Abstract
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. SimGlycan software was used in combination with MS(n) and permethylation to differentiate structural isomers present in ovalbumin glycans. The ion trap MS profile was acquired for permethylated ovalbumin glycans and specific precursors were targeted for MS(n) to differentiate structural isomers. Sequential MS(n) data were imported into SimGlycan software and various structural isomers of ovalbumin glycans were differentiated. SimGlycan differentiated structural isomers were verified using manual assignment and previously published data.