( ...)Characterization of Protein Oligosaccharides Using MSn

Andrew S.Weiskopf and Paul Vouros, Northeastern University, Boston, MA
David J. Harvey, University of Oxford, Oxford, UK

Protein Analysis

The data presented here can be acquired using the Thermo Finnigan LCQ Series of ion trap mass spectrometers.

Introduction

This application report provides a brief overview of protein oligosaccharides that present a unique analytical challenge among the families of biomolecules. Peptides and oligonucleotides are linear oligomers, so sequence information is all that is necessary for complete primary structure characterization. Oligosaccharides, on the other hand, are branched structures, with their constituent monosaccharides linked together by a variety of glycosidic bonds. As a result, while six amino acids can yield only 720 different peptides, six unique monosaccharides can be arranged to form many millions of oligosaccharides. Though much is understood about carbohydrate biosynthesis to eliminate most of these isomers from consideration, the permutations that remain still provide a formidable analytical problem.

Electrospray ionization tandem mass spectrometry (ESI-MS/MS) has become a valuable technique in oligosaccharide characterization.¹ Permethylation of the oligosaccharide before analysis more effectively directs fragmentation of the ion into various familiar series of product ions: glycosidic-bond fragments which indicate monosaccharide sequence and branching, and crossring fragments which identify the linkages between monosaccharides. However, interpretation is complicated by the relatively low abundance of these crossring fragments, and cleavage of especially labile bonds can suppress the formation of other fragments.

The MSⁿ capabilities of the LCQ Series present a powerful
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