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 -~----------~----~----~----~------~----~------~--~---
