question about IProphet output
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Andreas Quandt
Nov 10, 2009, 9:38:10 AM11/10/09
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dear list,
i was wondering if someone could explain me why there are 2 interprophet result entries for each of the 'hit_rank=1' tags in the pep.xml generated by iprophet?
cheers,
andreas
i was wondering if someone could explain me why there are 2 interprophet result entries for each of the 'hit_rank=1' tags in the pep.xml generated by iprophet?
cheers,
andreas
Dave Trudgian
Nov 10, 2009, 9:49:09 AM11/10/09
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Andreas,
I've just looked at some iprophet .pep.xml files and only see a single
interprophet result entry per search_hit tag.
These files are Mascot, Tandem, OMSSA searches, run individually through
PeptideProphet, combined with iProphet. What workflow gives two tags for
you?
DT
--
Dr. David Trudgian
Bioinformatician in Proteomics
University of Oxford
Mon-Thu: CCMP, Roosevelt Drive
Tel: (+44) (01865 2)87784
Friday : Dunn School of Pathology, S. Parks Rd.
Tel: (+44) (01865 2)75557
I've just looked at some iprophet .pep.xml files and only see a single
interprophet result entry per search_hit tag.
These files are Mascot, Tandem, OMSSA searches, run individually through
PeptideProphet, combined with iProphet. What workflow gives two tags for
you?
DT
Dr. David Trudgian
Bioinformatician in Proteomics
University of Oxford
Mon-Thu: CCMP, Roosevelt Drive
Tel: (+44) (01865 2)87784
Friday : Dunn School of Pathology, S. Parks Rd.
Tel: (+44) (01865 2)75557
Andreas Quandt
Nov 10, 2009, 10:30:47 AM11/10/09
to spctools...@googlegroups.com
hey dave,
i did something similar but combined multiple iprophet pep.xml's (in that case from 3 search engines) to a single iprophet result file.
here an example for a single spectrum
<!-- iprophet.pep.xml generated with mascot -->
<spectrum_query spectrum="B09-10149.c.01821.01821.2" start_scan="01821" end_scan="01821"
precursor_neutral_mass="958.5047" assumed_charge="2" index="354">
<search_result>
<search_hit hit_rank="1" peptide="NIVLLADDS" peptide_prev_aa="K" peptide_next_aa="S"
protein="gi|13622159|gb|AAK33905.1|" num_tot_proteins="1" num_matched_ions="3" tot_num_ions="16"
calc_neutral_pep_mass="958.4971" massdiff="+0.0076" num_tol_term="1" num_missed_cleavages="0"
is_rejected="0" protein_descr="putative lysin - phage associated [Streptococcus phage 370.3]">
<search_score name="ionscore" value="19.72"/>
<search_score name="identityscore" value="28.51"/>
<search_score name="star" value="0"/>
<search_score name="homologyscore" value="31.32"/>
<search_score name="expect" value="0.38"/>
<analysis_result analysis="peptideprophet">
<peptideprophet_result probability="0.3622" all_ntt_prob="(0.0000,0.3622,0.9790)">
<search_score_summary>
<parameter name="fval" value="-1.3378"/>
<parameter name="ntt" value="1"/>
<parameter name="nmc" value="0"/>
<parameter name="massd" value="0.008"/>
<parameter name="isomassd" value="0"/>
<parameter name="pI" value="3.56"/>
<parameter name="pI_zscore" value="-1.19"/>
</search_score_summary>
</peptideprophet_result>
</analysis_result>
<analysis_result analysis="interprophet">
<interprophet_result probability="0.0118374" all_ntt_prob="(0,0.0118374,0.495813)">
<search_score_summary>
<parameter name="nss" value="0"/>
<parameter name="nrs" value="0"/>
<parameter name="nse" value="0"/>
<parameter name="nsi" value="0"/>
<parameter name="nsm" value="0"/>
</search_score_summary>
</interprophet_result>
</analysis_result>
</search_hit>
</search_result>
</spectrum_query>
<!--iprophet.pep.xml generated with xtandem-->
