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.
chymotrypsin-low specificity and
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.
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.