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| author | galaxyp |
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| date | Wed, 15 Mar 2017 09:43:14 -0400 |
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<?xml version="1.0" encoding="ISO-8859-1"?> <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"> <analysis_summary analysis="PeptideShaker" version="1.15.1" time="2017-03-14T19:03:20Z"/> <analysis_summary analysis="ProteoWizard software" version="3.0.9934" time="2017-03-14T19:03:20Z"/> <msms_run_summary base_name="Mascot%20formatted%20MGF%20of%20data%2025" raw_data_type="" raw_data=""> <sample_enzyme name="Trypsin" independent="false" fidelity="specific"> <specificity sense="C" cut="KR" no_cut="P" min_spacing="0"/> </sample_enzyme> <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=""> <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"/> <enzymatic_search_constraint enzyme="Trypsin" max_num_internal_cleavages="2" min_number_termini="2"/> <aminoacid_modification aminoacid="C" massdiff="57.021464" mass="160.0306484778" variable="N" description="Carbamidomethyl"/> <aminoacid_modification aminoacid="K" massdiff="144.102062" mass="272.1970250177" variable="N" description="iTRAQ4plex"/> <terminal_modification terminus="n" massdiff="144.102062" mass="145.1098870321" variable="N" description="iTRAQ4plex"/> <aminoacid_modification aminoacid="M" massdiff="15.994915" mass="147.0353996062" variable="Y" description="Oxidation"/> <terminal_modification protein_terminus="n" terminus="n" massdiff="42.010565" mass="43.0183900321" variable="Y" description="Acetyl"/> <aminoacid_modification aminoacid="E" massdiff="-18.010565" mass="111.0320280962" peptide_terminus="n" variable="Y" description="Glu->pyro-Glu"/> <aminoacid_modification aminoacid="Q" massdiff="-17.026549" mass="111.0320285114" peptide_terminus="n" variable="Y" description="Gln->pyro-Glu"/> <aminoacid_modification aminoacid="C" massdiff="-17.026549" mass="85.9826354778" peptide_terminus="n" variable="Y" description="Ammonia-loss"/> </search_summary> <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"> <search_result> <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"> <modification_info mod_nterm_mass="145.1098870321"/> <search_score name="PeptideShaker PSM score" value="0.0"/> <search_score name="PeptideShaker PSM confidence" value="0.0"/> <search_score name="MS-GF:SpecEValue" value="0.0076572993"/> <search_score name="theoretical mass" value="1291.6489923533904"/> </search_hit> </search_result> </spectrum_query> <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"> <search_result> <search_hit hit_rank="1" peptide="FATQITRAAR" peptide_prev_aa="R" peptide_next_aa="R" protein="Q5JU85_REVERSED" num_tot_proteins="1" calc_neutral_pep_mass="1277.732602837914" massdiff="-0.005164228326" protein_descr="IQEC2_HUMAN IQ motif and SEC7 domain-containing protein 2 OS=Homo sapiens GN=IQSEC2 PE=1 SV=1-REVERSED" num_tol_term="2" num_missed_cleavages="1"> <modification_info mod_nterm_mass="145.1098870321"/> <search_score name="PeptideShaker PSM score" value="0.0"/> <search_score name="PeptideShaker PSM confidence" value="0.0"/> <search_score name="MS-GF:SpecEValue" value="0.0016835652"/> <search_score name="theoretical mass" value="1277.7326028380503"/> </search_hit> </search_result> </spectrum_query> <spectrum_query