OpenMS
2.4.0
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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.
The command line parameters of this tool are:
DigestorMotif -- digests a protein database in-silico Version: 2.4.0 Oct 29 2018, 15:52:19, Revision: 9690d06 To cite OpenMS: Rost HL, Sachsenberg T, Aiche S, Bielow C et al.. OpenMS: a flexible open-source software platform for mass spectrometry data analysis. Nat Meth. 2016; 13, 9: 741-748. doi:10.1038/nmeth.3959. 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: 'Trypsin', 'Arg-C', 'Arg-C/P', 'Chymotrypsin', 'Chymotrypsin/P', 'CNBr', 'Formic_acid', 'Lys-C', 'Lys-N', 'Lys-C/P', 'PepsinA', 'TrypChymo', 'Trypsin/P', 'V8-DE', 'V8- E', 'leukocyte elastase', 'proline endopeptidase', 'Alpha-lytic protease', 'glu tamyl endopeptidase', '2-iodobenzoate', 'iodosobenzoate', 'staphylococcal prote ase/D', 'proline-endopeptidase/HKR', 'Glu-C+P', 'PepsinA + P', 'cyanogen-bromid e', 'Clostripain/P', 'elastase-trypsin-chymotrypsin', 'no cleavage', 'unspecifi c cleavage', 'Asp-N', 'Asp-N/B', 'Asp-N_ambic') -motif <string> The motif for the restricted peptidome (default: 'M') Common UTIL 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: