<?xml version="1.0" encoding="UTF-8"?> <?xml-stylesheet type="text/xsl" href="/tools/bin/TPP/tpp/schema/pepXML_std.xsl"?> <msms_pipeline_analysis date="2006-07-20T17:23:26" xmlns="http://regis-web.systemsbiology.net/pepXML" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://regis-web.systemsbiology.net/pepXML /tools/bin/TPP/tpp/schema/pepXML_v18.xsd" summary_xml="000.xml"> <msms_run_summary base_name="/work/john/021112.EcoliSol37.1/000" msManufacturer="ThermoFinnigan" msModel="LCQ Classic" msIonization="ESI" msMassAnalyzer="Ion Trap" msDetector="UNKNOWN" 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="/work/john/021112.EcoliSol37.1/000" search_engine="SEQUEST" precursor_mass_type="average" fragment_mass_type="average" out_data_type="out" out_data=".tgz" search_id="1"> <search_database local_path="/work/ms/database/ecoli_K12.fasta" type="AA"/> <enzymatic_search_constraint enzyme="Trypsin" max_num_internal_cleavages="2" min_number_termini="2"/> <parameter name="peptide_mass_tol" value="1.500"/> <parameter name="fragment_ion_tol" value="0.000"/> <parameter name="ion_series" value=" 0 1 1 0.0 1.0 0.0 0.0 0.0 0.0 0.0 1.0 0.0"/> <parameter name="max_num_differential_AA_per_mod" value="4"/> <parameter name="nucleotide_reading_frame" value="0"/> <parameter name="num_output_lines" value="10"/> <parameter name="remove_precursor_peak" value="0"/> <parameter name="ion_cutoff_percentage" value="0.0"/> <parameter name="match_peak_count" value="0"/> <parameter name="match_peak_allowed_error" value="1"/> <parameter name="match_peak_tolerance" value="1.0"/> <parameter name="protein_mass_filter" value="0 0"/> <parameter name="sequence_header_filter" value=""/> </search_summary> <spectrum_query spectrum="000.100.100.1" start_scan="100" end_scan="100" precursor_neutral_mass="1074.5920" assumed_charge="1" index="1"> <search_result> <search_hit hit_rank="1" peptide="SIYFRNFK" peptide_prev_aa="R" peptide_next_aa="G" protein="gi|16130084|ref|NP_416651.1|" num_tot_proteins="1" num_matched_ions=" 4" tot_num_ions=" 14" calc_neutral_pep_mass="1074.1920" massdiff="+0.4" num_tol_term="2" num_missed_cleavages="1" is_rejected="0"> <search_score name="xcorr" value="0.400"/> <search_score name="deltacn" value="0.023"/> <search_score name="deltacnstar" value="0"/> <search_score name="spscore" value="78.8"/> <search_score name="sprank" value="1"/> </search_hit> </search_result> </spectrum_query> <spectrum_query spectrum="000.1000.1000.1" start_scan="1000" end_scan="1000" precursor_neutral_mass="663.1920" assumed_charge="1" index="2"> <search_result> <search_hit hit_rank="1" peptide="ALADFK" peptide_prev_aa="R" peptide_next_aa="S" protein="gi|16128765|ref|NP_415318.1|" num_tot_proteins="1" num_matched_ions=" 5" tot_num_ions=" 10" calc_neutral_pep_mass="663.7920" massdiff="-0.6" num_tol_term="2" num_missed_cleavages="0" is_rejected="0"> <search_score name="xcorr" value="0.965"/> <search_score name="deltacn" value="0.132"/> <search_score name="deltacnstar" value="0"/> <search_score name="spscore" value="81.1"/> <search_score name="sprank" value="1"/> </search_hit> </search_result> </spectrum_query> <spectrum_query spectrum="000.1002.1002.1" start_scan="1002" end_scan="1002" precursor_neutral_mass="1291.6920" assumed_charge="1" index="3"> <search_result> <search_hit hit_rank="1" peptide="EETEWRVQSK" peptide_prev_aa="R" peptide_next_aa="R" protein="gi|16128280|ref|NP_414829.1|" num_tot_proteins="1" num_matched_ions=" 10" tot_num_ions=" 18" calc_neutral_pep_mass="1291.3920" massdiff="+0.3" num_tol_term="2" num_missed_cleavages="1" is_rejected="0"> <search_score name="xcorr" value="0.904"/> <search_score name="deltacn" value="0.041"/> <search_score