Hi David, Using MINPROB=0 solved this problem. Thanks! Alex On Monday, April 6, 2020 at 4:11:47 PM UTC-7, David Shteynberg wrote: > > Hi Alex, > > PTMProphet by default will ignore any spectrum with less than 90% > probability (iProphet is used when available.) You can change this by > setting the option MINPROB= when you run the tool. Let me know if that > still fails for you. > > Thanks, > -David > > > > On Mon, Apr 6, 2020 at 3:27 PM Alex Zelter <aze...@uw.edu <javascript:>> > wrote: > >> I am running into a situation where MSFragger returns a massdiff but >> PTMProphet seems to ignore it. No modification_info or mod_aminoacid_mass >> position is reported by PTMProphet for some results, while for others >> things work as expected. >> Here are 2 PSMs as examples. I've included both MSFragger xml output and >> PTMProphet output. For scan number 49967 the open modification is localized >> and reported correctly by PTMProphet, but for scan 74042 that information >> is missing from the PTMProphet output, despite the MSFragger xml input >> being similar. >> Both the examples below are taken from the same results files and were >> thus treated identically. TPP v5.2.1-dev Flammagenitus, Build >> 202003241419-8041 was used. >> If you have any idea what might be causing this I'd be very grateful! >> Thanks, >> Alex >> >> MSFragger pep.xml output for scan 49967 (works as expected): >> >> <spectrum_query start_scan="49967" >> uncalibrated_precursor_neutral_mass="1847.0168" assumed_charge="3" >> spectrum="QEP2_2018_0812_AZ_033_az736_AZ.49967.49967.3" end_scan="49967" >> index="39256" precursor_neutral_mass="1847.0134" >> retention_time_sec="5830.280"> >> <search_result> >> <search_hit peptide="VTKCCTESLVNR" massdiff="495.3547" >> calc_neutral_pep_mass="1351.6587" peptide_next_aa="R" >> num_missed_cleavages="1" num_tol_term="2" num_tot_proteins="10" >> tot_num_ions="44" hit_rank="1" num_matched_ions="9" >> protein="sp|P02768|ALBU_HUMAN Serum albumin OS=Homo sapiens GN=ALB PE=1 >> SV=2" peptide_prev_aa="R" is_rejected="0"> >> <alternative_protein protein="tr|A0A087WWT3|A0A087WWT3_HUMAN Isoform of >> P02768, Serum albumin OS=Homo sapiens GN=ALB PE=1 SV=1" peptide_prev_aa="R" >> peptide_next_aa="R" num_tol_term="2"/> >> <alternative_protein protein="tr|A0A0C4DGB6|A0A0C4DGB6_HUMAN Isoform of >> P02768, Serum albumin OS=Homo sapiens GN=ALB PE=1 SV=1" peptide_prev_aa="R" >> peptide_next_aa="R" num_tol_term="2"/> >> <alternative_protein protein="tr|B7WNR0|B7WNR0_HUMAN Isoform of P02768, >> Serum albumin OS=Homo sapiens GN=ALB PE=1 SV=1" peptide_prev_aa="R" >> peptide_next_aa="R" num_tol_term="2"/> >> <alternative_protein protein="tr|C9JKR2|C9JKR2_HUMAN Isoform of P02768, >> Albumin, isoform CRA_k OS=Homo sapiens GN=ALB PE=1 SV=1" >> peptide_prev_aa="R" peptide_next_aa="R" num_tol_term="2"/> >> <alternative_protein protein="tr|D6RHD5|D6RHD5_HUMAN Isoform of P02768, >> Serum albumin OS=Homo sapiens GN=ALB PE=1 SV=1" peptide_prev_aa="R" >> peptide_next_aa="R" num_tol_term="2"/> >> <alternative_protein protein="tr|H0YA55|H0YA55_HUMAN Isoform of P02768, >> Serum albumin (Fragment) OS=Homo sapiens GN=ALB PE=1 SV=1" >> peptide_prev_aa="R" peptide_next_aa="R" num_tol_term="2"/> >> <alternative_protein protein="sp|P02768-2|ALBU_HUMAN Isoform of P02768, >> Isoform 2 of Serum albumin OS=Homo sapiens GN=ALB" peptide_prev_aa="R" >> peptide_next_aa="R" num_tol_term="2"/> >> <alternative_protein protein="sp|P02768-3|ALBU_HUMAN Isoform of P02768, >> Isoform 3 of Serum albumin OS=Homo sapiens GN=ALB" peptide_prev_aa="R" >> peptide_next_aa="R" num_tol_term="2"/> >> <alternative_protein protein="sp|ALBU_BOVIN|" peptide_prev_aa="R" >> peptide_next_aa="R" num_tol_term="2"/> >> <search_score name="hyperscore" value="15.283"/> >> <search_score name="nextscore" value="12.987"/> >> <search_score name="expect" value="1.670e-04"/> >> </search_hit> >> </search_result> >> </spectrum_query> >> >> PTMProphet output for the scan 49967: >> <spectrum_query start_scan="49967" >> uncalibrated_precursor_neutral_mass="1847.0168" assumed_charge="3" >> spectrum="QEP2_2018_0812_AZ_033_az736_AZ.49967.49967.3" end_scan="49967" >> index="34348" precursor_neutral_mass="1847.0134" >> retention_time_sec="5830.280"> >> <search_result> >> <search_hit peptide="VTKCCTESLVNR" massdiff="495.3547" >> calc_neutral_pep_mass="1351.6587" peptide_next_aa="R" >> num_missed_cleavages="1" num_tol_term="2" num_tot_proteins="10" >> tot_num_ions="44" hit_rank="1" num_matched_ions="9" >> protein="sp|P02768|ALBU_HUMAN" peptide_prev_aa="R" is_rejected="0" >> protein_descr="Serum albumin OS=Homo sapiens GN=ALB PE=1 SV=2"> >> <alternative_protein protein="tr|A0A087WWT3|A0A087WWT3_HUMAN" >> protein_descr="Isoform of P02768, Serum albumin OS=Homo sapiens GN=ALB PE=1 >> SV=1" num_tol_term="2" peptide_prev_aa="R" peptide_next_aa="R"/> >> <alternative_protein protein="tr|A0A0C4DGB6|A0A0C4DGB6_HUMAN" >> protein_descr="Isoform of P02768, Serum albumin OS=Homo sapiens GN=ALB PE=1 >> SV=1" num_tol_term="2" peptide_prev_aa="R" peptide_next_aa="R"/> >> <alternative_protein protein="tr|B7WNR0|B7WNR0_HUMAN" >> protein_descr="Isoform of P02768, Serum albumin OS=Homo sapiens GN=ALB PE=1 >> SV=1" num_tol_term="2" peptide_prev_aa="R" peptide_next_aa="R"/> >> <alternative_protein protein="tr|C9JKR2|C9JKR2_HUMAN" >> protein_descr="Isoform of P02768, Albumin, isoform CRA_k OS=Homo sapiens >> GN=ALB PE=1 SV=1" num_tol_term="2" peptide_prev_aa="R" peptide_next_aa="R"/> >> <alternative_protein protein="tr|D6RHD5|D6RHD5_HUMAN" >> protein_descr="Isoform of P02768, Serum albumin OS=Homo sapiens GN=ALB PE=1 >> SV=1" num_tol_term="2" peptide_prev_aa="R" peptide_next_aa="R"/> >> <alternative_protein protein="tr|H0YA55|H0YA55_HUMAN" >> protein_descr="Isoform of P02768, Serum albumin (Fragment) OS=Homo sapiens >> GN=ALB PE=1 SV=1" num_tol_term="2" peptide_prev_aa="R" peptide_next_aa="R"/> >> <alternative_protein protein="sp|P02768-2|ALBU_HUMAN" >> protein_descr="Isoform of P02768, Isoform 2 of Serum albumin OS=Homo >> sapiens GN=ALB" num_tol_term="2" peptide_prev_aa="R" peptide_next_aa="R"/> >> <alternative_protein protein="sp|P02768-3|ALBU_HUMAN" >> protein_descr="Isoform of P02768, Isoform 3 of Serum albumin OS=Homo >> sapiens GN=ALB" num_tol_term="2" peptide_prev_aa="R" peptide_next_aa="R"/> >> <alternative_protein protein="sp|ALBU_BOVIN|" num_tol_term="2" >> peptide_prev_aa="K" peptide_next_aa="R"/> >> <search_score name="hyperscore" value="15.283"/> >> <search_score name="nextscore" value="12.987"/> >> <search_score name="expect" value="1.670e-04"/> >> <analysis_result analysis="peptideprophet"> >> <peptideprophet_result probability="0.9495" >> all_ntt_prob="(0.0000,0.0020,0.9495)"> >> <search_score_summary> >> <parameter name="fval" value="6.0889"/> >> <parameter name="ntt" value="2"/> >> <parameter