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.
