The use of liquid chromatography-electrospray ionization-tandem mass spectrometry (LC-ESI-MS(n)) for the glycoproteomic characterization of glycopeptides is a growing field of research. The N- and O-glycosylated peptides (N- and O-glycopeptides) analyzed typically originate from protease-digested glycoproteins where many of them are expected to be biomedically important. Examples of LC-MS(2) and MS(3) fragmentation strategies used to pursue glycan structure, peptide identity and attachment-site identification analyses of glycopeptides are described in this review. MS(2) spectra, using the CID and HCD fragmentation techniques of a complex biantennary N-glycopeptide and a core 1 O-glycopeptide, representing two examples of commonly studied glycopeptide types, are presented. A few practical tips for accomplishing glycopeptide analysis using reversed-phase LC-MS(n) shotgun proteomics settings, together with references to the latest glycoproteomic studies, are presented.
Keywords: Collision-induced dissociation; Electron capture dissociation; Electron transfer dissociation; Glycopeptides; Glycoproteomics; Higher-energy collisional dissociation; Mass spectrometry; Oxonium ions.