Glycoproteomics: A Balance between High-Throughput and In-Depth Analysis

Glycoproteomics is an important subdiscipline of proteomics. Mass spectrometry (MS)-based glycoproteomics has relied so far on two levels of analysis, targeting either the released glycans or digested glycopeptides. However, limitations of these approaches, caused by the vast structural microheterogeneity that glycoproteins can exhibit, have become evident. Therefore, concomitant methods enabling deep characterization of all discrete glycoforms are essential to extend our functional understanding of the glycoproteome. Here, we discuss recent progress, particularly in protein-centric approaches. High-resolution native MS appears to be especially promising in revealing the glycoform profile of glycoproteins. We propose that systematically integrating MS data acquired at the glycan, glycopeptide, and glycoprotein levels best enhances our understanding of the glycoproteome.