spectrum="Mascot%20formatted%20MGF%20of%20data%2025.223.223.2" spectrumNativeID="index=223" start_scan="223" end_scan="223" precursor_neutral_mass="1247.58761906624" assumed_charge="2" index="3" retention_time_sec="-1.0"> <search_result> <search_hit hit_rank="1" peptide="CELCGPGRR" peptide_prev_aa="R" peptide_next_aa="T" protein="Q5JU85_REVERSED" num_tot_proteins="1" calc_neutral_pep_mass="1247.598494517214" massdiff="0.010875450974" protein_descr="IQEC2_HUMAN IQ motif and SEC7 domain-containing protein 2 OS=Homo sapiens GN=IQSEC2 PE=1 SV=1-REVERSED" num_tol_term="2" num_missed_cleavages="1"> <modification_info mod_nterm_mass="145.1098870321"> <mod_aminoacid_mass position="1" mass="160.0306484778"/> <mod_aminoacid_mass position="4" mass="160.0306484778"/> </modification_info> <search_score name="PeptideShaker PSM score" value="0.0"/> <search_score name="PeptideShaker PSM confidence" value="0.0"/> <search_score name="MS-GF:SpecEValue" value="3.1239502E-4"/> <search_score name="theoretical mass" value="1247.59849451735"/> </search_hit> </search_result> </spectrum_query> <spectrum_query spectrum="Mascot%20formatted%20MGF%20of%20data%2025.51.51.2" spectrumNativeID="index=51" start_scan="51" end_scan="51" precursor_neutral_mass="1008.52542506624" assumed_charge="2" index="4" retention_time_sec="-1.0"> <search_result> <search_hit hit_rank="1" peptide="SEAMALAR" peptide_prev_aa="T" peptide_next_aa="G" protein="Q7Z6Z7_REVERSED" num_tot_proteins="1" calc_neutral_pep_mass="1007.519164484014" massdiff="-1.006260582226" protein_descr="HUWE1_HUMAN E3 ubiquitin-protein ligase HUWE1 OS=Homo sapiens GN=HUWE1 PE=1 SV=3-REVERSED" num_tol_term="1" num_missed_cleavages="0"> <modification_info mod_nterm_mass="145.1098870321"> <mod_aminoacid_mass position="4" mass="147.0353996062"/> </modification_info> <search_score name="PeptideShaker PSM score" value="0.0"/> <search_score name="PeptideShaker PSM confidence" value="0.0"/> <search_score name="X!Tandem:expect" value="2.5"/> <search_score name="theoretical mass" value="1007.5191644841501"/> </search_hit> </search_result> </spectrum_query> <spectrum_query spectrum="Mascot%20formatted%20MGF%20of%20data%2025.1464.1464.3" spectrumNativeID="index=1464" start_scan="1464" end_scan="1464" precursor_neutral_mass="1779.94936059936" assumed_charge="3" index="5" retention_time_sec="-1.0"> <search_result> <search_hit hit_rank="1" peptide="ELEQGNSNKSNK" peptide_prev_aa="K" peptide_next_aa="N" protein="Q7Z6Z7_REVERSED" num_tot_proteins="1" calc_neutral_pep_mass="1778.948808484776" massdiff="-1.000552114584" 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="1"> <modification_info mod_nterm_mass="145.1098870321"> <mod_aminoacid_mass position="9" mass="272.1970250177"/> <mod_aminoacid_mass position="12" mass="272.1970250177"/> </modification_info> <search_score name="PeptideShaker PSM score" value="0.0"/> <search_score name="PeptideShaker PSM confidence" value="0.0"/> <search_score name="X!Tandem:expect" value="0.72"/> <search_score name="MS-GF:SpecEValue" value="4.8094043E-5"/> <search_score name="theoretical mass" value="1778.94880848498"/> </search_hit> </search_result> </spectrum_query> <spectrum_query spectrum="Mascot%20formatted%20MGF%20of%20data%2025.1721.1721.3" spectrumNativeID="index=1721" start_scan="1721" end_scan="1721" precursor_neutral_mass="1394.77711959936" assumed_charge="3" index="6" retention_time_sec="-1.0"> <search_result> <search_hit