Interpretation support for multistage MS: a mathematical method for theoretical generation of glycan fragments and calculation of their masses.

Glycan fragmentation forms an integral part of the current research in glycomics. Creation of a database of glycan fragments and their masses for known glycan structures is an important step in the interpretation of mass spectra for the identification of unknown glycan structures. This paper introduces the concept of positional nomenclature, gives a systematic representation of glycan structure of any size, and hence develops a method for theoretically generating all possible first and second generation fragments resulting from glycosidic and cross ring cleavages. Matrix equations are developed for the calculation of theoretical masses. Algorithm is presented for iterative generation of all fragments and calculation of their masses. This method is applicable to glycan analytical techniques using MS, MS/MS, and multistage MS (MSn) with different ionization methods, derivatives, or ions used. The method is adaptable to computer program and has been verified for theoretical masses reported in literature. Rules for the theoretical validation of the fragments are presented.