OpenMS
DigestorMotif

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: 3.2.0-pre-nightly-2024-07-21 Jul 22 2024, 02:13:52, Revision: b650df0
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', 'Clostripain/P', 'elastase-trypsin-chymotrypsin', 'no cleav
                              age', 'unspecific cleavage', 'Trypsin', 'Arg-C', 'staphylococcal protease/D', 
                              'proline-endopeptidase/HKR', 'Glu-C+P', 'PepsinA + P', 'cyanogen-bromide', 'leu
                              kocyte elastase', 'proline endopeptidase', 'Asp-N_ambic', 'Chymotrypsin', 'Chym
                              otrypsin/P', 'CNBr', 'Formic_acid', 'Lys-C', 'Lys-N', 'Lys-C/P', 'PepsinA', 
                              'TrypChymo', 'Trypsin/P', 'V8-DE', 'V8-E', 'glutamyl endopeptidase', 'Alpha-lyt
                              ic protease', '2-iodobenzoate', 'iodosobenzoate')
  -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
+DigestorMotifDigests a protein database in-silico
version3.2.0-pre-nightly-2024-07-21 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, Clostripain/P, elastase-trypsin-chymotrypsin, no cleavage, unspecific cleavage, Trypsin, Arg-C, staphylococcal protease/D, proline-endopeptidase/HKR, Glu-C+P, PepsinA + P, cyanogen-bromide, leukocyte elastase, proline endopeptidase, Asp-N_ambic, Chymotrypsin, Chymotrypsin/P, CNBr, Formic_acid, Lys-C, Lys-N, Lys-C/P, PepsinA, TrypChymo, Trypsin/P, V8-DE, V8-E, glutamyl endopeptidase, Alpha-lytic protease, 2-iodobenzoate, iodosobenzoate
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