BACKGROUND: Platelet (PLT) concentrates are routinely stored for 5 to 7 days. During storage they exhibit what has been termed PLT storage lesion (PSL), which is evident by a loss of hemostatic function when transfused into patients. The overall goal of this study was to obtain a comprehensive data set describing PLT metabolism during storage. STUDY DESIGN AND METHODS: The experimental approach adopted to achieve this goal combined a series of standard assays to monitor the quality of stored PLTs and a deep-coverage metabolomics study using liquid chromatography coupled with mass spectrometry performed on both the extracellular and the intracellular environments. During storage we measured 174 different variables in 6 PLT units, collected by apheresis. Samples were collected at eight different time points resulting in a data set containing more than 8000 measurements. RESULTS: Stored PLTs did not undergo a monotonic decay, but experienced systematic changes in metabolism reflected in three discrete metabolic phenotypes: The first (Days 0-3) was associated with active glycolysis, pentose phosphate pathway, and glutathione metabolism and down regulation of tricarboxylic acid (TCA) cycle. The second (Days 4-6) was associated with a more active TCA cycle as well as increased purine metabolism. A third metabolic phenotype of less clinical relevance (Days 7-10) was associated with a faster decay of cellular metabolism. CONCLUSION: PSL is not associated with a linear decay of metabolism, but rather with successive metabolic shifts. These findings may give new insight into the mechanisms underlying PSL and encourage the deployment of systems biology methods to PSL.