Rapid Peptides Generator: fast and efficient in silico protein digestion

Abstract

Recent developments in mass spectrometry techniques used in proteomics and proteogenomics have led to a constantly increasing interest in proteases. These proteases are used in different mass spectrometry analyses requiring protein digestions. To perform such digestions, one or multiple proteases are used. Few software exist that predict cleavage sites of proteases and simulate in silico digestions. In this work, Rapid Peptides Generator (RPG), a new software developed in order to predict proteases-induced cleavage sites on sequences, is presented. RPG offers extra features and overcomes most issues of existing software in different ways. First, for each generated peptide, RPG gives its sequence, length and estimation of mass, measurements already provided by other software, as well as the peptide’s isoelectric point. Moreover, contrary to existing software that limit the option of proteases to be used to a predefined list, users of RPG are able to easily define new proteases using a simple yet powerful grammar. This feature allows users to stay up-to-date to new or more specific proteases available on the market and optimizes time and effort before the actual mass spectrometry experiment. RPG is freely available through the well established package management system ‘pip’ and follows the standards for software development.