<spectrum_query spectrum="B09-10149.c.01821.01821.2" start_scan="1821" end_scan="1821" precursor_neutral_mass="958.5047"
assumed_charge="2" index="55" retention_time_sec="854.394">
<search_result>
<search_hit hit_rank="1" peptide="NLVNGEWK" peptide_prev_aa="K" peptide_next_aa="L"
protein="gi|13622481|gb|AAK34198.1|"
protein_descr="putative NADP-dependent glyceraldehyde-3-phosphate dehydrogenase [Streptococcus pyogenes M1 GAS]"
num_tot_proteins="1" num_matched_ions="14" tot_num_ions="14" calc_neutral_pep_mass="958.4877"
massdiff="0.017" num_tol_term="2" num_missed_cleavages="0" is_rejected="0">
<search_score name="hyperscore" value="343"/>
<search_score name="nextscore" value="296"/>
<search_score name="bscore" value="1"/>
<search_score name="yscore" value="1"/>
<search_score name="expect" value="1.7"/>
<analysis_result analysis="peptideprophet">
<peptideprophet_result probability="0.9881" all_ntt_prob="(0.0000,0.6710,0.9881)">
<search_score_summary>
<parameter name="fval" value="1.4464"/>
<parameter name="ntt" value="2"/>
<parameter name="nmc" value="0"/>
<parameter name="massd" value="0.017"/>
<parameter name="isomassd" value="0"/>
<parameter name="pI" value="6.00"/>
<parameter name="pI_zscore" value="0.25"/>
</search_score_summary>
</peptideprophet_result>
</analysis_result>
<analysis_result analysis="interprophet">
<interprophet_result probability="0.998354" all_ntt_prob="(0,0.937097,0.998354)">
<search_score_summary>
<parameter name="nss" value="0"/>
<parameter name="nrs" value="5"/>
<parameter name="nse" value="0"/>
<parameter name="nsi" value="0"/>
<parameter name="nsm" value="0"/>
</search_score_summary>
</interprophet_result>
</analysis_result>
</search_hit>
</search_result>
</spectrum_query>
<!--iprophet.pep.xml generated with omssa-->
<spectrum_query spectrum="B09-10149.c.01821.01821.2" start_scan="1821" end_scan="1821"
precursor_neutral_mass="958.505004882812" assumed_charge="2" index="1222">
<search_result>
<search_hit hit_rank="1" peptide="NLVNGEWK" peptide_prev_aa="K" peptide_next_aa="L"
protein="gi|13622481|gb|AAK34198.1|" num_tot_proteins="1" num_matched_ions="8" tot_num_ions="14"
calc_neutral_pep_mass="958.487" massdiff="0.017999999999996" is_rejected="0"
protein_descr="putative NADP-dependent glyceraldehyde-3-phosphate dehydrogenase [Streptococcus pyogenes M1 GAS]"
num_tol_term="2" num_missed_cleavages="0">
<search_score name="pvalue" value="0.006009478037955"/>
<search_score name="expect" value="13.803771053183747"/>
<analysis_result analysis="peptideprophet">
<peptideprophet_result probability="0.9829" all_ntt_prob="(0.0000,0.4742,0.9829)">
<search_score_summary>
<parameter name="fval" value="-2.3650"/>
<parameter name="ntt" value="2"/>
<parameter name="nmc" value="0"/>
<parameter name="massd" value="0.018"/>
</search_score_summary>
</peptideprophet_result>
</analysis_result>
<analysis_result analysis="interprophet">
<interprophet_result probability="0.997218" all_ntt_prob="(0,0.849045,0.997218)">
<search_score_summary>
<parameter name="nss" value="0"/>
<parameter name="nrs" value="5"/>
<parameter name="nse" value="0"/>
<parameter name="nsi" value="0"/>
<parameter name="nsm" value="0"/>
</search_score_summary>
</interprophet_result>
</analysis_result>
</search_hit>
<search_hit hit_rank="2" peptide="LNVGFIAPE" peptide_prev_aa="R" peptide_next_aa="T"
protein="DECOY_gi|13622856|gb|AAK34540.1|" num_tot_proteins="1" num_matched_ions="7" tot_num_ions="16"
calc_neutral_pep_mass="958.512" massdiff="-0.007000000000005" is_rejected="0"
protein_descr="DECOY_gi|13622856|gb|AAK34540.1| putative sucrose-specific PTS permease, enzyme II [Streptococcus pyogenes M1 GAS]"
num_tol_term="1" num_missed_cleavages="0">
