Search parameters (2012.01)

Comet search parameters are defined here. These are valid for Comet version 2012.01.X.

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

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.

Example:
add_A_alanine = 100.8

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.

Example:
add_B_user_amino_acid = 100.8

Comet parameter: add_C_cysteine

• Specify a static modification to the residue C.
• The specified mass is added to the unmodified mass of C.

Example:
add_C_cysteine = 57.02

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 17.0).

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 17.0).

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.

Example:
add_D_cysteine = 100.8

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.

Example:
add_E_cysteine = 100.8

Comet parameter: add_F_phenylalanine

• Specify a static modification to the residue F.
• The specified mass is added to the unmodified mass of F.

Example:
add_F_phenylalanine = 100.8

Comet parameter: add_G_glycine

• Specify a static modification to the residue G.
• The specified mass is added to the unmodified mass of G.

Example:
add_G_cysteine = 100.8

Comet parameter: add_H_histidine

• Specify a static modification to the residue H.
• The specified mass is added to the unmodified mass of H.

Example:
add_H_histidine = 100.8

Comet parameter: add_I_isoleucine

• Specify a static modification to the residue I.
• The specified mass is added to the unmodified mass of I.

Example:
add_I_isoleucine = 100.8

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.

Example:
add_J_user_amino_acid = 100.8

Comet parameter: add_K_lysine

• Specify a static modification to the residue K.
• The specified mass is added to the unmodified mass of K.

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.

Example:
add_L_leucine = 100.8

Comet parameter: add_M_methionine

• Specify a static modification to the residue M.
• The specified mass is added to the unmodified mass of M.

Example:
add_M_methionine = 100.8

Comet parameter: add_N_asparagine

• Specify a static modification to the residue N.
• The specified mass is added to the unmodified mass of N.

Example:
add_N_cysteine = 100.8

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).

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).

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.

Example:
add_O_ornithine = 100.8

Comet parameter: add_P_proline

• Specify a static modification to the residue P.
• The specified mass is added to the unmodified mass of P.

Example:
add_P_proline = 100.8

Comet parameter: add_Q_glutamine

• Specify a static modification to the residue Q.
• The specified mass is added to the unmodified mass of Q.

Example:
add_Q_glutamine = 100.8

Comet parameter: add_R_arginine

• Specify a static modification to the residue R.
• The specified mass is added to the unmodified mass of R.

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.

Example:
add_S_serine = 100.8

Comet parameter: add_T_threonine

• Specify a static modification to the residue T.
• The specified mass is added to the unmodified mass of T.

Example:
add_T_threonine = 100.8

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.

Example:
add_U_user_amino_acid = 100.8

Comet parameter: add_V_valine

• Specify a static modification to the residue V.
• The specified mass is added to the unmodified mass of V.

Example:
add_V_valine = 100.8

Comet parameter: add_W_tryptophan

• Specify a static modification to the residue W.
• The specified mass is added to the unmodified mass of W.

Example:
add_W_tryptophan = 100.8

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.

Example:
add_X_user_amino_acid = 100.8

Comet parameter: add_Y_tyrosine

• Specify a static modification to the residue Y.
• The specified mass is added to the unmodified mass of Y.

Example:
add_Y_tyrosine = 100.8

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.

Example:
add_Z_user_amino_acid = 100.8

Comet parameter: allowed_missed_cleage

• 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.

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

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.

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.

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

Comet parameter: decoy_search

• This parameter controls whether or not an internal decoy search is performed.
• 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.

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.

Example:
digest_mass_range = 0.0 10000.0     search all spectra with peptide masses between 0.0 and 10000.0
digest_mass_range = 600.0 5000.0     search only 600.0 to 5000.0 mass range

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 0.36, it is recommended to set fragment_bin_offset to 0.11. This is based on a brute force analysis of a yeast dataset.
• For high-res MS/MS data, one might use a fragment_bin_tol of 0.03 and a corresponding fragment_bin_offset of 0.0.
• Allowed values are positive decimal numbers (that must be less than the fragment_bin_tol value).

Example:
fragment_bin_offset = 0.11
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 724MB RAM with a 0.36 fragment_bin_tol value, 1.4GB RAM with a 0.10 value, and 9.6GB RAM with a 0.01 value.

Example:
fragment_bin_tol = 0.36
fragment_bin_tol = 0.03

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)

Example:
isotope_error = 0
isotope_error = 1
isotope_error = 2

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

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

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.

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.

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.

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.

