MS 2 and MS 3 spectra of thirteen previously identified saponin structures from Quillaja saponaria Molina were obtained by electrospray ionization ion trap multiple-stage mass spectrometry (ESI-ITMS n ) in positive ion mode. The spectra were analysed by partial least squares regression-discriminant analysis (PLS-DA) yielding a method that can classify the spectra according to saponin structure. For this method a referencing of the m/z axis was essential to obtain a correlation between peaks in the spectra and common structural elements. The MS 2 and MS 3 spectra could be classified according to the structures of the oligosaccharides at C-3 and C-28 of the corresponding saponins. Terminal residues with the same mass, such as β-d-Apif and β-d-Xylp, could also be distinguished. The PLS-DA method was applied on Quillaja saponins separated from a commercial bark extract by reversed-phase chromatography.The method outlined here is applied on a specific group of Quillaja saponins, but can be used on other types of glycoconjugates. Combination of this technique with chromatography would give a very powerful tool for rapid identification of components in complex mixtures.