Comparison of fragmentation modes for the structural determination of complex oligosaccharides ionized by matrix‐assisted laser desorption/ionization mass spectrometry

Fragment ions from underivatized N‐linked oligosaccharides ionized by matrix‐assisted laser desorption/ionization mass spectrometry were obtained by spontaneous fragmentation on a magnetic sector mass spectrometer, by post‐source decay (PSD) on a reflectron time‐of‐flight (TOF) instrument and by collision‐induced dissociation on a magnetic sector instrument fitted with an orthogonal‐TOF analyser. Spontaneous fragmentation on the magnetic sector instrument produced ions mainly by glycosidic cleavage together with two abundant ions formed by cross‐ring cleavage of the reducing‐terminal residue. The PSD spectra were similar, the majority of ions being formed by glycosidic cleavage. Internal fragment ions were abundant. High‐energy collision‐induced dissociation spectra, recorded with the orthogonal‐TOF analyser, differed considerably from the other types of spectra, particularly in the appearance of major fragment ions produced by cross‐ring cleavages of most of the constituent monosaccharide residues. These ions allowed much sequence and branching information to be obtained from the oligosaccharide.