glycoproteomics

Glycoproteomics is the branch of proteomics focused on the systematic study of glycosylated proteins and their attached carbohydrate structures. It investigates glycosylation sites, the structures of the glycans, and the heterogeneity of glycoforms across proteins, cells, tissues, and conditions. It complements glycomics, which analyzes released glycans, and traditional proteomics, which analyzes the protein backbone.

Typical goals include identifying glycosylation sites, characterizing the attached glycans, quantifying site-specific glycoforms, and comparing glycosylation patterns across biological states. Workflows combine sample preparation, selective enrichment of glycopeptides, and mass spectrometry to enable site- and glycan-resolved measurements.

Enrichment strategies include lectin affinity, hydrophilic interaction chromatography (HILIC), and chemical capture of glycopeptides. Glycans may be released enzymatically for deglycosylated proteomics or analyzed intact as glycopeptides. Mass spectrometry uses fragmentation methods such as higher-energy collision-induced dissociation (HCD) and electron-based techniques (ETD, ECD) to preserve or reveal glycan moieties. Specialized software and databases support identification and localization of glycosylation sites and glycan compositions, with tools such as Byonic, pGlyco, and GPQuest.

Analyses can be global (untargeted) or targeted to predefined glycoproteins or glycoforms. Quantitative approaches include label-free and isotopic labeling strategies to measure changes in glycosylation across samples.

Glycoproteomics has applications in biomarker discovery, cancer research, infectious diseases, and biopharmaceutical development, where glycosylation affects protein stability, activity, and immunogenicity. Challenges include extensive glycan heterogeneity, lability of glycosidic bonds, incomplete site localization, and the need for robust data analysis and standardized reporting.

Data repositories and resources such as GlycoPOST, PRIDE, UniCarb-DB, and GlyGen house glycoproteomics datasets and glycan information, supporting ongoing methodological advances to improve coverage and reproducibility.