Mass spectrometry is an established analytical technique in high-throughput metabolomics, often coupled with ultra-performance liquid chromatographic separation (UPLC). Since ion formation under ‘soft’ conditions is a complex phenomenon resulting in fragmentation, clustering and adduct formation, the extraction of meaningful information from holistic metabolomic profiling of biological samples requires the understanding of the physicochemical phenomena occurring inside an ionization source. In this paper we investigate the ionization dynamics of two ellagitannins (sanguiin H6 and lambertianin C) by combining state of the art mass spectrometric techniques (MALDI, ESI, APCI), ion mobility (IMS) and NMR. These compounds can be used as prototype of an important class of bio-active compound present in relevant concentrations in some food matrices. Copyright © 2011 John Wiley & Sons, Ltd.