The rapid separation of isomeric precursor ions of oligosaccharides prior to their analysis by MSn was demonstrated using an ambient pressure ion mobility spectrometer (IMS) interfaced with a quadrupole ion trap. Separations were not limited to specific types of isomers; representative isomers differing solely in the stereochemistry of sugars, in their anomeric configurations, and in their overall branching patterns and linkage positions could be resolved in the millisecond time frame. Physical separation of precursor ions permitted independent mass spectra of individual oligosaccharide isomers to be acquired to at least MS3, the number of stages of dissociation limited only practically by the abundance of specific product ions. IMS-MSn analysis was particularly valuable in the evaluation of isomeric oligosaccharides that yielded identical sets of product ions in MS/MS experiments, revealing pairs of isomers that would otherwise not be known to be present in a mixture if evaluated solely by MS dissociation methods alone. A practical example of IMS-MSn analysis of a set of isomers included within a single HPLC fraction of oligosaccharides released from bovine submaxillary mucin is described.
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