The files can be found here: https://we.tl/t-pa5MOH7aKr
Am Freitag, 6. März 2020 14:40:42 UTC+1 schrieb Alastair Skeffington: > > 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! > > > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To view this discussion on the web visit https://groups.google.com/d/msgid/spctools-discuss/f53d5455-ed3b-40ad-ae58-7bf810f8fd46%40googlegroups.com.