<search_score name="pvalue" value="0.247165546149053"/>
<search_score name="expect" value="567.739259504375696"/>
</search_hit>
<search_hit hit_rank="3" peptide="RAGMPNWQ" peptide_prev_aa="K" peptide_next_aa="I"
protein="gi|13623019|gb|AAK34688.1|" num_tot_proteins="1" num_matched_ions="8" tot_num_ions="14"
calc_neutral_pep_mass="958.444" massdiff="0.060999999999996" is_rejected="0"
protein_descr="gi|13623019|gb|AAK34688.1| hypothetical protein SPy_2006 [Streptococcus pyogenes M1 GAS]"
num_tol_term="1" num_missed_cleavages="0">
<search_score name="pvalue" value="0.32298820764574"/>
<search_score name="expect" value="741.903912962265508"/>
</search_hit>
<search_hit hit_rank="4" peptide="NIVLLADDS" peptide_prev_aa="K" peptide_next_aa="S"
protein="gi|13622159|gb|AAK33905.1|" num_tot_proteins="1" num_matched_ions="7" tot_num_ions="16"
calc_neutral_pep_mass="958.497" massdiff="0.007999999999996" is_rejected="0"
protein_descr="gi|13622159|gb|AAK33905.1| putative lysin - phage associated [Streptococcus phage 370.3]"
num_tol_term="1" num_missed_cleavages="0">
<search_score name="pvalue" value="0.726627699836322"/>
<search_score name="expect" value="1669.063826524031356"/>
</search_hit>
<search_hit hit_rank="5" peptide="RAVLFQLL" peptide_prev_aa="R" peptide_next_aa="Q"
protein="gi|13622381|gb|AAK34108.1|" num_tot_proteins="1" num_matched_ions="7" tot_num_ions="14"
calc_neutral_pep_mass="958.596" massdiff="-0.091000000000005" is_rejected="0"
protein_descr="gi|13622381|gb|AAK34108.1| conserved hypothetical protein [Streptococcus pyogenes M1 GAS]"
num_tol_term="1" num_missed_cleavages="0">
<search_score name="pvalue" value="2.042689741112156"/>
<search_score name="expect" value="4692.058335334622825"/>
</search_hit>
<search_hit hit_rank="6" peptide="LNVISEER" peptide_prev_aa="V" peptide_next_aa="S"
protein="gi|13622888|gb|AAK34569.1|" num_tot_proteins="1" num_matched_ions="7" tot_num_ions="14"
calc_neutral_pep_mass="958.509" massdiff="-0.004000000000004" is_rejected="0"
protein_descr="gi|13622888|gb|AAK34569.1| putative C3-degrading proteinase [Streptococcus pyogenes M1 GAS]"
num_tol_term="1" num_missed_cleavages="0">
<search_score name="pvalue" value="4.369044503054501"/>
<search_score name="expect" value="10035.69522351618798"/>
</search_hit>
<search_hit hit_rank="7" peptide="IRGVVFLGV" peptide_prev_aa="K" peptide_next_aa="A"
protein="DECOY_gi|13621344|gb|AAK33161.1|" num_tot_proteins="1" num_matched_ions="9" tot_num_ions="16"
calc_neutral_pep_mass="958.594" massdiff="-0.089000000000005" is_rejected="0"
protein_descr="DECOY_gi|13621344|gb|AAK33161.1| putative fatty acid/phospholipid synthesis protein [Streptococcus pyogenes M1 GAS]"
num_tol_term="1" num_missed_cleavages="1">
<search_score name="pvalue" value="10.271567255646678"/>
<search_score name="expect" value="23593.78998622042127"/>
</search_hit>
<search_hit hit_rank="8" peptide="QVRGLEEE" peptide_prev_aa="R" peptide_next_aa="P"
protein="gi|13621512|gb|AAK33314.1|" num_tot_proteins="1" num_matched_ions="6" tot_num_ions="14"
calc_neutral_pep_mass="958.473" massdiff="0.031999999999995" is_rejected="0"
protein_descr="gi|13621512|gb|AAK33314.1| conserved hypothetical protein [Streptococcus pyogenes M1 GAS]"
num_tol_term="1" num_missed_cleavages="1">
<search_score name="pvalue" value="10.710793674120096"/>
<search_score name="expect" value="24602.693069453860517"/>
</search_hit>
<search_hit hit_rank="9" peptide="KVQDQDVK" peptide_prev_aa="I" peptide_next_aa="T"
protein="gi|13622538|gb|AAK34250.1|" num_tot_proteins="1" num_matched_ions="7" tot_num_ions="14"
calc_neutral_pep_mass="958.509" massdiff="-0.004000000000004" is_rejected="0"
protein_descr="gi|13622538|gb|AAK34250.1| hypothetical protein SPy_1446 [Streptococcus pyogenes M1 GAS]"
