Recent advances in the use of liquid chromatography-mass spectrometry for the study of metabolomics are reviewed. Sample preparations of biofluids and practical aspects of ultra-high pressure liquid chromatography are discussed. Applicability of different kinds of mass spectrometers for metabolite profiling is described. New tools-ion mobility spectroscopy and automated chip-based nanoelectrospray system with potentials to be applied in the metabolomics analysis are described.