hit_rank="1" peptide="NKMEEPSK" peptide_prev_aa="R" peptide_next_aa="R" protein="Q7Z6Z7_REVERSED" num_tot_proteins="1" calc_neutral_pep_mass="1393.760068757086" massdiff="-1.017050842274" 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="1"> <modification_info mod_nterm_mass="145.1098870321"> <mod_aminoacid_mass position="2" mass="272.1970250177"/> <mod_aminoacid_mass position="8" mass="272.1970250177"/> </modification_info> <search_score name="PeptideShaker PSM score" value="0.0"/> <search_score name="PeptideShaker PSM confidence" value="0.0"/> <search_score name="MS-GF:SpecEValue" value="7.338132E-4"/> <search_score name="theoretical mass" value="1393.7600687572904"/> </search_hit> </search_result> </spectrum_query> <spectrum_query spectrum="Mascot%20formatted%20MGF%20of%20data%2025.1574.1574.2" spectrumNativeID="index=1574" start_scan="1574" end_scan="1574" precursor_neutral_mass="1105.63620306624" assumed_charge="2" index="7" retention_time_sec="-1.0"> <search_result> <search_hit hit_rank="1" peptide="ETLLSSRR" peptide_prev_aa="K" peptide_next_aa="I" protein="Q7Z6Z7_REVERSED" num_tot_proteins="1" calc_neutral_pep_mass="1104.637305470744" massdiff="-0.998897595496" 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="1"> <modification_info mod_nterm_mass="145.1098870321"/> <search_score name="PeptideShaker PSM score" value="0.0"/> <search_score name="PeptideShaker PSM confidence" value="0.0"/> <search_score name="X!Tandem:expect" value="0.3"/> <search_score name="MS-GF:SpecEValue" value="4.6369154E-5"/> <search_score name="theoretical mass" value="1104.6373054708802"/> </search_hit> </search_result> </spectrum_query> <spectrum_query spectrum="Mascot%20formatted%20MGF%20of%20data%2025.107.107.4" spectrumNativeID="index=107" start_scan="107" 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<search_score name="theoretical mass" value="2577.3408821007997"/> </search_hit> </search_result> </spectrum_query> <spectrum_query spectrum="Mascot%20formatted%20MGF%20of%20data%2025.986.986.3" spectrumNativeID="index=986" start_scan="986" end_scan="986" precursor_neutral_mass="1792.91707359936" assumed_charge="3" index="10" retention_time_sec="-1.0"> <search_result> <search_hit hit_rank="1" peptide="YHQYILNSNRANR" peptide_prev_aa="R" peptide_next_aa="R" protein="Q96JG8" num_tot_proteins="1" calc_neutral_pep_mass="1791.925048046986" massdiff="-0.992025552374" protein_descr="MAGD4_HUMAN Melanoma-associated antigen D4 OS=Homo sapiens GN=MAGED4 PE=1 SV=3" num_tol_term="2" num_missed_cleavages="1"> <modification_info mod_nterm_mass="145.1098870321"/> <search_score name="PeptideShaker PSM score" value="0.0"/> <search_score name="PeptideShaker PSM confidence" value="0.0"/> <search_score name="MS-GF:SpecEValue" value="0.0013160965"/> <search_score name="theoretical mass" 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name="MS-GF:SpecEValue" value="9.847712E-4"/> <search_score name="theoretical mass" value="2074.12928672665"/> </search_hit> </search_result> </spectrum_query> <spectrum_query spectrum="Mascot%20formatted%20MGF%20of%20data%2025.1878.1878.2" spectrumNativeID="index=1878" start_scan="1878" end_scan="1878" precursor_neutral_mass="1721.91757506624" assumed_charge="2" index="12" retention_time_sec="-1.0"> <search_result> <search_hit hit_rank="1" peptide="GLSRQMIGEFLGNR" peptide_prev_aa="K" peptide_next_aa="Q" protein="Q5JU85" num_tot_proteins="1" calc_neutral_pep_mass="1720.916457509305" massdiff="-1.001117556935" protein_descr="IQEC2_HUMAN