num_tol_term="1" num_missed_cleavages="1">
<search_score name="pvalue" value="20.644222337421816"/>
<search_score name="expect" value="47419.778709057914966"/>
</search_hit>
<search_hit hit_rank="10" peptide="ARKEAAKAD" peptide_prev_aa="K" peptide_next_aa="L"
protein="gi|13621916|gb|AAK33683.1|" num_tot_proteins="2" num_matched_ions="6" tot_num_ions="16"
calc_neutral_pep_mass="958.52" massdiff="-0.015000000000005" is_rejected="0"
protein_descr="gi|13621916|gb|AAK33683.1| putative extracellular matrix binding protein [Streptococcus pyogenes M1 GAS]"
num_tol_term="1" num_missed_cleavages="2">
<search_score name="pvalue" value="31.424525558323513"/>
<search_score name="expect" value="72182.135207469109446"/>
</search_hit>
<search_hit hit_rank="11" peptide="RGLKQVMK" peptide_prev_aa="N" peptide_next_aa="N"
protein="gi|13621847|gb|AAK33619.1|" num_tot_proteins="1" num_matched_ions="7" tot_num_ions="14"
calc_neutral_pep_mass="958.574" massdiff="-0.069000000000005" is_rejected="0"
protein_descr="gi|13621847|gb|AAK33619.1| hypothetical protein, phage associated [Streptococcus pyogenes M1 GAS]"
num_tol_term="1" num_missed_cleavages="2">
<search_score name="pvalue" value="31.947419722034656"/>
<search_score name="expect" value="73383.223101513605798"/>
</search_hit>
</search_result>
</spectrum_query>
<!-- iprophet.pep.xml generated from the previous iprophet.pep.xml's-->
<spectrum_query spectrum="B09-10149.c.01821.01821.2" start_scan="1821" end_scan="1821" precursor_neutral_mass="958.5047"
assumed_charge="2" index="55" retention_time_sec="854.394">
<search_result>
<search_hit hit_rank="1" peptide="NLVNGEWK" peptide_prev_aa="K" peptide_next_aa="L"
protein="gi|13622481|gb|AAK34198.1|"
protein_descr="putative NADP-dependent glyceraldehyde-3-phosphate dehydrogenase [Streptococcus pyogenes M1 GAS]"
num_tot_proteins="1" num_matched_ions="14" tot_num_ions="14" calc_neutral_pep_mass="958.4877"
massdiff="0.017" num_tol_term="2" num_missed_cleavages="0" is_rejected="0">
<search_score name="hyperscore" value="343"/>
<search_score name="nextscore" value="296"/>
<search_score name="bscore" value="1"/>
<search_score name="yscore" value="1"/>
<search_score name="expect" value="1.7"/>
<analysis_result analysis="peptideprophet">
<peptideprophet_result probability="0.9881" all_ntt_prob="(0.0000,0.6710,0.9881)">
<search_score_summary>
<parameter name="fval" value="1.4464"/>
<parameter name="ntt" value="2"/>
<parameter name="nmc" value="0"/>
<parameter name="massd" value="0.017"/>
<parameter name="isomassd" value="0"/>
<parameter name="pI" value="6.00"/>
<parameter name="pI_zscore" value="0.25"/>
</search_score_summary>
</peptideprophet_result>
</analysis_result>
<analysis_result analysis="interprophet">
<interprophet_result probability="0.994754" all_ntt_prob="(0,0.82324,0.994754)">
<search_score_summary>
<parameter name="nss" value="0.6207"/>
<parameter name="nrs" value="5"/>
<parameter name="nse" value="0"/>
<parameter name="nsi" value="0"/>
<parameter name="nsm" value="0"/>
</search_score_summary>
</interprophet_result>
</analysis_result>
<analysis_result analysis="interprophet">
<interprophet_result probability="0.998354" all_ntt_prob="(0,0.937097,0.998354)">
<search_score_summary>
<parameter name="nss" value="0"/>
<parameter name="nrs" value="5"/>
<parameter name="nse" value="0"/>
<parameter name="nsi" value="0"/>
<parameter name="nsm" value="0"/>
</search_score_summary>
</interprophet_result>
</analysis_result>
</search_hit>
</search_result>
</spectrum_query>
i did something similar but combined multiple iprophet pep.xml's (in that case from 3 search engines) to a single iprophet result file.
