Liquid chromatography ion trap mass spectrometric analysis of oligosaccharides using permethylated derivatives.

Reversed phase liquid chromatography was combined with the multiple stage mass analysis capability of an ion trap mass spectrometer for the characterization of permethylated oligosaccharide mixtures. The new method was used to separate the components of an unlabeled permethylated maltooligomer ladder, a 2-aminobenzamide-labeled (2-AB) maltooligomer ladder, a complex mixture of 2AB-labeled bi- (B), tri- (T), and tetraantennary (Q) standards, and a mixture of recombinant glycoprotein carbohydrates from soluble CD4 with varying sialic acid (S) content. Using reversed phase HPLC, permethylated mixture components including alpha and beta anomers were separated based on their structures. Fluorescent labeling with 2-aminobenzamide prior to permethylation was employed for off-line method development, but was not necessarily required for mass spectral analysis, as permethylation alone improved the ionization and fragmentation characteristics of the molecules. Antennae composition of permethylated derivatives was determined in MS(2) where the fragmentation patterns of the Y- and B-ion series predominated, and then further evaluated in MS(3), which provided additional information on branching obtained from A and X cross-ring fragmentation. Copyright 2001 John Wiley & Sons, Ltd.