Galaxy | (sandbox for testing) |

Changeset 1:37369e255465 (2017-03-15)

Previous changeset 0:0a77e0c00146 (2017-03-14)

Commit message:
Uploaded

modified:
probamconvert.xml

added:
test-data/test.mzid
test-data/test.pep.xml

diff -r 0a77e0c00146 -r 37369e255465 probamconvert.xml
--- a/probamconvert.xml Tue Mar 14 17:06:41 2017 -0400
+++ b/probamconvert.xml Wed Mar 15 09:43:14 2017 -0400

[

@@ -7,9 +7,9 @@
         <exit_code range="1:" />
     </stdio>
     <command><![CDATA[
-        #set $psm_file = input.${input.datatype.file_ext}
+        #set $psm_file = 'input.'+str($input.datatype.file_ext)
         ln -s "$input" $psm_file;
-        proBAM.py --name="converted" --file=$psm_file
+        proBAM.py --name="converted" --file=$psm_file --conversion_mode=$conversion_mode
         --database=$refsrc.database
         #if str($refsrc.database) == 'ENSEMBL':
             --species=$refsrc.species
@@ -17,15 +17,14 @@
                 --version=$refsrc.version
             #end if
         #end if
-        #if str($optional.decoy_annotation) != 'None':
+        #if str($optional.decoy_annotation) != '':
             --decoy_annotation='$optional.decoy_annotation'
         #end if
-        --pre_picked_annotation=$pre_picked_annotation
+        --pre_picked_annotation=$optional.pre_picked_annotation
         --mismatches=$optional.mismatches
         $optional.rm_duplicates
         $optional.three_frame_translation
         $optional.include_unmapped
-        --directory=outputs
     ]]></command>
     <inputs>
         <param name="input" type="data" format="mzid,pepxml" label="Peptide Indentification (mzIdentML or pepXML)"/>
@@ -87,21 +86,21 @@
          </section>
     </inputs>
     <outputs>
-        <data name="output_bam" format="pro.bam" label="" from_work_dir="outputs/converted.sorted.bam">
+        <data name="output_bam" format="bam" label="${conversion_mode} ${input.display_name}.pro.bam" from_work_dir="converted.sorted.bam">
             <filter>conversion_mode != 'proBED'</filter>
         </data>
-        <data name="output_bed" format="pro.bed" label="" from_work_dir="outputs/converted.pro.bed">
+        <data name="output_bed" format="bed" label="${conversion_mode} ${input.display_name}.pro.bed" from_work_dir="converted.pro.bed">
             <filter>conversion_mode == 'proBED'</filter>
         </data>
     </outputs>
     <tests>
         <test>
             <param name="input" ftype="mzid" value="test.mzid"/>
-            <param name="conversion_mode" value="proBAM_psm"/>
+            <param name="conversion_mode" value="proBED"/>
             <param name="database" value="ENSEMBL"/>
             <param name="species" value="homo_sapiens"/>
             <param name="version" value="87"/>
-            <output name="output_bam">
+            <output name="output_bed">
                 <assert_contents>
                     <has_text text="Q7Z6Z7_0" />
                 </assert_contents>

diff -r 0a77e0c00146 -r 37369e255465 test-data/test.mzid
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test.mzid Wed Mar 15 09:43:14 2017 -0400

