This application is used to digest a protein database to get all peptides given a cleavage enzyme. It will also produce peptide statistics given the mass accuracy of the instrument. You can extract peptides with specific motifs,e.g. onyl cysteine containing peptides for ICAT experiments. At the moment only trypsin is supported.

Note: Currently mzIdentML (mzid) is not directly supported as an input/output format of this tool. Convert mzid files to/from idXML using IDFileConverter if necessary.

The command line parameters of this tool are:

DigestorMotif -- Digests a protein database in-silico
Full documentation: http://www.openms.de/doxygen/nightly/html/TOPP_DigestorMotif.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:
  DigestorMotif <options>

Options (mandatory options marked with '*'):
  -in <file>*                 FASTA input file (valid formats: 'fasta')
  -out <file>*                Output file (peptides)
                               (valid formats: 'idXML')
  -missed_cleavages <number>  The number of allowed missed cleavages (default: '1') (min: '0')
  -mass_accuracy <number>     Give your mass accuracy in ppb (default: '1000')
  -min_length <number>        Minimum length of peptide (default: '6')
  -out_option <number>        Indicate 1 (peptide table only), 2 (statistics only) or (both peptide table + 
                              statistics) (default: '1')
  -enzyme <cleavage site>     The enzyme used for peptide digestion. (default: 'Trypsin') (valid: 'Arg-C/P', 
                              'Asp-N', 'Asp-N/B', 'Asp-N_ambic', 'Chymotrypsin', 'Clostripain/P', 'elastase-t
                              rypsin-chymotrypsin', 'no cleavage', 'unspecific cleavage', 'Trypsin', 'Arg-C',
                               'Chymotrypsin/P', 'CNBr', 'Formic_acid', 'Lys-C', 'Lys-N', 'Lys-C/P', 'PepsinA
                              ', 'TrypChymo', 'Trypsin/P', 'V8-DE', 'V8-E', 'leukocyte elastase', 'proline 
                              endopeptidase', 'glutamyl endopeptidase', 'Alpha-lytic protease', '2-iodobenzoa
                              te', 'iodosobenzoate', 'staphylococcal protease/D', 'proline-endopeptidase/HKR'
                              , 'Glu-C+P', 'PepsinA + P', 'cyanogen-bromide')
  -motif <string>             The motif for the restricted peptidome (default: 'M')
                              
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:

Legend:

required parameter

advanced parameter

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:

Name The identifier used in configuration files and on the command line.
Default value The value used if the parameter is not explicitly specified.
Description A short explanation describing the purpose and behavior of the parameter.
Tags Additional metadata associated with the parameter.
Restrictions Allowed value ranges for numeric parameters or valid options for string parameters.

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.

+DigestorMotifDigests a protein database in-silico

version3.6.0-pre-nightly-2026-03-06 Version of the tool that generated this parameters file.

++1Instance '1' section for 'DigestorMotif'

in FASTA input fileinput file*.fasta

out output file (peptides)
output file*.idXML

missed_cleavages1 the number of allowed missed cleavages0:∞

mass_accuracy1000 give your mass accuracy in ppb

min_length6 minimum length of peptide

out_option1 indicate 1 (peptide table only), 2 (statistics only) or (both peptide table + statistics)

enzymeTrypsin The enzyme used for peptide digestion.Arg-C/P, Asp-N, Asp-N/B, Asp-N_ambic, Chymotrypsin, Clostripain/P, elastase-trypsin-chymotrypsin, no cleavage, unspecific cleavage, Trypsin, Arg-C, Chymotrypsin/P, CNBr, Formic_acid, Lys-C, Lys-N, Lys-C/P, PepsinA, TrypChymo, Trypsin/P, V8-DE, V8-E, leukocyte elastase, proline endopeptidase, glutamyl endopeptidase, Alpha-lytic protease, 2-iodobenzoate, iodosobenzoate, staphylococcal protease/D, proline-endopeptidase/HKR, Glu-C+P, PepsinA + P, cyanogen-bromide

motifM the motif for the restricted peptidome

log Name of log file (created only when specified)

debug0 Sets the debug level

threads1 Sets the number of threads allowed to be used by the TOPP tool

no_progressfalse Disables progress logging to command linetrue, false

forcefalse Overrides tool-specific checkstrue, false

testfalse Enables the test mode (needed for internal use only)true, false