Deciphering Complex Natural Mixtures through Metabolome Mining of Mass Spectrometry Data: The Plant Specialized Metabolome as a Case Study

Plants contain manifold and structurally diverse specialized metabolites, also referred to as natural products. Many plant compound classes have important biological functions such as stimulating plant growth, maintaining plant health, and recruitment of a functional root microbiome. Analytical methods to study and map these specialized metabolites have been developed for a while. In recent years, mass spectrometry-based metabolomics technologies have been maturing and they are capturing increasingly information-dense spectral data. To couple structural information to the spectral and statistical metabolomics data to allow for biochemical interpretation, computational metabolomics tools are needed. In this chapter, we show how plant chemical diversity is increasingly captured through the coupling of untargeted mass spectrometry-based metabolomics acquisition methods and computational metabolomics workflows that perform metabolome mining and annotation. By showcasing examples from three different plant chemistry studies, it is shown how metabolomics data is transferred into information-rich molecular networks that enable us to answer key biological questions by linking plant taxonomy and herbivore resistance phenotypes to the plant specialized metabolite contents. We conclude that the further development and widespread implementation and democratization of computational metabolomics workflows will be needed to prepare metabolomics for the “big data” era that is looming on the horizon.