There is a demand for better tasting, healthier and safer food-stuffs which better meet the needs of both industry and the consumer. New technology has been required to monitor and improve the quality of food, metabolomics has become an important tool for food processing, plant breeding and so on. In-food science, comprehensive analysis of primary metabolites through to secondary metabolites is very important. However, there is no application which can analyze them at the same time. In this study, we developed the analytical methods using LC/MS/MS for monitoring the primary and secondary metabolites in foods, focus on the major compound's categories such as organic acids, amino acids, sugars, carotenoids and flavonoids.