Numerical Representations of Metabolic Systems

[Image: see text] Metabolomics is becoming a mature part of analytical chemistry as evidenced by the growing number of publications and attendees of international conferences dedicated to this topic. Yet, a systematic treatment of the fundamental structure and properties of metabolomics data is lagging behind. We want to fill this gap by introducing two fundamental theories concerning metabolomics data: data theory and measurement theory. Our approach is to ask simple questions, the answers of which require applying these theories to metabolomics. We show that we can distinguish at least four different levels of metabolomics data with different properties and warn against confusing data with numbers. This treatment provides a theoretical underpinning for preprocessing and postprocessing methods in metabolomics and also argues for a proper match between type of metabolomics data and the biological question to be answered. The approach can be extended to other omics measurements such as proteomics and is thus of relevance for a large analytical chemistry community.