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N-linked glycosylation is one of the most important protein post-translational modifications. Despite the importance of  N -glycans, the structural determination of  N -glycan isomers remains challenging. Here we develop a mass spectrometry method, logically derived sequence tandem mass spectrometry (LODES/MS n ), to determine the structures of  N -glycan isomers that cannot be determined using conventional mass spectrometry. In LODES/MS n , the sequences of successive collision-induced dissociation are derived from carbohydrate dissociation mechanisms and apply to  N -glycans in an ion trap for structural determination. We validate LODES/MS n  using synthesized  N -glycans and subsequently applied this method to  N -glycans extracted from soybean, ovalbumin, and IgY. Our method does not require permethylation, reduction, and labeling of  N -glycans, or the mass spectrum databases of oligosaccharides and  N -glycan standards. Moreover, it can be applied to all types of  N -glycans (high-mannose, hybrid, and complex), as well as the  N -glycans degraded from larger  N -glycans by any enzyme or acid hydrolysis.

Structural identification of N-glycan isomers using logically derived sequence tandem mass spectrometry