Search parameters (2014.01)

Comet search parameters are defined here. These are valid for Comet version 2014.01.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
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 = 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.
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 = 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.
The default value is "0.0" if this parameter is missing.

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 17.00274).
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 = 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.
The default value is "0.0" if this parameter is missing.

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.
The default value is "0.0" if this parameter is missing.

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.
The default value is "0.0" if this parameter is missing.

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.
The default value is "0.0" if this parameter is missing.

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.
The default value is "0.0" if this parameter is missing.

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.
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 = 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.
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 = 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.
The default value is "0.0" if this parameter is missing.

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.
The default value is "0.0" if this parameter is missing.

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).
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 = 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.
The default value is "0.0" if this parameter is missing.

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.
The default value is "0.0" if this parameter is missing.

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.
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 = 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.
The default value is "0.0" if this parameter is missing.

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.
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 = 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.
The default value is "0.0" if this parameter is missing.

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.
The default value is "0.0" if this parameter is missing.

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.
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 = 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.
The default value is "0.0" if this parameter is missing.

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.
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 = 100.8

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_no_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_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 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.
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_pinxmlfile

Controls whether to output search results in a Percolator-IN or "pin.xml" file. pin.xml files are used as inputs to Percolator.
When you choose to output a pin.xml file, you must also be performing a decoy_search or else the search will not run and an error will be reported.
The pin.xml format specifies the UniMod accession number for each modification. As this information is not available, Comet will write bogus values for the UniMod accession. Each variable modification will have the variable modification number (1 thru 6) as the UniMod accession. Each static modification will have the ASCII value of the residue as the UniMod accession. If you really care about having valid UniMod accession numbers, you'll have to handle the find and replace yourself on the produced pin.xml file.
Valid values are 0 (do not output) or 1 (output).
The default value is "0" if this parameter is missing.

Example:
output_pinxmlfile = 0
output_pinxmlfile = 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).
The default value is "0" if this parameter is missing.

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).
The default value is "0" if this parameter is missing.

Example:
output_sqt_stream = 0
output_sqt_stream = 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_txt_file

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_txt_file= 0
output_txt_file= 1

Here's a 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 2013.02 rev. 0   100  10/04/2013, 08:37:09 AM  /net/pr/vol1/ProteomicsResource/dbase/SGD/SGDyeast.fasta.20101117
scan  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
5129  1  599.9698  602.3136  1.73E+01  0.6847  0.0995  44.3  4  8  DAKNR  R.DAKNR.I   R  I  YML019W  0
5385  1  601.3290  603.3228  1.73E+01  0.5316  0.1905  70.9  3  8  NLTEK  R.NLTEK.T   R  T  YBL024W  1
5496  1  601.3358  599.3755  1.67E+01  0.4527  0.1315  6.6   2  8  VVNIR  R.VVNIR.L   R  L  YJL012C  0
5430  1  602.3329  605.2591  2.33E+01  0.4222  0.0854  73.2  4  8  DVGCR  K.DVGCR.I   K  I  YER085C  0
5829  1  616.4184  615.3414  5.26E+01  0.4321  0.0658  8.5   2  8  KPPMK  -.KPPM*K.Q  -  Q  DECOY__YBR025C  2

Comet's text output is different if Comet was compiled for Crux compatibility. Here's the example text output if you are running Comet in Crux. Note that up to 5 hits per spectrum are reported and there is just a single column header line.

