CometAdapter

Options

version

Version of the tool that generated this parameters file.

precursor_mass_tolerance

Precursor monoisotopic mass tolerance (Comet parameter: peptide_mass_tolerance). See also precursor_error_units to set the unit.

precursor_error_units

Unit of precursor monoisotopic mass tolerance for parameter precursor_mass_tolerance (Comet parameter: peptide_mass_units)

isotope_error

This parameter controls whether the peptide_mass_tolerance takes into account possible isotope errors in the precursor mass measurement. Use -8/-4/0/4/8 only for SILAC.

fragment_mass_tolerance

This is half the bin size, which is used to segment the MS/MS spectrum. Thus, the value should be a bit higher than for other search engines, since the bin might not be centered around the peak apex (see 'fragment_bin_offset').CAUTION: Low tolerances have heavy impact on RAM usage (since Comet uses a lot of bins in this case). Consider using use_sparse_matrix and/or spectrum_batch_size.

fragment_error_units

Fragment monoisotopic mass error units

fragment_bin_offset

Offset of fragment bins. Recommended by Comet: low-res: 0.4, high-res: 0.0

instrument

Comets theoretical_fragment_ions parameter: theoretical fragment ion peak representation, high-res: sum of intensities plus flanking bins, ion trap (low-res) ms/ms: sum of intensities of central M bin only

use_A_ions

use A ions for PSM

use_B_ions

use B ions for PSM

use_C_ions

use C ions for PSM

use_X_ions

use X ions for PSM

use_Y_ions

use Y ions for PSM

use_Z_ions

use Z ions for PSM

use_NL_ions

use neutral loss (NH3, H2O) ions from b/y for PSM

enzyme

The enzyme used for peptide digestion.

second_enzyme

Additional enzyme used for peptide digestion.

num_enzyme_termini

Specify the termini where the cleavage rule has to match

missed_cleavages

Number of possible cleavage sites missed by the enzyme. It has no effect if enzyme is unspecific cleavage.

min_peptide_length

Minimum peptide length to consider.

max_peptide_length

Maximum peptide length to consider.

num_hits

Number of peptide hits in output file

precursor_charge

Precursor charge range to search (if spectrum is not annotated with a charge or if override_charge!=keep any known): 0:[num] == search all charges, 2:6 == from +2 to +6, 3:3 == +3

override_charge

_keep any known_: keep any precursor charge state (from input), _ignore known_: ignore known precursor charge state and use precursor_charge parameter, _ignore outside range_: ignore precursor charges outside precursor_charge range, _keep known search unknown_: keep any known precursor charge state. For unknown charge states, search as singly charged if there is no signal above the precursor m/z or use the precursor_charge range

ms_level

MS level to analyze, valid are levels 2 (default) or 3

activation_method

If not ALL, only searches spectra of the given method

digest_mass_range

MH+ peptide mass range to analyze

max_fragment_charge

Set maximum fragment charge state to analyze as long as still lower than precursor charge - 1. (Allowed max 5)

max_precursor_charge

set maximum precursor charge state to analyze (allowed max 9)

clip_nterm_methionine

If set to true, also considers the peptide sequence w/o N-term methionine separately and applies appropriate N-term mods to it

spectrum_batch_size

max. number of spectra to search at a time; use 0 to search the entire scan range in one batch

mass_offsets

One or more mass offsets to search (values subtracted from deconvoluted precursor mass). Has to include 0.0 if you want the default mass to be searched.

minimum_peaks

Required minimum number of peaks in spectrum to search (default 10)

minimum_intensity

Minimum intensity value to read in

remove_precursor_peak

no = no removal, yes = remove all peaks around precursor m/z, charge_reduced = remove all charge reduced precursor peaks (for ETD/ECD). phosphate_loss = remove the HPO3 (-80) and H3PO4 (-98) precursor phosphate neutral loss peaks. See also remove_precursor_tolerance

remove_precursor_tolerance

one-sided tolerance for precursor removal in Thompson

clear_mz_range

for iTRAQ/TMT type data; will clear out all peaks in the specified m/z range, if not 0:0

fixed_modifications

Fixed modifications, specified using Unimod (www.unimod.org) terms, e.g. 'Carbamidomethyl (C)' or 'Oxidation (M)'

variable_modifications

Variable modifications, specified using Unimod (www.unimod.org) terms, e.g. 'Carbamidomethyl (C)' or 'Oxidation (M)'

binary_modifications

List of modification group indices. Indices correspond to the binary modification index used by comet to group individually searched lists of variable modifications. Note: if set, both variable_modifications and binary_modifications need to have the same number of entries as the N-th entry corresponds to the N-th variable_modification. if left empty (default), all entries are internally set to 0 generating all permutations of modified and unmodified residues. For a detailed explanation please see the parameter description in the Comet help.

max_variable_mods_in_peptide

Set a maximum number of variable modifications per peptide

require_variable_mod

If true, requires at least one variable modification per peptide

reindex

Recalculate peptide to protein association using OpenMS. Annotates target-decoy information.

log

Name of log file (created only when specified)

debug

Sets the debug level

threads

Sets the number of threads allowed to be used by the TOPP tool

no_progress

Disables progress logging to command line

force

Overrides tool-specific checks

test

Enables the test mode (needed for internal use only)

decoy_string

String that was appended (or prefixed - see 'decoy_string_position' flag below) to the accessions in the protein database to indicate decoy proteins. If empty (default), it's determined automatically (checking for common terms, both as prefix and suffix).

decoy_string_position

Is the 'decoy_string' prepended (prefix) or appended (suffix) to the protein accession? (ignored if decoy_string is empty)

missing_decoy_action

Action to take if NO peptide was assigned to a decoy protein (which indicates wrong database or decoy string): 'error' (exit with error, no output), 'warn' (exit with success, warning message), 'silent' (no action is taken, not even a warning)

write_protein_sequence

If set, the protein sequences are stored as well.

write_protein_description

If set, the protein description is stored as well.

keep_unreferenced_proteins

If set, protein hits which are not referenced by any peptide are kept.

unmatched_action

If peptide sequences cannot be matched to any protein: 1) raise an error; 2) warn (unmatched PepHits will miss target/decoy annotation with downstream problems); 3) remove the hit.

aaa_max

Maximal number of ambiguous amino acids (AAAs) allowed when matching to a protein database with AAAs. AAAs are 'B', 'J', 'Z' and 'X'.

mismatches_max

Maximal number of mismatched (mm) amino acids allowed when matching to a protein database. The required runtime is exponential in the number of mm's; apply with care. MM's are allowed in addition to AAA's.

IL_equivalent

Treat the isobaric amino acids isoleucine ('I') and leucine ('L') as equivalent (indistinguishable). Also occurrences of 'J' will be treated as 'I' thus avoiding ambiguous matching.

allow_nterm_protein_cleavage

Allow the protein N-terminus amino acid to clip.

name

Enzyme which determines valid cleavage sites - e.g. trypsin cleaves after lysine (K) or arginine (R), but not before proline (P). Default: deduce from input

specificity

Specificity of the enzyme. Default: deduce from input. 'full': both internal cleavage sites must match. 'semi': one of two internal cleavage sites must match. 'none': allow all peptide hits no matter their context (enzyme is irrelevant).

Views

CometAdapter Std Output

The text sent to standard out during the execution of CometAdapter.

CometAdapter Error Output

The text sent to standard error during the execution of CometAdapter. (If it appears in gray, it's the output of a previously failing run which is preserved for your trouble shooting.)

Workflows

• Proteomics_LFQOpenMS
• Proteomics_LFQKNIME Hub

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