In purine‐depleted environments, the de novo purine biosynthetic pathway is catalyzed to ultimately produce inosine monophosphate (IMP), a purine invisible using current optical microscopy methodology. These enzymes form a complex, termed the ‘purinosome,’ to replenish IMP levels. Before cellular chemical imaging may be applied to monitor the distributions and fluctuations in purine levels, it is necessary to develop a scheme to quantitatively detect purines. Here, IMP and other purines in biologically relevant matrices have been detected quantitatively. These methods provide a time‐of‐flight‐secondary ion mass spectrometry protocol using C60+ primary ions to determine the concentration of biomolecules in a cell, such as HeLa, at the nanomolar level. Copyright © 2012 John Wiley & Sons, Ltd.