Permethylation confers many advantages in the structural analysis of oligosaccharides by mass spectrometry. These include increased sensitivity by both MALDI and electrospray ionization, as well as branching and some linkage specificity in ion fragmentation analysis. In the past couple of years, a fundamental improvement in a method for oligosaccharide analysis has appeared. Skimmer-induced dissociation followed by MS/MS in a triple quadrupole and sustained off-resonance irradiation (SORI) MSn in an FT-ICR mass spectrometer have illustrated that dissociation of ion fragments, specifically di- and trisaccharide fragments, can provide linkage and monosaccharide details that are not accessible to tandem MS of larger oligomers. However, permethylation also stabilizes oligosaccharides to CID. In SORI FT-ICR, the high energy required for collisional dissociation of permethylated oligosaccharides results in large magnetron radii for the product ions and poor ion fragment reten tion. PID, although limited in its structural reach by the non-selective nature of the excitation, does not have the dynamical problems associated with collisional activation. This research examines MSn in FT-ICR by sequences of PID and fragment isolation for the structural analysis of oligosaccharides isolated from human milk.
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