Search Using Comet

To search using Comet:

  • Go the MS2 Dashboard.
  • 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 parameterDescriptionLabKey Server search protocol parameterComet Version
activation_method = ALL

activation method; used if activation method set;
allowable values include: ALL, CID, ECD, ETD, PQD, HCD, IRMPD

comet, activation_method2014 and later
add_A_alanine = 0.0000added to A - avg. 71.0779, mono. 71.03711residue, modification mass2014 and later
add_B_user_amino_acid = 0.0000added to B - avg. 0.0000, mono. 0.00000residue, modification mass2014 and later
add_C_cysteine = 57.021464added to C - avg. 103.1429, mono. 103.00918residue, modification mass2014 and later
add_Cterm_peptide = 0.0 residue, modification mass2014 and later
add_Cterm_protein = 0.0 residue, modification mass2014 and later
add_D_aspartic_acid = 0.0000added to D - avg. 115.0874, mono. 115.02694residue, modification mass2014 and later
add_E_glutamic_acid = 0.0000added to E - avg. 129.1140, mono. 129.04259residue, modification mass2014 and later
add_F_phenylalanine = 0.0000added to F - avg. 147.1739, mono. 147.06841residue, modification mass2014 and later
add_G_glycine = 0.0000added to G - avg. 57.0513, mono. 57.02146residue, modification mass2014 and later
add_H_histidine = 0.0000added to H - avg. 137.1393, mono. 137.05891residue, modification mass2014 and later
add_I_isoleucine = 0.0000added to I - avg. 113.1576, mono. 113.08406residue, modification mass2014 and later
add_J_user_amino_acid = 0.0000added to J - avg. 0.0000, mono. 0.00000residue, modification mass2014 and later
add_K_lysine = 0.0000added to K - avg. 128.1723, mono. 128.09496residue, modification mass2014 and later
add_L_leucine = 0.0000added to L - avg. 113.1576, mono. 113.08406residue, modification mass2014 and later
add_M_methionine = 0.0000added to M - avg. 131.1961, mono. 131.04048residue, modification mass2014 and later
add_N_asparagine = 0.0000added to N - avg. 114.1026, mono. 114.04293residue, modification mass2014 and later
add_Nterm_peptide = 0.0 residue, modification mass2014 and later
add_Nterm_protein = 0.0 residue, modification mass2014 and later
add_O_ornithine = 0.0000added to O - avg. 132.1610, mono 132.08988residue, modification mass2014 and later
add_P_proline = 0.0000added to P - avg. 97.1152, mono. 97.05276residue, modification mass2014 and later
add_Q_glutamine = 0.0000added to Q - avg. 128.1292, mono. 128.05858residue, modification mass2014 and later
add_R_arginine = 0.0000added to R - avg. 156.1857, mono. 156.10111residue, modification mass2014 and later
add_S_serine = 0.0000added to S - avg. 87.0773, mono. 87.03203residue, modification mass2014 and later
add_T_threonine = 0.0000added to T - avg. 101.1038, mono. 101.04768residue, modification mass2014 and later
add_U_user_amino_acid = 0.0000added to U - avg. 0.0000, mono. 0.00000residue, modification mass2014 and later
add_V_valine = 0.0000added to V - avg. 99.1311, mono. 99.06841residue, modification mass2014 and later
add_W_tryptophan = 0.0000added to W - avg. 186.0793, mono. 186.07931residue, modification mass2014 and later
add_X_user_amino_acid = 0.0000added to X - avg. 0.0000, mono. 0.00000residue, modification mass2014 and later
add_Y_tyrosine = 0.0000added to Y - avg. 163.0633, mono. 163.06333residue, modification mass2014 and later
add_Z_user_amino_acid = 0.0000added to Z - avg. 0.0000, mono. 0.00000residue, modification mass2014 and later
allowed_missed_cleavage = 2maximum value is 5; for enzyme searchscoring, maximum missed cleavage sites2014 and later
clear_mz_range = 0.0 0.0for iTRAQ/TMT type data; will clear out all peaks in the specified m/z rangecomet, clear_mz_range2014 and later
clip_nterm_methionine = 00=leave sequences as-is; 1=also consider sequence w/o N-term methioninecomet, clip_nterm_methionine2014 and later
database_name = c:\temp\comet\Bovine_mini.fasta pipeline, database2014 and later
decoy_prefix = DECOY_ comet, decoy_prefix2014 and later
decoy_search = 00=no (default), 1=concatenated search, 2=separate searchcomet, decoy_search2014 and later
digest_mass_range = 600.0 5000.0MH+ peptide mass range to analyzecomet, digest_mass_range2014 and later
fragment_bin_offset = 0.4offset position to start the binning (0.0 to 1.0)comet, fragment_bin_offset2014 and later
fragment_bin_tol = 1.0005binning to use on fragment ionsspectrum, fragment mass error2014 and later
