Hi Scott, I just checked in a fix to this error in SVN. The problem was the spectrum names were getting extra whitespace at the end in the .tandem files, which were being propagated to the pepXML. The workaround that I committed trims any extra whitespace surrounding the spectrum name. The fix is fairly benign and I have verified that it works on your data. Please give it a test and report back any issues.
Thanks, -David On Wed, Jul 29, 2009 at 12:04 PM, Natalie Tasman < [email protected]> wrote: > > Hi Scott, > > Thanks for your feedback and I'm glad David is taking a look. I just > want to remind everyone that svn trunk (which you're working with) is > development code. If you want stable results stick with the official > releases. > > -Natalie > > > 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 -~----------~----~----~----~------~----~------~--~---
