Molecules are everywhere. The diverse structures and functions of small and specialized molecules have always fascinated me. Specialized molecules play key roles in nature as inter-species and even inter-kingdom messengers or as chemical weapons to deter or eliminate competing organisms nearby. Furthermore, these specialized molecules are also important components of food often determining crop growth and fitness and their nutritional value. Knowing all small molecules and their functions would thus be of tremendous aid in scientific areas such as antibiotics discovery and the growing of healthy crops. However, these small molecules are seldom on their own and usually part of a complex metabolite mixture with molecules derived from various organisms and the environment. Thus, methods that quickly capture a complete picture of the small molecule profile of complex metabolite mixtures are needed. I recognise three paths to better understand complex metabolite mixtures: i) increased metabolite annotation power, ii) chemically-informed comparative metabolomics, and iii) linked metabolomics profiles to function and genotype/genomic information.