Collision-induced dissociation of ammonium-cationized alpha and beta acetyl pyranosidic isomers were studied and stereochemical dependence of the reactivity towards elimination of acetic acid from the anomeric position was found. It is shown that isomers that contain trans diacetyloxy groups at positions 1 and 2 of the pyranoside are more reactive, allowing anomeric distinction according to the relative abundance of the oxocarbenium product ion of this reaction in the spectrum. The higher reactivity of trans isomers is rationalized by neighboring group assistance that is possible only in the trans configuration. DFT calculations indicate that the lesser energetic reaction path occurs in an ammonium-cationized trans diequatorial 2,3-diacetoxy tetrahydropyran that was used as a model in order to study this process theoretically. It is also found that the configuration at position 4 of the carbohydrate plays a major role in the rate of formation and stability of oxocarbenium ions. Copyright © 2005 John Wiley & Sons, Ltd.