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<?xml version="1.0" encoding="UTF-8"?>
<?xml-stylesheet type="text/xsl" href="pepXML_std.xsl"?>
<msms_pipeline_analysis date="2009-05-25T12:33:22" summary_xml="/tmp/2ddb/84/1243269184.2280_0/B09-05181_p.xml" xmlns="http://regis-web.systemsbiology.net/pepXML" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://regis-web.systemsbiology.net/pepXML http://sashimi.sourceforge.net/schema_revision/pepXML/pepXML_v114.xsd">
<msms_run_summary base_name="B09-05181_p" msManufacturer="ThermoFinnigan" msModel="msModel" msIonization="msIonisation" msMassAnalyzer="msMassAnalyzer" msDetector="EMT" 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="B09-05181_p" search_engine="X! Tandem (k-score)" precursor_mass_type="monoisotopic" fragment_mass_type="monoisotopic" search_id="1">
<search_database local_path="./current.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-->
<!-- Input parameters -->
<parameter name="list path, default parameters" value="/usr/local/bin/default_input.xml"/>
<parameter name="list path, taxonomy information" value="./taxonomy.xml"/>
<parameter name="output, histogram column width" value="30"/>
<parameter name="output, histograms" value="no"/>
<parameter name="output, log path" value=""/>
<parameter name="output, maximum valid expectation value" value="0.1"/>
<parameter name="output, message" value="testing 1 2 3"/>
<parameter name="output, one sequence copy" value="yes"/>
<parameter name="output, parameters" value="yes"/>
<parameter name="output, path" value="B09-05181_p.mzXML.output.xml"/>
<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, sequence path" value=""/>
<parameter name="output, sequences" value="no"/>
<parameter name="output, sort results by" value="spectrum"/>
<parameter name="output, spectra" value="yes"/>
<parameter name="output, xsl path" value="tandem-style.xsl"/>
<parameter name="protein, C-terminal residue modification mass" value="0.0"/>
<parameter name="protein, N-terminal residue modification mass" value="0.0"/>
<parameter name="protein, cleavage C-terminal mass change" value="+17.002735"/>
<parameter name="protein, cleavage N-terminal mass change" value="+1.007825"/>
<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="current"/>
<parameter name="refine" value="yes"/>
<parameter name="refine, cleavage semi" value="yes"/>
<parameter name="refine, maximum valid expectation value" value="0.1"/>
<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, sequence path" value=""/>
<parameter name="refine, spectrum synthesis" value="yes"/>
<parameter name="refine, tic percent" value="20"/>
<parameter name="refine, unanticipated cleavage" value="yes"/>
<parameter name="refine, use potential modifications for full refinement" value="yes"/>
<parameter name="residue, modification mass" value="57.021464@C"/>
<parameter name="residue, potential modification mass" value="15.99491@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="1000.0"/>
<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="150.0"/>
<parameter name="spectrum, minimum parent m+h" value="300.0"/>
<parameter name="spectrum, minimum peaks" value="6"/>
<parameter name="spectrum, parent monoisotopic mass error minus" value="25.0"/>
<parameter name="spectrum, parent monoisotopic mass error plus" value="25.0"/>
<parameter name="spectrum, parent monoisotopic mass error units" value="ppm"/>
<parameter name="spectrum, parent monoisotopic mass isotope error" value="no"/>
<parameter name="spectrum, path" value="B09-05181_p.mzXML"/>
<parameter name="spectrum, sequence batch size" value="1000"/>
<parameter name="spectrum, threads" value="1"/>
<parameter name="spectrum, total peaks" value="50"/>
<parameter name="spectrum, use conditioning" value="no"/>
<parameter name="spectrum, use noise suppression" value="yes"/>
<!-- Unused input parameters -->
<parameter name="scoring, pluggable scoring" value="yes"/>
<parameter name="spectrum, maximum parent m+h" value="4094.0"/>
<!-- Performance parameters -->
<parameter name="list path, sequence source #1" value="./current.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="69092616"/>
<parameter name="modelling, total proteins used" value="119798"/>
<parameter name="modelling, total spectra used" value="11023"/>
<parameter name="process, start time" value="2009:05:25:12:33:22"/>
