Comet

Comet parameter: activation_method

• This parameter specifies which scan types are searched.
• If "ALL" is specified, no filtering based on the activation method is applied.
• If any other allowed entry is chosen, only spectra with activation method matching the specified entry are searched.
• This parameter is valid only for mzXML, mzML and mz5 input.
• Allowed values are: ALL, CID, ECD, ETD, PQD, HCD, IRMPD
• The default value is "ALL" if this parameter is missing.

Example:
activation_method = ALL
activation_method = CID
activation_method = ETD
activation_method = HCD

Comet parameter: add_A_alanine

• Specify a static modification to the residue A.
• The specified mass is added to the unmodified mass of A.
• The default value is "0.0" if this parameter is missing.

Example:
add_A_alanine = 15.9949

Comet parameter: add_B_user_amino_acid

• This parameter allows users to define their own custom residue. Just encode the letter 'B' in the input FASTA file and specify its mass here.
• The letter 'B' has no default mass. So the mass entered here will be its residue mass.
• The default value is "0.0" if this parameter is missing. If any peptide contains the letter 'B' while this parameter value is set to 0.0, that peptide will not be analyzed.

Example:
add_B_user_amino_acid = 15.9949

Comet parameter: add_C_cysteine

• Specify a static modification to the residue C.
• The specified mass is added to the unmodified mass of C.
• The default value is "0.0" if this parameter is missing. If Comet was compiled for Crux compatibility, the default value is "57.021464". Note that in the example parameter file produced by Comet using the "-p" command line option, this parameter entry has a value of 57.021464 for cysteine carbamidomethylation.

Example:
add_C_cysteine = 57.021464

Comet parameter: add_Cterm_peptide

• Specify a static modification to the C-terminus of all peptides.
• The specified mass is added to the unmodified C-terminal mass (mass of OH or 17.00274).
• The default value is "0.0" if this parameter is missing.

Example:
add_Cterm_peptide = 14.01

Comet parameter: add_Cterm_protein

• Specify a static modification to the C-terminal peptide of each protein entry.
• The specified mass is added to the unmodified C-terminal mass (mass of OH or 17.00274).
• The default value is "0.0" if this parameter is missing.

Example:
add_Cterm_protein = 14.01

Comet parameter: add_D_aspartic_acid

• Specify a static modification to the residue D.
• The specified mass is added to the unmodified mass of D.
• The default value is "0.0" if this parameter is missing.

Example:
add_D_cysteine = 15.9949

Comet parameter: add_E_glutamic_acid

• Specify a static modification to the residue E.
• The specified mass is added to the unmodified mass of E.
• The default value is "0.0" if this parameter is missing.

Example:
add_E_cysteine = 15.9949

Comet parameter: add_F_phenylalanine

• Specify a static modification to the residue F.
• The specified mass is added to the unmodified mass of F.
• The default value is "0.0" if this parameter is missing.

Example:
add_F_phenylalanine = 15.9949

Comet parameter: add_G_glycine

• Specify a static modification to the residue G.
• The specified mass is added to the unmodified mass of G.
• The default value is "0.0" if this parameter is missing.

Example:
add_G_cysteine = 15.9949

Comet parameter: add_H_histidine

• Specify a static modification to the residue H.
• The specified mass is added to the unmodified mass of H.
• The default value is "0.0" if this parameter is missing.

Example:
add_H_histidine = 15.9949

Comet parameter: add_I_isoleucine

• Specify a static modification to the residue I.
• The specified mass is added to the unmodified mass of I.
• The default value is "0.0" if this parameter is missing.

Example:
add_I_isoleucine = 15.9949

Comet parameter: add_J_user_amino_acid

• This parameter allows users to define their own custom residue. Just encode the letter 'J' in the input FASTA file and specify its mass here.
• The letter 'J' has no default mass. So the mass entered here will be its residue mass.
• The default value is "0.0" if this parameter is missing. If any peptide contains the letter 'J' while this parameter value is set to 0.0, that peptide will not be analyzed.

Example:
add_J_user_amino_acid = 15.9949

Comet parameter: add_K_lysine

• Specify a static modification to the residue K.
• The specified mass is added to the unmodified mass of K.
• The default value is "0.0" if this parameter is missing.

Example:
add_K_lysine = 14.01

Comet parameter: add_L_leucine

• Specify a static modification to the residue L.
• The specified mass is added to the unmodified mass of L.
• The default value is "0.0" if this parameter is missing.

Example:
add_L_leucine = 15.9949

Comet parameter: add_M_methionine

• Specify a static modification to the residue M.
• The specified mass is added to the unmodified mass of M.
• The default value is "0.0" if this parameter is missing.

Example:
add_M_methionine = 15.9949

Comet parameter: add_N_asparagine

• Specify a static modification to the residue N.
• The specified mass is added to the unmodified mass of N.
• The default value is "0.0" if this parameter is missing.

Example:
add_N_cysteine = 15.9949

Comet parameter: add_Nterm_peptide

• Specify a static modification to the N-terminus of all peptides.
• The specified mass is added to the unmodified N-terminal mass (mass of H or 1.007825).
• The default value is "0.0" if this parameter is missing.

Example:
add_Nterm_peptide = 14.01

Comet parameter: add_Nterm_protein

• Specify a static modification to the N-terminal peptide of each protein entry.
• The specified mass is added to the unmodified N-terminal mass (mass of H or 1.007825).
• The default value is "0.0" if this parameter is missing.

Example:
add_Nterm_protein = 14.01

Comet parameter: add_O_ornithine

• Specify a static modification to the residue O.
• The specified mass is added to the unmodified mass of O.
• The default value is "0.0" if this parameter is missing.

Example:
add_O_ornithine = 15.9949

Comet parameter: add_P_proline

• Specify a static modification to the residue P.
• The specified mass is added to the unmodified mass of P.
• The default value is "0.0" if this parameter is missing.

Example:
add_P_proline = 15.9949

Comet parameter: add_Q_glutamine

• Specify a static modification to the residue Q.
• The specified mass is added to the unmodified mass of Q.
• The default value is "0.0" if this parameter is missing.

Example:
add_Q_glutamine = 15.9949

Comet parameter: add_R_arginine

• Specify a static modification to the residue R.
• The specified mass is added to the unmodified mass of R.
• The default value is "0.0" if this parameter is missing.

Example:
add_R_arginine = 28.03

Comet parameter: add_S_serine

• Specify a static modification to the residue S.
• The specified mass is added to the unmodified mass of s.
• The default value is "0.0" if this parameter is missing.

Example:
add_S_serine = 15.9949

Comet parameter: add_T_threonine

• Specify a static modification to the residue T.
• The specified mass is added to the unmodified mass of T.
• The default value is "0.0" if this parameter is missing.

Example:
add_T_threonine = 15.9949

Comet parameter: add_U_user_amino_acid

• This parameter allows users to define their own custom residue. Just encode the letter 'U' in the input FASTA file and specify its mass here.
• The letter 'U' has no default mass. So the mass entered here will be its residue mass.
• The default value is "0.0" if this parameter is missing. If any peptide contains the letter 'U' while this parameter value is set to 0.0, that peptide will not be analyzed.

Example:
add_U_user_amino_acid = 15.9949

Comet parameter: add_V_valine

• Specify a static modification to the residue V.
• The specified mass is added to the unmodified mass of V.
• The default value is "0.0" if this parameter is missing.

Example:
add_V_valine = 15.9949

Comet parameter: add_W_tryptophan

• Specify a static modification to the residue W.
• The specified mass is added to the unmodified mass of W.
• The default value is "0.0" if this parameter is missing.

Example:
add_W_tryptophan = 15.9949

Comet parameter: add_X_user_amino_acid

• This parameter allows users to define their own custom residue. Just encode the letter 'X' in the input FASTA file and specify its mass here.
• The letter 'X' has no default mass. So the mass entered here will be its residue mass.
• The default value is "0.0" if this parameter is missing. If any peptide contains the letter 'X' while this parameter value is set to 0.0, that peptide will not be analyzed.

Example:
add_X_user_amino_acid = 15.9949

Comet parameter: add_Y_tyrosine

• Specify a static modification to the residue Y.
• The specified mass is added to the unmodified mass of Y.
• The default value is "0.0" if this parameter is missing.

Example:
add_Y_tyrosine = 15.9949

Comet parameter: add_Z_user_amino_acid

• This parameter allows users to define their own custom residue. Just encode the letter 'Z' in the input FASTA file and specify its mass here.
• The letter 'Z' has no default mass. So the mass entered here will be its residue mass.
• The default value is "0.0" if this parameter is missing. If any peptide contains the letter 'Z' while this parameter value is set to 0.0, that peptide will not be analyzed.

Example:
add_Z_user_amino_acid = 15.9949

Comet parameter: allowed_missed_cleavage

• Number of allowed missed enzyme cleavages in a peptide.
• Parameter is not applied of the no-enzyme option is specified in the search_enzyme_number parameter.
• The default value is "2" if this parameter is missing.

Example:
allowed_missed_cleavage = 0     for no missed cleavages
allowed_missed_cleavage = 2     allow two missed cleavages

Comet parameter: clear_mz_range

• This parameter is intended for iTRAQ/TMT type data where one might want to remove the reporter ion signals in the MS/MS spectra prior to searching.
• Defines the m/z range to clear out in each MS/MS spectra
• This parameter has two decimal values.
• The first value is the lower mass cutoff and the second value is the high mass cutoff.
• Valid values are two decimal numbers where the first number must be less or equal to the second number.
• All peaks between the two decimal values are cleared out.
• The default value is "0.0 0.0" if this parameter is missing.

Example:
clear_mz_range = 0.0 0.0     parameter is ignored
clear_mz_range = 112.5 121.5     ignore all peaks between 112.5 and 121.5 m/z for iTRAQ 8-plex
clear_mz_range = 125.5 131.5     ignore all peaks between 125.5 and 131.5 m/z for TMT

Comet parameter: clip_nterm_methionine

• This parameter controls whether Comet will automatically remove the N-terminal methionine from a sequence entry.
• If set to 0, the sequence is analyzed as-is.
• If set to 1, any sequence with an N-terminal methionine will be analyzed as-is as well as with the methionine removed. This means that any N-terminal modifications will also apply (if appropriate) to the peptide that is generated after the removal of the methionine.
• Valid values are 0 and 1.
• The default value is "0" if this parameter is missing.

Example:
clip_nterm_methionine = 0
clip_nterm_methionine = 1

Comet parameter: database_name

• A full or relative path to the sequence database, in FASTA format, to search. Example databases include RefSeq or UniProt.
• Database can contain amino acid sequences or nucleic acid sequences. If sequences are amino acid sequences, set the parameter "nucleotide_reading_frame = 0". If the sequences are nucleic acid sequences, you must instruct Comet to translate these to amino acid sequences. Do this by setting "nucleotide_reading_frame" to a value between 1 and 9.
• There is no default value if this parameter is missing.

Example:
database_name = /usr/local/db/yeast.fasta
database_name = c:\local\db\yeast.fasta
database_name = yeast.fasta

Comet parameter: decoy_prefix

• This parameter specifies the prefix string that is pre-pended to the protein identifier and reported for decoy hits.
• This parameter is only valid when a decoy_search is performed.
• For example, if the prefix parameter is set to "decoy_prefix = reverse_", a match to a decoy peptide from protein "ALBU_HUMAN" would return "reverse_ALBU_HUMAN" as the protein identifier.
• The default value is "DECOY_" if this parameter is missing.

Example:
decoy_prefix = DECOY_
decoy_prefix = rev_
decoy_prefix = --any_string_you_want_without_spaces--

Comet parameter: decoy_search

• This parameter controls whether or not an internal decoy search is performed.
• Comet generates decoys by reversing each target peptide sequence, keeping the N-terminal or C-terminal amino acid in place (depending on the "sense" value of the digestion enzyme specified by search_enzyme_number). For example, peptide DIGSESTK becomes decoy peptide TSESGIDK for a tryptic search and peptide DVINHKGGA becomes DAGGKHNIV for an Asp-N search.
• Valid parameter values are 0, 1, or 2:
  • 0 = no decoy search (default)
  • 1 = concatenated decoy search. Target and decoy entries will be scored against each other and a single result is performed for each spectrum query.
  • 2 = separate decoy search. Target and decoy entries will be scored separately and separate target and decoy search results will be reported.
• The default value is "0" if this parameter is missing.

Example:
decoy_search = 0
decoy_search = 1
decoy_search = 2

Comet parameter: digest_mass_range

• Defines the mass range of peptides to search (based on MH+ or the singly protonated mass).
• This parameter has two decimal values.
• The first value is the lower mass cutoff and the second value is the high mass cutoff.
• Only spectra with experimental MH+ masses in within the defined mass ranges are searched.
• Valid values are two decimal numbers where the first number must be less or equal to the second number.
• The default value is "0.0 10000.0" if this parameter is missing.

Example:
digest_mass_range = 600.0 5000.0     search only 600.0 to 5000.0 mass range
digest_mass_range = 0.0 6500.0     search all spectra with peptide masses between 0.0 and 6000.0

Comet parameter: fragment_bin_offset

• This parameter controls how each fragment bin of size fragment_bin_tol is defined in terms of where each bin starts.
• For example, assume a fragment_bin_tol of 1.0. Most intuitively, the fragment bins would be 0.0 to 1.0, 1.0 to 2.0, 2.0 to 3.0, etc. This set of bins corresponds to a fragment_bin_offset of 0.0. However, consider if we set fragment_bin_offset to 0.5; this would cause the bins to be 0.5 to 1.5, 1.5 to 2.5, 2.5 to 3.5, etc.
• So this fragment_bin_offset gives one a mechanism to define where each bin starts and is centered.
• For ion trap data with a fragment_bin_tol of 1.0005, it is recommended to set fragment_bin_offset to 0.4.
• For high-res MS/MS data, one might use a fragment_bin_tol of 0.02 and a corresponding fragment_bin_offset of 0.0.
• Allowed values are between 0.0 and 1.0. The actual offset value is scaled by the fragment_bin_tol value.
• I know this is esoteric and any normal user should not give this parameter any thought beyond using the recommended settings.
• The default value is "0.4" if this parameter is missing.

Example:
fragment_bin_offset = 0.4
fragment_bin_offset = 0.0

Comet parameter: fragment_bin_tol

• This parameter controls the bin size associated with fragment ions.
• The bin size defines the mass width associated with a single MS/MS peak as it is stored internally in an array element.
• Although it's not explicitly a fragment ion tolerance, it's probably easiest to think of it as such.
• Note, there is a direct correlation between the value selected for the fragment_bin_tol and the memory used in a search. The lower the fragment_bin_tol setting, the more memory a search will use. A test of 4,515 query spectra used ~700MB RAM with a 0.4 fragment_bin_tol value, ~1.5GB RAM with a 0.10 value, and ~9GB RAM with a 0.01 value. For small fragment_bin_tol values where computer memory becomes an issue, either set use_sparse_matrix to true and/or make use of the spectrum_batch_size parameter
• The minimum allowed value is 0.01.
• The default value is "1.0005" if the parameter is missing.

Example:
fragment_bin_tol = 1.0005
fragment_bin_tol = 0.4
fragment_bin_tol = 0.02

Comet parameter: isotope_error

• This parameter controls whether the peptide_mass_tolerance takes into account possible isotope errors in the precursor mass measurement.
• It is possible that an accurately read precursor mass is not measured on the monoisotopic peak of a precursor isotopic pattern. In these cases, the precursor mass is measured on the first isotope peak (one C13 atom) or possibly even the second or third isotope peak. To address this problem, this "isotope_error" parameter allows you to perform an accurate mass search (say 10 ppm) even if the precursor mass measurement is off by one or more C13 offsets.
• Valid values are 0, 1, and 2:
  • 0 performs no isotope error searches
  • 1 searches -1, 0, +1, +2, and +3 isotope offsets
  • 2 searches -8, -4, 0, +4, +8 isotope offsets (for +4/+8 stable isotope labeling)
• The default value is "0" if this parameter is missing.

Example:
isotope_error = 0
isotope_error = 1
isotope_error = 2

Comet parameter: mass_offsets

• This parameter allows the user to specify one or more "mass offsets" to apply.
• This value is effective subtracted from each precursor mass such that peptides that are smaller than the precursor mass by the offset value can still be matched to the respective spectrum. The application of this parameter is for those uses cases where say a chemical tag is applied and always falls off the peptide before/during fragmentation.
• Only positive numbers only are allowed.
• When this parameter is applied, one must add the offset "0.0" if you want the search to also analyze peptides that match the base precursor mass.

Example:
mass_offsets = 42.0123 48.3812 82.030
mass_offsets = 0.0 42.0123 48.3812 82.030

Comet parameter: mass_type_fragment

• Controls the mass type, average or monoisotopic, applied to fragment ion calculations.
• Valid values are 0 or 1:
  • 0 for average masses
  • 1 for monoisotopic masses
• The default value is "1" if this parameter is missing.

