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]"
...
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