RPG

RPG predicts protease-induced cleavage sites on amino acid sequences to simulate in silico protein digestion for mass spectrometry–based proteomics and proteogenomics.

Key Features:

• Predictive Capabilities: Predicts protease cleavage sites on protein sequences to generate peptide fragments for downstream mass spectrometry analyses.
• Comprehensive Peptide Information: Reports peptide sequence, length, estimated mass, and isoelectric point for each generated peptide.
• Customizable Protease Definitions: Supports user-defined proteases via a configurable protease grammar to specify cleavage rules.

Scientific Applications:

• Proteomics sample preparation: Simulates enzymatic digestions to inform peptide generation and selection prior to mass spectrometry workflows.
• Proteogenomics: Enables in silico digestion of translated genomic or transcriptomic sequences to support peptide identification and variant discovery.
• Mass spectrometry experiment design: Provides peptide property estimates to aid selection of proteases and predicted peptides for targeted or discovery MS experiments.

Methodology:

Uses an algorithmic approach to predict cleavage sites based on user-defined protease rules expressed via a protease grammar and computes peptide sequence, length, estimated mass, and isoelectric point.