Thank you, Jimmy. I'll try what you suggested. -Bob On Tuesday, March 22, 2016 at 11:49:23 AM UTC-4, Jimmy Eng wrote: > > Besides using a very old version of Comet, there's nothing wrong with the > parameter settings that would indicate why you might see an extremely long > search. As Brian and Mike suggested, it's likely Comet's not even running > right now for whatever reason. > > You're using version 2014.02 rev. 2 that was released in September 2014. > Before doing anything else, it's in your best interest to update to the > latest 2016.01 rev. 0 release that you can download from here: > > https://sourceforge.net/projects/comet-ms/files/ > > Grab the file comet_binaries_2016010.zip. Find your current Comet binary > (should be at c:\inetpub\tpp-bin\comet.exe) and replace it with the binary > in this zip file (rename comet.2016010.win64.exe to > c:\inetpub\tpp-bin\comet.exe). Then generate a new comet.params file or > grab the comet.params.low-low > <http://comet-ms.sourceforge.net/parameters/parameters_201601/comet.params.low-low> > > from link below and rename to comet.params in the appropriate directory and > attempt a search again. > > http://comet-ms.sourceforge.net/parameters/parameters_201601/ > > This search should complete in well under 10 minutes and not hours or > days. Try the search again with the current Comet binary and report back > if you still have issues. > > - Jimmy > > On Tue, Mar 22, 2016 at 8:16 AM, <bx20...@gmail.com <javascript:>> wrote: > >> Hi Jimmy, Brian and Mike, >> >> Thank you all for your replies. Please see below the content of my >> comet.params file (again, this came with TPP installation, I did not modify >> it). >> >> Thanks, >> >> Bob >> >> # comet_version 2014.02 rev. 2 >> # Comet MS/MS search engine parameters file. >> # Everything following the '#' symbol is treated as a comment. >> >> database_name = /some/path/db.fasta >> decoy_search = 0 # 0=no (default), 1=concatenated >> search, 2=separate search >> >> num_threads = 0 # 0=poll CPU to set num threads; >> else specify num threads directly (max 64) >> >> # >> # masses >> # >> peptide_mass_tolerance = 3.00 >> peptide_mass_units = 0 # 0=amu, 1=mmu, 2=ppm >> mass_type_parent = 1 # 0=average masses, 1=monoisotopic >> masses >> mass_type_fragment = 1 # 0=average masses, 1=monoisotopic >> masses >> isotope_error = 0 # 0=off, 1=on -1/0/1/2/3 (standard >> C13 error), 2= -8/-4/0/4/8 (for +4/+8 labeling) >> >> # >> # search enzyme >> # >> search_enzyme_number = 1 # choose from list at end of this >> params file >> num_enzyme_termini = 2 # valid values are 1 >> (semi-digested), 2 (fully digested, default), 8 N-term, 9 C-term >> allowed_missed_cleavage = 2 # maximum value is 5; for enzyme >> search >> >> # >> # Up to 9 variable modifications are supported >> # format: <mass> <residues> <0=variable/1=binary> <max_mods_per_peptide> >> <term_distance> <n/c-term> >> # e.g. 79.966331 STY 0 3 -1 0 >> # >> variable_mod01 = 15.9949 M 0 3 -1 0 >> variable_mod02 = 0.0 X 0 3 -1 0 >> variable_mod03 = 0.0 X 0 3 -1 0 >> variable_mod04 = 0.0 X 0 3 -1 0 >> variable_mod05 = 0.0 X 0 3 -1 0 >> variable_mod06 = 0.0 X 0 3 -1 0 >> variable_mod07 = 0.0 X 0 3 -1 0 >> variable_mod08 = 0.0 X 0 3 -1 0 >> variable_mod09 = 0.0 X 0 3 -1 0 >> max_variable_mods_in_peptide = 5 >> >> # >> # fragment ions >> # >> # ion trap ms/ms: 1.0005 tolerance, 0.4 offset (mono masses), >> theoretical_fragment_ions = 1 >> # high res ms/ms: 0.02 tolerance, 0.0 offset (mono masses), >> theoretical_fragment_ions = 0 >> # >> fragment_bin_tol = 1.0005 # binning to use on fragment ions >> fragment_bin_offset = 0.4 # offset position to start the >> binning (0.0 to 1.0) >> theoretical_fragment_ions = 1 # 0=use flanking peaks, 1=M peak >> only >> use_A_ions = 0 >> use_B_ions = 1 >> use_C_ions = 0 >> use_X_ions = 0 >> use_Y_ions = 1 >> use_Z_ions = 0 >> use_NL_ions = 1 # 0=no, 1=yes to consider NH3/H2O >> neutral loss peaks >> use_sparse_matrix = 0 >> >> # >> # output >> # >> output_sqtstream = 0 # 0=no, 1=yes write sqt to >> standard output >> output_sqtfile = 0 # 0=no, 1=yes write sqt file >> output_txtfile = 0 # 0=no, 1=yes write tab-delimited >> txt file >> output_pepxmlfile = 1 # 0=no, 1=yes write pep.xml file >> output_percolatorfile = 0 # 0=no, 1=yes write Percolator >> tab-delimited input file >> output_outfiles = 0 # 0=no, 1=yes write .out files >> print_expect_score = 1 # 0=no, 1=yes to replace Sp with >> expect in out & sqt >> num_output_lines = 5 # num peptide results to show >> show_fragment_ions = 0 # 0=no, 1=yes for out files only >> >> sample_enzyme_number = 1 # Sample enzyme which is possibly >> different than the one applied to the search. >> # Used to calculate NTT & NMC in >> pepXML output (default=1 for trypsin). >> >> # >> # mzXML parameters >> # >> scan_range = 0 0 # start and scan scan range to >> search; 0 as 1st entry ignores parameter >> precursor_charge = 0 0 # precursor charge range to >> analyze; does not override any existing charge; 0 as 1st entry ignores >> parameter >> override_charge = 0 # 0=no, 1=yes to override existing >> precursor charge states with precursor_charge parameter >> ms_level = 2 # MS level to analyze, valid are >> levels 2 (default) or 3 >> activation_method = ALL # activation method; used if >> activation method set; allowed ALL, CID, ECD, ETD, PQD, HCD, IRMPD >> >> # >> # misc parameters >> # >> digest_mass_range = 600.0 5000.0 # MH+ peptide mass range to analyze >> num_results = 50 # number of search hits to store >> internally >> skip_researching = 1 # for '.out' file output only, >> 0=search everything again (default), 1=don't search if .out exists >> max_fragment_charge = 3 # set maximum fragment charge >> state to analyze (allowed max 5) >> max_precursor_charge = 6 # set maximum precursor charge >> state to analyze (allowed max 9) >> nucleotide_reading_frame = 0 # 0=proteinDB, 1-6, 7=forward >> three, 8=reverse three, 9=all six >> clip_nterm_methionine = 0 # 0=leave sequences as-is; 1=also >> consider sequence w/o N-term methionine >> spectrum_batch_size = 0 # max. # of spectra to search at a >> time; 0 to search the entire scan range in one loop >> decoy_prefix = DECOY_ # decoy entries are denoted by >> this string which is pre-pended to each protein accession >> output_suffix = # add a suffix to output base >> names i.e. suffix "-C" generates base-C.pep.xml from base.mzXML input >> >> # >> # spectral processing >> # >> minimum_peaks = 10 # required minimum number of peaks >> in spectrum to search (default 10) >> minimum_intensity = 0 # minimum intensity value to read >> in >> remove_precursor_peak = 0 # 0=no, 1=yes, 2=all charge >> reduced precursor peaks (for ETD) >> remove_precursor_tolerance = 1.5 # +- Da tolerance for precursor >> removal >> clear_mz_range = 0.0 0.0 # for iTRAQ/TMT type data; will >> clear out all peaks in the specified m/z range >> >> # >> # additional modifications >> # >> >> add_Cterm_peptide = 0.0 >> add_Nterm_peptide = 0.0 >> add_Cterm_protein = 0.0 >> add_Nterm_protein = 0.0 >> >> add_G_glycine = 0.0000 # added to G - avg. 57.0513, >> mono. 57.02146 >> add_A_alanine = 0.0000 # added to A - avg. 71.0779, >> mono. 71.03711 >> add_S_serine = 0.0000 # added to S - avg. 87.0773, >> mono. 87.03203 >> add_P_proline = 0.0000 # added to P - avg. 97.1152, >> mono. 97.05276 >> add_V_valine = 0.0000 # added to V - avg. 99.1311, >> mono. 99.06841 >> add_T_threonine = 0.0000 # added to T - avg. 101.1038, >> mono. 101.04768 >> add_C_cysteine = 57.021464 # added to C - avg. 103.1429, >> mono. 103.00918 >> add_L_leucine = 0.0000 # added to L - avg. 