here an example for a single spectrum
<!-- iprophet.pep.xml generated with mascot -->
<spectrum_query spectrum="B09-10149.c.01821.01821.2" start_scan="01821" end_scan="01821"
precursor_neutral_mass="958.5047" assumed_charge="2" index="354">
<search_result>
<search_hit hit_rank="1" peptide="NIVLLADDS" peptide_prev_aa="K" peptide_next_aa="S"
protein="gi|13622159|gb|AAK33905.1|" num_tot_proteins="1" num_matched_ions="3" tot_num_ions="16"
calc_neutral_pep_mass="958.4971" massdiff="+0.0076" num_tol_term="1" num_missed_cleavages="0"
is_rejected="0" protein_descr="putative lysin - phage associated [Streptococcus phage 370.3]">
<search_score name="ionscore" value="19.72"/>
<search_score name="identityscore" value="28.51"/>
<search_score name="star" value="0"/>
<search_score name="homologyscore" value="31.32"/>
<search_score name="expect" value="0.38"/>
<analysis_result analysis="peptideprophet">
<peptideprophet_result probability="0.3622" all_ntt_prob="(0.0000,0.3622,0.9790)">
<search_score_summary>
<parameter name="fval" value="-1.3378"/>
<parameter name="ntt" value="1"/>
<parameter name="nmc" value="0"/>
<parameter name="massd" value="0.008"/>
<parameter name="isomassd" value="0"/>
<parameter name="pI" value="3.56"/>
<parameter name="pI_zscore" value="-1.19"/>
</search_score_summary>
</peptideprophet_result>
</analysis_result>
<analysis_result analysis="interprophet">
<interprophet_result probability="0.0118374" all_ntt_prob="(0,0.0118374,0.495813)">
<search_score_summary>
<parameter name="nss" value="0"/>
<parameter name="nrs" value="0"/>
<parameter name="nse" value="0"/>
<parameter name="nsi" value="0"/>
<parameter name="nsm" value="0"/>
</search_score_summary>
</interprophet_result>
</analysis_result>
</search_hit>
</search_result>
</spectrum_query>
<!--iprophet.pep.xml generated with xtandem-->
<spectrum_query spectrum="B09-10149.c.01821.01821.2" start_scan="1821" end_scan="1821" precursor_neutral_mass="958.5047"
assumed_charge="2" index="55" retention_time_sec="854.394">
<search_result>
<search_hit hit_rank="1" peptide="NLVNGEWK" peptide_prev_aa="K" peptide_next_aa="L"
protein="gi|13622481|gb|AAK34198.1|"
protein_descr="putative NADP-dependent glyceraldehyde-3-phosphate dehydrogenase [Streptococcus pyogenes M1 GAS]"
num_tot_proteins="1" num_matched_ions="14" tot_num_ions="14" calc_neutral_pep_mass="958.4877"
massdiff="0.017" num_tol_term="2" num_missed_cleavages="0" is_rejected="0">
<search_score name="hyperscore" value="343"/>
<search_score name="nextscore" value="296"/>
<search_score name="bscore" value="1"/>
<search_score name="yscore" value="1"/>
<search_score name="expect" value="1.7"/>
<analysis_result analysis="peptideprophet">
<peptideprophet_result probability="0.9881" all_ntt_prob="(0.0000,0.6710,0.9881)">
<search_score_summary>
<parameter name="fval" value="1.4464"/>
<parameter name="ntt" value="2"/>
<parameter name="nmc" value="0"/>
<parameter name="massd" value="0.017"/>
<parameter name="isomassd" value="0"/>
<parameter name="pI" value="6.00"/>
<parameter name="pI_zscore" value="0.25"/>
</search_score_summary>
</peptideprophet_result>
</analysis_result>
<analysis_result analysis="interprophet">
