Thanks a lot, David! I then realized that it may be my own problem. I merged the pepXML files from replicates, and it reported the problem. If I ran PeptideProphet for each replicate separately, they all passed successfully.
-Han On Friday, August 7, 2015 at 2:52:48 PM UTC-4, David Shteynberg wrote: > > 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] <javascript:>> 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] >> <javascript:>> 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] <javascript:>. >>> To post to this group, send email to [email protected] >>> <javascript:>. >>> 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.