Example:
minimum_intensity = 1000.0

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.
• Valid values are any integer number.

Example:
minimum_peaks = 20

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 MS^3 scans.
• This parameter is only valid for mzXML, mzML, and mz5 input files.
• Allowed values are 2 or 3.

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.
• 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.
• Valid values are 0 through 9.

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 and 2.

  Example:
  num_enzyme_termini = 1
  num_enzyme_termini = 2

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 each per query, set this value to 1.
• The maximum possible number of reported hits is hardcoded into each binary and that value is currently set to 100.
• Valid values are any positive integer 1 or greater.

Example:
num_output_lines = 1
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).
• The maximum num_results value possible is hardcoded into Comet and is currently 100.
• Valid values are any integer greater than zero.

Example:
num_results = 10

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 32.
• A value of 0 will cause Comet to poll the system and launch the same number of threads as CPU cores. This is the default setting.
• To set an explicit thread count, enter any value between 1 and 32.

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).

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).

Example:
output_pepxmlfile= 0
output_pepxmlfile= 1

Comet parameter: output_sqt_file

• Controls whether to output search results into an SQT file (.sqt).
• Valid values are 0 (do not output) or 1 (output).

Example:
output_sqt_file= 0
output_sqt_file= 1

Comet parameter: output_sqt_stream

• 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).

Example:
output_sqt_stream = 0
output_sqt_stream = 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".

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:
  • 0 for amu
  • 1 for mmu
  • 2 for ppm

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
• If the first input value is not 0 then all charge states between (and inclusive of) the first and second input values are searched.

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.
• Valid values are 0 or 1:
  • 0 applied to singly charged mass (MH+)
  • 1 applied to m/z

Example:
precursor_tolerance_type = 0
precursor_tolerance_type = 1

For example, assume a 2.1 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 1248.3 to 1252.5.

If "precursor_tolerance_type = 1" for a 10 ppm peptide_mass_tolerance, then the 10 ppm tolerance is applied at the precursor m/z level. Assuming the precursor charge is 3+ for the 1320.8 MH+ mass, this means the precursor m/z is 440.93855. +/- 10 ppm on 440.93855 gives the range 440.9341 to 440.94296. This range corresponds to peptides with MH+ masses between 1320.7868 and 1320.8132.

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, 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.

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. of 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.

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.

Example:
remove_precursor_tolerance = 0.75
remove_precursor_tolerance = 1.5

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.

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.
• 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.

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.

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

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.

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.
• Valid values are 0 and 1.

Example:
skip_researching = 0
skip_researching = 1

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.

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.

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.

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.

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.

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.

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.

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.

Example:
use_Z_ions = 0
use_Z_ions = 1

Comet parameter: variable_C_terminus_distance

• This parameter affects how the variable_C_terminus parameter is applied.
• The variable modification on the c-terminus can be applied to
  • all peptides analyzed by entering a value of -1
  • only peptides containing the protein's c-terminus by entering a value of 0
  • any positive interger N will have the program consider modifications on the c-terminus and next N residues (effectively N+1 residues).

Example:
variable_C_terminus_distance = -1   Applied to all peptides
variable_C_terminus_distance = 0     Applied only to peptides containing protein's c-terminus
variable_C_terminus_distance = 3     Applied on any peptide who's c-terminus is one of last 4 residues (c-term & next 3)
variable_C_terminus_distance = 20   Applied on any peptide who's c-terminus is one of last 21 residues (c-term & next 20)

Comet parameter: variable_C_terminus

• Specify a variable modification to peptide's c-terminus.
• Works in conjunction with variable_C_terminus_distance to specify scope of which peptides this parameter is applied to.

Example:
variable_C_terminus = 14.0

Comet parameter: variable_mod1

• This parameter specifies the 1st of 6 variable modifications.
• There are 4 entries that are associated with this parameter:
  • 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.
  • The third entry is a integer 0 or 1 to specify whether the modification is a variable modification (0) or a binary modification (1).
    • A variable modification analyzes all permutations of modified and unmodified residues.
    • A binary modification analyzes peptides where all residues are either modified or all residues are not modified.
  • The fourth entry is an integer specifying the maximum number of modified residues possible in a peptide for this modification entry.
• In the output, this first modification is encoded with the character '*' in the peptide string.

