Configure Comet Parameters |
2024-04-19 |
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Comet is an open source sequence search engine for tandem mass spectrometry. It is developed and maintained by the University of Washington. Detailed information and source and binary downloads can be obtained at the Comet project on Sourceforge.
Search Using Comet
To search using Comet:
- Go the main page of your MS2 folder.
- In the Data Pipeline panel, click Process and Import Data.
- In the Files panel, select one or more mass spec data files.
- Click Comet Peptide Search.
- Then select or create an analysis protocol to use and click Search.
Comet Versions
LabKey Server 16.1 supports parameters from Comet 2015 and 2014 releases. Prior versions only support Comet 2014. By default, 2015 will be assumed, but you can specify that the server should generate a comet.params for 2014 versions using:
<note label="comet, version" type="input">2014</note>
Comet Parameters
To set the value of a parameter, add a line to your search protocol such as:
<note label="comet, activation_method" type="input">CID</note>
For details on setting default (and overriding) Comet parameters, see Set Up Comet.
| comet.params parameter | Description | LabKey Server search protocol parameter | Comet Version |
| activation_method = ALL |
activation method; used if activation method set; |
comet, activation_method | 2014 and later |
| add_A_alanine = 0.0000 | added to A - avg. 71.0779, mono. 71.03711 | residue, modification mass | 2014 and later |
| add_B_user_amino_acid = 0.0000 | added to B - avg. 0.0000, mono. 0.00000 | residue, modification mass | 2014 and later |
| add_C_cysteine = 57.021464 | added to C - avg. 103.1429, mono. 103.00918 | residue, modification mass | 2014 and later |
| add_Cterm_peptide = 0.0 | residue, modification mass | 2014 and later | |
| add_Cterm_protein = 0.0 | residue, modification mass | 2014 and later | |
| add_D_aspartic_acid = 0.0000 | added to D - avg. 115.0874, mono. 115.02694 | residue, modification mass | 2014 and later |
| add_E_glutamic_acid = 0.0000 | added to E - avg. 129.1140, mono. 129.04259 | residue, modification mass | 2014 and later |
| add_F_phenylalanine = 0.0000 | added to F - avg. 147.1739, mono. 147.06841 | residue, modification mass | 2014 and later |
| add_G_glycine = 0.0000 | added to G - avg. 57.0513, mono. 57.02146 | residue, modification mass | 2014 and later |
| add_H_histidine = 0.0000 | added to H - avg. 137.1393, mono. 137.05891 | residue, modification mass | 2014 and later |
| add_I_isoleucine = 0.0000 | added to I - avg. 113.1576, mono. 113.08406 | residue, modification mass | 2014 and later |
| add_J_user_amino_acid = 0.0000 | added to J - avg. 0.0000, mono. 0.00000 | residue, modification mass | 2014 and later |
| add_K_lysine = 0.0000 | added to K - avg. 128.1723, mono. 128.09496 | residue, modification mass | 2014 and later |
| add_L_leucine = 0.0000 | added to L - avg. 113.1576, mono. 113.08406 | residue, modification mass | 2014 and later |
| add_M_methionine = 0.0000 | added to M - avg. 131.1961, mono. 131.04048 | residue, modification mass | 2014 and later |
| add_N_asparagine = 0.0000 | added to N - avg. 114.1026, mono. 114.04293 | residue, modification mass | 2014 and later |
| add_Nterm_peptide = 0.0 | residue, modification mass | 2014 and later | |
| add_Nterm_protein = 0.0 | residue, modification mass | 2014 and later | |
| add_O_ornithine = 0.0000 | added to O - avg. 132.1610, mono 132.08988 | residue, modification mass | 2014 and later |
| add_P_proline = 0.0000 | added to P - avg. 97.1152, mono. 97.05276 | residue, modification mass | 2014 and later |
| add_Q_glutamine = 0.0000 | added to Q - avg. 128.1292, mono. 128.05858 | residue, modification mass | 2014 and later |
