Has anyone been able to feed OMSSA native pepXML output (using -op option) through PeptideProphet? I don't know if anyone has tested this or if OMSSA has only been tested using a separate converter.
Replacing the protein word was to address the error message having no DECOY entries. This fix hopefully addressed that one point which is seems to have done. So to address the follow-up problem, minimally you'll want to include the diagnostic output from PeptideProphetParser in case anything obvious shows up from that info. Possibly you'll need to have a developer, who knows more than I do, take a closer look at your data. - Jimmy Ping wrote: > Jimmy, > > As you suggested, I replace the value in the "protein" with the first > word from the "protein_descr" in each search_hit entry. But when I run > PeptideProphetParser, it still gives the error message: > > ERROR: NAN probability density detected. Please alert the > developer !!! > > Is there anything else I need to fix? > > Thanks! > > Ping > > > Here is the example of the result after I replace protein/ > protein_descr > > for not decoy string, it looks like this: > > <search_hit hit_rank="1" peptide="YPSRPLPPPPPFGLGFVPPPPPPYGPGR" > peptide_prev_aa="R" peptide_next_aa="I" protein="gi|73975149|ref| > XP_862242.1|" num_tot_proteins="3" num_matched_ions="15" > tot_num_ions="54" calc_neutral_pep_mass="2949.569" > massdiff="0.59985990298992" is_rejected="0" protein_descr="gi| > 73975149| > ref|XP_862242.1| PREDICTED: hypothetical protein XP_857149 isoform 2 > [Canis familiaris]" num_tol_term="2" num_missed_cleavages="0"> > <alternative_protein protein="gi|73975151|ref|XP_862273.1|" > protein_descr="gi|73975151|ref|XP_862273.1| PREDICTED: hypothetical > protein XP_857180 isoform 3 [Canis familiaris]"/> > <alternative_protein protein="gi|73975153|ref|XP_862298.1|" > protein_descr="gi|73975153|ref|XP_862298.1| PREDICTED: hypothetical > protein XP_857205 isoform 4 [Canis familiaris]"/> > <search_score name="pvalue" value="0.000002382663488"/> > <search_score name="expect" value="0.028320338214958"/> > </search_hit> > > For decoy string, it looks like this: > > <search_hit hit_rank="2" peptide="QESARYSAKVTVAGLEESATEAQQQIR" > peptide_prev_aa="K" peptide_next_aa="S" protein="decoy_2098 > 2" num_tot_proteins="1" num_matched_ions="17" tot_num_ions="52" > calc_neutral_pep_mass="2949.481" massdiff="0.9728599071700 > 05" is_rejected="0" protein_descr="decoy_20982"> > <search_score name="pvalue" value="0.000014221885248"/> > <search_score name="expect" value="0.168173793062284"/> > </search_hit> > > > On Jul 2, 4:44 pm, Jimmy Eng <[email protected]> wrote: >> Ping, >> >> I just downloaded OMSSA 2.1.4 and tried the direct pep.xml export >> myself. I do see a problem with the resulting pep.xml file that the >> "-op" option generates that's causing the problem you're seeing. >> >> The key error message in your output is this: >> WARNING: No decoys with label DECOY were found in this dataset. >> >> Looking at the generated pep.xml files, OMSSA seems to be placing some >> number in the protein="" attribute of each search_hit element. Whereas >> PeptideProphet expects this protein attribute to contain some protein >> identifier that includes the DECOY string for those decoy matches. In >> the converters we use, the value of the protein attribute is the first >> word of the protein definition line. >> >> As for a fix, we need someone at NCBI to address this and hopefully >> someone here will contact them about this. For you in the short term, >> you're going to need a developer to modify you pep.xml files to replace >> the value in the "protein" attribute with the first word from the >> "protein_descr" attribute of each search_hit entry. >> >> - Jimmy >> >> Ping wrote: >>> Hi, >>> I am trying to run the xinteract on the omssa pep.xml output files. my >>> omssa's version is 2.1.4, my TPP version is 4.2.1. But I couldn't get >>> it through. I search the old post, there is a similar post, but the >>> problem was solved by specifying enzyme to xinteract. >>> I tried it, but is still not working. InteractParse went through, but >>> PeptideProphetParser got stuck by a segmentation fault. >>> Any help would be greatly appreciated! >>> Many Thanks, >>> Ping >>> ***** output for interactParser and PeptideProphetParser >>> InteractParser 'interact.pep.xml' 'omssa.pep.xml' -L'7' -E'trypsin' -C >>> -P >>> file 1: ParoSaliv_SHAM_03.pep.xml >>> processed altogether 2623 results >>> PeptideProphetParser 'interact.pep.xml' DECOY=DECOY MINPROB=0 >>> NONPARAM >>> Using Decoy Label "DECOY". >>> Using non-parametric distributions >>> (OMSSA) (minprob 0) >>> WARNING!! The discriminant function for OMSSA is not yet complete. It >>> is presented here to help facilitate trial and discussion. Reliance >>> on this code for publishable scientific results is not recommended. >>> init with OMSSA Trypsin >>> MS Instrument info: Manufacturer: UNKNOWN, Model: UNKNOWN, Ionization: >>> UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN >>> PeptideProphet (TPP v4.2 JETSTREAM rev 1, Build 200905131510 >>> (linux)) akel...@isb >>> read in 75 1+, 1790 2+, 749 3+, 0 4+, 0 5+, 0 6+, and 0 7+ spectra. >>> Initialising statistical models ... >>> WARNING: No decoys with label DECOY were found in this dataset. >>> reverting to fully unsupervised method. >>> Iterations: .........10.........20 >>> Segmentation fault > > --~--~---------~--~----~------------~-------~--~----~ You received this message because you are subscribed to the Google Groups "spctools-discuss" group. 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