scan  charge  spectrum precursor m/z  spectrum neutral mass  matches/spectrum  peptide mass  e-value  xcorr score  xcorr rank  delta_cn  sp score  sp rank  b/y ions matched  b/y ions total  sequence  flanking aa  protein id
5129  1  600.9771  599.9698  5440  602.3136  1.73E+01  0.6847  1  0.0995  44.3   19  4  8   DAKNR   RI  YML019W
5129  1  600.9771  599.9698  5440  602.3249  1.96E+01  0.6714  2  0.1016  46.1   17  5  10  RTGGGR  RI  YGR054W
5129  1  600.9771  599.9698  5440  602.3136  1.99E+01  0.6698  3  0.1131  77.6   6   5  8   NISNR   KV  YMR033W
5129  1  600.9771  599.9698  5440  601.2820  2.16E+01  0.6612  4  0.1240  38.6   22  4  8   EPSNR   RD  YPL161C
5129  1  600.9771  599.9698  5440  600.3231  0.00E+00  0.6532  5  0.1389  104.6  3   6  8   IESPR   KM  YLL021W
5385  1  602.3363  601.3290  6518  603.3228  1.73E+01  0.5316  1  0.1905  70.9   2   3  8   NLTEK   RT  YBL024W
5385  1  602.3363  601.3290  6518  600.3707  1.86E+01  0.5249  2  0.2022  31.0   8   3  8   ARNIK   KT  DECOY_YIL159W
5385  1  602.3363  601.3290  6518  602.3249  2.02E+01  0.5173  3  0.2134  47.4   4   3  8   ARNSR   KI  DECOY_YLL040C
5385  1  602.3363  601.3290  6518  601.3184  2.19E+01  0.5100  4  0.2148  7.1    19  2  10  GAVNNK  KS  DECOY_YMR125W
5385  1  602.3363  601.3290  6518  599.4119  0.00E+00  0.5091  5  0.2148  28.3   9   3  8   ALLKR   RI  YML107C

Comet parameter: override_charge

This parameter specifies the whether to override existing precursor charge state information when present in the input files with the charge range specified by the "precursor_charge" parameter.
Valid values are 0 and 1.
To keep any known charge state values in the input files, set the value to 0.
To ignore any known charge values in the input files and instead use the charge state range specified by the "precursor_charge" parameter, set the value to 1.
The default value is "0" if this parameter is missing.
This parameter was implemented in version 2014.01 rev. 1.

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
If the first input value is not 0 then all charge states between (and inclusive of) the first and second input values are searched.
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.
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 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 (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. 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.
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 "2.0" if this parameter is missing.

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.
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.
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

The format of the parameter definition looks like the following:

[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

The first column of the parameter definition is the enzyme number. This number list must start from 0 and sequentially increase by 1. The second column is the enzyme name; no spaces are allowed in this name field. The third column is the digestion "sense" i.e. a value of "0" specifies cleavage N-teriminal to (before) the specified residues in column 4 and a value of "1" specifies cleavage C-terminal to (after) the specified residues in column 4. Column 4 contains the residue(s) that the enzyme cleaves at. Column 5 contains the flanking residue(s) that negate cleavage.

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 "0" 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_sparse_matrix

Controls whether or not internal sparse matrix data representation is used.
The sparse matrix data representation will use a significantly smaller amount of memory/RAM for small fragment_bin_tol settings such as 0.05 or 0.01. We're talking going from tens of GB (gigabytes) down to a few hundred megabytes (MB)!
In this release, the sparse matrix searches will always be slower than the classical data representation (i.e. use_sparse_matrix = 0). So it should be used only when memory is an issue. Alternately, the spectrum_batch_size parameter can also be used to mitigate memory issues.
Valid values are 0 and 1.
To not use sparse matrix, set the value to 0.
To use sparse matrix, set the value to 1.
The default value is "0" if this parameter is missing.

Example:
use_sparse_matrix = 0
use_sparse_matrix = 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 "0" 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_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).
The default value is "-1" if this parameter is missing.

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.
The default value is "0.0" if this parameter is missing.

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.
The default value is "0.0 null 0 4" if this parameter is missing.

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.
The default value is "0.0 null 0 4" if this parameter is missing.

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.
The default value is "0.0 null 0 4" if this parameter is missing.

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.
The default value is "0.0 null 0 4" if this parameter is missing.

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.
The default value is "0.0 null 0 4" if this parameter is missing.

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.
The default value is "0.0 null 0 4" if this parameter is missing.

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).
The default value is "-1" if this parameter is missing.

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.
The default value is "0.0" if this parameter is missing.

Example:
variable_N_terminus = 14.0

Comet

MS/MS database search