| add_R_arginine = 0.0000 | added to R - avg. 156.1857, mono. 156.10111 | residue, modification mass | 2014 and later |
| add_S_serine = 0.0000 | added to S - avg. 87.0773, mono. 87.03203 | residue, modification mass | 2014 and later |
| add_T_threonine = 0.0000 | added to T - avg. 101.1038, mono. 101.04768 | residue, modification mass | 2014 and later |
| add_U_user_amino_acid = 0.0000 | added to U - avg. 0.0000, mono. 0.00000 | residue, modification mass | 2014 and later |
| add_V_valine = 0.0000 | added to V - avg. 99.1311, mono. 99.06841 | residue, modification mass | 2014 and later |
| add_W_tryptophan = 0.0000 | added to W - avg. 186.0793, mono. 186.07931 | residue, modification mass | 2014 and later |
| add_X_user_amino_acid = 0.0000 | added to X - avg. 0.0000, mono. 0.00000 | residue, modification mass | 2014 and later |
| add_Y_tyrosine = 0.0000 | added to Y - avg. 163.0633, mono. 163.06333 | residue, modification mass | 2014 and later |
| add_Z_user_amino_acid = 0.0000 | added to Z - avg. 0.0000, mono. 0.00000 | residue, modification mass | 2014 and later |
| allowed_missed_cleavage = 2 | maximum value is 5; for enzyme search | scoring, maximum missed cleavage sites | 2014 and later |
| clear_mz_range = 0.0 0.0 | for iTRAQ/TMT type data; will clear out all peaks in the specified m/z range | comet, clear_mz_range | 2014 and later |
| clip_nterm_methionine = 0 | 0=leave sequences as-is; 1=also consider sequence w/o N-term methionine | comet, clip_nterm_methionine | 2014 and later |
| database_name = c:\temp\comet\Bovine_mini.fasta | pipeline, database | 2014 and later | |
| decoy_prefix = DECOY_ | comet, decoy_prefix | 2014 and later | |
| decoy_search = 0 | 0=no (default), 1=concatenated search, 2=separate search | comet, decoy_search | 2014 and later |
| digest_mass_range = 600.0 5000.0 | MH+ peptide mass range to analyze | comet, digest_mass_range | 2014 and later |
| fragment_bin_offset = 0.4 | offset position to start the binning (0.0 to 1.0) | comet, fragment_bin_offset | 2014 and later |
| fragment_bin_tol = 1.0005 | binning to use on fragment ions | spectrum, fragment mass error | 2014 and later |
| 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) | comet, isotope_error | 2014 and later |
| mass_offsets | one or more mass offsets to search (values substracted from deconvoluted precursor mass) | comet, mass_offsets | 2015 and later |
| mass_type_parent = 1 | 0=average masses, 1=monoisotopic masses | comet, mass_type_parent | 2014 and later |
| max_fragment_charge = 3 | set maximum fragment charge state to analyze (allowed max 5) | comet, max_fragment_charge | 2014 and later |
| max_precursor_charge = 6 | set maximum precursor charge state to analyze (allowed max 9) | comet, max_precursor_charge | 2014 and later |
| max_variable_mods_in_peptide = 5 | comet, max_variable_mods_in_peptide | 2014 and later | |
| minimum_intensity = 0 | minimum intensity value to read in | comet, minimum_intensity | 2014 and later |
| minimum_peaks = 10 | minimum num. of peaks in spectrum to search (default 10) | comet, minimum_peaks | 2014 and later |
| ms_level = 2 | MS level to analyze, valid are levels 2 (default) or 3 | comet, ms_level | 2014 and later |
| nucleotide_reading_frame = 0 | 0=proteinDB, 1-6, 7=forward three, 8=reverse three, 9=all six | N/A | 2014 and later |
| num_enzyme_termini = 2 | valid values are 1 (semi-digested), 2 (fully digested, default), 8 N-term, 9 C-term | comet, num_enzyme_termini | 2014 and later |
| num_output_lines = 5 | num peptide results to show | comet, num_output_lines | 2014 and later |
| num_results = 50 | number of search hits to store internally | comet, num_results | 2014 and later |
| num_threads = 0 | 0=poll CPU to set num threads; else specify num threads directly (max 32) | comet, num_threads | 2014 and later |
