Metabolomics studies offer a better, faster path to medication discovery than the traditional natural product research methodology. By using such a method, one not only avoids the problems of the traditional methodologies employed in natural product research, but also gains a deeper understanding of the biochemical status and gene activities of the organisms being examined. In plant research, transcriptomics and metabolomics have been used to identify candidate genes with functions that control the entire biological apparatus and establish the relationship between genotype and phenotype in response to a variety of environmental factors, such as climate, ecotype differences, and abiotic/biotic stress conditions. The majority of metabolomics researches give phenotypic data since small-molecule metabolite databases are used in several dimensions and untargeted metabolomics investigations are becoming more common. As a result, a novel approach in functional metabolomics is required for investigating the underlying mechanisms of the deregulated small-molecule metabolism found in various biological systems.