<parameter name="process, version" value="x! tandem TORNADO (2008.02.01.3)"/>
<parameter name="quality values" value="723 528 401 358 269 165 117 63 44 32 21 12 4 1 1 1 0 0 0 0"/>
<parameter name="refining, # input models" value="1640"/>
<parameter name="refining, # input spectra" value="9694"/>
<parameter name="refining, # partial cleavage" value="190"/>
<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="30"/>
<parameter name="timing, initial modelling total (sec)" value="226.33"/>
<parameter name="timing, initial modelling/spectrum (sec)" value="0.021"/>
<parameter name="timing, load sequence models (sec)" value="0.21"/>
<parameter name="timing, refinement/spectrum (sec)" value="0.029"/>
</search_summary>
<spectrum_query spectrum="B09-05181_p.00002.00002.3" start_scan="2" end_scan="2" precursor_neutral_mass="1612.7918" assumed_charge="3" index="1" retention_time_sec="1.3653">
<search_result>
<search_hit hit_rank="1" peptide="ELNKEMAAEKAKAAAG" peptide_prev_aa="R" peptide_next_aa="E" protein="ddb000449223" num_tot_proteins="3" num_matched_ions="17" tot_num_ions="60" calc_neutral_pep_mass="1612.8247" massdiff="-0.033" num_tol_term="1" num_missed_cleavages="3" is_rejected="0">
<alternative_protein protein="ddb000394137" num_tol_term="1"/>
<alternative_protein protein="ddb000015734" num_tol_term="1"/>
<modification_info>
<mod_aminoacid_mass position="1" mass="111.0320" />
</modification_info>
<search_score name="hyperscore" value="329"/>
<search_score name="nextscore" value="323"/>
<search_score name="bscore" value="1"/>
<search_score name="yscore" value="1"/>
<search_score name="expect" value="8"/>
</search_hit>
</search_result>
</spectrum_query>
<spectrum_query spectrum="B09-05181_p.00003.00003.2" start_scan="3" end_scan="3" precursor_neutral_mass="1273.7547" assumed_charge="2" index="2" retention_time_sec="1.719">
<search_result>
<search_hit hit_rank="1" peptide="QLPGVNIKPVVK" peptide_prev_aa="R" peptide_next_aa="V" protein="ddb000014286" num_tot_proteins="1" num_matched_ions="11" tot_num_ions="22" calc_neutral_pep_mass="1273.7757" massdiff="-0.021" num_tol_term="2" num_missed_cleavages="0" is_rejected="0">
<modification_info>
<mod_aminoacid_mass position="1" mass="111.0321" />
</modification_info>
<search_score name="hyperscore" value="173"/>
<search_score name="nextscore" value="167"/>
<search_score name="bscore" value="0"/>
<search_score name="yscore" value="0"/>
<search_score name="expect" value="7.7"/>
</search_hit>
</search_result>
</spectrum_query>
<spectrum_query spectrum="B09-05181_p.00004.00004.2" start_scan="4" end_scan="4" precursor_neutral_mass="1354.7538" assumed_charge="2" index="3" retention_time_sec="2.0436">
<search_result>
<search_hit hit_rank="1" peptide="IFQAALYAAPYK" peptide_prev_aa="K" peptide_next_aa="S" protein="ddb000517740" num_tot_proteins="1" num_matched_ions="16" tot_num_ions="22" calc_neutral_pep_mass="1354.7287" massdiff="0.025" num_tol_term="2" num_missed_cleavages="0" is_rejected="0">
<search_score name="hyperscore" value="274"/>
<search_score name="nextscore" value="250"/>
<search_score name="bscore" value="1"/>
<search_score name="yscore" value="0"/>
<search_score name="expect" value="4.9"/>
</search_hit>
</search_result>
</spectrum_query>
<spectrum_query spectrum="B09-05181_p.00006.00006.3" start_scan="6" end_scan="6" precursor_neutral_mass="2285.1617" assumed_charge="3" index="4" retention_time_sec="2.7843">
<search_result>
<search_hit hit_rank="1" peptide="EISPDTTLLDLQNNDISELR" peptide_prev_aa="K" peptide_next_aa="K" protein="ddb000026697" num_tot_proteins="4" num_matched_ions="40" tot_num_ions="76" calc_neutral_pep_mass="2285.1387" massdiff="0.023" num_tol_term="2" num_missed_cleavages="0" is_rejected="0">
<alternative_protein protein="ddb000626345" num_tol_term="2"/>
<alternative_protein protein="ddb000626346" num_tol_term="2"/>
<alternative_protein protein="ddb005168372" num_tol_term="2"/>
<search_score name="hyperscore" value="807"/>
<search_score name="nextscore" value="446"/>
<search_score name="bscore" value="2"/>
<search_score name="yscore" value="2"/>
<search_score name="expect" value="0.00091"/>
</search_hit>
</search_result>
</spectrum_query>
<spectrum_query spectrum="B09-05181_p.00007.00007.2" start_scan="7" end_scan="7" precursor_neutral_mass="2285.1754" assumed_charge="2" index="5" retention_time_sec="3.085">
