The protonated and sodium cationized pseudomolecular ions of a series of reducing and non‐reducing oligosaccharides possessing aldopentopyranosyl, 6‐deoxyaldohexopyranosyl, ketohexofuranosyl, 4‐O‐methyl glucuronopyranosyl methyl ester and N‐acetyl 2‐deoxyglucopyranosylamine units were studied using collision‐induced dissociation (CID) fast atom bombardment (FAB) mass spectrometry. The CID spectra of the [M + H]+ ions provide information about the sequence of the monosaccharide units, while dissociation of the [M + Na]+ ions by two‐bond ring cleavage processes gives rise to fragment ions which allow differentiation of 1 → 2 and 1 → 4 linkages. The influence of the structure of the constituent monosaccharides on the dissociation of the [M + H]+ and [M + Na]+ ions is discussed. An unusual type of fragmentation, which we suggest involves the elimination of internal monosaccharides residues, has not only been observed in the FAB mass spectra but also in the unimolecular decomposition and CID spectra of both [M + H]+ ions and oxonium ions from several oligosaccharides containing monosaccharide residues with different masses.

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The phenomenon of 'internal residue loss' of protonated native- and per-O-methylated oligosaccharides has recently been described as occurring on high-energy collision conditions. Awareness of this phenomenon in the mass spectrometric analysis of oligosaccharides is of great importance since the rearrangement ions produced by this process may complicate monosaccharide sequence assignment. In this research, oligosaccharides having N-acetyl-glucosamine residues as the reducing or non-reducing terminal residue have been included in our MS/MS analyses in order to try to better understand the factors that influence 'internal residue loss'. Native and per-O-methylated compounds were submitted to positive and negative MS/MS, selecting protonated, sodium-cationized, or de-protonated pseudomolecular ions as precursors. High- and low-energy collision induced dissociation tandem mass spectrometry experiments were performed using a four sector instrument and a hybrid quadrupole time-of-flight mass spectrometer respectively. The phenomenon of 'internal residue loss' was not observed on either high- or low-energy CID-MS/MS when sodium-cationized precursor ions of either native or per-O-methylated oligosaccharides were examined. Similarly, MS/MS analysis performed in the negative ionization mode also failed to generate ions resulting from 'internal residue loss'. This combination of experiments therefore offers a way to be sure whether ions observed in the tandem mass spectra of protonated native or per-O-methylated oligosaccharides originate from 'internal residue loss' or from direct glycosidic linkage fragmentation.

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