Structural Analysis of Glycosylated Peptides in Complex Mixtures with Ion Trap MSⁿ

Shiaw-Lin Wu, Pavel Bondarenko, Tom Shaler, Paul Shieh, and William S. Hancock

Protein Glycosylation

The data presented here can be acquired using any Thermo Finnigan LCQTMion trap mass spectrometer with MSⁿ capability. Introduction In humans, glycoproteins on cell surfaces are important for communication between cells, maintaining cell structure and self-recognition by the immune system. Of particular clinical concern is how viruses, bacteria and parasites bind to cell-surface glycoproteins and use them as portals of entry into cells. Understanding the detailed structure of glycoproteins at the molecular level may provide insights to aid in combating glycoprotein- mediated induction of disease.

A variety of mass spectrometry-based approaches have been applied to the fundamental study of glycoproteins. Typically, a glycoprotein is enzymatically digested, the resulting peptide fragments are separated using HPLC and the peptides are identified by on-line MS analysis using electrospray ionization. Alternatively, fractions may be collected after the HPLC separation and analyzed off-line by matrix-assisted laser desorption ionization (MALDI) or nanospray ionization.

Peptides that do not correspond to predicted masses may be present in a glycosylated form. These putative glycopeptides are treated with a glycosidase to cleave the bond between the peptide and the oligosaccharide. The difference in mass following cleavage is used to infer the carbohyd
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