<interprophet_result probability="0.998354" all_ntt_prob="(0,0.937097,0.998354)">
<search_score_summary>
<parameter name="nss" value="0"/>
<parameter name="nrs" value="5"/>
<parameter name="nse" value="0"/>
<parameter name="nsi" value="0"/>
<parameter name="nsm" value="0"/>
</search_score_summary>
</interprophet_result>
</analysis_result>
</search_hit>
</search_result>
</spectrum_query>
<!--iprophet.pep.xml generated with omssa-->
<spectrum_query spectrum="B09-10149.c.01821.01821.2" start_scan="1821" end_scan="1821"
precursor_neutral_mass="958.505004882812" assumed_charge="2" index="1222">
<search_result>
<search_hit hit_rank="1" peptide="NLVNGEWK" peptide_prev_aa="K" peptide_next_aa="L"
protein="gi|13622481|gb|AAK34198.1|" num_tot_proteins="1" num_matched_ions="8" tot_num_ions="14"
calc_neutral_pep_mass="958.487" massdiff="0.017999999999996" is_rejected="0"
protein_descr="putative NADP-dependent glyceraldehyde-3-phosphate dehydrogenase [Streptococcus pyogenes M1 GAS]"
num_tol_term="2" num_missed_cleavages="0">
<search_score name="pvalue" value="0.006009478037955"/>
<search_score name="expect" value="13.803771053183747"/>
<analysis_result analysis="peptideprophet">
<peptideprophet_result probability="0.9829" all_ntt_prob="(0.0000,0.4742,0.9829)">
<search_score_summary>
<parameter name="fval" value="-2.3650"/>
<parameter name="ntt" value="2"/>
<parameter name="nmc" value="0"/>
<parameter name="massd" value="0.018"/>
</search_score_summary>
</peptideprophet_result>
</analysis_result>
<analysis_result analysis="interprophet">
<interprophet_result probability="0.997218" all_ntt_prob="(0,0.849045,0.997218)">
<search_score_summary>
<parameter name="nss" value="0"/>
<parameter name="nrs" value="5"/>
<parameter name="nse" value="0"/>
<parameter name="nsi" value="0"/>
<parameter name="nsm" value="0"/>
</search_score_summary>
</interprophet_result>
</analysis_result>
</search_hit>
<search_hit hit_rank="2" peptide="LNVGFIAPE" peptide_prev_aa="R" peptide_next_aa="T"
protein="DECOY_gi|13622856|gb|AAK34540.1|" num_tot_proteins="1" num_matched_ions="7" tot_num_ions="16"
calc_neutral_pep_mass="958.512" massdiff="-0.007000000000005" is_rejected="0"
protein_descr="DECOY_gi|13622856|gb|AAK34540.1| putative sucrose-specific PTS permease, enzyme II [Streptococcus pyogenes M1 GAS]"
num_tol_term="1" num_missed_cleavages="0">
<search_score name="pvalue" value="0.247165546149053"/>
<search_score name="expect" value="567.739259504375696"/>
</search_hit>
<search_hit hit_rank="3" peptide="RAGMPNWQ" peptide_prev_aa="K" peptide_next_aa="I"
protein="gi|13623019|gb|AAK34688.1|" num_tot_proteins="1" num_matched_ions="8" tot_num_ions="14"
calc_neutral_pep_mass="958.444" massdiff="0.060999999999996" is_rejected="0"
protein_descr="gi|13623019|gb|AAK34688.1| hypothetical protein SPy_2006 [Streptococcus pyogenes M1 GAS]"
num_tol_term="1" num_missed_cleavages="0">
<search_score name="pvalue" value="0.32298820764574"/>
<search_score name="expect" value="741.903912962265508"/>
</search_hit>
<search_hit hit_rank="4" peptide="NIVLLADDS" peptide_prev_aa="K" peptide_next_aa="S"
protein="gi|13622159|gb|AAK33905.1|" num_tot_proteins="1" num_matched_ions="7" tot_num_ions="16"
calc_neutral_pep_mass="958.497" massdiff="0.007999999999996" is_rejected="0"
