There is also a clear problem with the way Tide has reported the modification on the peptide in pepXML:
On Fri, Aug 7, 2015 at 11:51 AM, David Shteynberg < [email protected]> wrote: > Hi Han, > > It is possible the reported scores are not all that PeptideProphet expects > in this type of pepXML file. If you can post the file for download I can > test the actual issue. > > Thanks, > -David > > On Fri, Aug 7, 2015 at 11:02 AM, Han Hu <[email protected]> wrote: > >> Hi, >> >> I was trying to run PeptideProphet on Tide results and got following >> results >> >> The data (interact.tide.pep.xml) looks like >> <spectrum_query spectrum="20130510_EXQ1_IgPa_QC_UPS1_04.63208.63208.4" >> start_scan="63208" end_scan="63208" precursor_neutral_mass="3949.8508" >> assumed_charge="4" index="317452"> >> <search_result> >> <search_hit hit_rank="1" peptide="LFMREMFEFWVYVFSLGICLVCGWWLFWGR" >> peptide_prev_aa="K" peptide_next_aa="F" protein="sp|Q46867|YGIZ_ECOLI" >> num_tot_proteins="1" num_matched_ions="1" tot_num_ions="174" >> calc_neutral_pep_mass="3949.8796" massdiff="-0.0288" num_tol_term="2" >> num_missed_cleavages="1" num_matched_peptides="2" is_rejected="0" >> protein_descr="Inner membrane protein YgiZ OS=Escherichia coli (strain K12) >> GN=ygiZ PE=1 SV=1"> >> <modification_info modified_peptide="LFM[16]REMFEFWVYVFSLGICLVCGWWLFWGR"> >> <mod_aminoacid_mass position="3" mass="15.99"/> >> </modification_info> >> <modification_info modified_peptide="LFMREMFEFWVYVFSLGICLVCGWWLFWGR"> >> <mod_aminoacid_mass position="19" mass="57.02"/> >> <mod_aminoacid_mass position="22" mass="57.02"/> >> </modification_info> >> <search_score name="spscore" value="0.19079092"/> >> <search_score name="sprank" value="1"/> >> <search_score name="xcorr_score" value="0.20136720"/> >> <search_score name="xcorr_rank" value="1"/> >> <search_score name="deltacn" value="0.00247400"/> >> </search_hit> >> </search_result> >> </spectrum_query> >> <spectrum_query spectrum="20130510_EXQ1_IgPa_QC_UPS1_04.62879.62879.4" >> start_scan="62879" end_scan="62879" precursor_neutral_mass="3949.8508" >> assumed_charge="4" index="317453"> >> <search_result> >> <search_hit hit_rank="1" peptide="LFMREMFEFWVYVFSLGICLVCGWWLFWGR" >> peptide_prev_aa="K" peptide_next_aa="F" protein="sp|Q46867|YGIZ_ECOLI" >> num_tot_proteins="1" num_matched_ions="0" tot_num_ions="174" >> calc_neutral_pep_mass="3949.8796" massdiff="-0.0288" num_tol_term="2" >> num_missed_cleavages="1" num_matched_peptides="2" is_rejected="0" >> protein_descr="Inner membrane protein YgiZ OS=Escherichia coli (strain K12) >> GN=ygiZ PE=1 SV=1"> >> <modification_info modified_peptide="LFMREM[16]FEFWVYVFSLGICLVCGWWLFWGR"> >> <mod_aminoacid_mass position="6" mass="15.99"/> >> </modification_info> >> <modification_info modified_peptide="LFMREMFEFWVYVFSLGICLVCGWWLFWGR"> >> <mod_aminoacid_mass position="19" mass="57.02"/> >> <mod_aminoacid_mass position="22" mass="57.02"/> >> </modification_info> >> <search_score name="spscore" value="0.00000000"/> >> <search_score name="sprank" value="1"/> >> <search_score name="xcorr_score" value="0.09289770"/> >> <search_score name="xcorr_rank" value="1"/> >> <search_score name="deltacn" value="0.00039120"/> >> </search_hit> >> </search_result> >> </spectrum_query> >> >> --------------------------------------------------------------------------------------------------------------------------------------------------------------------- >> $ PeptideProphetParser interact.tide.pep.xml MINPROB=0 FORCEDISTR >> Forcing output of mixture model >> (Crux) (minprob 0) >> init with Crux trypsin >> MS Instrument info: Manufacturer: NA, Model: NA, Ionization: NA, >> Analyzer: UNKNOWN, Detector: UNKNOWN >> >> PeptideProphet (TPP v4.8.0 PHILAE, Build 201506081212-exported >> (RedHatEnterpriseServer-x86_64)) AKeller@ISB >> read in 0 1+, 0 2+, 0 3+, 0 4+, 0 5+, 0 6+, and 0 7+ spectra. >> read in no data >> >> Does anyone know the reason? Is it because of the format, low score or >> something else. >> >> Thanks a lot, >> >> >> -Han >> >> >> >> -- >> 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 [email protected]. >> To post to this group, send email to [email protected]. >> Visit this group at http://groups.google.com/group/spctools-discuss. >> For more options, visit https://groups.google.com/d/optout. >> > > -- 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 [email protected]. To post to this group, send email to [email protected]. Visit this group at http://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout.
