Protein cleaver: an interactive web interface for in silico prediction and systematic annotation of protein digestion-derived peptides

Proteolytic digestion is an essential process in mass spectrometry-based proteomics for converting proteins into peptides, hence crucial for protein identification and quantification. In a typical proteomics experiment, digestion reagents are selected without prior evaluation of their optimality for detecting proteins or peptides of interest, partly due to the lack of comprehensive and user-friendly predictive tools. In this work, we introduce Protein Cleaver, a web-based application that systematically assesses regions of proteins that are likely or unlikely to be identified, along with extensive sequence and structure annotation and visualization features. We showcase practical examples of Protein Cleaver's usability in drug discovery and highlight proteins that are typically difficult to detect using the most common proteolytic enzymes. We evaluate trypsin and chymotrypsin for identifying G-protein-coupled receptors and discover that chymotrypsin produces significantly more identifiable peptides than trypsin. We perform a bulk digestion analysis and assess 36 proteolytic enzymes for their ability to detect most of cysteine-containing peptides in the human proteome. We anticipate Protein Cleaver to be a valuable auxiliary tool for proteomics scientists.