Gas‐phase dissociation of glycosylated peptide ions

Among the myriad of protein post‐translational modifications (PTMs), glycosylation presents a singular analytical challenge. On account of the extraordinary diversity of protein‐linked carbohydrates and the great complexity with which they decorate glycoproteins, the rigorous establishment of glycan–protein connectivity is often an arduous experimental venture. Consequently, elaborating the interplay between structures of oligosaccharides and functions of proteins they modify is usually not a straightforward task. A more mature biochemical appreciation of carbohydrates as PTMs will significantly hinge upon analytical advances in the field of glycoproteomics. Undoubtedly, the analysis of glycosylated peptides by tandem mass spectrometry (MS/MS) will play a pivotal role in this regard. The goal of this review is to summarize, from an analytical and tutorial perspective, the present state of knowledge regarding the dissociation of glycopeptide ions as accomplished by various MS/MS methods. In addition, this review will endeavor to harmonize some seemingly disparate findings to provide a more complete and broadly applicable description of glycopeptide ion fragmentation. A fuller understanding of the rich variety of glycopeptide dissociation behaviors will allow glycoproteomic researchers to maximize the information yielded by MS/MS experiments, while also paving the way to new innovations in MS‐based glycoproteomics. © 2012 Wiley Periodicals, Inc. Mass Spec Rev 31:666–682, 2012