As analytical techniques and data pre-processing methods continue to improve, the bottleneck of metabolomics is shifting towards later stages of data analysis and biological interpretation. High-coverage metabolomics is only possible when combining data from multiple platforms necessitating efficient methods for data integration. Metabolomic data sets with high coverage provide a unique opportunity to estimate and study metabolic networks. Once established, these networks can provide a backbone for systems biology approaches where the aim is to construct fundamental models of metabolic regulation. In this chapter, we provide an overview of status of these topics and describe current methods and tools, their drawbacks and advantages for integrative plant metabolomics.