Ultraviolet matrix-assisted laser desorption/ionization mass spectrometric (UV-MALDI-MS) analysis of highly acidic, thermally labile species such as glycosaminoglycan-derived oligosaccharides is complicated by their poor ionization efficiency and tendency to fragment through the loss of sulfo groups. We have utilized a systematic approach to evaluate the effect of alkali metal counterions on the degree of fragmentation through SO3 loss from a highly sulfated model compound, sucrose octasulfate (SOS). The lithium, sodium, potassium, rubidium, and cesium salts of SOS were analyzed by UV-MALDI-time-of-flight (TOF)MS using an ionic liquid matrix, bis-1,1,3,3-tetramethylguanidinium alpha-cyano-4-hydroxycinnamate. The positive-ion and negative-ion MALDI mass spectra of five alkali metal salts of SOS were compared in terms of the degree of analyte fragmentation through the SO3 loss and the absolute intensity of a molecular ion signal. Experimental results demonstrate that the lithium, sodium, and potassium salts of SOS undergo some degree of fragmentation through the loss of SO3, whereas the fragmentation through the loss of SO3 in the rubidium and cesium salts of SOS is suppressed. A high detection sensitivity associated with the stability of sulfate half-esters was achieved for the cesium salt of SOS using positive-ion detection. Finally, the cesium salt of chondroitin sulfate A disaccharide was successfully analyzed using UV-MALDI-TOFMS.