Premium Feature - This is a legacy feature available with Premium Editions of LabKey Server. Learn more or contact LabKey.

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;
allowable values include: ALL, CID, ECD, ETD, PQD, HCD, IRMPD

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
refine, potential C-terminus modifications
refine, potential N-terminus modifications
comet, variable_C_terminus_distance
comet, variable_N_terminus_distance 

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

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