In silico digestions were performed using the PDMQ Application. A version of this application is free to use. This version contains only three enzymes, i.e. trypsin, chymotrypsin-low specificity and pepsin-pH 1.3.

When using this tool, a reference should be provided as:

Reka Haraszi, Csongor Tasi, Angela Juhasz and Szabolcs Makai (2015) PDMQ – Protein Digestion Multi Query software tool to perform in silico digestion of protein/peptide sequences, bioRxiv Full text.

A modified version of PDMQ was used to generate peptide entries in ProPepper™ and that contains six enzymes as selectable cleavage tools, i.e. trypsin, chymotrypsin-low specificity, pepsin-pH 1.3, LysC, thermolysin and proteinase K. The used enzyme combinations for the ProPepper™ peptides are described in the ProPepper™ reference paper:

Angela Juhasz, Reka Haraszi and Csaba Maulis (2015) ProPepper: a curated database for identification and analysis of peptide and immune-responsive epitope composition of cereal grain protein families, Database Full text.