name="nmc" value="1"/> >> <parameter name="massd" value="-0.303"/> >> <parameter name="isomassd" value="3"/> >> </search_score_summary> >> </peptideprophet_result> >> </analysis_result> >> <analysis_result analysis="interprophet"> >> <interprophet_result probability="0.919585" >> all_ntt_prob="(0,0.00121737,0.919585)"> >> <search_score_summary> >> <parameter name="nrs" value="-8.8028"/> >> <parameter name="nsi" value="0.999"/> >> <parameter name="nsm" value="2.9825"/> >> <parameter name="nsp" value="20"/> >> </search_score_summary> >> </interprophet_result> >> </analysis_result> >> *<modification_info modified_peptide="VTK[623]CCTESLVNR">* >> *<mod_aminoacid_mass position="3" mass="623.4497"/>* >> </modification_info> >> <analysis_result analysis="ptmprophet"> >> <parameter name="mass_ppm_offset" value="-2.43401"/> >> <parameter name="mass_ppm_tolerance" value="11.2026"/> >> <ptmprophet_result ptm="MASSDIFF" prior="0.0833333" >> ptm_peptide="V(0.024)T(0.024)K(0.777)C(0.035)C(0.035)T(0.023)E(0.018)S(0.015)L(0.013)V(0.013)N(0.011)R(0.011)"> >> <parameter name="mean_best_prob" value="0.777"/> >> <parameter name="norm_info_gain" value="0.580"/> >> <parameter name="localized_mods" value="0.580"/> >> <mod_aminoacid_probability position="1" probability="2.436e-02" >> oscore="0.071" mscore="0.250" direct_oscore="0.500" direct_mscore="0.500" >> cterm_score="0.500" nterm_score="0.000"/> >> <mod_aminoacid_probability position="2" probability="2.436e-02" >> oscore="0.071" mscore="0.250" direct_oscore="0.500" direct_mscore="0.500" >> cterm_score="0.500" nterm_score="0.000"/> >> <mod_aminoacid_probability position="3" probability="7.774e-01" >> oscore="0.928" mscore="0.667" direct_oscore="0.500" direct_mscore="0.500" >> cterm_score="0.500" nterm_score="0.000"/> >> <mod_aminoacid_probability position="4" probability="3.531e-02" >> oscore="0.072" mscore="0.333" direct_oscore="0.500" direct_mscore="0.500" >> cterm_score="0.500" nterm_score="0.000"/> >> <mod_aminoacid_probability position="5" probability="3.531e-02" >> oscore="0.072" mscore="0.333" direct_oscore="0.500" direct_mscore="0.500" >> cterm_score="0.500" nterm_score="0.000"/> >> <mod_aminoacid_probability position="6" probability="2.256e-02" >> oscore="0.043" mscore="0.250" direct_oscore="0.500" direct_mscore="0.500" >> cterm_score="0.462" nterm_score="0.000"/> >> <mod_aminoacid_probability position="7" probability="1.758e-02" >> oscore="0.033" mscore="0.200" direct_oscore="0.500" direct_mscore="0.500" >> cterm_score="0.417" nterm_score="0.000"/> >> <mod_aminoacid_probability position="8" probability="1.491e-02" >> oscore="0.025" mscore="0.167" direct_oscore="0.500" direct_mscore="0.500" >> cterm_score="0.364" nterm_score="0.000"/> >> <mod_aminoacid_probability position="9" probability="1.349e-02" >> oscore="0.024" mscore="0.143" direct_oscore="0.500" direct_mscore="0.500" >> cterm_score="0.300" nterm_score="0.000"/> >> <mod_aminoacid_probability position="10" probability="1.255e-02" >> oscore="0.023" mscore="0.125" direct_oscore="0.500" direct_mscore="0.500" >> cterm_score="0.222" nterm_score="0.000"/> >> <mod_aminoacid_probability position="11" probability="1.131e-02" >> oscore="0.019" mscore="0.100" direct_oscore="0.101" direct_mscore="0.333" >> cterm_score="0.000" nterm_score="0.000"/> >> <mod_aminoacid_probability