Hello Scott, It sounds like the model PeptideProphet generates with the SVN version of the TPP fails the model quality controls on your data. I cannot be sure of the reason without seeing the data. Please post the file to our FTP site, instructions here:
http://tools.proteomecenter.org/wiki/index.php?title=TPP:Frequently_Asked_Questions#How_do_I_upload_files_to_the_SPC_tools_team.3F Thanks, -David On Tue, Jul 28, 2009 at 6:35 PM, Scott Stansfield<[email protected]> wrote: > > Hi All, > > I've just my updated TPP (version 4.4) from the svn last night, > unfortunately when I run xinteract on my sets of TANDEM search results > "0" is returned for all peptide prophet probabilities for all > spectra. What's upsetting is it worked in the last version I had (TPP > 4.2.1), peptide prophet reports the models and the graphs for each > charge model are saved in the directory. Does anyone know where this > problem could have arisen? > > Cheers, > > Scott. > > I run xinteract on my files like this: > >>xinteract -OdP -dREV -p0 -eT -E20090409_1a_n1_v2 >>-N/data/tpp/data/processing/stansfie/20090409_1a_n1_v2/TANDEM.interact.pep.xml >> *.TANDEM.pep.xml > > bits of the TANDEM.interact.pep.xml output look like this: > > ...cropped... (there's a model) > > <roc_data_point min_prob="0.99" sensitivity="0.8941" error="0.0008" > num_corr="1501" num_incorr="1"/> > <roc_data_point min_prob="0.98" sensitivity="0.9298" error="0.0013" > num_corr="1561" num_incorr="2"/> > <roc_data_point min_prob="0.95" sensitivity="0.9651" error="0.0024" > num_corr="1620" num_incorr="4"/> > <roc_data_point min_prob="0.90" sensitivity="0.9835" error="0.0036" > num_corr="1651" num_incorr="6"/> > > ...cropped...(this should be better than zero since it's the largest > hyperscore in the dataset) > > </search_hit> > </search_result> > </spectrum_query> > <spectrum_query spectrum="20090409_1a_n1_K4-AMG_C10.01455.01455.3" > start_scan="95" end_scan="95" precursor_neutral_mass="2209.9282" > assumed_charge="3" index="1837" retention_time_sec="96.952" > experiment_label="20090409_1a_n1_v2"> > <search_result> > <search_hit hit_rank="1" peptide="LGEHNIDVLEGNEQFINAAK" > peptide_prev_aa="R" peptide_next_aa="I" protein="sp|TRYP_PIG|" > num_tot_proteins="3" num_matched_ions="25" tot_num_ions="76" > calc_neutral_pep_mass="2210.0967" massdiff="-0.169" num_tol_term="2" > num_missed_cleavages="0" is_rejected="0"> > <alternative_protein protein="sp|TRYP_PIG|" num_tol_term="2" > peptide_prev_aa="R" peptide_next_aa="I"/> > <alternative_protein protein="sp|TRYP_PIG|" num_tol_term="2" > peptide_prev_aa="R" peptide_next_aa="I"/> > <search_score name="hyperscore" value="977"/> > <search_score name="nextscore" value="412"/> > <search_score name="bscore" value="2"/> > <search_score name="yscore" value="2"/> > <search_score name="expect" value="0.0023"/> > <analysis_result analysis="peptideprophet"> > <peptideprophet_result probability="0" all_ntt_prob="(0,0,0)" > analysis="none"/> > </analysis_result> > </search_hit> > > ...cropped... > > > > --~--~---------~--~----~------------~-------~--~----~ You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To post to this group, send email to [email protected] To unsubscribe from this group, send email to [email protected] For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en -~----------~----~----~----~------~----~------~--~---
