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, <[email protected]> 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, <[email protected]> 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 [email protected]. >>> To post to this group, send email to [email protected]. >>> 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 [email protected]. > To post to this group, send email to [email protected]. > 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. 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