Mass Spectrometry-Based Proteomics Methods for Systematic Identification and Quantification of Protein...

Protein O-glycosylation is one of the most common and important modifications in human cells. It regulates protein folding, trafficking, stability, and interactions with other molecules, and its dysregulation is directly related to numerous diseases such as cancer and neurodegenerative diseases. Modern mass spectrometry (MS)-based proteomics provides a unique opportunity to systematically characterize O-glycosylated proteins. However, it is still extremely challenging due to the low abundance of many glycoproteins, the heterogeneity of O-glycans, and the complexity of biological samples. In this review, we discuss recent advances in MS-based proteomics methods designed to overcome the challenges for global and site-specific characterization of protein O-glycosylation. We begin with an overview of the biosynthetic pathways underlying the major classes of protein O-glycosylation. Then, we discuss different methods to enrich O-glycopeptides with diverse structures of O-glycans. Furthermore, various MS dissociation techniques for intact glycopeptide profiling are covered. In addition, different quantitative approaches are included for studying protein O-glycosylation in biological and biomedical research. We also discuss computational tools for intact O-glycopeptide identification, highlighting the challenges in search space requirement, false discovery rate control, and glycosylation site localization. The advancements of MS-based glycoproteomics are critical for gaining insights into the critical roles of protein O-glycosylation in biology and human disease.