Recipe 2.5. Digesting a protein

You want to digest a protein and get the peptide digests.

You first have to get a peptidase, make a digester with it and digest the protein/peptide.

// get the peptidase
Peptidase trypsin = Peptidase.getInstance("Trypsin");

// create the digester
digester = Digester.newInstance(trypsin);

// the peptide to digest
Peptide aas = new Peptide.Builder("MQRSTATGCFKL").build();

// make the digestion
digester.digest(aas);

// get the digests
Set<Peptide> digests = digester.getUniqueDigests();

You can also define missed cleavage on the digester before calling digest().

...
digester.setNumberOfMissedCleavage(2);
digester.digest(aas);