Abstract: Metabonomics is a science to measure as many metabolites as possible in an organism (tissue, body fluids) or cell. The most common tools are the NMR and MS. Metabonomics study usually includes the sample collection, sample pretreatment, metabonome data collection, multivariate data analysis, metabolite marker finding and identification, and final biological explanation. Among them, the identification of metabolic biomarkers is one bottleneck. In this lecture, we shall report an integrated method for comprehensive identification of defined metabolite markers from the multivariate analysis based on the LC-MS.