Lately I've been encountering a problem with peptide prophet were it seems to fail and discard some peptides due to a mixture model quality problem. Since i am merely a software developer / administrator and NOT the person actually running the mass specs, I can't really comment on what's going on with the experimenters.
Can anyone tell me what the mixture model represents and how to improve its quality experimentally? Or maybe is there a way to bypass the mixture model test in Peptide Prophet? I tried the -OF option and it still fails. We are using LTQ -> Sequest / Mascot -> TPP. Here is the output, you can see that a lot is getting thrown out: /opt/tpp/`uname -p`/bin/xinteract -Ninteract.xml -Ol -dREV *.xml uname -p /opt/tpp/x86_64/bin/xinteract (TPP v4.2 JETSTREAM rev 0, Build 200903231240 (linux)) running: "/opt/tpp/x86_64/bin/InteractParser 'interact.xml' 'cox-2- h_G_C-1_090307035947.pep.xml' 'cox-2-h_S_C-1_090307023841.pep.xml' 'cox-2M_H_G_C.pep.xml' 'cox-2M_H_S_C.pep.xml' -L'7'" file 1: cox-2-h_G_C-1_090307035947.pep.xml file 2: cox-2-h_S_C-1_090307023841.pep.xml file 3: cox-2M_H_G_C.pep.xml file 4: cox-2M_H_S_C.pep.xml processed altogether 4105 results results written to file /data/www/htdocs/qInteract/data2/ xuanwen_20090305121123/xuanwen_3626/interact.shtml command completed in 1 sec running: "/opt/tpp/x86_64/bin/PeptideProphetParser 'interact.xml' LEAVE DECOY=REV" Using Decoy Label "REV". (SEQUEST) (leaving deltacn* entries) init with SEQUEST trypsin MS Instrument info: Manufacturer: Thermo Scientific, Model: LTQ FT, Ionization: ESI, Analyzer: FTMS, Detector: unknown PeptideProphet (TPP v4.2 JETSTREAM rev 0, Build 200903231240 (linux)) akel...@isb read in 0 1+, 3416 2+, 469 3+, 60 4+, 1 5+, 0 6+, and 0 7+ spectra. Initialising statistical models ... Iterations: .........10.........20.... WARNING: Mixture model quality test failed for charge (1+). 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+). WARNING: Mixture model quality test failed for charge (6+). WARNING: Mixture model quality test failed for charge (7+). model complete after 25 iterations command completed in 1 sec running: "/opt/tpp/x86_64/bin/ProphetModels.pl -i interact.xml" Analyzing interact.xml ... Parsing search results "cox-2-h_G_C-1_090307035947 (SEQUEST)"... => Total of 35 hits. Parsing search results "cox-2-h_S_C-1_090307023841 (SEQUEST)"... => Total of 52 hits. Parsing search results "cox-2M_H_G_C (SEQUEST)"... => Total of 3 hits. Parsing search results "cox-2M_H_S_C (SEQUEST)"... => Total of 34 hits. Warning: empty y range [0:0], adjusting to [0:1] command completed in 0 sec running: "/opt/tpp/x86_64/bin/DatabaseParser 'interact.xml'" command completed in 0 sec running: "/opt/tpp/x86_64/bin/RefreshParser 'interact.xml' '/data/www/ htdocs/qInteract/dblib/IPI.HUMAN.20081112.REV/ipi.HUMAN. 20081112.rev.fasta'" - Building Commentz-Walter keyword tree... - Searching the tree... - Linking duplicate entries... - Printing results... command completed in 2 sec running: "/opt/tpp/x86_64/cgi-bin/PepXMLViewer.cgi -I /data/www/htdocs/ qInteract/data2/xuanwen_20090305121123/xuanwen_3626/interact.xml" command completed in 0 sec /opt/tpp/x86_64/bin/InteractParser 'interact.xml' 'cox-2- h_G_C-1_090307035947.pep.xml' 'cox-2-h_S_C-1_090307023841.pep.xml' 'cox-2M_H_G_C.pep.xml' 'cox-2M_H_S_C.pep.xml' -L'7' 1 sec /opt/tpp/x86_64/bin/PeptideProphetParser 'interact.xml' LEAVE DECOY=REV 1 sec /opt/tpp/x86_64/bin/ProphetModels.pl -i interact.xml 0 sec /opt/tpp/x86_64/bin/RefreshParser 'interact.xml' '/data/www/htdocs/ qInteract/dblib/IPI.HUMAN.20081112.REV/ipi.HUMAN.20081112.rev.fasta' 2 sec /opt/tpp/x86_64/cgi-bin/PepXMLViewer.cgi -I /data/www/htdocs/qInteract/ data2/xuanwen_20090305121123/xuanwen_3626/interact.xml 0 sec job completed in 4 sec /opt/tpp/`uname -p`/bin/ProteinProphet interact.xml interact-prot.xml DB_REFRESH MINPROB0.05 EXCLUDE_ZEROS uname -p ProteinProphet (C++) by Insilicos LLC and LabKey Software, after the original Perl by A. Keller (TPP v4.2 JETSTREAM rev 0, Build 200903231240 (linux)) (xml input) (report Protein Length) (using degen pep info) (database refresh) (exclude zero prob entries) . . . reading in /data/www/htdocs/qInteract/data2/ xuanwen_20090305121123/xuanwen_3626/interact.xml. . . - Building Commentz-Walter keyword tree... - Searching the tree... - Linking duplicate entries... - Printing results... . . . read in 0 1+, 124 2+, 0 3+, 0 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.05 INFO: mu=1.14443e-06, db_size=124778066 protein probabilities written to file /data/www/htdocs/qInteract/ data2/xuanwen_20090305121123/xuanwen_3626/interact-prot.xml direct your browser to http://p//data/www/htdocs/qInteract/data2/xuanwen_20090305121123/xuanwen_3626/interact-prot.shtml --~--~---------~--~----~------------~-------~--~----~ You received this message because you are subscribed to the Google Groups "spctools-discuss" group. 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