All of your peptides have probabilities of 0 and since the setting shows MINPROB=0.05, all of the spetra are filtered from the resulting interact.pep.xml file. This message is very telling "Found 11360 Decoys, and 10614 Non-Decoys", assuming your decoy rate is 0.5 (rate of decoys amongst random matches) then you have 0 correct results in this search.
-David On Mon, Mar 10, 2014 at 10:41 AM, <[email protected]> wrote: > One of my data failed and the return code 65280. The details are copied > below. > > I noticed that I have more decoys than non-decoys. However, I found many > good MS2 spectra when I manually check my raw data. > > What settings should I use to get the real good peptides validated through > TPP (I used semi- when I did the database search using X!Tandem)? > > Thanks. > > Xianyin. > > > ------------------------------------------------------------------------------------------------------------------------------------------------------- > c:\Inetpub\tpp-bin\xinteract (TPP v4.6 OCCUPY rev 3, Build 201307241109 > (MinGW)) > PPM mode in Accurate Mass Model ... > running: "C:/Inetpub/tpp-bin/InteractParser "interact.pep.xml" > "20140307_12A.tandem.pep.xml" -L"7"" > file 1: 20140307_12A.tandem.pep.xml > SUCCESS: CORRECTED data file > c:/Inetpub/wwwroot/ISB/data/20140307_12A.mzXML in msms_run_summary tag ... > processed altogether 22005 results > INFO: Results written to file: c:/Inetpub/wwwroot/ISB/data/interact.pep.xml > command completed in 6 sec > running: "C:/Inetpub/tpp-bin/DatabaseParser "interact.pep.xml"" > command completed in 1 sec > running: "C:/Inetpub/tpp-bin/RefreshParser "interact.pep.xml" > "c:/Inetpub/wwwroot/ISB/data/RAT20140219T_DECOY.fasta"" > - Searching the tree... > - Linking duplicate entries... - Printing results... > - Building Commentz-Walter keyword tree...command completed in 9 sec > running: "C:/Inetpub/tpp-bin/PeptideProphetParser "interact.pep.xml" > MINPROB=0.05 PPM ACCMASS DECOY=DECOY" > using Accurate Mass Bins > using PPM mass difference > Using Decoy Label "DECOY". > (X! Tandem (k-score)) > adding Accurate Mass mixture distr > init with X! Tandem (k-score) trypsin > MS Instrument info: Manufacturer: Thermo Scientific, Model: LTQ Orbitrap > Velos, Ionization: electrospray ionization, Analyzer: radial ejection > linear ion trap, Detector: electron multiplier > PeptideProphet (TPP v4.6 OCCUPY rev 3, Build 201307241109 (MinGW)) > AKeller@ISB > read in 0 1+, 6945 2+, 6638 3+, 4461 4+, 3930 5+, 0 6+, and 0 7+ spectra. > Initialising statistical models ... > Found 11360 Decoys, and 10614 Non-Decoys > Iterations: .........10.........20.........30.. > WARNING: Mixture model quality test failed for charge (2+). > WARNING: Mixture model quality test failed for charge (3+). > WARNING: Mixture model quality test failed for charge (4+). > WARNING: Mixture model quality test failed for charge (5+). > model complete after 33 iterations > command completed in 34 sec > running: "C:/Inetpub/tpp-bin/ProphetModels.pl -i interact.pep.xml -d > "DECOY"" > Analyzing interact.pep.xml ... > Reading Accurate Mass Model model +1 ... > Reading Accurate Mass Model model +2 ... > Reading Accurate Mass Model model +3 ... > Reading Accurate Mass Model model +4 ... > Reading Accurate Mass Model model +5 ... > Reading Accurate Mass Model model +6 ... > Reading Accurate Mass Model model +7 ... > Parsing search results "c:/Inetpub/wwwroot/ISB/data/20140307_12A (X! > Tandem (k-score))"... > => Found 0 hits. (0 decoys, 0 excluded) > => Total so far: 0 hits. (0 decoys, 0 excluded) > The system cannot find the path specified. > command completed in 1 sec > running: "c:/Inetpub/wwwroot/../tpp-bin/PepXMLViewer.cgi -I > c:/Inetpub/wwwroot/ISB/data/interact.pep.xml" > command "c:/Inetpub/wwwroot/../tpp-bin/PepXMLViewer.cgi -I > c:/Inetpub/wwwroot/ISB/data/interact.pep.xml" failed: Unknown error > command "c:/Inetpub/wwwroot/../tpp-bin/PepXMLViewer.cgi -I > c:/Inetpub/wwwroot/ISB/data/interact.pep.xml" exited with non-zero exit > code: 255 > QUIT - the job is incomplete > command "c:\Inetpub\tpp-bin\xinteract -Ninteract.pep.xml -p0.05 -l7 -PPM > -OAp -dDECOY 20140307_12A.tandem.pep.xml" failed: Unknown error > > -- > 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. > -- 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.