name="deltacnstar" value="0"/> <search_score name="spscore" value="140.0"/> <search_score name="sprank" value="1"/> </search_hit> </search_result> </spectrum_query> <spectrum_query spectrum="000.1003.1003.1" start_scan="1003" end_scan="1003" precursor_neutral_mass="769.3920" assumed_charge="1" index="4"> <search_result> <search_hit hit_rank="1" peptide="NIGLLNK" peptide_prev_aa="R" peptide_next_aa="I" protein="gi|16129238|ref|NP_415793.1|" num_tot_proteins="1" num_matched_ions=" 8" tot_num_ions=" 12" calc_neutral_pep_mass="770.8920" massdiff="-1.5" num_tol_term="2" num_missed_cleavages="0" is_rejected="0"> <search_score name="xcorr" value="0.887"/> <search_score name="deltacn" value="0.115"/> <search_score name="deltacnstar" value="0"/> <search_score name="spscore" value="153.1"/> <search_score name="sprank" value="2"/> </search_hit> </search_result> </spectrum_query> <spectrum_query spectrum="000.1004.1004.2" start_scan="1004" end_scan="1004" precursor_neutral_mass="1252.2920" assumed_charge="2" index="5"> <search_result> <search_hit hit_rank="1" peptide="QLTYTAHGPHK" peptide_prev_aa="R" peptide_next_aa="A" protein="gi|16131568|ref|NP_418155.1|" num_tot_proteins="1" num_matched_ions=" 7" tot_num_ions=" 20" calc_neutral_pep_mass="1252.3920" massdiff="-0.1" num_tol_term="2" num_missed_cleavages="0" is_rejected="0"> <search_score name="xcorr" value="1.066"/> <search_score name="deltacn" value="0.172"/> <search_score name="deltacnstar" value="0"/> <search_score name="spscore" value="125.2"/> <search_score name="sprank" value="10"/> </search_hit> </search_result> </spectrum_query> <spectrum_query spectrum="000.1004.1004.3" start_scan="1004" end_scan="1004" precursor_neutral_mass="1878.4920" assumed_charge="3" index="6"> <search_result> <search_hit hit_rank="1" peptide="AGNARVVNSNAMSFLAQK" peptide_prev_aa="K" peptide_next_aa="G" protein="gi|16131337|ref|NP_417922.1|" num_tot_proteins="1" num_matched_ions=" 16" tot_num_ions=" 68" calc_neutral_pep_mass="1878.0920" massdiff="+0.4" num_tol_term="2" num_missed_cleavages="1" is_rejected="0"> <search_score name="xcorr" value="1.370"/> <search_score name="deltacn" value="0.199"/> <search_score name="deltacnstar" value="0"/> <search_score name="spscore" value="245.0"/> <search_score name="sprank" value="2"/> </search_hit> </search_result> </spectrum_query> <spectrum_query spectrum="000.1006.1006.2" start_scan="1006" end_scan="1006" precursor_neutral_mass="888.1920" assumed_charge="2" index="7"> <search_result> <search_hit hit_rank="1" peptide="GNSRDIVK" peptide_prev_aa="R" peptide_next_aa="A" protein="gi|16131041|ref|NP_417618.1|" num_tot_proteins="1" num_matched_ions=" 9" tot_num_ions=" 14" calc_neutral_pep_mass="887.9920" massdiff="+0.2" num_tol_term="2" num_missed_cleavages="1" is_rejected="0"> <search_score name="xcorr" value="0.982"/> <search_score name="deltacn" value="0.006"/> <search_score name="deltacnstar" value="0"/> <search_score name="spscore" value="267.3"/> <search_score name="sprank" value="6"/> </search_hit> </search_result> </spectrum_query> <spectrum_query spectrum="000.1006.1006.3" start_scan="1006" end_scan="1006" precursor_neutral_mass="1332.2920" assumed_charge="3" index="8"> <search_result> <search_hit hit_rank="1" peptide="MAAGENPAAEMIK" peptide_prev_aa="K" peptide_next_aa="S" protein="gi|16132265|ref|NP_418563.1|" num_tot_proteins="2" num_matched_ions=" 16" tot_num_ions=" 48" calc_neutral_pep_mass="1332.5920" massdiff="-0.3" num_tol_term="2" num_missed_cleavages="0" is_rejected="0"> <search_score name="xcorr" value="1.058"/> <search_score name="deltacn" value="0.191"/> <search_score name="deltacnstar" value="0"/> <search_score