 |
OpenMS
|
Digests a protein database in-silico.
| pot. predecessor tools | → Digestor → | pot. successor tools |
|---|---|---|
| none (FASTA input) | IDFilter (peptide blacklist) |
This application is used to digest a protein database to get all peptides given a cleavage enzyme.
The output can be used e.g. as a blacklist filter input to IDFilter, to remove certain peptides.
The command line parameters of this tool are:
Digestor -- Digests a protein database in-silico.
Full documentation: http://www.openms.de/doxygen/nightly/html/TOPP_Digestor.html
Version: 3.6.0-pre-nightly-2026-03-06 Mar 7 2026, 01:46:19, Revision: c92c980
To cite OpenMS:
+ Pfeuffer, J., Bielow, C., Wein, S. et al.. OpenMS 3 enables reproducible analysis of large-scale mass spec
trometry data. Nat Methods (2024). doi:10.1038/s41592-024-02197-7.
Usage:
Digestor <options>
Options (mandatory options marked with '*'):
-in <file>* Input file (valid formats: 'fasta')
-out <file>* Output file (peptides) (valid formats: 'idXML', 'fasta')
-out_type <type> Set this if you cannot control the filename of 'out', e.g., in TOPPAS. (valid:
'idXML', 'fasta')
-missed_cleavages <number> The number of allowed missed cleavages (default: '1') (min: '0')
-min_length <number> Minimum length of peptide (default: '6')
-max_length <number> Maximum length of peptide (default: '40')
-enzyme <string> The type of digestion enzyme (default: 'Trypsin') (valid: 'Arg-C/P', 'Asp-N',
'Asp-N/B', 'Asp-N_ambic', 'Chymotrypsin', 'Clostripain/P', 'elastase-trypsin-c
hymotrypsin', 'no cleavage', 'unspecific cleavage', 'Trypsin', 'Arg-C', 'Chymo
trypsin/P', 'CNBr', 'Formic_acid', 'Lys-C', 'Lys-N', 'Lys-C/P', 'PepsinA',
'TrypChymo', 'Trypsin/P', 'V8-DE', 'V8-E', 'leukocyte elastase', 'proline endo
peptidase', 'glutamyl endopeptidase', 'Alpha-lytic protease', '2-iodobenzoate'
, 'iodosobenzoate', 'staphylococcal protease/D', 'proline-endopeptidase/HKR',
'Glu-C+P', 'PepsinA + P', 'cyanogen-bromide')
Options for FASTA output files:
-FASTA:ID <option> Identifier to use for each peptide: copy from parent protein (parent); a conse
cutive number (number); parent ID + consecutive number (both) (default: 'paren
t') (valid: 'parent', 'number', 'both')
-FASTA:description <option> Keep or remove the (possibly lengthy) FASTA header description. Keeping it
can increase resulting FASTA file significantly. (default: 'remove') (valid:
'remove', 'keep')
-replace_ambiguous Replace ambiguous amino acids with a random unambiguous amino acid. This is
useful for generating an output file that mimics a search engine result (since
they usually do not contain ambiguous amino acids).
Common TOPP options:
-ini <file> Use the given TOPP INI file
-threads <n> Sets the number of threads allowed to be used by the TOPP tool (default: '1')
-write_ini <file> Writes the default configuration file
--help Shows options
--helphelp Shows all options (including advanced)
INI file documentation of this tool:
This section lists all parameters supported by the tool. Parameters are organized into hierarchical subsections that group related settings together. Subsections may contain further subsections or individual parameters.
Each parameter entry contains the following information:
Parameter tags provide additional information about how a parameter is used. Some tags indicate whether a parameter is required or intended for advanced configuration, while others may be used internally by OpenMS or workflow tools.
Parameters highlighted as required must be specified for the tool to run successfully. Parameters marked as advanced allow fine-tuning of algorithm behavior and are typically not needed for standard workflows.
1.9.8