Hello,
I'm combining some Mascot and comet search results with TPP and have the
problem that it doesn't seem to be identifying decoys correctly.
I'm running TPP.5.1.0 on ubuntu 16.
The comet and the mascot search are done with decoy search turned off, but
I added decoys to the database with the prefix "XXX_"
Then I continue to run TPP like this:
InteractParser H1_EhN_cm2.pep.xml H1_ma_EhN.pep.xml H1_co_EhN2.pep.xml
-D../../Databases/EhuxAllproteins_MCC_decoy.fasta -s -XH1 -Etrypsin
DatabaseParser H1_EhN_cm2.pep.xml
RefreshParser H1_EhN_cm2.pep.xml
../../Databases/EhuxAllproteins_MCC_decoy.fasta
PeptideProphetParser H1_EhN_cm2.pep.xml RT DECOY=XXX_ NONPARAM
ProphetModels.pl -i H1_EhN_cm2.pep.xml
tpp_models.pl H1_EhN_cm2.pep.xml
And get the following printed to stdout:
../../../../Databases/EhuxAllproteins_MCC_decoy.fasta,../../Databases/EhuxAllproteins_MCC_decoy.fasta
- Building Commentz-Walter keyword tree...
- Searching the tree...
- Linking duplicate entries...
- Printing results...
using RT
Using Decoy Label "XXX_".
Using non-parametric distributions
(MASCOT)
error: -1.0 ion score
Analyzing H1_EhN_cm2.pep.xml ...
Parsing search results
"/home/mpimp-golm.mpg.de/skeffington/winhome/proteomics2/CAP/CAPdata/mascot/Ehnew/H1
(MASCOT)"...
=> Found 23168 hits. (0 decoys, 0 excluded)
=> Total so far: 23168 hits. (0 decoys, 0 excluded)
Parsing search results
"/home/mpimp-golm.mpg.de/skeffington/winhome/proteomics2/CAP/CAPdata/H1
(Comet)"...
=> Found 21343 hits. (0 decoys, 0 excluded)
=> Total so far: 44511 hits. (0 decoys, 0 excluded)
File: H1_EhN_cm2.pep.xml
- in ms run:
/home/mpimp-golm.mpg.de/skeffington/winhome/proteomics2/CAP/CAPdata/mascot/Ehnew/H1...
- in ms run:
/home/mpimp-golm.mpg.de/skeffington/winhome/proteomics2/CAP/CAPdata/H1...
-------------------------------------------------------------------------------
TPP DASHBOARD -- started at Fri Mar 6 14:18:51 2020
-------------------------------------------------------------------------------
File H1_EhN_cm2.pep.xml is pepxml
--> Trying to write file H1_EhN_cm2.pep-MODELS.html
-------------------------------------------------------------------------------
Finished at Fri Mar 6 14:18:54 2020 with 0 errors.
-------------------------------------------------------------------------------
So I don't understand why it doesn't find the decoys when they are clearly
there in the search results, when they are clearly there in the .pep.xml
file:
<spectrum_query spectrum="H1.27890.27890.4" start_scan="27890"
end_scan="27890" precursor_neutral_mass="1899.7835" assumed_charge="4"
index="13563" experiment_label="H1">
<search_result>
<search_hit hit_rank="1" peptide="SWHGEAASKTVDSLPR" peptide_prev_aa="R"
peptide_next_aa="F" protein="XXX_44165" num_tot_proteins="1"
num_matched_ions="6" tot_num_ions="60" calc_neutral_pep_mass="1899.7996"
massdiff="-0.0160" num_tol_term="2" num_missed_cleavages="1"
is_rejected="0">
<modification_info modified_peptide="S[167]WHGEAASKTVDS[167]LPR">
<mod_aminoacid_mass position="1" mass="166.998359"/>
<mod_aminoacid_mass position="13" mass="166.998359"/>
</modification_info>
<search_score name="ionscore" value="15.77"/>
<search_score name="identityscore" value="33.71"/>
<search_score name="star" value="0"/>
<search_score name="homologyscore" value="27.00"/>
<search_score name="expect" value="3.1107"/>
</search_hit>
</search_result>
</spectrum_query>
Any ideas would be much appreciated!
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