Xianyin, This recently happened to me. In my case it turned out that the majority of proteins in the sample were not present in the search database. Once I determined this and added in the correct species into the original search database, xinteract completed successfully. Only a few proteins were from the targeted species were present in the sample and the vast majority of proteins in the sample were from the background species. Without the protein sequences from the "background species" in the search database the analysis by the Prophets failed.
Brian Hampton Protein Analysis Lab Center for Vascular and Inflammatory Diseases University of Maryland School of Medicine 655 West Baltimore Street BRB 7-018 Baltimore MD 21201 V: 410-706-8207 On Mon, Mar 10, 2014 at 2:19 PM, David Shteynberg < [email protected]> wrote: > 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. > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. 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