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.
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