Brian, The fact that the analysis gives you no peptides when there are no peptides to be had should be classified as a WIN! Otherwise, you could be misled to publish erroneous conclusions based on false positive "identifications".
Cheers, -David On Mon, Mar 10, 2014 at 11:38 AM, Brian Hampton <[email protected]>wrote: > 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. > 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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