Mechanisms of fragmentation of glycosyl bond linkages in various saccharides were investigated by using computational calculations to find general rules of fragmentation of sodiated oligosaccharides in mass spectrometry. The calculations revealed that alpha-Glc, alpha-Gal, beta-Man, alpha-Fuc, beta-GlcNAc, and beta-GalNAc linkages were cleaved more easily than beta-Glc, beta-Gal, and alpha-Man linkages because the transition states of the former were stabilized by the anomeric effect. The 1-6 linkage was more stable than the others, since saccharides with flexible 1-6 linkages were more stabilized in energy than the other linkages by the sodium cation. The sialyl linkage was the most labile of all the linkages investigated. Comparison of activation energies and binding affinities to the sodium cation revealed an increase in activation energy in proportion to the increment in binding affinity. The calculated stabilities of glycosyl bonds were: alpha-Man (Manalpha1-3Man, Manalpha1-4Man, Manalpha1-6Man) > beta-Gal (Galbeta1-4Gal) > alpha-GalNAc (GalNAcalpha1-4GalNAc) > beta-Man (Manbeta1-4GlcNAc) > alpha-Gal (Galalpha1-3Gal, Galalpha1-4Gal, Galalpha1-6Gal) > beta-Man (Manbeta1-4Man) > beta-GalNAc (GalNAcbeta1-4GalNAc) > alpha-Fuc (Fucalpha1-6GlcNAc) > alpha-Fuc (Fucalpha1-4GlcNAc) > beta-GlcNAc (GlcNAcbeta1-4GlcNAc) > alpha-Fuc (Fucalpha1-3GlcNAc) > alpha-NeuNAc (NeuNAcalpha2-3Gal, NeuNAcalpha2-6Gal); this result was close to the experimentally deduced trend. These theoretically and experimentally derived general rules for fragmentation should be useful for analyzing the experimentally obtained mass spectra of oligosaccharides.