isotope_error = 00=off, 1=on -1/0/1/2/3 (standard C13 error), 2= -8/-4/0/4/8 (for +4/+8 labeling)comet, isotope_error2014 and later
mass_offsetsone or more mass offsets to search (values substracted from deconvoluted precursor mass)comet, mass_offsets2015 and later
mass_type_parent = 10=average masses, 1=monoisotopic massescomet, mass_type_parent2014 and later
max_fragment_charge = 3set maximum fragment charge state to analyze (allowed max 5)comet, max_fragment_charge2014 and later
max_precursor_charge = 6set maximum precursor charge state to analyze (allowed max 9)comet, max_precursor_charge2014 and later
max_variable_mods_in_peptide = 5 comet, max_variable_mods_in_peptide2014 and later
minimum_intensity = 0minimum intensity value to read incomet, minimum_intensity2014 and later
minimum_peaks = 10minimum num. of peaks in spectrum to search (default 10)comet, minimum_peaks2014 and later
ms_level = 2MS level to analyze, valid are levels 2 (default) or 3comet, ms_level2014 and later
nucleotide_reading_frame = 00=proteinDB, 1-6, 7=forward three, 8=reverse three, 9=all sixN/A2014 and later
num_enzyme_termini = 2valid values are 1 (semi-digested), 2 (fully digested, default), 8 N-term, 9 C-termcomet, num_enzyme_termini2014 and later
num_output_lines = 5num peptide results to showcomet, num_output_lines2014 and later
num_results = 50number of search hits to store internallycomet, num_results2014 and later
num_threads = 00=poll CPU to set num threads; else specify num threads directly (max 32)comet, num_threads2014 and later
override_charge0=no, 1=override precursor charge states, 2=ignore precursor charges outside precursor_charge range, 3=see onlinecomet, override_charge2015 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 = 00=amu, 1=mmu, 2=ppmspectrum, parent monoisotopic mass error units2014 and later
precursor_charge = 0 0precursor charge range to analyze; does not override mzXML charge; 0 as 1st entry ignores parametercomet, precursor_charge2014 and later
precursor_tolerance_type = 00=MH+ (default), 1=precursor m/zcomet, precursor_tolerance_type2014 and later
print_expect_score = 10=no, 1=yes to replace Sp with expect in out & sqtcomet, print_expect_score2014 and later
remove_precursor_peak = 00=no, 1=yes, 2=all charge reduced precursor peaks (for ETD)comet, remove_precursor_peak2014 and later
remove_precursor_tolerance = 1.5+- Da tolerance for precursor removalcomet, remove_precursor_tolerance2014 and later
require_variable_mod N/A2015 and later 
sample_enzyme_number = 1Sample enzyme which is possibly different than the one applied to the search.protein, cleavage site2014 and later
scan_range = 0 0start and scan scan range to search; 0 as 1st entry ignores parametercomet, scan_range2014 and later
search_enzyme_number = 1choose from list at end of this params fileprotein, cleavage site2014 and later
show_fragment_ions = 00=no, 1=yes for out files onlycomet, show_fragment_ions2014 and later
skip_researching = 1for '.out' file output only, 0=search everything again (default), 1=don't search if .out existsN/A2014 and later
spectrum_batch_size = 0max. of spectra to search at a time; 0 to search the entire scan range in one loopcomet, spectrum_batch_size2014 and later
theoretical_fragment_ions = 10=default peak shape, 1=M peak onlycomet, theoretical_fragment_ions2014 and later
use_A_ions = 0 scoring, a ions2014 and later
use_B_ions = 1 scoring, b ions2014 and later
use_C_ions = 0 scoring, c ions2014 and later
use_NL_ions = 10=no, 1=yes to consider NH3/H2O neutral loss peakscomet, use_NL_ions2014 and later
use_sparse_matrix = 0 N/A2014 and later
use_X_ions = 0 scoring, x ions2014 and later
use_Y_ions = 1 scoring, y ions2014 and later
use_Z_ions = 0 scoring, z ions2014 and later
variable_C_terminus = 0.0 residue, potential modification mass2014
variable_C_terminus_distance = -1-1=all peptides, 0=protein terminus, 1-N = maximum offset from C-terminuscomet, variable_N_terminus_distance2014
variable_mod1 = 15.9949 M 0 3 residue, potential modification2014
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 mass2014
variable_N_terminus_distance = -1-1=all peptides, 0=protein terminus, 1-N = maximum offset from N-terminuscomet, variable_N_terminus_distance2014
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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