The role of small molecules, in particular of secondary metabolites, in plant-pathogen and plant-symbiont interactions is already obvious but still by far underestimated, simply because the majority of these compounds is not known. Furthermore, the synthesis of most secondary metabolites is limited to specific tissues or cell types and is often only stimulated during specific developmental stages or under certain environmental conditions. The broad structural diversity of secondary metabolites makes it virtually impossible to detect all compound classes by one analytical technique. However, a metabolomics platform combining GC- and LC-MS technologies allows detection and efficient profiling of all six classes of secondary metabolites described for Arabidopsis (von Roepenack-Lahaye et al., 2004). A workshop will provide training particular in CapLC-ESI-QTOF-MS-based profiling of secondary metabolites in Arabidopsis including data management {von Roepenack-Lahaye, 2004 #1206}{von Roepenack-Lahaye, 2004 #1206}.