A new method was here developed for the determination of O-18-labeling ratios in metabolic oligophosphates, such as ATP, at different phosphoryl moieties (alpha-, beta-, and gamma-ATP) using sensitive and rapid electrospray ionization mass spectrometry (ESI-MS). The ESI-MS-based method for monitoring of O-18/O-16 exchange was validated with gas chromatography-mass spectrometry and 2D P-31 NMR correlation spectroscopy, the current standard methods in labeling studies. Significant correlation was found between isotopomer selective 2D P-31 NMR spectroscopy and isotopomer less selective ESI-MS method. Results demonstrate that ESI-MS provides a robust analytical platform for simultaneous determination of levels, O-18-labeling kinetics and turnover rates of alpha-, beta-, and gamma-phosphoryls in ATP molecule. Such method is advantageous for large scale dynamic phosphometabolomic profiling of metabolic networks and acquiring information on the status of probed cellular energetic system.