Natural products such as medicinal plants, foods, and fungi have been traditionally used for human health. Bioactive ingredients in the natural products have been identified to search for the mechanism, and the unique structures of active compounds have been elucidated so far. Recently, the omics techniques were used to search for secondary metabolites and to conduct a comprehensive analysis of the mechanism of bioactivity. The target proteins could be identified using thermal shift assay with the proteomics analysis using LC–MS2. We could also comprehensively analyze secondary metabolites by using the database of the fragmentations of LC–MS2. These innovative methods make it possible to elucidate the ingredients and mechanism effectively and quickly. Recent studies on isolation and identification of compounds from natural products and the search for the mechanism were introduced in this section.