This programs allows you to input one or more protein sequences and to specify one proteolytic agent from a list, which might be a proteolytic enzyme or other reagent. It will then write a report file containing the positions where the agent cuts, together with the peptides produced.
By default pepdigest uses average molecular weights. The -mono option will use monoisotopic weights.
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The header information contains the program name, date of run, name of the reagent used to digest the protein and the number of fragments reported. The header will report if complete or partial digestion was chosen.
The rest of the file consists of columns holding the following data:
If you wish to emulate a partial digestion, then using the -overlap qualifier will display the results from a digest in which all cut sites are used and in which one site at a time is not cut. Thus the resulting peptide fragments from the cut sites numbered 1, 2, 3, 4 etc. are shown, plus the fragments produced by cutting at the sites 1 to 3, 2 to 4, etc. In other words, this option will reveal fragments containing one potential cut site.
If you wish to emulate a very partial digestion (!) then using the -allpartials qualifier will do what -overlap did, but also show all possible fragments from using all possible combinations of cut sites. For example, fragments from the cut sites numbered 1, 2, 3, 4, 5 and from the fragments produced by cutting between sites 1..3, 1..4, 1..5, 2..4, 2..5, 3..5, etc. In other words, this option will reveal fragments containing one or more potential cut site.
If the boolean -ragging is specified then terminal digest fragments are also shown; this can be useful for mass spectrometry. Ragging is further controlled by the -termini option which allows you to select removal of residues from the N and/or C termini.
Each proteolytic enzyme has favoured as well as unfavoured cut sites. For example, Trypsin will not normally cut after a K if it is followed by (e.g.) another K or a P. By default, only data for favoured cut sites is generated. Specifying the qualifier -unfavoured produces data for unfavoured cut sites as well.