b'@@ -0,0 +1,679888 @@\n+<?xml version="1.0" encoding="UTF-8"?>\n+<MzIdentML id="PeptideShaker v1.15.1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://psidev.info/psi/pi/mzIdentML/1.1 http://www.psidev.info/files/mzIdentML1.1.0.xsd" xmlns="http://psidev.info/psi/pi/mzIdentML/1.1" version="1.1.0" creationDate="2017-03-14T14:00:05">\n+\t<cvList>\n+\t\t<cv id="PSI-MS" uri="https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo" fullName="PSI-MS"/>\n+\t\t<cv id="UNIMOD" uri="http://www.unimod.org/obo/unimod.obo" fullName="UNIMOD"/>\n+\t\t<cv id="UO" uri="https://raw.githubusercontent.com/bio-ontology-research-group/unit-ontology/master/unit.obo" fullName="UNIT-ONTOLOGY"/>\n+\t\t<cv id="PRIDE" uri="https://github.com/PRIDE-Utilities/pride-ontology/blob/master/pride_cv.obo" fullName="PRIDE"/>\n+\t</cvList>\n+\t<AnalysisSoftwareList>\n+\t\t<AnalysisSoftware name="PeptideShaker" version="1.15.1" id="ID_software" uri="http://compomics.github.io/projects/peptide-shaker.html">\n+\t\t\t<ContactRole contact_ref="PS_DEV">\n+\t\t\t\t<Role>\n+\t\t\t\t\t<cvParam cvRef="PSI-MS" accession="MS:1001267" name="software vendor"/>\n+\t\t\t\t</Role>\n+\t\t\t</ContactRole>\n+\t\t\t<SoftwareName>\n+\t\t\t\t<cvParam cvRef="PSI-MS" accession="MS:1002458" name="PeptideShaker"/>\n+\t\t\t</SoftwareName>\n+\t\t\t<Customizations>No customisations</Customizations>\n+\t\t</AnalysisSoftware>\n+\t</AnalysisSoftwareList>\n+\t<Provider id="PROVIDER">\n+\t\t<ContactRole contact_ref="PROVIDER">\n+\t\t\t<Role>\n+\t\t\t\t<cvParam cvRef="PSI-MS" accession="MS:1001271" name="researcher"/>\n+\t\t\t</Role>\n+\t\t</ContactRole>\n+\t</Provider>\n+\t<AuditCollection>\n+\t\t<Person firstName="Proteomics" lastName="Galaxy" id="PROVIDER">\n+\t\t\t<cvParam cvRef="PSI-MS" accession="MS:1000587" name="contact address" value="galaxyp@umn.edu"/>\n+\t\t\t<cvParam cvRef="PSI-MS" accession="MS:1000589" name="contact email" value="galaxyp@umn.edu"/>\n+\t\t\t<Affiliation organization_ref="ORG_DOC_OWNER"/>\n+\t\t</Person>\n+\t\t<Organization name="University of Minnesota" id="ORG_DOC_OWNER">\n+\t\t\t<cvParam cvRef="PSI-MS" accession="MS:1000586" name="contact name" value="University of Minnesota"/>\n+\t\t\t<cvParam cvRef="PSI-MS" accession="MS:1000587" name="contact address" value="Minneapolis, MN 55455, Vereinigte Staaten"/>\n+\t\t\t<cvParam cvRef="PSI-MS" accession="MS:1000589" name="contact email" value="galaxyp@umn.edu"/>\n+\t\t</Organization>\n+\t\t<Organization name="PeptideShaker developers" id="PS_DEV">\n+\t\t\t<cvParam cvRef="PSI-MS" accession="MS:1000586" name="contact name" value="PeptideShaker developers"/>\n+\t\t\t<cvParam cvRef="PSI-MS" accession="MS:1000587" name="contact address" value="Proteomics Unit, Building for Basic Biology, University of Bergen, Jonas Liesvei 91, N-5009 Bergen, Norway"/>\n+\t\t\t<cvParam cvRef="PSI-MS" accession="MS:1000588" name="contact URL" value="http://compomics.github.io/projects/peptide-shaker.html"/>\n+\t\t\t<cvParam cvRef="PSI-MS" accession="MS:1000589" name="contact email" value="peptide-shaker@googlegroups.com"/>\n+\t\t</Organization>\n+\t</AuditCollection>\n+\t<SequenceCollection>\n+\t\t<DBSequence id="Q8IYD1" accession="Q8IYD1" searchDatabase_ref="SearchDB_1" >\n+\t\t\t<cvParam cvRef="PSI-MS" accession="MS:1001088" name="protein description" value="ERF3B_HUMAN Eukaryotic peptide chain release factor GTP-binding subunit ERF3B OS=Homo sapiens GN=GSPT2 PE=1 SV=2"/>\n+\t\t</DBSequence>\n+\t\t<DBSequence id="Q8IYD1_REVERSED" accession="Q8IYD1_REVERSED" searchDatabase_ref="SearchDB_1" >\n+\t\t\t<cvParam cvRef="PSI-MS" accession="MS:1001088" name="protein description" value="ERF3B_HUMAN Eukaryotic peptide chain release factor GTP-binding subunit ERF3B OS=Homo sapiens GN=GSPT2 PE=1 SV=2-REVERSED"/>\n+\t\t</DBSequence>\n+\t\t<DBSequence id="Q7Z6Z7" accession="Q7Z6Z7" searchDatabase_ref="SearchDB_1" >\n+\t\t\t<cvParam cvRef="PSI-MS" accession="MS:1001088" name="protein description" value="HUWE1_HUMAN E3 ubiquitin-protein ligase HUWE1 OS=Homo sapiens GN=HUWE1 PE=1 SV=3"/>\n+\t\t</DBSequence>\n+\t\t<DBSequence id="Q7Z6Z7_REVERSED" accession="Q7Z6Z7_REVERSED" searchDatabase_ref="SearchDB_'..b'eptideEvidence_ref="PepEv_748">\n+\t\t\t\t\t\t<SpectrumIdentificationItemRef spectrumIdentificationItem_ref="SII_9016_1"/>\n+\t\t\t\t\t\t<SpectrumIdentificationItemRef spectrumIdentificationItem_ref="SII_9368_1"/>\n+\t\t\t\t\t</PeptideHypothesis>\n+\t\t\t\t\t<PeptideHypothesis peptideEvidence_ref="PepEv_3277">\n+\t\t\t\t\t\t<SpectrumIdentificationItemRef spectrumIdentificationItem_ref="SII_9037_1"/>\n+\t\t\t\t\t</PeptideHypothesis>\n+\t\t\t\t\t<PeptideHypothesis peptideEvidence_ref="PepEv_1146">\n+\t\t\t\t\t\t<SpectrumIdentificationItemRef spectrumIdentificationItem_ref="SII_9171_1"/>\n+\t\t\t\t\t</PeptideHypothesis>\n+\t\t\t\t\t<PeptideHypothesis peptideEvidence_ref="PepEv_2543">\n+\t\t\t\t\t\t<SpectrumIdentificationItemRef spectrumIdentificationItem_ref="SII_9182_1"/>\n+\t\t\t\t\t</PeptideHypothesis>\n+\t\t\t\t\t<PeptideHypothesis peptideEvidence_ref="PepEv_4978">\n+\t\t\t\t\t\t<SpectrumIdentificationItemRef spectrumIdentificationItem_ref="SII_9188_1"/>\n+\t\t\t\t\t</PeptideHypothesis>\n+\t\t\t\t\t<PeptideHypothesis peptideEvidence_ref="PepEv_2207">\n+\t\t\t\t\t\t<SpectrumIdentificationItemRef spectrumIdentificationItem_ref="SII_9267_1"/>\n+\t\t\t\t\t</PeptideHypothesis>\n+\t\t\t\t\t<PeptideHypothesis peptideEvidence_ref="PepEv_3692">\n+\t\t\t\t\t\t<SpectrumIdentificationItemRef spectrumIdentificationItem_ref="SII_9328_1"/>\n+\t\t\t\t\t</PeptideHypothesis>\n+\t\t\t\t\t<PeptideHypothesis peptideEvidence_ref="PepEv_3296">\n+\t\t\t\t\t\t<SpectrumIdentificationItemRef spectrumIdentificationItem_ref="SII_9352_1"/>\n+\t\t\t\t\t</PeptideHypothesis>\n+\t\t\t\t\t<PeptideHypothesis peptideEvidence_ref="PepEv_3026">\n+\t\t\t\t\t\t<SpectrumIdentificationItemRef spectrumIdentificationItem_ref="SII_9414_1"/>\n+\t\t\t\t\t</PeptideHypothesis>\n+\t\t\t\t\t<PeptideHypothesis peptideEvidence_ref="PepEv_4114">\n+\t\t\t\t\t\t<SpectrumIdentificationItemRef spectrumIdentificationItem_ref="SII_9433_1"/>\n+\t\t\t\t\t</PeptideHypothesis>\n+\t\t\t\t\t<PeptideHypothesis peptideEvidence_ref="PepEv_1135">\n+\t\t\t\t\t\t<SpectrumIdentificationItemRef spectrumIdentificationItem_ref="SII_9502_1"/>\n+\t\t\t\t\t</PeptideHypothesis>\n+\t\t\t\t\t<PeptideHypothesis peptideEvidence_ref="PepEv_4165">\n+\t\t\t\t\t\t<SpectrumIdentificationItemRef spectrumIdentificationItem_ref="SII_9594_1"/>\n+\t\t\t\t\t</PeptideHypothesis>\n+\t\t\t\t\t<PeptideHypothesis peptideEvidence_ref="PepEv_4890">\n+\t\t\t\t\t\t<SpectrumIdentificationItemRef spectrumIdentificationItem_ref="SII_5388_1"/>\n+\t\t\t\t\t</PeptideHypothesis>\n+\t\t\t\t\t<PeptideHypothesis peptideEvidence_ref="PepEv_1955">\n+\t\t\t\t\t\t<SpectrumIdentificationItemRef spectrumIdentificationItem_ref="SII_5910_1"/>\n+\t\t\t\t\t</PeptideHypothesis>\n+\t\t\t\t\t<PeptideHypothesis peptideEvidence_ref="PepEv_4348">\n+\t\t\t\t\t\t<SpectrumIdentificationItemRef spectrumIdentificationItem_ref="SII_8087_1"/>\n+\t\t\t\t\t</PeptideHypothesis>\n+\t\t\t\t\t<PeptideHypothesis peptideEvidence_ref="PepEv_1369">\n+\t\t\t\t\t\t<SpectrumIdentificationItemRef spectrumIdentificationItem_ref="SII_7937_1"/>\n+\t\t\t\t\t\t<SpectrumIdentificationItemRef spectrumIdentificationItem_ref="SII_9497_1"/>\n+\t\t\t\t\t</PeptideHypothesis>\n+\t\t\t\t\t<PeptideHypothesis peptideEvidence_ref="PepEv_2127">\n+\t\t\t\t\t\t<SpectrumIdentificationItemRef spectrumIdentificationItem_ref="SII_1408_1"/>\n+\t\t\t\t\t</PeptideHypothesis>\n+\t\t\t\t\t<cvParam cvRef="PSI-MS" accession="MS:1002403" name="group representative"/>\n+\t\t\t\t\t<cvParam cvRef="PSI-MS" accession="MS:1002401" name="leading protein"/>\n+\t\t\t\t\t<cvParam cvRef="PSI-MS" accession="MS:1001093" name="sequence coverage" value="0.034"/>\n+\t\t\t\t</ProteinDetectionHypothesis>\n+\t\t\t\t<cvParam cvRef="PSI-MS" accession="MS:1002470" name="PeptideShaker protein group score" value="100.0"/>\n+\t\t\t\t<cvParam cvRef="PSI-MS" accession="MS:1002471" name="PeptideShaker protein group confidence" value="100.0"/>\n+\t\t\t\t<cvParam cvRef="PSI-MS" accession="MS:1002542" name="PeptideShaker protein confidence type" value="Doubtful"/>\n+\t\t\t\t<cvParam cvRef="PSI-MS" accession="MS:1002415" name="protein group passes threshold" value="true"/>\n+\t\t\t</ProteinAmbiguityGroup>\n+\t\t\t<cvParam cvRef="PSI-MS" accession="MS:1002404" name="count of identified proteins" value="3"/>\n+\t\t</ProteinDetectionList>\n+\t</AnalysisData>\n+</DataCollection>\n+</MzIdentML>\n\\ No newline at end of file\n'