Example:
mass_type_fragment = 0
mass_type_fragment = 1

Comet parameter: mass_type_parent

• Controls the mass type, average or monoisotopic, applied to peptide mass calculations.
• Valid values are 0 or 1:
  • 0 for average masses
  • 1 for monoisotopic masses
• The default value is "1" if this parameter is missing.

Example:
mass_type_parent = 0
mass_type_parent = 1

Comet parameter: max_fragment_charge

• This parameter sets the maximum fragment charge state that will be considered in the analysis.
• Typically, the fragment charge state range that is analyzed is from 1+ to one charge less than the precursor charge state.
• For high precursor charge states (i.e. 6+), the default behavior would analyze fragment ions with 1+ through 5+ charges on them. This parameter is a mechanism to limit the fragment charge range that is analyzed.
• For example, if max_fragment_charge is set to 3 then the maximum fragment charge state that will be analyzed is 3+. However, the default rule will still limit 1+ and 2+ precursor ions to only have 1+ fragments considered. And similarly 3+ precursors will still only have 1+ and 2+ fragments considered.
• Valid values are any non-zero integer.
• The default value is "3" if this parameter is missing. A maximum allowed value of "5" is enforced for this parameter.

Example:
max_fragment_charge = 3

Comet parameter: max_precursor_charge

• This parameter defines the maximum precursor charge state that will be analyzed.
• Only spectra with this number of precursor charges or less will be searched.
• Valid values are any integer greater than 1.
• The default value is "6" if this parameter is missing. A maximum allowed value of "9" is enforced for this parameter.

Example:
max_precursor_charge = 5

Comet parameter: max_variable_mods_in_peptide

• Specifies the total/maximum number of residues that can be modified in a peptide.
• As opposed to specifying the maximum number of variable modifications for each of the 6 possible variable modifications, this entry limits the global number of variable mods possible in each peptide.
• The default value is "10" if this parameter is missing.

Example:
max_variable_mods_in_peptide = 6
max_variable_mods_in_peptide = 10

Comet parameter: minimum_intensity

• A floating point number indicating the minimum intensity value for input the input peaks.
• If an experimental MS/MS peak intensity is less than this value, it will not be read in and used in the analysis.
• This is one mechanism to get rid of systemmatic background noise that has a near contant peak intensity.
• If a peak does not pass this minimum intensity threshold, it will also not be counted towards the minimum_peaks parameter.
• Valid values are any floating point number.
• The default value is "0.0" if this parameter is missing.

Example:
minimum_intensity = 100.0

Comet parameter: minimum_peaks

• An integer value indicating the minimum number of m/z-intensity pairs that must be present in a spectrum before it is searched.
• This parameter can be used to avoid searching nearly sparse spectra that will not likely yield an indentification.
• This parameter is checked against the spectrum after clear_mz_range is applied but before any other spectral processing occurs (i.e. remove_precursor_peak).
• Valid values are any integer number.
• The default value is "10" if this parameter is missing.

Example:
minimum_peaks = 10

Comet parameter: ms_level

• This parameter specifies which scans are searched.
• An input value of 2 will search MS/MS scans.
• An input value of 3 will search MS3 scans.
• This parameter is only valid for mzXML, mzML, and mz5 input files.
• Allowed values are 2 or 3.
• The default value is "2" if this parameter is missing or any value other than 2 or 3 is entered.

Example:
ms_level = 2
ms_level = 3

Comet parameter: nucleotide_reading_frame

• This parameter is used to search nucleotide sequence databases.
• It controls how the nucleotides are translated specifically which sets of reading frames are translated.
• Valid values are 0 through 9.
• Set this parameter to 0 for a protein sequence database.
• Set this parameter to 1 to search the 1st forward reading frame.
• Set this parameter to 2 to search the 2nd forward reading frame.
• Set this parameter to 3 to search the 3rd forward reading frame.
• Set this parameter to 4 to search the 1st reverse reading frame.
• Set this parameter to 5 to search the 2nd reverse reading frame.
• Set this parameter to 6 to search the 3rd reverse reading frame.
• Set this parameter to 7 to search all 3 forward reading frames.
• Set this parameter to 8 to search all 3 reverse reading frames.
• Set this parameter to 9 to search all 6 reading frames.
• The default value is "0" if this parameter is missing.

Example:
nucleotide_reading_frame = 0
nucleotide_reading_frame = 9

Comet parameter: num_enzyme_termini

• This parameter specifies the number of enzyme termini a peptide must have.
• For example, if trypsin were specified as the search enzyme, only fully tryptic peptides would be analyzed if "num_enzyme_termini = 2" whereas semi-tryptic peptides would be analyzed if "num_enzyme_termini = 1".
• This parameter is unused if a no-enzyme search is specified.
• Valid values are 1, 2, 8, 9.
• Set this parameter to 1 for a semi-enzyme search.
• Set this parameter to 2 for a full-enzyme search.
• Set this parameter to 8 for a semi-enzyme search, unspecific cleavage on peptide's C-terminus. The N-terminus of each peptide will be enzyme specific and the C-terminus can be enzyme unspecific.
• Set this parameter to 9 for a semi-enzyme search, unspecific cleavage on peptide's N-terminus. The C-terminus of each peptide will be enzyme specific and the N-terminus can be enzyme unspecific.
• The default value is "2" if this parameter is missing.

Example:
num_enzyme_termini = 1
num_enzyme_termini = 2
num_enzyme_termini = 8
num_enzyme_termini = 9

Comet parameter: num_output_lines

• This parameter controls the number of search result hits (peptides) that are reported for each spectrum query.
• If you are only interested in seeing one top hit each per query, set this value to 1.
• This parameter value cannot be larger than the value entered for "num_results" which itself is limited to a maximum value of 100.
• Valid values are any positive integer 1 or greater.
• If a value less than 1 is entered, this parameter is set to 1.
• The default value is "10" if this parameter is missing.

Example:
num_output_lines = 1
num_output_lines = 5
num_output_lines = 10

Comet parameter: num_results

• This parameter controls the number of peptide search results that are stored internally.
• Depending on what post-processing tools are used, one may want to set this to the same value as num_output_lines.
• When this parameter is set to a value greater than num_output_lines, it allows the SpRank value to span a larger range which may be helpful for tools like PeptideProphet or Percolator (not likely though).
• Valid values are any integer between 1 and 100.
• The default value is "100" if this parameter is missing.

Example:
num_results = 50

Comet parameter: num_threads

• This parameter controls the number of processing threads that will be spawned for a search. Ideally the number of threads is set to the same value as the number of CPU cores available.
• Valid values range for this parameter are numbers ranging from 0 to 64.
• A value of 0 will cause Comet to poll the system and launch the same number of threads as CPU cores.
• To set an explicit thread count, enter any value between 1 and 64.
• The default value is "0" if this parameter is missing.

Example:
num_threads = 0
num_threads = 8

Comet parameter: output_outfiles

• Controls whether to output search results as individual .out files.
• Valid values are 0 (do not output) or 1 (output).
• The default value is "0" if this parameter is missing.

Example:
output_outfiles = 0
output_outfiles = 1

Comet parameter: output_pepxmlfile

• Controls whether to output search results in a pepXML file.
• Valid values are 0 (do not output) or 1 (output).
• The default value is "1" if this parameter is missing.

Example:
output_pepxmlfile = 0
output_pepxmlfile = 1

Comet parameter: output_percolatorfile

• Controls whether to output search results in a Percolator's tab-delimited input format.
• Valid values are 0 (do not output) or 1 (output).
• The default value is "0" if this parameter is missing.
• The created file will have a ".tsv" file extension.
• This parameter replaces the now defunct "output_pinxmlfile".

Example:
output_percolatorfile = 0
output_percolatorfile = 1

Comet parameter: output_sqtfile

• Controls whether to output search results into an SQT file (.sqt).
• Valid values are 0 (do not output) or 1 (output).
• The default value is "0" if this parameter is missing.

Example:
output_sqtfile = 0
output_sqtfile = 1

Comet parameter: output_sqtstream

• Controls whether to output search results to standard out (i.e. to the screen unless otherwise directed) in SQT format.
• Just the search results (M and L lines and not any H lines) are output to standard out.
• Valid values are 0 (do not output) or 1 (output).
• The default value is "0" if this parameter is missing.

Example:
output_sqtstream = 0
output_sqtstream = 1

Comet parameter: output_suffix

• This parameter specifies the suffix string that is appended to the base output name for the pep.xml, pin.xml, txt and sqt output files.
• Use this parameter to give output files a unique suffix base name.
• For example, if the output_suffix parameter is set to "output_suffix = _000", then a search of the file base.mzXML will generate output files named base_000.pep.xml, base_000.pin.xml, base_000.txt, and/or base_000.sqt.
• Note that using this parameter could break downstream tools that expect the output base name to be the same as the input file base name.
• The default value is blank if this parameter is missing i.e. base.mzXML will generate base.pep.xml.

Example:
output_suffix =
output_suffix = _some_suffix
output_suffix = any_string_you_want_without_spaces

Comet parameter: output_txtfile

• Controls whether to output search results into a tab-delimited text file (.txt).
• Valid values are 0 (do not output) or 1 (output).
• The default value is "0" if this parameter is missing.

Example:
output_txtfile = 0
output_txtfile = 1

Here's snippet of sample output below. The first line of the output file is a header line which contains the Comet version, search start time/date, and search database. The second line contains the column headers.

CometVersion 2015.01 rev. 0     BASE_NAME_OF_FILE_0000000       02/23/2015, 12:15:44 PM /net/database/path/YEAST.fasta.20141030
scan  num   charge   exp_neutral_mass  calc_neutral_mass e-value  xcorr delta_cn sp_score ions_matched   ions_total  plain_peptide  peptide  prev_aa  next_aa  protein  duplicate_protein_count
4  1  3  4916.768332 4917.845271 1.03E+01 0.8477   0.0015   31.8  10 164   NISMDDDDALNSPDMGQEYEGRDADDVVMMASSTNEELEELK   K.NISMDDDDALNSPDMGQEY[80.0]EGRDADDVVMMAS[80.0]ST[80.0]NEELEELK.K  K  K  sp|Q03954|SPC19_YEAST   0
6  1  2  3454.696629 3452.657825 1.78E+01 0.8366   0.0133   44.2  7  52 ENFVFLQYQYESRNAQPYLQFYHLNNK   K.ENFVFLQYQYESRNAQPYLQFYHLNNK.D  K  D  sp|Q06682|UBX5_YEAST 0
9  1  2  3081.173191 3079.219382 1.04E+00 0.9564   0.1603   33.3  7  48 TGGWIYSCNTRDMSGNPIMLEKGPR  R.T[80.0]GGWIY[80.0]S[80.0]CNTRDMSGNPIMLEKGPR.T R  T  sp|P40012|PPOX_YEAST 0
19 1  2  3481.657810 3478.707612 8.53E+00 0.7803   0.0457   14.0  4  50 TKYLNYYTPLVLLIFTVLFITYNIWK R.TKYLNYYTPLVLLIFT[80.0]VLFIT[80.0]Y[80.0]NIWK.H   R  H  sp|P32386|YBT1_YEAST 0
23 1  2  3277.656834 3274.649977 3.38E+00 0.9774   0.0012   28.2  8  64 LVAGGAAQNTARGAAYVLGAGQVVYFGSVGKDK   K.LVAGGAAQNTARGAAYVLGAGQVVY[80.0]FGSVGKDK.F  K  F  sp|P47143|ADK_YEAST  0

Comet parameter: override_charge

• This parameter specifies the whether to override existing precursor charge state information when present in the files with the charge range specified by the "precursor_charge" parameter.
• Valid values are 0, 1, 2, and 3:
  • 0 = keep any known precursor charge state values in the input files
  • 1 = ignore known precursor charge state values in the input files and instead use the charge state range specified by the "precursor_charge" parameter
  • 2 = only search precursor charge state values that are within the range specified by the "precursor_charge" parameter
  • 3 = keep any known precursor charge state values. For unknown charge states, search as singly charged if there is no signal above the precursor m/z or use the "precursor_charge" range otherwise.

