Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS), has been used for structure characterization of 1-aminopyrene-3,6,8-trisulfonate (APTS)-derivatized oligosaccharides previously separated by capillary electrophoresis (CE). The resolved components were first isolated by employing an automated high-resolution fraction collector. Using on-probe sample cleanup with a cation-exchange resin and a matrix mixture of (1:1) 6-hydroxypicolinic acid and 3-hydroxypicolinic acid, APTS-labeled oligosaccharides were successfully detected by MALDI-TOF MS in the negative ionization mode. Each APTS-labeled oligosaccharide produced single [M-H]-1 peaks. Detection limits for standard APTS-derivatized oligosaccharide (maltoheptaose) were down to 30 fmol. APTS labeled maltooligosaccharides and various standard carbohydrates were separated and collected by CE, followed by molecular weight determination with MALDI-TOF MS. The mass spectral characterization enhances the power of the CE analysis of oligosaccharides.