time_sec="1426.62"> <search_result> <search_hit hit_rank="1" peptide="VIEIAVK" peptide_prev_aa="R" peptide_next_aa="G" protein="sp|P0AA10|RL13_ECOLI" protein_descr="50S ribosomal protein L13 OS=Escherichia coli (strain K12) GN=rplM" num_tot_proteins="1" num_matched_ions="12" tot_num_ions="12" calc_neutral_pep_mass="770.4897" massdiff="0.356" num_tol_term="2" num_missed_cleavages="0" is_rejected="0"> <search_score name="hyperscore" value="353"/> <search_score name="nextscore" value="274"/> <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="0.9003" all_ntt_prob="(0.0017,0.1478,0.9003)"> <search_score_summary> <parameter name="fval" value="2.5317"/> <parameter name="ntt" value="2"/> <parameter name="nmc" value="0"/> <parameter name="massd" value="0.356"/> </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_3481.08560.08560.2" start_scan="8560" end_scan="8560" precursor_neutral_mass="770.9039" assumed_charge="2" index="21" retention_time_sec="1446.22"> <search_result> <search_hit hit_rank="1" peptide="VIEIAVK" peptide_prev_aa="R" peptide_next_aa="G" protein="sp|P0AA10|RL13_ECOLI" protein_descr="50S ribosomal protein L13 OS=Escherichia coli (strain K12) GN=rplM" num_tot_proteins="1" num_matched_ions="11" tot_num_ions="12" calc_neutral_pep_mass="770.4897" massdiff="0.414" num_tol_term="2" num_missed_cleavages="0" is_rejected="0"> <search_score name="hyperscore" value="374"/> <search_score name="nextscore" value="307"/> <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="1.8"/> <analysis_result analysis="peptideprophet"> <peptideprophet_result probability="0.8664" all_ntt_prob="(0.0012,0.1107,0.8664)"> <search_score_summary> <parameter name="fval" value="2.3295"/> <parameter name="ntt" value="2"/> <parameter name="nmc" value="0"/> <parameter name="massd" value="0.414"/> </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_3481.08572.08572.2" start_scan="8572" end_scan="8572" precursor_neutral_mass="770.9631" assumed_charge="2" index="22" retention_time_sec="1448.14"> <search_result> <search_hit hit_rank="1" peptide="VIEIAVK" peptide_prev_aa="R" peptide_next_aa="G" protein="sp|P0AA10|RL13_ECOLI" protein_descr="50S ribosomal protein L13 OS=Escherichia coli (strain K12) GN=rplM" num_tot_proteins="1" num_matched_ions="13" tot_num_ions="12" calc_neutral_pep_mass="770.4897" massdiff="0.473" num_tol_term="2" num_missed_cleavages="0" is_rejected="0"> <search_score name="hyperscore" value="349"/> <search_score name="nextscore" value="278"/> <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="0.7"/> <analysis_result analysis="peptideprophet"> <peptideprophet_result probability="0.8512" all_ntt_prob="(0.0011,0.0990,0.8512)"> <search_score_summary> <parameter name="fval" value="2.2542"/> <parameter name="ntt" value="2"/> <parameter name="nmc" value="0"/> <parameter name="massd" value="0.473"/> </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_3481.04007.04007.2" start_scan="4007" end_scan="4007" precursor_neutral_mass="772.9554" assumed_charge="2" index="23" retention_time_sec="706.85"> <search_result> <search_hit hit_rank="1" peptide="IATLTVR" peptide_prev_aa="R" peptide_next_aa="D" protein="sp|P36662|TORD_ECOLI" protein_descr="Chaperone protein torD OS=Escherichia coli (strain K12) GN=torD" num_tot_proteins="1" num_matched_ions="10" tot_num_ions="12" calc_neutral_pep_mass="772.4807" massdiff="0.475" num_tol_term="2" num_missed_cleavages="0" is_rejected="0"> <search_score name="hyperscore" value="292"/> <search_score name="nextscore" value="248"/> <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="0.65"/> <analysis_result analysis="peptideprophet"> <peptideprophet_result probability="0.2967" all_ntt_prob="(0.0001,0.0080,0.2967)"> <search_score_summary> <parameter name="fval" value="0.8046"/> <parameter name="ntt" value="2"/> <parameter name="nmc" value="0"/> <parameter name="massd" value="0.475"/> </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_3481.04801.04801.2" start_scan="4801" end_scan="4801" precursor_neutral_mass="773.5116" assumed_charge="2" index="24" retention_time_sec="836.39"> <search_result> <search_hit hit_rank="1" peptide="SNTIVLK" peptide_prev_aa="K" peptide_next_aa="V" protein="sp|P0ADZ0|RL23_ECOLI" protein_descr="50S ribosomal protein L23 OS=Escherichia coli (strain K12) GN=rplW" num_tot_proteins="1" num_matched_ions="10" tot_num_ions="12" calc_neutral_pep_mass="773.4647" massdiff="0.047" num_tol_term="2" num_missed_cleavages="0" is_rejected="0"> <search_score name="hyperscore" value="268"/> <search_score name="nextscore" value="242"/> <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="0.82"/> <analysis_result