Hi Brian, This message is quite telling: 10751 Decoys, and 11603 Non-Decoys
Assuming 50% of the wrong ones are Decoys there are less than 900 correct matches in this dataset. That said, I don't think using the default parameteric option is the best choice here due to the extended tail of the negative distribution and the relatively small number of correct IDs. I would suggest you try the semi-parametric (non-parametric option), also run with minimum probability 0 and perhaps set a CLEVEL of 1 with advanced option -c1 or -c2 (higher is more conservative) to help keep the positive distribution of the model on the shoulder. Finally, I would recommend you try the latest version 4.7.0, which is due out today. Cheers, -David On Fri, Feb 28, 2014 at 3:09 PM, Brian Hampton <[email protected]> wrote: > I am trying to squeak additional mass accuracy out of an LTQ by collecting > MS1 data with Enhanced Scan and in Profile mode so the data will have > isotopic resolution. This had the expected result of shifting the > frequency of peptides observed at a particular error down from ~0.75 (when > collected using normal scan rate and centroid mode) to center the curve > over an error of 0 (when collected using enhanced scan rate and profile > mode). Nice. > > I processed the raw files with msconvert and used the --filter > "peakPicking true 1-1" argument and run it through TPP v 4.6.2 with Tandem > as the search engine. This has worked fine on samples until today when > this latest data set (which is a pull down experiment), xinteract fails to > produce a pep.xml file and results in a warning that says: > > WARNING: Mixture model quality test failed for charge (1+). > WARNING: Mixture model quality test failed for charge (2+). > WARNING: Mixture model quality test failed for charge (3+). > > The tandem.pep.xml file contains many high scoring peptides. And there > are good +1,+2 & +3 spectral matches. > > I am wondering if there is an argument to msconvert that I am missing. Or > maybe my approach to collecting the data is incompatible with TPP? Or > could this be a problem with K-score vs native tandem scoring? I haven't > tried another search using native Tandem scoring yet. > > Below is the output from TPP. > > Thanks in advance for any help. > > Cheers, > Brian > > > > > > EXECUTING: cd /usr/local/tpp/data/projects/lindsey/xiap-ide12; > /usr/local/tpp/bin/xinteract -Ninteract-XIAP-IDE12.pep.xml -p0.05 -l5 -Op > -dDECOY 140226-XIAP-IDE12-5pct.tandem.pep.xml > > /usr/local/tpp/bin/xinteract (TPP v4.6 OCCUPY rev 2, Build 201302151642 > (linux)) > > running: "/usr/local/tpp/bin/InteractParser 'interact-XIAP-IDE12.pep.xml' > '140226-XIAP-IDE12-5pct.tandem.pep.xml' -L'5'" > file 1: 140226-XIAP-IDE12-5pct.tandem.pep.xml > SUCCESS: CORRECTED data file > /usr/local/tpp/data/projects/lindsey/xiap-ide12/140226-XIAP-IDE12-5pct.mzML > in msms_run_summary tag ... > processed altogether 22365 results > INFO: Results written to file: > /usr/local/tpp/data/projects/lindsey/xiap-ide12/interact-XIAP-IDE12.pep.xml > command completed in 6 sec > > running: "/usr/local/tpp/bin/DatabaseParser 'interact-XIAP-IDE12.pep.xml'" > command completed in 1 sec > > running: "/usr/local/tpp/bin/RefreshParser 'interact-XIAP-IDE12.pep.xml' > '/usr/local/tpp/data/dbase/ixodes-plus-crap_DECOY.fasta'" > - Building Commentz-Walter keyword tree... - Searching the tree... > - Linking duplicate entries... - Printing results... > > command completed in 6 sec > > running: "/usr/local/tpp/bin/PeptideProphetParser > 'interact-XIAP-IDE12.pep.xml' MINPROB=0.05 DECOY=DECOY" > Using Decoy Label "DECOY". > (X! Tandem (k-score)) > init with X! Tandem (k-score) trypsin > MS Instrument info: Manufacturer: Thermo Scientific, Model: UNKNOWN, > Ionization: nanoelectrospray, Analyzer: radial ejection linear ion trap, > Detector: electron multiplier > > PeptideProphet (TPP v4.6 OCCUPY rev 2, Build 201302151642 (linux)) > AKeller@ISB > read in 2445 1+, 9959 2+, 9950 3+, 0 4+, 0 5+, 0 6+, and 0 7+ spectra. > Initialising statistical models ... > Found 10751 Decoys, and 11603 Non-Decoys > Iterations: .........10.........20........ > WARNING: Mixture model quality test failed for charge (1+). > WARNING: Mixture model quality test failed for charge (2+). > WARNING: Mixture model quality test failed for charge (3+). > model complete after 29 iterations > command completed in 4 sec > > running: "/usr/local/tpp/bin/ProphetModels.pl -i > interact-XIAP-IDE12.pep.xml -d DECOY" > Analyzing interact-XIAP-IDE12.pep.xml ... > Parsing search results > "/usr/local/tpp/data/projects/lindsey/xiap-ide12/140226-XIAP-IDE12-5pct (X! > Tandem (k-score))"... > => Total of 0 hits. > => Total of 0 decoy hits. > => Total of 0 excluded hits. > Warning: empty y range [0:0], adjusting to [0:1] > Warning: empty y range [0:0], adjusting to [0:1] > > plot "interact-XIAP-IDE12.pep_FVAL.tsv" using 1:17 title "Observed" with > line lc -1 , "interact-XIAP-IDE12.pep_FVAL.tsv" using 1:18 title "Model > Pos" with line lc 3 , "interact-XIAP-IDE12.pep_FVAL.tsv" using 1:19 title > "Model Neg" with line lc 1 > > ^ > "interact-XIAP-IDE12.pep_FVAL.gp", line 23: warning: Skipping data file > with no valid points > Warning: empty y range [0:0], adjusting to [0:1] > > plot "interact-XIAP-IDE12.pep_FVAL.tsv" using 1:20 title "Observed" with > line lc -1 , "interact-XIAP-IDE12.pep_FVAL.tsv" using 1:21 title "Model > Pos" with line lc 3 , "interact-XIAP-IDE12.pep_FVAL.tsv" using 1:22 title > "Model Neg" with line lc 1 > > ^ > "interact-XIAP-IDE12.pep_FVAL.gp", line 25: warning: Skipping data file > with no valid points > Warning: empty y range [0:0], adjusting to [0:1] > > plot "interact-XIAP-IDE12.pep_PPPROB.tsv" using 2:1 title "PeptideProphet" > with line lt 1 lc 3 , x notitle with line lt 0 lc -1 > > ^ > "interact-XIAP-IDE12.pep_PPPROB.gp", line 17: warning: Skipping data file > with no valid points > > plot "interact-XIAP-IDE12.pep_IPPROB.tsv" using 2:1 title "iProphet" with > line lt 1 lc 3 , "interact-XIAP-IDE12.pep_PPPROB.tsv" using 2:1 title > "PeptideProphet" with line lt 1 lc 1 , x notitle with line lt 0 lc -1 > > ^ > "interact-XIAP-IDE12.pep_IPPROB.gp", line 17: warning: Skipping data file > with no valid points > > plot "interact-XIAP-IDE12.pep_IPPROB.tsv" using 2:1 title "iProphet" with > line lt 1 lc 3 , "interact-XIAP-IDE12.pep_PPPROB.tsv" using 2:1 title > "PeptideProphet" with line lt 1 lc 1 , x notitle with line lt 0 lc -1 > > > ^ > "interact-XIAP-IDE12.pep_IPPROB.gp", line 17: warning: Skipping data file > with no valid points > command completed in 0 sec > > running: "/usr/local/tpp/cgi-bin/PepXMLViewer.cgi -I > /usr/local/tpp/data/projects/lindsey/xiap-ide12/interact-XIAP-IDE12.pep.xml" > Segmentation fault (core dumped) > > command "/usr/local/tpp/cgi-bin/PepXMLViewer.cgi -I > /usr/local/tpp/data/projects/lindsey/xiap-ide12/interact-XIAP-IDE12.pep.xml" > exited with non-zero exit code: 35584 > QUIT - the job is incomplete > > Command FAILED > RETURN CODE:35584 > > -- > 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/groups/opt_out. > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. 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