name="spscore" value="177.5"/> <search_score name="sprank" value="8"/> </search_hit> </search_result> </spectrum_query> <spectrum_query spectrum="000.1007.1007.1" start_scan="1007" end_scan="1007" precursor_neutral_mass="867.2920" assumed_charge="1" index="9"> <search_result> <search_hit hit_rank="1" peptide="GALLHVEK" peptide_prev_aa="K" peptide_next_aa="M" protein="gi|16128020|ref|NP_414567.1|" num_tot_proteins="1" num_matched_ions=" 4" tot_num_ions=" 14" calc_neutral_pep_mass="865.9920" massdiff="+1.3" num_tol_term="2" num_missed_cleavages="0" is_rejected="0"> <search_score name="xcorr" value="0.467"/> <search_score name="deltacn" value="0.011"/> <search_score name="deltacnstar" value="0"/> <search_score name="spscore" value="39.4"/> <search_score name="sprank" value="30"/> </search_hit> </search_result> </spectrum_query> <spectrum_query spectrum="000.1008.1008.2" start_scan="1008" end_scan="1008" precursor_neutral_mass="691.0920" assumed_charge="2" index="10"> <search_result> <search_hit hit_rank="1" peptide="RLFTR" peptide_prev_aa="R" peptide_next_aa="A" protein="gi|16130457|ref|NP_417027.1|" num_tot_proteins="1" num_matched_ions=" 5" tot_num_ions=" 8" calc_neutral_pep_mass="691.7920" massdiff="-0.7" num_tol_term="2" num_missed_cleavages="0" is_rejected="0"> <search_score name="xcorr" value="0.903"/> <search_score name="deltacn" value="0.333"/> <search_score name="deltacnstar" value="0"/> <search_score name="spscore" value="172.8"/> <search_score name="sprank" value="1"/> </search_hit> </search_result> </spectrum_query> <spectrum_query spectrum="000.1008.1008.3" start_scan="1008" end_scan="1008" precursor_neutral_mass="1036.7920" assumed_charge="3" index="11"> <search_result> <search_hit hit_rank="1" peptide="VHEGLNTLR" peptide_prev_aa="R" peptide_next_aa="L" protein="gi|16128370|ref|NP_414919.1|" num_tot_proteins="1" num_matched_ions=" 6" tot_num_ions=" 32" calc_neutral_pep_mass="1038.1920" massdiff="-1.4" num_tol_term="2" num_missed_cleavages="0" is_rejected="0"> <search_score name="xcorr" value="0.767"/> <search_score name="deltacn" value="0.089"/> <search_score name="deltacnstar" value="0"/> <search_score name="spscore" value="66.1"/> <search_score name="sprank" value="18"/> </search_hit> </search_result> </spectrum_query> <spectrum_query spectrum="000.1010.1010.1" start_scan="1010" end_scan="1010" precursor_neutral_mass="869.4920" assumed_charge="1" index="12"> <search_result> <search_hit hit_rank="1" peptide="HFRALVK" peptide_prev_aa="K" peptide_next_aa="H" protein="gi|16130926|ref|NP_417502.1|" num_tot_proteins="1" num_matched_ions=" 7" tot_num_ions=" 12" calc_neutral_pep_mass="870.0920" massdiff="-0.6" num_tol_term="2" num_missed_cleavages="1" is_rejected="0"> <search_score name="xcorr" value="0.995"/> <search_score name="deltacn" value="0.065"/> <search_score name="deltacnstar" value="0"/> <search_score name="spscore" value="152.2"/> <search_score name="sprank" value="1"/> </search_hit> </search_result> </spectrum_query> <spectrum_query spectrum="000.1011.1011.1" start_scan="1011" end_scan="1011" precursor_neutral_mass="734.4920" assumed_charge="1" index="13"> <search_result> <search_hit hit_rank="1" peptide="FRDGLK" peptide_prev_aa="R" peptide_next_aa="E" protein="gi|16132019|ref|NP_418618.1|" num_tot_proteins="1" num_matched_ions=" 7" tot_num_ions=" 10" calc_neutral_pep_mass="734.8920" massdiff="-0.4" num_tol_term="2" num_missed_cleavages="1" is_rejected="0"> <search_score name="xcorr" value="1.467"/> <search_score name="deltacn" value="0.396"/> <search_score name="deltacnstar" value="0"/> <search_score name="spscore" value="140.5"/> <search_score