Thanks David, I'll try your suggestions. Also, I'm thinking there might be proteins from another species in the sample that are not represented in the database I'm searching.
Thanks, Brian > On Feb 28, 2014, at 6:18 PM, David Shteynberg > <[email protected]> wrote: > > 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. > 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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