diff -r 0a77e0c00146 -r 37369e255465 test-data/test.pep.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test.pep.xml Wed Mar 15 09:43:14 2017 -0400

b'@@ -0,0 +1,126144 @@\n+<?xml version="1.0" encoding="ISO-8859-1"?>\n+<msms_pipeline_analysis date="2017-03-14T14:00:05" summary_xml="outdir/Mascot formatted MGF of data 25.pepXML" xmlns="http://regis-web.systemsbiology.net/pepXML" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://sashimi.sourceforge.net/schema_revision/pepXML/pepXML_v117.xsd">\n+ <analysis_summary analysis="PeptideShaker" version="1.15.1" time="2017-03-14T19:03:20Z"/>\n+ <analysis_summary analysis="ProteoWizard software" version="3.0.9934" time="2017-03-14T19:03:20Z"/>\n+ <msms_run_summary base_name="Mascot%20formatted%20MGF%20of%20data%2025" raw_data_type="" raw_data="">\n+ <sample_enzyme name="Trypsin" independent="false" fidelity="specific">\n+ <specificity sense="C" cut="KR" no_cut="P" min_spacing="0"/>\n+ </sample_enzyme>\n+ <search_summary base_name="Mascot%20formatted%20MGF%20of%20data%2025" search_engine="PeptideShaker" precursor_mass_type="monoisotopic" fragment_mass_type="monoisotopic" out_data_type="" out_data="">\n+ <search_database local_path="file:/panfs/roc/galaxy/GALAXYP/job_working_directory/000/131/131606/working/PeptideShakerCLI/.PeptideShaker_unzip_temp/peptideshaker_output_PeptideShaker_temp/data/input_database.fasta" database_name="SearchDB_1" size_in_db_entries="10" type="AA"/>\n+ <enzymatic_search_constraint enzyme="Trypsin" max_num_internal_cleavages="2" min_number_termini="2"/>\n+ <aminoacid_modification aminoacid="C" massdiff="57.021464" mass="160.0306484778" variable="N" description="Carbamidomethyl"/>\n+ <aminoacid_modification aminoacid="K" massdiff="144.102062" mass="272.1970250177" variable="N" description="iTRAQ4plex"/>\n+ <terminal_modification terminus="n" massdiff="144.102062" mass="145.1098870321" variable="N" description="iTRAQ4plex"/>\n+ <aminoacid_modification aminoacid="M" massdiff="15.994915" mass="147.0353996062" variable="Y" description="Oxidation"/>\n+ <terminal_modification protein_terminus="n" terminus="n" massdiff="42.010565" mass="43.0183900321" variable="Y" description="Acetyl"/>\n+ <aminoacid_modification aminoacid="E" massdiff="-18.010565" mass="111.0320280962" peptide_terminus="n" variable="Y" description="Glu->pyro-Glu"/>\n+ <aminoacid_modification aminoacid="Q" massdiff="-17.026549" mass="111.0320285114" peptide_terminus="n" variable="Y" description="Gln->pyro-Glu"/>\n+ <aminoacid_modification aminoacid="C" massdiff="-17.026549" mass="85.9826354778" peptide_terminus="n" variable="Y" description="Ammonia-loss"/>\n+ </search_summary>\n+ <spectrum_query spectrum="Mascot%20formatted%20MGF%20of%20data%2025.2256.2256.2" spectrumNativeID="index=2256" start_scan="2256" end_scan="2256" precursor_neutral_mass="1292.64157506624" assumed_charge="2" index="1" retention_time_sec="-1.0">\n+ <search_result>\n+ <search_hit hit_rank="1" peptide="SDAGSIAVASDR" peptide_prev_aa="R" peptide_next_aa="T" protein="Q7Z6Z7_REVERSED" num_tot_proteins="1" calc_neutral_pep_mass="1291.648992353254" massdiff="-0.992582712986" protein_descr="HUWE1_HUMAN E3 ubiquitin-protein ligase HUWE1 OS=Homo sapiens GN=HUWE1 PE=1 SV=3-REVERSED" num_tol_term="2" num_missed_cleavages="0">\n+ <modification_info mod_nterm_mass="145.1098870321"/>\n+ <search_score name="PeptideShaker PSM score" value="0.0"/>\n+ <search_score name="PeptideShaker PSM confidence" value="0.0"/>\n+ <search_score name="MS-GF:SpecEValue" value="0.0076572993"/>\n+ <search_score name="theoretical mass" value="1291.6489923533904"/>\n+ </search_hit>\n+ </search_result>\n+ </spectrum_query>\n+ <spectrum_query spectrum="Mascot%20formatted%20MGF%20of%20data%2025.1139.1139.2" spectrumNativeID="index=1139" start_scan="1139" end_scan="1139" precursor_neutral_mass="1277.73776706624" assumed_charge="2" index="2" retention_time_sec="-1.0">\n+ <search_result>\n+ <search_hit hit_rank="1" peptide="FATQITRAAR" peptide_prev_aa="R" peptide'..b'core" value="0.0"/>\n+ <search_score name="PeptideShaker PSM confidence" value="0.0"/>\n+ <search_score name="X!Tandem:expect" value="490.0"/>\n+ <search_score name="MS-GF:SpecEValue" value="4.6683443E-4"/>\n+ <search_score name="theoretical mass" value="2376.36068103791"/>\n+ </search_hit>\n+ </search_result>\n+ </spectrum_query>\n+ <spectrum_query spectrum="Mascot%20formatted%20MGF%20of%20data%2025.2073.2073.4" spectrumNativeID="index=2073" start_scan="2073" end_scan="2073" precursor_neutral_mass="2158.14203813248" assumed_charge="4" index="9808" retention_time_sec="-1.0">\n+ <search_result>\n+ <search_hit hit_rank="1" peptide="STIGGQIMFLTGMVDKR" peptide_prev_aa="K" peptide_next_aa="T" protein="Q8IYD1" num_tot_proteins="1" calc_neutral_pep_mass="2157.152964797448" massdiff="-0.989073335032" protein_descr="ERF3B_HUMAN Eukaryotic peptide chain release factor GTP-binding subunit ERF3B OS=Homo sapiens GN=GSPT2 PE=1 SV=2" num_tol_term="2" num_missed_cleavages="1">\n+ <modification_info mod_nterm_mass="145.1098870321">\n+ <mod_aminoacid_mass position="16" mass="272.1970250177"/>\n+ <mod_aminoacid_mass position="13" mass="147.0353996062"/>\n+ </modification_info>\n+ <search_score name="PeptideShaker PSM score" value="0.0"/>\n+ <search_score name="PeptideShaker PSM confidence" value="0.0"/>\n+ <search_score name="X!Tandem:expect" value="1900.0"/>\n+ <search_score name="MS-GF:SpecEValue" value="1.3698231E-4"/>\n+ <search_score name="theoretical mass" value="2157.1529647977204"/>\n+ </search_hit>\n+ </search_result>\n+ </spectrum_query>\n+ <spectrum_query spectrum="Mascot%20formatted%20MGF%20of%20data%2025.3470.3470.3" spectrumNativeID="index=3470" start_scan="3470" end_scan="3470" precursor_neutral_mass="1487.91701259936" assumed_charge="3" index="9809" retention_time_sec="-1.0">\n+ <search_result>\n+ <search_hit hit_rank="1" peptide="QIKPLLSASSR" peptide_prev_aa="K" peptide_next_aa="L" protein="Q7Z6Z7" num_tot_proteins="1" calc_neutral_pep_mass="1486.907495845736" massdiff="-1.009516753624" protein_descr="HUWE1_HUMAN E3 ubiquitin-protein ligase HUWE1 OS=Homo sapiens GN=HUWE1 PE=1 SV=3" num_tol_term="2" num_missed_cleavages="0">\n+ <modification_info mod_nterm_mass="145.1098870321">\n+ <mod_aminoacid_mass position="3" mass="272.1970250177"/>\n+ </modification_info>\n+ <search_score name="PeptideShaker PSM score" value="0.0"/>\n+ <search_score name="PeptideShaker PSM confidence" value="0.0"/>\n+ <search_score name="X!Tandem:expect" value="5.2"/>\n+ <search_score name="MS-GF:SpecEValue" value="1.1932847E-4"/>\n+ <search_score name="theoretical mass" value="1486.90749584594"/>\n+ </search_hit>\n+ </search_result>\n+ </spectrum_query>\n+ <spectrum_query spectrum="Mascot%20formatted%20MGF%20of%20data%2025.3887.3887.3" spectrumNativeID="index=3887" start_scan="3887" end_scan="3887" precursor_neutral_mass="1946.17159059936" assumed_charge="3" index="9810" retention_time_sec="-1.0">\n+ <search_result>\n+ <search_hit hit_rank="1" peptide="LLAELVRSYVGIATLIA" peptide_prev_aa="R" peptide_next_aa="N" protein="Q7Z6Z7" num_tot_proteins="1" calc_neutral_pep_mass="1945.173383384557" massdiff="-0.998207214803" protein_descr="HUWE1_HUMAN E3 ubiquitin-protein ligase HUWE1 OS=Homo sapiens GN=HUWE1 PE=1 SV=3" num_tol_term="1" num_missed_cleavages="1">\n+ <modification_info mod_nterm_mass="145.1098870321"/>\n+ <search_score name="PeptideShaker PSM score" value="0.0"/>\n+ <search_score name="PeptideShaker PSM confidence" value="0.0"/>\n+ <search_score name="X!Tandem:expect" value="44.0"/>\n+ <search_score name="theoretical mass" value="1945.1733833847607"/>\n+ </search_hit>\n+ </search_result>\n+ </spectrum_query>\n+ </msms_run_summary>\n+</msms_pipeline_analysis>\n'