Fast and Comprehensive N- and O-glycoproteomics analysis with MSFragger-Glyco

Abstract Glycosylation is a ubiquitous and heterogeneous post-translational modification (PTM) used to accomplish a wide variety of critical cellular tasks. Recent advances in methods for enrichment and mass spectrometric analysis of intact glycopeptides have produced large-scale, high-quality glycoproteomics datasets, but interpreting this data remains challenging. In addition to being large, complex, and heterogeneous, glycans undergo fragmentation during vibrational activation, making common PTM search strategies ineffective for their identification. We present a computational tool called MSFragger-Glyco for fast and highly sensitive identification of N- and O-linked glycopeptides using open and glycan mass offset search strategies. Reanalysis of recently published N-glycoproteomics data resulted in annotation of 83% more glycopeptide-spectrum matches (glycoPSMs) than in previous results, which translated to substantial increases in the numbers of glycoproteins and glycosites that could be identified. In published O-glycoproteomics data, our method more than doubled the number of glycoPSMs annotated when searching the same peptides as the original search and resulted in up to a 6-fold increase when expanding searches to include large numbers of possible glycan compositions and other modifications. Expanded searches revealed trends in glycan composition and crosstalk with phosphorylation that remained hidden to the original search. With greatly improved spectral annotation, coupled with the fast speed of fragment ion index-based scoring, MSFragger-Glyco makes it possible to comprehensively interrogate glycoproteomics data and illuminate the many roles of glycosylation.