see if the info on the last message of this thread helps http://groups.google.com/group/spctools-discuss/browse_thread/thread/9a6aafd2c59d88bf/95c07178c24373c3
On Mon, Sep 6, 2010 at 5:55 PM, Jagan Kommineni <[email protected]> wrote: > > > On Fri, Sep 3, 2010 at 2:51 PM, Jagan Kommineni <[email protected]> > wrote: >> >> Dear All, >> >> I have taken RAW file generated by Instrument info: Manufacturer: Thermo >> Finnigan, Model: LCQ Deca, Ionization: nanoelectrospray, Analyzer: >> quadrupole ion trap, Detector: electron multiplier and run standard search >> using Mascot, X!tandem and OMSSA and fed the data through TPP pipeline then >> I found that 0 (zero) decoy and 130 non-decoy entries for the search results >> of OMSSA whereas 545 Decoys and 785 Non-Decoys entries for Mascot search >> results and 536 Decoys and 833 Non-Decoys entries for x!tandem search. >> >> I found total hits retruned from Mascot and X!tandem search result sets >> respectively are of 303 and 351. >> >> >> For OMSSA based search results, the PeptideProphetParser program quitted >> with exit code of 11. >> >> Here is the complete STDOUT of OMSSA and TPP pipeleine ... >> >> ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- >> >> /home/APCF/tpp/bin/xinteract -Njagan-J1370.pepprophet.xml -eT -d'sp|decoy' >> -p0.05 -l7 -x20 -R -OP jagan-J1370.pep.xml >> >> /home/APCF/tpp/bin/xinteract (TPP v4.4 JETSTREAM (unstable development >> prerelease) rev 0, Build 201007011135 (linux)) >> >> running: "/mnt/sanfs/APCF/APCF_WEB/tpp/bin/InteractParser >> 'jagan-J1370.pepprophet.xml' 'jagan-J1370.pep.xml' -P -L'7' -E'trypsin'" >> file 1: jagan-J1370.pep.xml >> processed altogether 130 results >> >> >> results written to file >> /mnt/sanfs/APCF/results/tpp/2010-09-03/jagan-J1370.pepprophet.shtml >> >> >> >> command completed in 0 sec >> >> running: "/mnt/sanfs/APCF/APCF_WEB/tpp/bin/PeptideProphetParser >> 'jagan-J1370.pepprophet.xml' DECOY='sp|decoy' MINPROB=0.05 EXTRAITRS=20 >> NONPARAM" >> Using Decoy Label "sp|decoy". >> Using non-parametric distributions >> (OMSSA) >> 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 v4.4 JETSTREAM (unstable development prerelease) rev >> 0, Build 201007011135 (linux)) akel...@isb >> read in 0 1+, 99 2+, 31 3+, 0 4+, 0 5+, 0 6+, and 0 7+ spectra. >> Initialising statistical models ... >> Found 0 Decoys, and 130 Non-Decoys >> WARNING: No decoys with label sp|decoy were found in this dataset. >> reverting to fully unsupervised method. >> Iterations: .........10.........20 >> >> command "/mnt/sanfs/APCF/APCF_WEB/tpp/bin/PeptideProphetParser >> 'jagan-J1370.pepprophet.xml' DECOY='sp|decoy' MINPROB=0.05 EXTRAITRS=20 >> NONPARAM" exited with non-zero exit code: 11 >> QUIT - the job is incomplete >> >> ============================================================================================== >> >> I wonder is there any requirement to have at least few decoy entries for >> PeptideProphetParser to continue without fail? >> >> Further study with pep XML generated by different algorithm search >> results, I found that there is only one decoy entry for xml tag of >> search_hit which I am here with enclosing in this mail ... >> >> ------------------------------------------------------------ >> <search_hit hit_rank="2" peptide="LGDSEVDIGIMANLDIVESKR" >> peptide_prev_aa="K" peptide_next_aa="L" protein="520685" >> num_tot_proteins="2" num_matched_ions="21" tot_num_ions="40" >> calc_neutral_pep_mass="2273.156" massdiff="0.041999999999865" >> is_rejected="0" protein_descr="sp|decoy_C1ERL6|ACDH_BACC3 Reverse sequence, >> was Acetaldehyde dehydrogenase OS=Bacillus cereus (strain 03BB102) >> GN=BCA_2154 PE=3 SV=1"> >> <alternative_protein protein="520683" >> protein_descr="sp|decoy_A0RD69|ACDH_BACAH Reverse sequence, was Acetaldehyde >> dehydrogenase OS=Bacillus thuringiensis (strain Al Hakam) GN=BALH_1843 PE=3 >> SV=1"/> >> <search_score name="pvalue" value="0.000012588862528"/> >> <search_score name="expect" value="0.648238298133515"/> >> </search_hit> >> ----------------------------------------------------------- >> >> whereas I found 581 and 572 similar tags in Mascot and X!tandem based >> results, >> >> with regards, >> >> -- >> Dr. Jagan Kommineni >> Ludwig Institute for Cancer research >> Pakville VIC 3145 >> Australia. > > > > -- > 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. 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