name="sprank" value="1"/> </search_hit> </search_result> </spectrum_query> <spectrum_query spectrum="000.1012.1012.1" start_scan="1012" end_scan="1012" precursor_neutral_mass="899.3920" assumed_charge="1" index="14"> <search_result> <search_hit hit_rank="1" peptide="RQLAERK" peptide_prev_aa="R" peptide_next_aa="Q" protein="gi|16129398|ref|NP_415956.1|" num_tot_proteins="1" num_matched_ions=" 6" tot_num_ions=" 12" calc_neutral_pep_mass="899.9920" massdiff="-0.6" num_tol_term="2" num_missed_cleavages="0" is_rejected="0"> <search_score name="xcorr" value="0.797"/> <search_score name="deltacn" value="0.156"/> <search_score name="deltacnstar" value="0"/> <search_score name="spscore" value="37.7"/> <search_score name="sprank" value="8"/> </search_hit> </search_result> </spectrum_query> <spectrum_query spectrum="000.1014.1014.1" start_scan="1014" end_scan="1014" precursor_neutral_mass="869.5920" assumed_charge="1" index="15"> <search_result> <search_hit hit_rank="1" peptide="HFRALVK" peptide_prev_aa="K" peptide_next_aa="H" protein="gi|16130926|ref|NP_417502.1|" num_tot_proteins="1" num_matched_ions=" 6" tot_num_ions=" 12" calc_neutral_pep_mass="870.0920" massdiff="-0.5" num_tol_term="2" num_missed_cleavages="1" is_rejected="0"> <search_score name="xcorr" value="0.908"/> <search_score name="deltacn" value="0.005"/> <search_score name="deltacnstar" value="0"/> <search_score name="spscore" value="110.4"/> <search_score name="sprank" value="12"/> </search_hit> </search_result> </spectrum_query> <spectrum_query spectrum="000.1015.1015.1" start_scan="1015" end_scan="1015" precursor_neutral_mass="1077.9920" assumed_charge="1" index="16"> <search_result> <search_hit hit_rank="1" peptide="KVYQLAETK" peptide_prev_aa="K" peptide_next_aa="T" protein="gi|16128363|ref|NP_414912.1|" num_tot_proteins="1" num_matched_ions=" 8" tot_num_ions=" 16" calc_neutral_pep_mass="1079.2920" massdiff="-1.3" num_tol_term="2" num_missed_cleavages="0" is_rejected="0"> <search_score name="xcorr" value="0.897"/> <search_score name="deltacn" value="0.056"/> <search_score name="deltacnstar" value="0"/> <search_score name="spscore" value="125.1"/> <search_score name="sprank" value="1"/> </search_hit> </search_result> </spectrum_query> <spectrum_query spectrum="000.1016.1016.1" start_scan="1016" end_scan="1016" precursor_neutral_mass="871.6920" assumed_charge="1" index="17"> <search_result> <search_hit hit_rank="1" peptide="VGAITAANR" peptide_prev_aa="K" peptide_next_aa="I" protein="gi|16129608|ref|NP_416167.1|" num_tot_proteins="1" num_matched_ions=" 9" tot_num_ions=" 16" calc_neutral_pep_mass="871.9920" massdiff="-0.3" num_tol_term="2" num_missed_cleavages="0" is_rejected="0"> <search_score name="xcorr" value="1.028"/> <search_score name="deltacn" value="0.115"/> <search_score name="deltacnstar" value="0"/> <search_score name="spscore" value="238.6"/> <search_score name="sprank" value="1"/> </search_hit> </search_result> </spectrum_query> <spectrum_query spectrum="000.1018.1018.1" start_scan="1018" end_scan="1018" precursor_neutral_mass="919.7920" assumed_charge="1" index="18"> <search_result> <search_hit hit_rank="1" peptide="DFLIATLK" peptide_prev_aa="K" peptide_next_aa="P" protein="gi|16131978|ref|NP_418577.1|" num_tot_proteins="1" num_matched_ions=" 7" tot_num_ions=" 14" calc_neutral_pep_mass="920.0920" massdiff="-0.3" num_tol_term="1" num_missed_cleavages="0" is_rejected="0"> <search_score name="xcorr" value="1.010"/> <search_score name="deltacn" value="0.156"/> <search_score name="deltacnstar" value="0"/> <search_score name="spscore" value="79.2"/> <search_score name="sprank" value="7"/> </search_hit> </search_result> </spectrum_query> </msms_run_summary> </msms_pipeline_analysis>