analysis="peptideprophet"> <peptideprophet_result probability="0.0551" all_ntt_prob="(0.0000,0.0011,0.0551)"> <search_score_summary> <parameter name="fval" value="-0.2005"/> <parameter name="ntt" value="2"/> <parameter name="nmc" value="0"/> <parameter name="massd" value="0.047"/> </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_3481.06440.06440.2" start_scan="6440" end_scan="6440" precursor_neutral_mass="776.3973" assumed_charge="2" index="25" retention_time_sec="1102.50"> <search_result> <search_hit hit_rank="1" peptide="FSVEAPK" peptide_prev_aa="K" peptide_next_aa="T" protein="sp|P60723|RL4_ECOLI" protein_descr="50S ribosomal protein L4 OS=Escherichia coli (strain K12) GN=rplD" num_tot_proteins="1" num_matched_ions="14" tot_num_ions="12" calc_neutral_pep_mass="776.4068" massdiff="-0.010" num_tol_term="2" num_missed_cleavages="0" is_rejected="0"> <search_score name="hyperscore" value="377"/> <search_score name="nextscore" value="249"/> <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="0.036"/> <analysis_result analysis="peptideprophet"> <peptideprophet_result probability="0.7684" all_ntt_prob="(0.0006,0.0599,0.7684)"> <search_score_summary> <parameter name="fval" value="4.1140"/> <parameter name="ntt" value="2"/> <parameter name="nmc" value="0"/> <parameter name="massd" value="-0.010"/> </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_3481.06285.06285.2" start_scan="6285" end_scan="6285" precursor_neutral_mass="776.4254" assumed_charge="2" index="26" retention_time_sec="1077.43"> <search_result> <search_hit hit_rank="1" peptide="FSVEAPK" peptide_prev_aa="K" peptide_next_aa="T" protein="sp|P60723|RL4_ECOLI" protein_descr="50S ribosomal protein L4 OS=Escherichia coli (strain K12) GN=rplD" num_tot_proteins="1" num_matched_ions="13" tot_num_ions="12" calc_neutral_pep_mass="776.4067" massdiff="0.019" num_tol_term="2" num_missed_cleavages="0" is_rejected="0"> <search_score name="hyperscore" value="412"/> <search_score name="nextscore" value="295"/> <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="0.41"/> <analysis_result analysis="peptideprophet"> <peptideprophet_result probability="0.9866" all_ntt_prob="(0.0136,0.5855,0.9866)"> <search_score_summary> <parameter name="fval" value="3.9455"/> <parameter name="ntt" value="2"/> <parameter name="nmc" value="0"/> <parameter name="massd" value="0.019"/> </search_score_summary> </peptideprophet_result> </analysis_result> </search_hit> </search_result> </spectrum_query> </msms_run_summary> </msms_pipeline_analysis> /default:msms_pipeline_analysis/default:analysis_summary/default:peptideprophet_summary/default:roc_error_data[position()=1]/default:roc_data_point/@sensitivity 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.InvokeRead_Text_Filefileurl0filecontents00 This component uses the standard Beanshell to read the PepXML file from PeptideProphet. 2013-01-28 12:45:15.149 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.InvokeCalculate_AUCROC1AUC00 This small Rshell component calculates the area under the ROC curve using the sensitivity data and the interval lengths (non-uniform but fixed). If in the future, PeptideProphet alters the histogram binning or make it data-dependent, this script should extract also this information and use it in the AUC calculation. 2013-01-28 12:49:02.691 UTC net.sf.taverna.t2.activitiesrshell-activity1.4net.sf.taverna.t2.activities.rshell.RshellActivity ROC 1 false AUC 0 0 false localhost 6311 false false ROC DOUBLE_LIST AUC DOUBLE 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_Sensitivityxml_textRead_Text_FilefilecontentsRead_Text_FilefileurlInteract_pepXMLCalculate_AUCROCExtract_SensitivitynodelistROC_AUCCalculate_AUCAUC 9ce09e4a-f4d3-4013-8af7-e681e89854a3 2013-01-28 12:18:33.998 UTC c707e634-1e85-477e-8f8a-bab0db5fa608 2013-01-28 12:10:13.864 UTC 0639aa15-b00f-45e8-b61e-91e97b5d2019 2013-01-28 12:05:11.874 UTC This small workflow extracts the area under the curve (AUC) from the receiver operating characteristic (ROC) curve for all charge states analyzed by PeptideProphet. This measure can be used to compare the sensitivity and specificity of different search engines for matching tandem mass spectra to peptides. 2013-01-28 12:43:55.386 UTC b9b06add-89cd-4444-bba0-2e5034193f07 2013-01-28 11:55:23.222 UTC eb654d69-06b1-4aa7-9c15-6b52d31db227 2013-01-28 12:20:16.70 UTC Magnus Palmblad 2013-01-28 12:43:59.130 UTC 4e79fdac-b03c-476b-91a5-082c0f3be1d1 2013-01-28 12:32:45.741 UTC 1d63ba8f-0548-40b6-bdf3-a5af98c66a41 2013-01-28 12:18:45.433 UTC f16da9e2-263c-41ac-86d2-28cd800f2ff0 2013-01-28 12:50:18.117 UTC ROC_AUC_Workflow 2013-01-28 12:44:24.605 UTC