protein_descr="gi|13622159|gb|AAK33905.1| putative lysin - phage associated [Streptococcus phage 370.3]"
num_tol_term="1" num_missed_cleavages="0">
<search_score name="pvalue" value="0.726627699836322"/>
<search_score name="expect" value="1669.063826524031356"/>
</search_hit>
<search_hit hit_rank="5" peptide="RAVLFQLL" peptide_prev_aa="R" peptide_next_aa="Q"
protein="gi|13622381|gb|AAK34108.1|" num_tot_proteins="1" num_matched_ions="7" tot_num_ions="14"
calc_neutral_pep_mass="958.596" massdiff="-0.091000000000005" is_rejected="0"
protein_descr="gi|13622381|gb|AAK34108.1| conserved hypothetical protein [Streptococcus pyogenes M1 GAS]"
num_tol_term="1" num_missed_cleavages="0">
<search_score name="pvalue" value="2.042689741112156"/>
<search_score name="expect" value="4692.058335334622825"/>
</search_hit>
<search_hit hit_rank="6" peptide="LNVISEER" peptide_prev_aa="V" peptide_next_aa="S"
protein="gi|13622888|gb|AAK34569.1|" num_tot_proteins="1" num_matched_ions="7" tot_num_ions="14"
calc_neutral_pep_mass="958.509" massdiff="-0.004000000000004" is_rejected="0"
protein_descr="gi|13622888|gb|AAK34569.1| putative C3-degrading proteinase [Streptococcus pyogenes M1 GAS]"
num_tol_term="1" num_missed_cleavages="0">
<search_score name="pvalue" value="4.369044503054501"/>
<search_score name="expect" value="10035.69522351618798"/>
</search_hit>
<search_hit hit_rank="7" peptide="IRGVVFLGV" peptide_prev_aa="K" peptide_next_aa="A"
protein="DECOY_gi|13621344|gb|AAK33161.1|" num_tot_proteins="1" num_matched_ions="9" tot_num_ions="16"
calc_neutral_pep_mass="958.594" massdiff="-0.089000000000005" is_rejected="0"
protein_descr="DECOY_gi|13621344|gb|AAK33161.1| putative fatty acid/phospholipid synthesis protein [Streptococcus pyogenes M1 GAS]"
num_tol_term="1" num_missed_cleavages="1">
<search_score name="pvalue" value="10.271567255646678"/>
<search_score name="expect" value="23593.78998622042127"/>
</search_hit>
<search_hit hit_rank="8" peptide="QVRGLEEE" peptide_prev_aa="R" peptide_next_aa="P"
protein="gi|13621512|gb|AAK33314.1|" num_tot_proteins="1" num_matched_ions="6" tot_num_ions="14"
calc_neutral_pep_mass="958.473" massdiff="0.031999999999995" is_rejected="0"
protein_descr="gi|13621512|gb|AAK33314.1| conserved hypothetical protein [Streptococcus pyogenes M1 GAS]"
num_tol_term="1" num_missed_cleavages="1">
<search_score name="pvalue" value="10.710793674120096"/>
<search_score name="expect" value="24602.693069453860517"/>
</search_hit>
<search_hit hit_rank="9" peptide="KVQDQDVK" peptide_prev_aa="I" peptide_next_aa="T"
protein="gi|13622538|gb|AAK34250.1|" num_tot_proteins="1" num_matched_ions="7" tot_num_ions="14"
calc_neutral_pep_mass="958.509" massdiff="-0.004000000000004" is_rejected="0"
protein_descr="gi|13622538|gb|AAK34250.1| hypothetical protein SPy_1446 [Streptococcus pyogenes M1 GAS]"
num_tol_term="1" num_missed_cleavages="1">
<search_score name="pvalue" value="20.644222337421816"/>
<search_score name="expect" value="47419.778709057914966"/>
</search_hit>
<search_hit hit_rank="10" peptide="ARKEAAKAD" peptide_prev_aa="K" peptide_next_aa="L"
protein="gi|13621916|gb|AAK33683.1|" num_tot_proteins="2" num_matched_ions="6" tot_num_ions="16"
