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.