position="12" probability="1.082e-02" >> oscore="0.014" mscore="0.091" direct_oscore="0.101" direct_mscore="0.333" >> cterm_score="0.000" nterm_score="0.000"/> >> </ptmprophet_result> >> </analysis_result> >> </search_hit> >> </search_result> >> </spectrum_query> >> >> >> >> MSFragger pep.xml output for scan 74042 (does not work as expected): >> <spectrum_query start_scan="74042" >> uncalibrated_precursor_neutral_mass="1494.4763" assumed_charge="2" >> spectrum="QEP2_2018_0812_AZ_033_az736_AZ.74042.74042.2" end_scan="74042" >> index="61738" precursor_neutral_mass="1494.4722" >> retention_time_sec="8409.789"> >> <search_result> >> <search_hit peptide="VTKCCTESLVNR" massdiff="142.8135" >> calc_neutral_pep_mass="1351.6587" peptide_next_aa="R" >> num_missed_cleavages="1" num_tol_term="2" num_tot_proteins="10" >> tot_num_ions="22" hit_rank="1" num_matched_ions="11" >> protein="sp|P02768|ALBU_HUMAN Serum albumin OS=Homo sapiens GN=ALB PE=1 >> SV=2" peptide_prev_aa="R" is_rejected="0"> >> <alternative_protein protein="tr|A0A087WWT3|A0A087WWT3_HUMAN Isoform of >> P02768, Serum albumin OS=Homo sapiens GN=ALB PE=1 SV=1" peptide_prev_aa="R" >> peptide_next_aa="R" num_tol_term="2"/> >> <alternative_protein protein="tr|A0A0C4DGB6|A0A0C4DGB6_HUMAN Isoform of >> P02768, Serum albumin OS=Homo sapiens GN=ALB PE=1 SV=1" peptide_prev_aa="R" >> peptide_next_aa="R" num_tol_term="2"/> >> <alternative_protein protein="tr|B7WNR0|B7WNR0_HUMAN Isoform of P02768, >> Serum albumin OS=Homo sapiens GN=ALB PE=1 SV=1" peptide_prev_aa="R" >> peptide_next_aa="R" num_tol_term="2"/> >> <alternative_protein protein="tr|C9JKR2|C9JKR2_HUMAN Isoform of P02768, >> Albumin, isoform CRA_k OS=Homo sapiens GN=ALB PE=1 SV=1" >> peptide_prev_aa="R" peptide_next_aa="R" num_tol_term="2"/> >> <alternative_protein protein="tr|D6RHD5|D6RHD5_HUMAN Isoform of P02768, >> Serum albumin OS=Homo sapiens GN=ALB PE=1 SV=1" peptide_prev_aa="R" >> peptide_next_aa="R" num_tol_term="2"/> >> <alternative_protein protein="tr|H0YA55|H0YA55_HUMAN Isoform of P02768, >> Serum albumin (Fragment) OS=Homo sapiens GN=ALB PE=1 SV=1" >> peptide_prev_aa="R" peptide_next_aa="R" num_tol_term="2"/> >> <alternative_protein protein="sp|P02768-2|ALBU_HUMAN Isoform of P02768, >> Isoform 2 of Serum albumin OS=Homo sapiens GN=ALB" peptide_prev_aa="R" >> peptide_next_aa="R" num_tol_term="2"/> >> <alternative_protein protein="sp|P02768-3|ALBU_HUMAN Isoform of P02768, >> Isoform 3 of Serum albumin OS=Homo sapiens GN=ALB" peptide_prev_aa="R" >> peptide_next_aa="R" num_tol_term="2"/> >> <alternative_protein protein="sp|ALBU_BOVIN|" peptide_prev_aa="R" >> peptide_next_aa="R" num_tol_term="2"/> >> <search_score name="hyperscore" value="19.365"/> >> <search_score name="nextscore" value="17.327"/> >> <search_score name="expect" value="1.083e-05"/> >> </search_hit> >> </search_result> >> </spectrum_query> >> >> PTMProphet pep.xml output for scan 74042 (does not work as expected): >> <spectrum_query start_scan="74042" >> uncalibrated_precursor_neutral_mass="1494.4763" assumed_charge="2" >> spectrum="QEP2_2018_0812_AZ_033_az736_AZ.74042.74042.2" end_scan="74042" >> index="54976" precursor_neutral_mass="1494.4722" >> retention_time_sec="8409.789"> >> <search_result> >> <search_hit peptide="VTKCCTESLVNR" massdiff="142.8135" >> calc_neutral_pep_mass="1351.6587" peptide_next_aa="R" >> num_missed_cleavages="1" num_tol_term="2" num_tot_proteins="10" >> tot_num_ions="22" hit_rank="1" num_matched_ions="11" >> protein="sp|P02768|ALBU_HUMAN" peptide_prev_aa="R" is_rejected="0" >> protein_descr="Serum