Mass spectrometry (MS) has emerged as a powerful tool for the structural elucidation of glycans. The use of permethylaytion in combination with multistage fragmentation (MSn) is a critical aspect for glycan structural characterization. Only MSn truly characterizes a glycan structure as it allows identification of branching patterns, linkages and resolution of isobaric structures which are otherwise indistinguishable in MS/MS spectra. However, MSn analysis is complicated by large number of spectra generated for a single structure. It is very common that one must acquire MS6 or MS7 level of fragmentation to differentiate potential glycan structural isomers. Here we present the use of a bioinformatics tool (SimGlycan) for glycan structural isomer differentiation from MSn data.