Glycosylation is the most prevalent and varied form of post-translational protein modifications. Protein glycosylation regulates multiple cellular functions, including protein folding, cell adhesion, molecular trafficking and clearance, receptor activation, signal transduction, and endocytosis. In particular,
membrane proteins are frequently highly glycosylated, which is both linked to physiological processes and of high relevance in various disease mechanisms. The cellular glycome is increasingly considered to be a therapeutic target. Here we describe a new strategy to compare membrane glycoproteomes, thereby identifying
proteins with altered
glycan structures and the respective glycosites. The workflow started with an optimized procedure for the digestion of
membrane proteins followed by the
lectin-based isolation of
glycopeptides. Since alterations in the
glycan part of a
glycopeptide cause mass alterations, analytical size exclusion chromatography was applied to detect these mass shifts. N-
glycosidase treatment combined with nanoUPLC-coupled mass spectrometry identified the altered
glycoproteins and respective glycosites. The methodology was established using the
colon cancer cell line
CX1, which was treated with 2-deoxy-glucose-a modulator of N-glycosylation. The described methodology is not restricted to cell culture, as it can also be adapted to tissue samples or body fluids. Altogether, it is a useful module in various experimental settings that target
glycan functions.