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Tandem mass spectrometry has been recognized as a useful technique for the characterization of the glycan structures. However, current softwares for automated interpretation of tandem mass spectra of glycans are limited by the size, biosynthetic rules, and fragmenting type of glycans. We developed a robust, fully-automated computer software program, GlycoMaster, to determine the glycan structure from mass spectra, in which a heuristic dynamic algorithm is used. Experiments showed that GlycoMaster can very accurately elucidate glycan structures from tandem mass spectra with those limitations. In this paper, we describe the algorithm.