IQ motif and SEC7 domain-containing protein 2 OS=Homo sapiens GN=IQSEC2 PE=1 SV=1" num_tol_term="2" num_missed_cleavages="1"> <modification_info mod_nterm_mass="145.1098870321"/> <search_score name="PeptideShaker PSM score" value="0.0"/> <search_score name="PeptideShaker PSM confidence" value="0.0"/> <search_score name="MS-GF:SpecEValue" value="0.005105595"/> <search_score name="theoretical mass" value="1720.9164575094405"/> </search_hit> </search_result> </spectrum_query> <spectrum_query spectrum="Mascot%20formatted%20MGF%20of%20data%2025.901.901.2" spectrumNativeID="index=901" start_scan="901" end_scan="901" precursor_neutral_mass="1014.58121106624" assumed_charge="2" index="13" retention_time_sec="-1.0"> <search_result> <search_hit hit_rank="1" peptide="VENVLAVQ" peptide_prev_aa="K" peptide_next_aa="A" protein="Q7Z6Z7_REVERSED" num_tot_proteins="1" calc_neutral_pep_mass="1014.583144639564" massdiff="0.001933573324" protein_descr="HUWE1_HUMAN E3 ubiquitin-protein ligase HUWE1 OS=Homo sapiens GN=HUWE1 PE=1 SV=3-REVERSED" num_tol_term="1" num_missed_cleavages="0"> <modification_info mod_nterm_mass="145.1098870321"/> <search_score name="PeptideShaker PSM score" value="0.0"/> <search_score name="PeptideShaker PSM confidence" value="0.0"/> <search_score name="X!Tandem:expect" value="0.22"/> <search_score name="theoretical 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</search_hit> </search_result> </spectrum_query> <spectrum_query spectrum="Mascot%20formatted%20MGF%20of%20data%2025.1048.1048.2" spectrumNativeID="index=1048" start_scan="1048" end_scan="1048" precursor_neutral_mass="1253.72287306624" assumed_charge="2" index="15" retention_time_sec="-1.0"> <search_result> <search_hit hit_rank="1" peptide="RLDGLFPHR" peptide_prev_aa="K" peptide_next_aa="V" protein="Q96JG8_REVERSED" num_tot_proteins="1" calc_neutral_pep_mass="1253.711473470514" massdiff="-0.011399595726" protein_descr="MAGD4_HUMAN Melanoma-associated antigen D4 OS=Homo sapiens GN=MAGED4 PE=1 SV=3-REVERSED" num_tol_term="2" num_missed_cleavages="1"> <modification_info mod_nterm_mass="145.1098870321"/> <search_score name="PeptideShaker PSM score" value="0.0"/> <search_score name="PeptideShaker PSM confidence" value="0.0"/> <search_score name="MS-GF:SpecEValue" value="0.010934511"/> <search_score name="theoretical mass" value="1253.7114734706502"/> </search_hit> </search_result> </spectrum_query> <spectrum_query spectrum="Mascot%20formatted%20MGF%20of%20data%2025.1002.1002.3" spectrumNativeID="index=1002" start_scan="1002" end_scan="1002" precursor_neutral_mass="1132.65971859936" assumed_charge="3" index="16" retention_time_sec="-1.0"> <search_result> <search_hit hit_rank="1" peptide="QTLNLIMR" peptide_prev_aa="S" peptide_next_aa="T" protein="Q7Z6Z7_REVERSED" num_tot_proteins="1" calc_neutral_pep_mass="1131.655598387106" massdiff="-1.004120212254" protein_descr="HUWE1_HUMAN E3 ubiquitin-protein ligase HUWE1 OS=Homo sapiens GN=HUWE1 PE=1 SV=3-REVERSED" num_tol_term="1" num_missed_cleavages="0"> <modification_info mod_nterm_mass="145.1098870321"/> <search_score name="PeptideShaker PSM score" value="0.0"/> <search_score name="PeptideShaker PSM confidence" value="0.0"/> <search_score name="X!Tandem:expect" value="1.9"/> <search_score name="theoretical mass" value="1131.65559838731"/> </search_hit> </search_result> </spectrum_query> <spectrum_query 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