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Abstract Matrix‐assisted laser desorption/ionization tandem time‐of‐flight mass spectrometry （MALDI‐TOF/TOF‐MS） has been introduced in recent years as a valuable tool for the structural characterization of permethylated oligosaccharides. In this report, we describe the combination of MALDI in‐source decay （ISD） with the subsequent TOF/TOF‐MS analyses of specific fragments, allowing the detailed characterization of the selected part of the oligosaccharide molecule. Part of the second‐generation fragment ions were different from those observed in conventional MALDI‐TOF/TOF‐MS experiments. Other fragments, which had already been observed in conventional MALDI‐TOF/TOF‐MS and again showed up in second‐generation fragment analysis, could be assigned to specific parts of the molecule. Our approach disclosed different structural features of the oligosaccharides: due to permethylation, the glycosidic linkage fragments allowed the distinction between terminal, monosubstituted and disubstituted monosaccharides and indicated the oligosaccharide sequence. Moreover, substitution positions were deduced based on characteristic cross‐ring fragmentation by high‐energy collision‐induced fragmentation. In conclusion, combination of MALDI‐ISD with TOF/TOF‐MS allows the detailed characterization of specific moieties of permethylated oligosaccharides and is, therefore, a powerful technique for structural glycomics. Copyright ? 2006 John Wiley & Sons, Ltd.
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