Breastfeeding is regarded as the ideal way to nourish infants. However, feeding with formula milk is also common in much of the West. Despite this, the function of the molecular components of breast- and formula milks are not fully understood, less still the relationship between the composition of the milk and the infant’s metabolism and how this influences the infant’s development. The Biotechnology and Biological Sciences Research Council (BBSRC)-funded project ‘The validation of biomarkers of metabolic efficacy in infant nutrition’ aims to identify lipid biomarkers that can be used to study the effect of diet on growth and development of infants. In this work, we have been able to validate these markers. Here, we present an approach to biomarker discovery that has new depth and will inform research questions about how metabolism is governed, and which species can be used to identify situations where metabolism is becoming defective.