O-acetylated N-glycans from fish serum of Atlantic salmon (Salmo salar) are characterized by capillary electrophoresis (CE) in conjunction with both laser-induced fluorescence (LIF) and mass spectrometry (MS) detection methods. Glycans derivatized with negatively charged fluorescent label 8-aminopyrene-1,2,6-trisulfonate (APTS) were separated to obtain a CE-LIF profile of the complex glycan mixture, and the profile concurs with that obtained by using electrospray mass spectrometry. The identity of the APTS-labeled glycans was confirmed by CE-MS. The same glycans can be identified also in their native state by CE-MS without derivatization. The structural variations of O-acetylated sialic acid isomers in fish serum glycans are investigated by CE-MS/MS. Selected ion monitoring provided useful structural information of the underivatized glycans from fragmentation spectra. New complex fish serum glycans that are not reported previously were observed and characterized. These methods may be useful not only for the characterization of acetylation of complex glycans but also to study other types of glycan modifications, as well as to allow determination of overall glycan composition in glycoproteins.