Metabolomics is defined as the quantitative measurement of the dynamic multiparametric metabolites. Recent technological advances in the quantification of cellular metabolites, such as capillary electrophoresis (CE) -TOFMS, have prompted the comprehensive analysis of the global metabolism. Now, metabolomics has been used in the identification of new biomarker for toxicology and disease diagnosis, and the elucidation of fermentation processes. Moreover, it is considered that metabolomics would be a powerful tool for the target identification of small molecular bioactive compounds. Here we introduce our recent study that metabolomics was applied to identify the molecular target of glucopiericidin A, which was isolated through a screening of natural products for an inhibitor of cellular filopodia protrusion in carcinoma cells.