| override_charge | 0=no, 1=override precursor charge states, 2=ignore precursor charges outside precursor_charge range, 3=see online | comet, override_charge | 2015 and later |
| peptide_mass_tolerance = 3.00 | spectrum, parent monoisotopic mass error minus spectrum, parent monoisotopic mass error plus |
2014 and later | |
| peptide_mass_units = 0 | 0=amu, 1=mmu, 2=ppm | spectrum, parent monoisotopic mass error units | 2014 and later |
| precursor_charge = 0 0 | precursor charge range to analyze; does not override mzXML charge; 0 as 1st entry ignores parameter | comet, precursor_charge | 2014 and later |
| precursor_tolerance_type = 0 | 0=MH+ (default), 1=precursor m/z | comet, precursor_tolerance_type | 2014 and later |
| print_expect_score = 1 | 0=no, 1=yes to replace Sp with expect in out & sqt | comet, print_expect_score | 2014 and later |
| remove_precursor_peak = 0 | 0=no, 1=yes, 2=all charge reduced precursor peaks (for ETD) | comet, remove_precursor_peak | 2014 and later |
| remove_precursor_tolerance = 1.5 | +- Da tolerance for precursor removal | comet, remove_precursor_tolerance | 2014 and later |
| require_variable_mod | N/A | 2015 and later | |
| sample_enzyme_number = 1 | Sample enzyme which is possibly different than the one applied to the search. | protein, cleavage site | 2014 and later |
| scan_range = 0 0 | start and scan scan range to search; 0 as 1st entry ignores parameter | comet, scan_range | 2014 and later |
| search_enzyme_number = 1 | choose from list at end of this params file | protein, cleavage site | 2014 and later |
| show_fragment_ions = 0 | 0=no, 1=yes for out files only | comet, show_fragment_ions | 2014 and later |
| skip_researching = 1 | for '.out' file output only, 0=search everything again (default), 1=don't search if .out exists | N/A | 2014 and later |
| spectrum_batch_size = 0 | max. of spectra to search at a time; 0 to search the entire scan range in one loop | comet, spectrum_batch_size | 2014 and later |
| theoretical_fragment_ions = 1 | 0=default peak shape, 1=M peak only | comet, theoretical_fragment_ions | 2014 and later |
| use_A_ions = 0 | scoring, a ions | 2014 and later | |
| use_B_ions = 1 | scoring, b ions | 2014 and later | |
| use_C_ions = 0 | scoring, c ions | 2014 and later | |
| use_NL_ions = 1 | 0=no, 1=yes to consider NH3/H2O neutral loss peaks | comet, use_NL_ions | 2014 and later |
| use_sparse_matrix = 0 | N/A | 2014 and later | |
| use_X_ions = 0 | scoring, x ions | 2014 and later | |
| use_Y_ions = 1 | scoring, y ions | 2014 and later | |
| use_Z_ions = 0 | scoring, z ions | 2014 and later | |
| variable_C_terminus = 0.0 | residue, potential modification mass | 2014 | |
| variable_C_terminus_distance = -1 | -1=all peptides, 0=protein terminus, 1-N = maximum offset from C-terminus | comet, variable_N_terminus_distance | 2014 |
| variable_mod1 = 15.9949 M 0 3 | residue, potential modification | 2014 | |
| variable_mod2 = 0.0 X 0 3 | |||
| variable_mod3 = 0.0 X 0 3 | |||
| variable_mod4 = 0.0 X 0 3 | |||
| variable_mod5 = 0.0 X 0 3 | |||
| variable_mod6 = 0.0 X 0 3 | |||
| variable_N_terminus = 0.0 | residue, potential modification mass | 2014 | |
| variable_N_terminus_distance = -1 | -1=all peptides, 0=protein terminus, 1-N = maximum offset from N-terminus | comet, variable_N_terminus_distance | 2014 |
| variable_mod01 = 15.9949 M 0 3 -1 0 0 | <mass> <residues> <0=variable/else binary> <max_mods_per_peptide> <term_distance> <n/c-term> <required> |
residue, potential modification |
2015 and later |
| variable_mod02 = 0.0 X 0 3 -1 0 0 | |||
| variable_mod03 = 0.0 X 0 3 -1 0 0 | |||
| variable_mod04 = 0.0 X 0 3 -1 0 0 | |||
| variable_mod05 = 0.0 X 0 3 -1 0 0 | |||
| variable_mod06 = 0.0 X 0 3 -1 0 0 | |||
| variable_mod07 = 0.0 X 0 3 -1 0 0 | |||
| variable_mod08 = 0.0 X 0 3 -1 0 0 | |||
| variable_mod09 = 0.0 X 0 3 -1 0 0 |