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.
