The circadian clock governs body time and regulates many physiological functions including sleep and wake cycles, body temperature, feeding, and hormone secretion. Alignment of drug dosing time to body time can maximize the pharmacological effect and minimize untoward effects. Therefore, a simple and robust method for estimating body time is important for drug efficacy or “chronotherapy”. We previously reported that a metabolite timetable could estimate body time with good accuracy. A metabolite timetable was constructed by profiling metabolites in human and mouse with capillary electrophoresis-mass spectrometry (CE-MS) and liquid chromatography–mass spectrometry (LC-MS). In this chapter, we describe practical methods to profile and identify oscillating metabolites.