113.1576, >> mono. 113.08406 >> add_I_isoleucine = 0.0000 # added to I - avg. 113.1576, >> mono. 113.08406 >> add_N_asparagine = 0.0000 # added to N - avg. 114.1026, >> mono. 114.04293 >> add_D_aspartic_acid = 0.0000 # added to D - avg. 115.0874, >> mono. 115.02694 >> add_Q_glutamine = 0.0000 # added to Q - avg. 128.1292, >> mono. 128.05858 >> add_K_lysine = 0.0000 # added to K - avg. 128.1723, >> mono. 128.09496 >> add_E_glutamic_acid = 0.0000 # added to E - avg. 129.1140, >> mono. 129.04259 >> add_M_methionine = 0.0000 # added to M - avg. 131.1961, >> mono. 131.04048 >> add_O_ornithine = 0.0000 # added to O - avg. 132.1610, mono >> 132.08988 >> add_H_histidine = 0.0000 # added to H - avg. 137.1393, >> mono. 137.05891 >> add_F_phenylalanine = 0.0000 # added to F - avg. 147.1739, >> mono. 147.06841 >> add_R_arginine = 0.0000 # added to R - avg. 156.1857, >> mono. 156.10111 >> add_Y_tyrosine = 0.0000 # added to Y - avg. 163.0633, >> mono. 163.06333 >> add_W_tryptophan = 0.0000 # added to W - avg. 186.0793, >> mono. 186.07931 >> add_B_user_amino_acid = 0.0000 # added to B - avg. 0.0000, >> mono. 0.00000 >> add_J_user_amino_acid = 0.0000 # added to J - avg. 0.0000, >> mono. 0.00000 >> add_U_user_amino_acid = 0.0000 # added to U - avg. 0.0000, >> mono. 0.00000 >> add_X_user_amino_acid = 0.0000 # added to X - avg. 0.0000, >> mono. 0.00000 >> add_Z_user_amino_acid = 0.0000 # added to Z - avg. 0.0000, >> mono. 0.00000 >> >> # >> # COMET_ENZYME_INFO _must_ be at the end of this parameters file >> # >> [COMET_ENZYME_INFO] >> 0. No_enzyme 0 - - >> 1. Trypsin 1 KR P >> 2. Trypsin/P 1 KR - >> 3. Lys_C 1 K P >> 4. Lys_N 0 K - >> 5. Arg_C 1 R P >> 6. Asp_N 0 D - >> 7. CNBr 1 M - >> 8. Glu_C 1 DE P >> 9. PepsinA 1 FL P >> 10. Chymotrypsin 1 FWYL P >> >> >> On Monday, March 21, 2016 at 5:39:46 PM UTC-4, Jimmy Eng wrote: >>> >>> It would be helpful if you post (or send me) the search parameters which >>> is the contents of the comet.params file. >>> >>> On Mon, Mar 21, 2016 at 2:11 PM, <bx20...@gmail.com> wrote: >>> >>>> Hi everyone, >>>> >>>> I started a Comet search in TPP three days ago and it is still going >>>> three days later. I must have messed up something without knowing because >>>> TPP did not generate any error message. Did anyone else have similar >>>> experience? Please see my system and TPP info below. >>>> >>>> HP Z600 Workstation >>>> Windows 7 Professional >>>> Processor: Intel(R) Xeon(R) CPU E5640 @ 2.67GHz 2.66 GHz >>>> Installed memory (RAM): 24.0 GB >>>> System type: 64-bit Operating System >>>> >>>> TPP v4.8.0 PHILAE, Build 201411201551-6764 (mingw-i686) >>>> >>>> Comet search >>>> >>>> mzXML input file: mydata.mzXML (110 MB) >>>> generated using command line msconvert >>>> C:/Inetpub/tpp-bin/msconvert mydata.raw --mzXML >>>> --filter "mslevel 2" --filter "threshold count 100 most-intense" >>>> >>>> Comet Parameters file: comet.params (default, came with TPP >>>> installation) >>>> Sequence database: human_uniprot_sprot.fasta >>>> >>>> Any advice/pointer is greatly appreciated. >>>> >>>> Thanks, >>>> >>>> Bob Xiong >>>> >>>> -- >>>> 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 spctools-discu...@googlegroups.com. >>>> To post to this group, send email to spctools...@googlegroups.com. >>>> Visit this group at https://groups.google.com/group/spctools-discuss. >>>> For more options, visit https://groups.google.com/d/optout. >>>> >>> >>> -- >> 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 spctools-discu...@googlegroups.com <javascript:>. >> To post to this group, send email to spctools...@googlegroups.com >> <javascript:>. >> Visit this group at https://groups.google.com/group/spctools-discuss. >> For more options, visit https://groups.google.com/d/optout. >> > >
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