Glycomic Mass Spectrometric Analysis and Data Interpretation Tools

Glycosylation is one of the most pronounced posttranslational modifications to a protein. With the requirement of one gene-many functions of the gene product, understanding the process of the non template-driven process, such as glycosylation, is a prerequisite for understanding the functional aspects of expressed proteins. This chapter describes the current mass spectrometric technologies of both MALDI-MS and ESI-MS used for the analysis of O-linked and N-linked type glycosylation. We hope it will serve as an introduction for newcomers to the field of glycomics and glycobioinformatics and help in the understanding of the rationale of the analysis. Specifically the chapter addresses how the high data content of mass spectrometric based glycosylation analysis can be utilized to obtain biologically relevant information for glycobiomarker discovery, glycoprotein characterization and for a fundamental understanding of the glycosylation process. Concepts about the relationship between molecular mass and monosaccharide composition are introduced and we show how the mass spectrometric measurement of the intact molecular weight of released oligosaccharides and glycopeptides can be combined with fragmentation mass spectrometry to gain information on oligosaccharide sequence and the location of glycosylation sites within a glycopeptide. The chapter also introduces the basic terminology for oligosaccharide fragmentation and describes factors that direct the fragmentation process of glycoconjugates. The usefulness of derivatisation and chemical modification techniques of glycoconjugates for mass spectrometric analysis is discussed, including reductive amination, reduction, peracetylation, permethylation, enzymatic and chemical degradation. As in proteomics, the development of informatic tools that facilitate the interpretation of the mass spectrometric data is crucial to increasing the value of the data and to extending the glycoanalytical capability into more laboratories. The interpretation needs to be both at the level of determining the branched structure of the oligosaccharides in terms of sequence and linkage as well as in the determination of the heterogeneity present at each site on the peptide. The chapter describes current trends and software being developed in glycobioinformatics for translating the mass spectrometric glycoanalytical data into oligosaccharide structural information. This aspect of the field needs increased attention and resourcing since the the development and availability of these tools will provide the impetus for new research into glycobiology and the role of glycosylation in life science.