albumin OS=Homo sapiens GN=ALB PE=1 SV=2"> >> <alternative_protein protein="tr|A0A087WWT3|A0A087WWT3_HUMAN" >> protein_descr="Isoform of P02768, Serum albumin OS=Homo sapiens GN=ALB PE=1 >> SV=1" num_tol_term="2" peptide_prev_aa="R" peptide_next_aa="R"/> >> <alternative_protein protein="tr|A0A0C4DGB6|A0A0C4DGB6_HUMAN" >> protein_descr="Isoform of P02768, Serum albumin OS=Homo sapiens GN=ALB PE=1 >> SV=1" num_tol_term="2" peptide_prev_aa="R" peptide_next_aa="R"/> >> <alternative_protein protein="tr|B7WNR0|B7WNR0_HUMAN" >> protein_descr="Isoform of P02768, Serum albumin OS=Homo sapiens GN=ALB PE=1 >> SV=1" num_tol_term="2" peptide_prev_aa="R" peptide_next_aa="R"/> >> <alternative_protein protein="tr|C9JKR2|C9JKR2_HUMAN" >> protein_descr="Isoform of P02768, Albumin, isoform CRA_k OS=Homo sapiens >> GN=ALB PE=1 SV=1" num_tol_term="2" peptide_prev_aa="R" peptide_next_aa="R"/> >> <alternative_protein protein="tr|D6RHD5|D6RHD5_HUMAN" >> protein_descr="Isoform of P02768, Serum albumin OS=Homo sapiens GN=ALB PE=1 >> SV=1" num_tol_term="2" peptide_prev_aa="R" peptide_next_aa="R"/> >> <alternative_protein protein="tr|H0YA55|H0YA55_HUMAN" >> protein_descr="Isoform of P02768, Serum albumin (Fragment) OS=Homo sapiens >> GN=ALB PE=1 SV=1" num_tol_term="2" peptide_prev_aa="R" peptide_next_aa="R"/> >> <alternative_protein protein="sp|P02768-2|ALBU_HUMAN" >> protein_descr="Isoform of P02768, Isoform 2 of Serum albumin OS=Homo >> sapiens GN=ALB" num_tol_term="2" peptide_prev_aa="R" peptide_next_aa="R"/> >> <alternative_protein protein="sp|P02768-3|ALBU_HUMAN" >> protein_descr="Isoform of P02768, Isoform 3 of Serum albumin OS=Homo >> sapiens GN=ALB" num_tol_term="2" peptide_prev_aa="R" peptide_next_aa="R"/> >> <alternative_protein protein="sp|ALBU_BOVIN|" num_tol_term="2" >> peptide_prev_aa="K" peptide_next_aa="R"/> >> <search_score name="hyperscore" value="19.365"/> >> <search_score name="nextscore" value="17.327"/> >> <search_score name="expect" value="1.083e-05"/> >> <analysis_result analysis="peptideprophet"> >> <peptideprophet_result probability="0.9504" >> all_ntt_prob="(0.0000,0.9728,0.9504)"> >> <search_score_summary> >> <parameter name="fval" value="6.1669"/> >> <parameter name="ntt" value="2"/> >> <parameter name="nmc" value="1"/> >> <parameter name="massd" value="0.337"/> >> <parameter name="isomassd" value="3"/> >> </search_score_summary> >> </peptideprophet_result> >> </analysis_result> >> <analysis_result analysis="interprophet"> >> <interprophet_result probability="0.865139" >> all_ntt_prob="(0,0.922921,0.865139)"> >> <search_score_summary> >> <parameter name="nrs" value="-15"/> >> <parameter name="nsi" value="0.9975"/> >> <parameter name="nsm" value="2.9825"/> >> <parameter name="nsp" value="20"/> >> </search_score_summary> >> </interprophet_result> >> </analysis_result> >> </search_hit> >> </search_result> >> </spectrum_query> >> >> -- >> You received this message because you are subscribed to the Google Groups >> "spctools-discuss" group. >> To unsubscribe from this group and stop receiving emails from it, send an >> email to spctools...@googlegroups.com <javascript:>. >> To view this discussion on the web visit >> https://groups.google.com/d/msgid/spctools-discuss/c957b746-ceb3-4591-a47a-0fbfd6a40167%40googlegroups.com >> >> 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