Hi Jagan, It appears that the QC filters were triggered on the PeptideProphet MixtureModel. This is likely due to too few data points in the analysis for good stats: read in 0 1+, 82 2+, 44 3+, 0 4+, 0 5+, 0 6+, and 0 7+ spectra.
With OMSSA this could be due to too low e-value setting which filters out many results which the model can utilize to better model the negative and positive distributions. Set your OMSSA e-value to a high value like 1e6 and this problem will likely go away. Unless you don't have very many correct results due to wrong parameters or bad data or something else. Hope this helps. -David On Fri, Jul 2, 2010 at 1:02 AM, Jagan Kommineni <[email protected]> wrote: > Dear All, > > I have created decoy database for the SwisPlot database using decoyFASTA of > the TPPDistribution and run the following TPP commands after the omssa > search with decoy database and here is the output on STDOUT ... > > --------------------------------------- > [r...@compute-3-0 run-on-compute]# > /mnt/sanfs/APCF/APCF_WEB/tpp/bin/InteractParser 'jagan-J128.pepprophet.xml' > 'jagan-J128.pep.xml' > -D'/home/APCF/databases/SwissProt/uniprot_sprot_Jan2009/decoy/decoy_uniprot_sprot.fasta' > -L'7' -E'trypsin' -C -P > file 1: jagan-J128.pep.xml > processed altogether 126 results > > > results written to file > /mnt/sanfs/APCF/results/omssa/decoy_test_run/run-on-compute/jagan-J128.pepprophet.shtml > > > > [r...@compute-3-0 run-on-compute]# > /mnt/sanfs/APCF/APCF_WEB/tpp/bin/PeptideProphetParser > 'jagan-J128.pepprophet.xml' DECOY=decoy MINPROB=0 NONPARAM > Using Decoy Label "decoy". > Using non-parametric distributions > (OMSSA) (minprob 0) > WARNING!! The discriminant function for OMSSA is not yet complete. It is > presented here to help facilitate trial and discussion. Reliance on this > code for publishable scientific results is not recommended. > init with OMSSA Trypsin > MS Instrument info: Manufacturer: UNKNOWN, Model: UNKNOWN, Ionization: > UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN > > PeptideProphet (TPP v4.3 JETSTREAM rev 1, Build 201003241044 (linux)) > akel...@isb > read in 0 1+, 82 2+, 44 3+, 0 4+, 0 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 (2+). > 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 26 iterations > [r...@compute-3-0 run-on-compute]# > /mnt/sanfs/APCF/APCF_WEB/tpp/bin/RefreshParser 'jagan-J128.pepprophet.xml' > '/home/APCF/databases/SwissProt/uniprot_sprot_Jan2009/decoy/decoy_uniprot_sprot.fasta' > - Building Commentz-Walter keyword tree... - Searching the tree... > - Linking duplicate entries... - Printing results... > > [r...@compute-3-0 run-on-compute]# > /mnt/sanfs/APCF/APCF_WEB/tpp/bin/ProteinProphet 'jagan-J128.pepprophet.xml' > 'jagan-J128.prot.xml' > ProteinProphet (C++) by Insilicos LLC and LabKey Software, after the > original Perl by A. Keller (TPP v4.3 JETSTREAM rev 1, Build 201003241044 > (linux)) > (xml input) (report Protein Length) (using degen pep info) > . . . reading in > /mnt/sanfs/APCF/results/omssa/decoy_test_run/run-on-compute/jagan-J128.pepprophet.xml. > . . > . . . read in 0 1+, 0 2+, 33 3+, 0 4+, 0 5+, 0 6+, 0 7+ spectra with min > prob 0.05 > Could not find/open font when opening font "arial", using internal > non-scalable font > INFO: mu=6.3014e-09, db_size=584667857 > > protein probabilities written to file > /mnt/sanfs/APCF/results/omssa/decoy_test_run/run-on-compute/jagan-J128.prot.xml > direct your browser to > http://nfs//mnt/sanfs/APCF/results/omssa/decoy_test_run/run-on-compute/jagan-J128.prot.shtml > > [r...@compute-3-0 run-on-compute]# > > ------------------------------------- > > I noticed there are some warning messages indicating some tests are failed, > how critical are these messages. > > > with regards, > > > Dr. Jagan Kommineni > Ludwig Institute for Cancer research > Pakville VIC 3145 > Australia. > > -- > You received this message because you are subscribed to the Google Groups > "spctools-discuss" group. > To post to this group, send email to [email protected]. > To unsubscribe from this group, send email to > [email protected]. > For more options, visit this group at > http://groups.google.com/group/spctools-discuss?hl=en. > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To post to this group, send email to [email protected]. To unsubscribe from this group, send email to [email protected]. For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en.
