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CometAdapter (version 2.8+galaxy0)

Input file:

select mzml data sets(s)

FASTA file:

select fasta data sets(s)

Default Comet params file:

All parameters of this take precedence. A template file can be generated using 'comet.exe -p' select txt data sets(s)

Precursor monoisotopic mass tolerance (Comet parameter: peptide_mass_tolerance):

See also precursor_error_units to set the unit

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

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

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 monoisotopic mass error units:

Offset of fragment bins:

Recommended by Comet: low-res: 0.4, high-res: 0.0

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:

The enzyme used for peptide digestion:

Specify the termini where the cleavage rule has to match:

Number of possible cleavage sites missed by the enzyme:

It has no effect if enzyme is unspecific cleavage

Minimum peptide length to conside:

Maximum peptide length to conside:

Number of peptide hits in output file:

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:

_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 to analyze, valid are levels 2 (default) or 3:

If not ALL, only searches spectra of the given method:

Set maximum fragment charge state to analyze as long as still lower than precursor charge - 1:

(Allowed max 5)

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

Fixed modifications, specified using Unimod (www.unimod.org) terms:

e.g. 'Carbamidomethyl (C)' or 'Oxidation (M)'

Variable modifications, specified using Unimod (www.unimod.org) terms:

e.g. 'Carbamidomethyl (C)' or 'Oxidation (M)'

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 (space separated list, in order to allow for spaces in list items surround them by single quotes)

Recalculate peptide to protein association using OpenMS:

Annotates target-decoy information

Advanced Options

Advanced Options 0

Optional outputs: