Comprehensive characterisation of disease-related metabolomic phenotypes and drug effects requires monitoring metabolite levels and their turnover rates. Tandem application of stable isotope 18O-assisted 31P NMR and mass spectrometric techniques uniquely allow simultaneous measurements of phosphorus-containing metabolite levels and their dynamics in tissue and blood samples. The 18O labelling procedure is based on incorporation of the 18O atom, provided from H218O, into Pi with each act of ATP hydrolysis and the subsequent distribution of 18O-labelled phosphoryls amongst phosphate-carrying molecules. Essentially, all major phosphometabolites and their turnover rates can be quantified using 18O-assisted 31P NMR spectroscopy and mass spectrometry. This technology permits the simultaneous recording of ATP synthesis and utilisation, phosphotransfer fluxes through adenylate kinase, creatine kinase and glycolytic pathways, as well as mitochondrial nucleotide dynamics and glycogen turnover. Another advantage of 18O methodology is that it can measure almost every phosphotransfer and hydrolytic reaction taking place in the cell including the turnover of small pools of signalling molecules, and the dynamics of energetic signal communication. Our studies demonstrate that 18O-assisted 31P NMR/mass spectrometry is a valuable tool for phosphometabolomic and fluxomic profiling of transgenic models of human diseases, providing valuable data which reveals system-wide adaptations in metabolic networks.