HI David, I should have said, .... Prophets failed as they should have since no targets were in the database. You are correct that it is indeed a win.
Brian On Mon, Mar 10, 2014 at 2:41 PM, David Shteynberg < [email protected]> wrote: > 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. > 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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