TermineR: Bioinformatic processing of shotgun proteomics data for the annotation and quantitation of protein termini

Proteolytic processing shapes protein function through irreversible cleavage events that are often overlooked in standard shotgun proteomics workflows. In this methods chapter, we describe a comprehensive strategy for the identification, annotation, and quantitation of proteolytic products and terminal peptides using semi-specific database searches. We present practical guidelines for spectral data processing using the FragPipe software suite, leveraging modern rescoring tools such as Percolator and MSBooster to improve sensitivity. Building upon this, we introduce TermineR, an R-based framework for downstream annotation and statistical evaluation of proteolytic termini. Together, these tools enable the extraction of biologically meaningful insights into proteolytic activity from complex proteomics datasets, without the need for biochemical enrichment.