I have recently participated in the Metabolomics workshop organized by EMBO at the Wageningen University and Research, the Netherlands. This course has provided an overview of key issues that affect metabolomics studies, handling datasets and procedures for the analysis of metabolomics data using bioinformatics tools. It was delivered using a mixture of lectures, computer-based practical sessions and interactive discussions. The course provided a platform for discussion of the key questions and challenges in the field of metabolomics, from study design to metabolite identification. Special thanks to the organizers Reza Salek (Bruker GmbH, Germany), Jos Hageman (Wageningen University and Research), Ron Wehrens (Wageningen University and Research) and all the trainers.