Example:
override_charge = 0
override_charge = 1
override_charge = 2
override_charge = 3

Comet parameter: override_charge

• This parameter specifies the whether to override existing precursor charge state information when present in the files with the charge range specified by the "precursor_charge" parameter.
• Valid values are 0, 1, and 2:
  • 0 = keep any known precursor charge state values in the input files
  • 1 = ignore known precursor charge state values in the input files and instead use the charge state range specified by the "precursor_charge" parameter
  • 2 = only search precursor charge state values that are within the range specified by the "precursor_charge" parameter

Example:
override_charge = 0
override_charge = 1

Comet parameter: peptide_mass_tolerance

• This parameter controls the mass tolerance value.
• The mass tolerance is set at +/- the specified number i.e. an entered value of "1.0" applies a -1.0 to +1.0 tolerance.
• The units of the mass tolerance is controlled by the parameter "peptide_mass_units".
• The default value is "1.0" if this parameter is missing.

Example:
peptide_mass_tolerance = 3.0
peptide_mass_tolerance = 10.0

Comet parameter: peptide_mass_units

• This parameter controls the units applied to the peptide_mass_tolerance parameter.
• Valid values are 0, 1, and 2.
• Set this parameter to 0 for amu.
• Set this parameter to 1 for mmu.
• Set this parameter to 2 for ppm.
• The default value is "0" if this parameter is missing.

Example:
peptide_mass_units = 0
peptide_mass_units = 1
peptide_mass_units = 2

Comet parameter: precursor_charge

• This parameter specifies the precursor charge range to search.
• This parameter expects to integer values as input.
• If the first input value is 0 then this parameter is ignored and all charge states are searched
• Only in the case where a spectrum does not have a precursor charge will all charges in the specified charge range be searched.
• If the first input value is not 0 then all charge states between (and inclusive of) the first and second input values are searched. Again, only for those spectra with no specified precursor charge state.
• If a precursor charge is present for a particular spectrum, this parameter will not override that charge state and that spectrum will always be searched.
• With the default "0 0" values and a spectrum with no precursor charge, Comet will either search the spectrum as a 1+ or a 2+/3+.
• The default value is "0 0" if this parameter is missing.

Example:
precursor_charge = 0 0     search all charge ranges
precursor_charge = 0 2     search all charge ranges (because first entry is 0)
precursor_charge = 2 6     search 2+ to 6+ precursors
precursor_charge = 3 3     search 3+ precursors

Comet parameter: precursor_tolerance_type

• This parameter controls how the peptide_mass_tolerance parameter is applied. That tolerance can be applied to the singly charged peptide mass or it can be applied to the precursor m/z.
• Note that this parameter is applied only when amu or mmu tolerances are specified. It is ignored when ppm tolerances are specified.
• Valid values are 0 or 1.
• Set this parameter to 0 to specify that the mass tolerance is applied to the singly charged peptide mass.
• Set this parameter to 1 to specify that the mass tolerance is applied to the precursor m/z.
• The default value is "0" if this parameter is missing.

Example:
precursor_tolerance_type = 0
precursor_tolerance_type = 1

For example, assume a 1.0 Da peptide_mass_tolerance was specified. If "precursor_tolerance_type = 0" then a peptide with MH+ mass of 1250.4 will be queried against peptide sequences with MH+ masses between 1249.4 to 1251.4. If "precursor_tolerance_type = 1" then say the 2+ m/z is 625.7 so the search mass range would be 624.7 m/z to 626.7 m/z which corresponds to MH+ masses between 1248.4 and 1252.4, effectively scaling the mass tolerance by the charge state.

Comet parameter: print_expect_score

• A boolean flag this determines whether or not the expectation score (E-value) is reported in .out and SQT formats. Note that the E-value is always reported in pepXML output.
• This parameter is only pertinant for results reported in .out and SQT formats.
• If expect scores are chosen to be reported (i.e. value set to 1), they will replace the number reported for the traditional "spscore" i.e. "spscore" will be replaced by an E-value. Also an expectation value histogram will be output at the end of each .out file; this histogram is not present for SQT output.
• Valid values are 0 and 1.
• The default value is "0" if this parameter is missing.

Example:
print_expect_score = 0
print_expect_score = 1

Comet parameter: remove_precursor_peak

• This parameter controls excluding/removing any precursor signals from the input MS/MS spectrum.
• An input value of 0 will not perform any precursor removal.
• An input value of 1 will remove all peaks around the precursor m/z.
• An input value of 2 will remove all charge reduced precursor peaks as expected to be present for ETD/ECD spectra.
• This parameter works in conjuction with remove_precursor_tolerance to specify the tolerance around each precuror m/z that will be removed.
• Valid values are 0, 1, and 2.
• The default value is "0" if this parameter is missing.

Example:
remove_precursor_peak = 0
remove_precursor_peak = 1
remove_precursor_peak = 2

Comet parameter: remove_precursor_tolerance

• This parameter specifies the mass tolerance around each precursor m/z that would be removed when the remove_precursor_peak option is invoked.
• The mass tolerance units is in Da (or Th if you prefer).
• Any non-negative, non-zero floating point number is valid.
• The default value is "1.5" if this parameter is missing.

