N-glycosylation of proteins is the predominant glycosylation in mammals and confers specific conformations, localization, and functions to proteins. High-throughput proteomics techniques have focused on the identification of proteins through amino acid sequence determination, with little attention paid to their post-translational modification, in particular, glycosylation. High-throughput mass spectrometric data often contain information about glycosylation, but this is systematically discarded by proteomic search engines. We have developed an algorithm, StrOligo (for STRucture of OLIGOsaccharides), capable of automated analysis of oligosaccharide composition and possible structures by mass spectrometry. The algorithm analyzes tandem mass spectrometry (MS/MS) data in an automated three-step process and provides possible structures and a discrimination score. In the first step, the algorithm constructs a relationship tree of the monosaccharide moiety losses observed in the MS/MS spectrum. In the second step, the algorithm uses the tree to propose possible compositions and structures from combinations of adduct and fragment ions as well as a discrimination score, which reflects the fit with the experimental results. Finally, an interface is available to visualize the proposed structures and their scores. As well, the MS/MS spectrum is displayed with relevant peaks labeled for the proposed structure with the highest discrimination score, using a modified nomenclature.