calc_neutral_pep_mass="958.52" massdiff="-0.015000000000005" is_rejected="0"
protein_descr="gi|13621916|gb|AAK33683.1| putative extracellular matrix binding protein [Streptococcus pyogenes M1 GAS]"
num_tol_term="1" num_missed_cleavages="2">
<search_score name="pvalue" value="31.424525558323513"/>
<search_score name="expect" value="72182.135207469109446"/>
</search_hit>
<search_hit hit_rank="11" peptide="RGLKQVMK" peptide_prev_aa="N" peptide_next_aa="N"
protein="gi|13621847|gb|AAK33619.1|" num_tot_proteins="1" num_matched_ions="7" tot_num_ions="14"
calc_neutral_pep_mass="958.574" massdiff="-0.069000000000005" is_rejected="0"
protein_descr="gi|13621847|gb|AAK33619.1| hypothetical protein, phage associated [Streptococcus pyogenes M1 GAS]"
num_tol_term="1" num_missed_cleavages="2">
<search_score name="pvalue" value="31.947419722034656"/>
<search_score name="expect" value="73383.223101513605798"/>
</search_hit>
</search_result>
</spectrum_query>
<!-- iprophet.pep.xml generated from the previous iprophet.pep.xml's-->
<spectrum_query spectrum="B09-10149.c.01821.01821.2" start_scan="1821" end_scan="1821" precursor_neutral_mass="958.5047"
assumed_charge="2" index="55" retention_time_sec="854.394">
<search_result>
<search_hit hit_rank="1" peptide="NLVNGEWK" peptide_prev_aa="K" peptide_next_aa="L"
protein="gi|13622481|gb|AAK34198.1|"
protein_descr="putative NADP-dependent glyceraldehyde-3-phosphate dehydrogenase [Streptococcus pyogenes M1 GAS]"
num_tot_proteins="1" num_matched_ions="14" tot_num_ions="14" calc_neutral_pep_mass="958.4877"
massdiff="0.017" num_tol_term="2" num_missed_cleavages="0" is_rejected="0">
<search_score name="hyperscore" value="343"/>
<search_score name="nextscore" value="296"/>
<search_score name="bscore" value="1"/>
<search_score name="yscore" value="1"/>
<search_score name="expect" value="1.7"/>
<analysis_result analysis="peptideprophet">
<peptideprophet_result probability="0.9881" all_ntt_prob="(0.0000,0.6710,0.9881)">
<search_score_summary>
<parameter name="fval" value="1.4464"/>
<parameter name="ntt" value="2"/>
<parameter name="nmc" value="0"/>
<parameter name="massd" value="0.017"/>
<parameter name="isomassd" value="0"/>
<parameter name="pI" value="6.00"/>
<parameter name="pI_zscore" value="0.25"/>
</search_score_summary>
</peptideprophet_result>
</analysis_result>
<analysis_result analysis="interprophet">
<interprophet_result probability="0.994754" all_ntt_prob="(0,0.82324,0.994754)">
<search_score_summary>
<parameter name="nss" value="0.6207"/>
<parameter name="nrs" value="5"/>
<parameter name="nse" value="0"/>
<parameter name="nsi" value="0"/>
<parameter name="nsm" value="0"/>
</search_score_summary>
</interprophet_result>
</analysis_result>
<analysis_result analysis="interprophet">
<interprophet_result probability="0.998354" all_ntt_prob="(0,0.937097,0.998354)">
<search_score_summary>
<parameter name="nss" value="0"/>
<parameter name="nrs" value="5"/>
<parameter name="nse" value="0"/>
<parameter name="nsi" value="0"/>
<parameter name="nsm" value="0"/>
</search_score_summary>
</interprophet_result>
</analysis_result>
</search_hit>
</search_result>
</spectrum_query>
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