Example:
remove_precursor_tolerance = 0.75
remove_precursor_tolerance = 1.5

Comet parameter: require_variable_mod

• This parameter takes in one input value.
• The input value is an integer that controls whether the analyzed peptides must contain at least one variable modification i.e. force all reported peptides to have a variable modifiation.
  • 0 = consider both modified and unmodified peptides (default)
  • 1 = analyze only peptides that contain a variable modification

Example:
require_variable_mod = 0     ... modifications not required
require_variable_mod = 1     ... peptides must contain a variable modification

Comet parameter: sample_enzyme_number

• This parameter is relevant only for pepXML output i.e. when output_pepxmlfile is set to 1.
• The pepXML format encodes the enzyme that is applied to the sample i.e. trypsin. This enzyme is written to the "sample_enzyme" element.
• The sample enzyme could be different from the search enzyme i.e. the sample enzyme is "trypsin" yet the search enzyme is "No-enzyme" for a non-specific search. Hence the need for this separate parameter.
• Valid values are any integer represented in the enzyme list.
• The default value is "0" if this parameter is missing.

Example:
sample_enzyme_number = 1
sample_enzyme_number = 3

Comet parameter: scan_range

• Defines the scan range to search. Only spectra within (and inclusive) of the specified scan range are searched.
• This parameter works only with mzXML and mzML inputs files.
• Two digits are specified for this parameter. The first digit is the start scan and the second digit is the end scan.
• As of now, it looks like the first digit must be an MS/MS scan.
• When the start scan is set to 0, this parameter setting is ignored irrespective of what the end scan is set to.
• When the end scan is less than the start scan, this parameter setting is ignored.
• The default value is "0 0" if this parameter is missing.

Example:
scan_range = 0 0     search all scans
scan_range = 0 1000     search all scans (because first entry is 0)
scan_range = 1000 1500     search only scans 1000 to 1500

Comet parameter: search_enzyme_number

• The search enzyme is specified by this parameter.
• The list of search enzymes is specified at the end of the comet.params file beginning with the line [COMET_ENZYME_INFO]. The actual enzyme list and digestion parameters are read here. So one can edit/add/delete enzyme definitions simply be changing the enzyme information.
• This parameter works in conjection with the num_enzyme_termini parameter to define the cleavage rule for fully-digested vs. semi-digested search options.
• This parameter works in conjection with the allowed_missed_cleavage parameter to define the miss cleavage rule.
• The default value is "0" if this parameter is missing.

Example:
search_enzyme_number = 0     typically no-enzyme
search_enzyme_number = 1     typically trypsin

[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

Comet parameter: show_fragment_ions

• This parameter affects .out files only i.e. output_outfiles set to 1.
• This parameter controls whether or not the theoretical fragment ion masses for the top peptide hit are calculated and dislayed at the end of an .out file.
• Valid values are 0 and 1.
• The default value is "0" if this parameter is missing.

Example:
show_fragment_ions = 0
show_fragment_ions = 1

Comet parameter: skip_researching

• This parameter is valid only when output_outfiles is set to 1 and each of output_pepxmlfile, output_sqtfile, and output_sqtstream are set to 0.
• When .out files only are set to be exported, this parameter will look to see if an .out file already exists for each query spectrum. If so, it will not re-search that particular spectrum.
• When set to 0, all spectra are re-searched. When set to 1, the search is skipped for those spectra where an .out file already exists.
• Valid values are 0 and 1.
• The default value is "0" if this parameter is missing.

Example:
skip_researching = 0
skip_researching = 1

Comet parameter: spectrum_batch_size

• When this parameter is set to a non-zero value, say 5000, this causes Comet to load and search about 5000 spectra at a time, looping through sets of 5000 spectra until all data have been analyzed.
• This parameter was implemented to simplify searching large datasets that might not fit into memory if searched all at once.
• The loaded batch sizes might be a little larger than the specified parameter value (i.e. 5014 spectra loaded when the parameter is set to 5000) due to both threading and potential charge state considerations when precursor charge state is not known.
• Valid values are 0 or any positive integer.
• Set this parameter to 0 to load and search all spectra at once.
• Set this parameter to any other positive integer to loop through searching this number of spectra at a time until all spectra have been analyzed.
• The default value is "0" if this parameter is missing.

Example:
spectrum_batch_size = 0
spectrum_batch_size = 1000
spectrum_batch_size = 5000

Comet parameter: theoretical_fragment_ions

• This parameter specifies how theoretical fragment ion peaks are represented.
• Even though Comet does not generate/store a theoretical spectrum, it does calculate fragment ion masses and this parameter controls how the acquired spectrum intensities at these theoretical mass locations contribute to the correlation score.
• A value of 0 indicates that the fast correlation score will be a sum of the intensities at each theortical fragment mass bin and half the intensity of each flanking bin.
• A value of 1 indicates that the fast correlation score will be the sum of the intensities at each theoretical fragment mass bin.
• For extremely coarse fragment_bin_tol values such as the historical ~1 Da bins, a theoretical_fragment_ions value of 1 is optimal.
• But for narrower bins, such as ~0.3 for ion trap data or ~0.03 for high-res MS/MS spectra, a value of 0 is optimal to incorporate intensities from the flanking bins.
• Allowed values are 0 or 1.
• The default value is "1" if this parameter is missing.

Example:
theoretical_fragment_ions = 0
theoretical_fragment_ions = 1

Comet parameter: use_A_ions

• Controls whether or not A-ions are considered in the search.
• Valid values are 0 and 1.
• To not use A-ions, set the value to 0.
• To use A-ions, set the value to 1.
• The default value is "0" if this parameter is missing.

Example:
use_A_ions = 0
use_A_ions = 1

Comet parameter: use_B_ions

• Controls whether or not B-ions are considered in the search.
• Valid values are 0 and 1.
• To not use B-ions, set the value to 0.
• To use B-ions, set the value to 1.
• The default value is "1" if this parameter is missing.