<search_result>
<search_hit hit_rank="1" peptide="EISPDTTLLDLQNNDISELR" peptide_prev_aa="K" peptide_next_aa="K" protein="ddb000026697" num_tot_proteins="4" num_matched_ions="29" tot_num_ions="38" calc_neutral_pep_mass="2285.1387" massdiff="0.037" num_tol_term="2" num_missed_cleavages="0" is_rejected="0">
<alternative_protein protein="ddb000626345" num_tol_term="2"/>
<alternative_protein protein="ddb000626346" num_tol_term="2"/>
<alternative_protein protein="ddb005168372" num_tol_term="2"/>
<search_score name="hyperscore" value="705"/>
<search_score name="nextscore" value="309"/>
<search_score name="bscore" value="1"/>
<search_score name="yscore" value="2"/>
<search_score name="expect" value="7.9e-05"/>
</search_hit>
</search_result>
</spectrum_query>
<spectrum_query spectrum="B09-05181_p.00008.00008.3" start_scan="8" end_scan="8" precursor_neutral_mass="2307.1422" assumed_charge="3" index="6" retention_time_sec="3.4018">
<search_result>
<search_hit hit_rank="1" peptide="RSHTILNSSQSFAKGCVQCK" peptide_prev_aa="K" peptide_next_aa="H" protein="rev000025591" num_tot_proteins="3" num_matched_ions="20" tot_num_ions="76" calc_neutral_pep_mass="2307.1207" massdiff="0.022" num_tol_term="2" num_missed_cleavages="1" is_rejected="0">
<alternative_protein protein="rev000001143" num_tol_term="2"/>
<alternative_protein protein="rev000450478" num_tol_term="2"/>
<modification_info>
<mod_aminoacid_mass position="16" mass="160.0306" />
<mod_aminoacid_mass position="19" mass="160.0306" />
</modification_info>
<search_score name="hyperscore" value="350"/>
<search_score name="nextscore" value="349"/>
<search_score name="bscore" value="1"/>
<search_score name="yscore" value="1"/>
<search_score name="expect" value="14"/>
</search_hit>
</search_result>
</spectrum_query>
<spectrum_query spectrum="B09-05181_p.00010.00010.3" start_scan="10" end_scan="10" precursor_neutral_mass="2269.2134" assumed_charge="3" index="7" retention_time_sec="4.4573">
<search_result>
<search_hit hit_rank="1" peptide="VSLPNYPAIPSDATLEVQSLR" peptide_prev_aa="K" peptide_next_aa="S" protein="ddb000622429" num_tot_proteins="3" num_matched_ions="21" tot_num_ions="80" calc_neutral_pep_mass="2269.1957" massdiff="0.018" num_tol_term="2" num_missed_cleavages="0" is_rejected="0">
<alternative_protein protein="ddb000622428" num_tol_term="2"/>
<alternative_protein protein="ddb000450900" num_tol_term="2"/>
<search_score name="hyperscore" value="463"/>
<search_score name="nextscore" value="431"/>
<search_score name="bscore" value="1"/>
<search_score name="yscore" value="1"/>
<search_score name="expect" value="0.65"/>
</search_hit>
</search_result>
</spectrum_query>
<spectrum_query spectrum="B09-05181_p.00011.00011.2" start_scan="11" end_scan="11" precursor_neutral_mass="1612.7726" assumed_charge="2" index="8" retention_time_sec="4.8288">
<search_result>
<search_hit hit_rank="1" peptide="NALWHTGDTESQVR" peptide_prev_aa="R" peptide_next_aa="L" protein="ddb000409092" num_tot_proteins="3" num_matched_ions="23" tot_num_ions="26" calc_neutral_pep_mass="1612.7597" massdiff="0.013" num_tol_term="2" num_missed_cleavages="0" is_rejected="0">
<alternative_protein protein="ddb000394916" num_tol_term="2"/>
<alternative_protein protein="ddb000012684" num_tol_term="2"/>
<search_score name="hyperscore" value="478"/>
<search_score name="nextscore" value="278"/>
<search_score name="bscore" value="1"/>
<search_score name="yscore" value="1"/>
<search_score name="expect" value="0.0046"/>
</search_hit>
</search_result>
</spectrum_query>
<spectrum_query spectrum="B09-05181_p.00012.00012.2" start_scan="12" end_scan="12" precursor_neutral_mass="1023.5534" assumed_charge="2" index="9" retention_time_sec="5.1785">
<search_result>
<search_hit hit_rank="1" peptide="SSLKNYANK" peptide_prev_aa="R" peptide_next_aa="I" protein="rev000409159" num_tot_proteins="2" num_matched_ions="9" tot_num_ions="16" calc_neutral_pep_mass="1023.5347" massdiff="0.019" num_tol_term="2" num_missed_cleavages="1" is_rejected="0">
<alternative_protein protein="rev000459115" num_tol_term="2"/>
<search_score name="hyperscore" value="266"/>
<search_score name="nextscore" value="228"/>
<search_score name="bscore" value="1"/>
<search_score name="yscore" value="1"/>
<search_score name="expect" value="1.1"/>
</search_hit>
</search_result>
</spectrum_query>
</msms_run_summary>
</msms_pipeline_analysis>
|
