Identification of side-reaction products generated during the ammonia-catalyzed release of N-glycans

N-linked glycosylation is one of the most important post translational modification of proteins. Various analytical techniques are used for the structural identification of the N-glycans released from proteins through various enzymatic and chemical methods. Although very few side-reaction products are generated during the enzymatic release of N-glycans, this method is expensive and suitable only for small quantities of samples. By contrast, chemical methods can be used for large quantities of samples; however, various side-reaction products are generated when chemical methods are used. Recently, the ammonia-catalyzed release of N-glycans from proteins has been reported to be associated with no typical side reactions. In the present study, we discovered a new side reaction: the epimerization of N-acetylglucosamine present at the reducing end of N-glycans to N-acetylmannosamine. The product of this side reaction interfered with the structural identification N-glycans. We propose a simple method that can help identify this artifact N-glycan isomer and eliminate the aforementioned interference. This simple method widens the applicability of ammonia-catalyzed reactions for N-glycan release from proteins, and is also suitable for N-glycans released using any other alkaline solutions.