From mass spectrometry-based glycosylation analysis to glycomics and glycoproteomics

Mass spectrometry (MS) is the pivotal technique driving most current day protein glycosylation analysis. It is unrivaled in combining high sensitivity, resolution, and precision for de novo identification and therefore most conducive to discovery mapping of new or biologically implicated glyco-epitopes. This chapter attempts to provide an account of current advances and limitations in MS-based glycosylation analysis as it rapidly evolves into all-encompassing glycomics and glycoproteomics. Given the omic-scale complexity, an urgent need is to orchestrate advances in chromatographic separation, chemical derivatization, and innovative online LC-MS/MS scan functions for more penetrative and purposeful data acquisition, along with empowering computational tools to overcome the bottleneck in automated data analysis, in order to increase the breadth and depth of glycomic coverage. This entails not only MS (n) -level resolution and mapping of isomeric variations but also addressing often overlooked structural features such as poly-N-acetyllactosamine extension and the widespread occurrence of sulfation in relation to immuno-activation and malignant transformation. Only then can functional glycotopes of relevance be uncovered, and further localized to particular glycan and protein carriers, the latter by means of target glycoproteomics. Mapping of site occupancy without addressing the full range of occupying glycans by direct sequencing of glycopeptides is essentially inadequate for any glycobiology driven venture. This chapter aims to conceptualize the required experimental workflows from glycomics to glycoproteomics, with MS analysis of permethylated glycans occupying the central node.