High energy (4keV) collision-induced dissociation (CID) product ion spectra have been obtained for a series of isomeric sugar molecules of close structural similarity. The reproducibility of the approach has been established and the spectra shown to have significant differences. These differences have been rationalised in terms of conventional mass spectrometric fragmentation rules. The data have also been subjected to analysis using chemometric methods, which require no specialist mass spectrometric input. The resulting classification of the data shows good agreement with the conventional interpretation approach.