Example:
variable_mod1 = 15.9949 M 0 3
variable_mod1 = 79.966331 STY 0 3

Comet parameter: variable_mod2

• This parameter specifies the 2nd of 6 variable modifications.
• There are 4 entries that are associated with this parameter.
  • 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.
  • The third entry is a integer 0 or 1 to specify whether the modification is a variable modification (0) or a binary modification (1).
    • A variable modification analyzes all permutations of modified and unmodified residues.
    • A binary modification analyzes peptides where all residues are either modified or all residues are not modified.
  • The fourth entry is an integer specifying the maximum number of modified residues possible in a peptide for this modification entry.
• In the output, this first modification is encoded with the character '#' in the peptide string.

Example:
variable_mod2 = 15.9949 M 0 3
variable_mod2 = 79.966331 STY 0 3

Comet parameter: variable_mod3

• This parameter specifies the 3rd of 6 variable modifications.
• There are 4 entries that are associated with this parameter.
  • 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.
  • The third entry is a integer 0 or 1 to specify whether the modification is a variable modification (0) or a binary modification (1).
    • A variable modification analyzes all permutations of modified and unmodified residues.
    • A binary modification analyzes peptides where all residues are either modified or all residues are not modified.
  • The fourth entry is an integer specifying the maximum number of modified residues possible in a peptide for this modification entry.
• In the output, this first modification is encoded with the character '@' in the peptide string.

Example:
variable_mod3 = 15.9949 M 0 3
variable_mod3 = 79.966331 STY 0 3

Comet parameter: variable_mod4

• This parameter specifies the 4th of 6 variable modifications.
• There are 4 entries that are associated with this parameter.
  • 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.
  • The third entry is a integer 0 or 1 to specify whether the modification is a variable modification (0) or a binary modification (1).
    • A variable modification analyzes all permutations of modified and unmodified residues.
    • A binary modification analyzes peptides where all residues are either modified or all residues are not modified.
  • The fourth entry is an integer specifying the maximum number of modified residues possible in a peptide for this modification entry.
• In the output, this first modification is encoded with the character '^' in the peptide string.

Example:
variable_mod4 = 15.9949 M 0 3
variable_mod4 = 79.966331 STY 0 3

Comet parameter: variable_mod5

• This parameter specifies the 5th of 6 variable modifications.
• There are 4 entries that are associated with this parameter.
  • 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.
  • The third entry is a integer 0 or 1 to specify whether the modification is a variable modification (0) or a binary modification (1).
    • A variable modification analyzes all permutations of modified and unmodified residues.
    • A binary modification analyzes peptides where all residues are either modified or all residues are not modified.
  • The fourth entry is an integer specifying the maximum number of modified residues possible in a peptide for this modification entry.
• In the output, this first modification is encoded with the character '~' in the peptide string.

Example:
variable_mod5 = 15.9949 M 0 3
variable_mod5 = 79.966331 STY 0 3

Comet parameter: variable_mod6

• This parameter specifies the 6th of 6 variable modifications.
• There are 4 entries that are associated with this parameter.
  • 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.
  • The third entry is a integer 0 or 1 to specify whether the modification is a variable modification (0) or a binary modification (1).
    • A variable modification analyzes all permutations of modified and unmodified residues.
    • A binary modification analyzes peptides where all residues are either modified or all residues are not modified.
  • The fourth entry is an integer specifying the maximum number of modified residues possible in a peptide for this modification entry.
• In the output, this first modification is encoded with the character '$' in the peptide string.

Example:
variable_mod6 = 15.9949 M 0 3
variable_mod6 = 79.966331 STY 0 3

Comet parameter: variable_N_terminus_distance

• This parameter affects how the variable_N_terminus parameter is applied.
• The variable modification on the n-terminus can be applied to
  • all peptides analyzed by entering a value of -1
  • only peptides containing the protein's n-terminus by entering a value of 0
  • any positive integer N will have the program consider modifications on the n-terminus and the next N residues (effectively the first N+1 residues).

Example:
variable_N_terminus_distance = -1   Applied to all peptides
variable_N_terminus_distance = 0     Applied only to peptides containing protein's n-terminus
variable_N_terminus_distance = 1     Applied on any peptide who's n-terminus is one of first 2 residues (n-term & next 1)
variable_N_terminus_distance = 12   Applied on any peptide who's n-terminus is one of first 13 residues (n-term & next 12)

Comet parameter: variable_N_terminus

• Specify a variable modification to peptide's n-terminus.
• Works in conjunction with variable_N_terminus_distance to specify scope of which peptides this parameter is applied to.

Example:
variable_N_terminus = 14.0