Analysis of Mucin‐Domain Glycoproteins Using Mass Spectrometry

Abstract Mucin‐domain glycoproteins are characterized by their high density of glycosylated serine and threonine residues, which complicates their analysis by mass spectrometry. The dense glycosylation renders the protein backbone inaccessible to workhorse proteases like trypsin, the vast heterogeneity of glycosylation often results in ion suppression from unmodified peptides, and search algorithms struggle to confidently analyze and site‐localize O‐glycosites. We have made a number of advances to address these challenges, rendering mucinomics possible for the first time. Here, we summarize these contributions and provide a detailed protocol for mass spectrometric analysis of mucin‐domain glycoproteins. © 2024 Wiley Periodicals LLC. Basic Protocol 1 : Enrichment of mucin‐domain glycoproteins Basic Protocol 2 : Enzymatic digestion of mucin‐domain glycoprotein(s) Basic Protocol 3 : Mass spectrometry data collection for O‐glycopeptides Basic Protocol 4 : Mass spectrometry data analysis of O‐glycopeptides