Example:
use_B_ions = 0
use_B_ions = 1

Comet parameter: use_C_ions

• Controls whether or not C-ions are considered in the search.
• Valid values are 0 and 1.
• To not use C-ions, set the value to 0.
• To use C-ions, set the value to 1.
• The default value is "0" if this parameter is missing.

Example:
use_C_ions = 0
use_C_ions = 1

Comet parameter: use_NL_ions

• Controls whether or not neutral loss ions (-NH3 and -H2O from b- and y-ions) are considered in the search.
• Valid values are 0 and 1.
• To not use neutral loss ions, set the value to 0.
• To use neutral loss ions, set the value to 1.
• The default value is "0" if this parameter is missing.

Example:
use_NL_ions = 0
use_NL_ions = 1

Comet parameter: use_X_ions

• Controls whether or not X-ions are considered in the search.
• Valid values are 0 and 1.
• To not use X-ions, set the value to 0.
• To use X-ions, set the value to 1.
• The default value is "0" if this parameter is missing.

Example:
use_X_ions = 0
use_X_ions = 1

Comet parameter: use_Y_ions

• Controls whether or not Y-ions are considered in the search.
• Valid values are 0 and 1.
• To not use Y-ions, set the value to 0.
• To use Y-ions, set the value to 1.
• The default value is "1" if this parameter is missing.

Example:
use_Y_ions = 0
use_Y_ions = 1

Comet parameter: use_Z_ions

• Controls whether or not Z-dot ions are considered in the search.
• Valid values are 0 and 1.
• To not use Z-dot ions, set the value to 0.
• To use Z-dot ions, set the value to 1.
• The default value is "0" if this parameter is missing.

Example:
use_Z_ions = 0
use_Z_ions = 1

Comet parameter: variable_mod01 through variable_mod09

• There are 7 entries/settings that are associated with these parameters:
  • The first entry is a decimal value specifying the modification mass difference.
  • The second entry is the residue(s) that the modifications are possibly applied to. If more than a single residue is modified by the same mass difference, list them all as a string. Use 'n' for N-terminal modfication and 'c' for C-terminal modification.
  • The third entry is a integer to specify whether the modification is a variable modification (0) or a binary modification (non-zero value).
    • 0 = variable modification analyzes all permutations of modified and unmodified residues.
    • non-zero value = A binary modification analyzes peptides where all residues are either modified or all residues are not modified.
    Note that if you set the same binary modification value in multiple "variable_mod?" parameter entries, Comet will treat those variable modifications as a "binary set". This means that all modifiable residues in the "binary set" must be unmodified or modified. Multiple "binary sets" can be specified by setting a different binary modification value e.g. use "1" for all modifications in set 1, and "2" or all modifications in set 2. Binary groups were added with version 2015.02 rev. 1.
  • The fourth entry is an integer specifying the maximum number of modified residues possible in a peptide for this modification entry.
  • The fifth entry specifies the distance the modification is applied to from the respective terminus:
    • -1 = no distance contraint
    • 0 = only applies to terminal residue
    • 1 = only applies to terminal residue and next residue
    • 2 = only applies to terminal residue through next 2 residues
    • N = only applies to terminal residue through next N residues where N is a positive integer
  • The sixth entry specifies which terminus the distance constraint is applied to:
    • 0 = protein N-terminus
    • 1 = protein C-terminus
    • 2 = peptide N-terminus
    • 3 = peptide C-terminus
  • The seventh entry specifies whether peptides are must contain this modification
    • 0 = not forced to be present
    • 1 = modification is required
• Modification codes for variable_mod01 through variable_mod09 (for some outputs): *, #, @, ^, ~, $, %, !, +
• The default value is "0.0 null 0 4 -1 0 0" if this parameter is missing.

Example:
variable_mod01 = 15.9949 M 0 3 -1 0 0
variable_mod02 = 79.966331 STY 0 3 -1 0 0     ... possible phosphorylation on any S, T, Y residue
variable_mod02 = 79.966331 STY 0 3 -1 0 1     ... force peptide IDs to contain at least one phosphorylation mod
variable_mod01 = 42.010565 nK 0 3 -1 0 0     ... acetylation mod to lysine and N-terminus of all peptides
variable_mod01 = 15.994915 n 0 3 0 0 0     ... oxidation of protein's N-terminus
variable_mod01 = 28.0 c 0 3 8 1 0     ... modification applied to C-terminus as long as the C-term residue is one of last 9 residues in protein
variable_mod03 = -17.026549 Q 0 1 0 2 0     ... cyclization of N-terminal glutamine to form pyroglutamic acid (elimination of NH3)
variable_mod04 = -18.010565 E 0 1 0 2 0     ... cyclization of N-terminal glutamic acid to form pyroglutamic acid (elimination of H2O)

Here is a binary modification search example of triple SILAC plus acetylation of lysine. The SILAC modifications are "R +6 and K +4" (medium) and "R +10 and K +8" (heavy). In conjunction with K +42 acetylation, the binary modification sets would be "R +6, K +4, K +4+42" for SILAC medium (binary group 1) and "R +10, K +8, K +8+42" for SILAC heavy (binary group 2). Mass values are listed with no precision for clarity; definitely use precise modification masses in practice.
variable_mod01 = 42.0 K 0 3 -1 0 0
variable_mod02 =  6.0 R 1 3 -1 0 0
variable_mod03 =  4.0 K 1 3 -1 0 0
variable_mod04 = 46.0 K 1 3 -1 0 0
variable_mod05 = 10.0 R 2 3 -1 0 0
variable_mod06 =  8.0 K 2 3 -1 0 0
variable_mod07 = 50.0 K 2 3 -1 0 0
variable_mod08 =  0.0 X 0 3 -1 0 0
variable_mod09 =  0.0 X 0 3 -1 0 0