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Metabolomics, the time related qualitative and quantitative analysis of metabolome is a new paradigm of research bridging the phenotype-genotype gap and linking gene to function. It has great potential for the improvement of the compositional quality of crops. Metabolomics involves non-biased identification and quantification of all metabolites in a biological system at a specific time and enable large-scale and parallel interrogation of cell states under different stages of development and defined environmental conditions to reveal novel interactions among various pathways using a new array of analytical methodologies and technologies, particularly the GC-TOFMS (Gas Chromatography with Time of Flight Mass Spectrometry) and LC-MS (Liquid Chromatography with Mass Spectrometry). FT-IR (Fourier Transform Infrared Spectroscopy) and NMR (Nuclear Magnetic Resonance) spectroscopy provide rapid and non-destructive high-throughput methods. The strategies in metabolomics involve metabolite profiling, metabolic fingerprinting and metabolite target analysis. The success of plant metabolomics depends on collection and preprocessing the data for direct comparison of data sets from comparative analyses; processing and mining the data to extract the components of interest; presenting complex data in a readily understandable way using dedicated visualization strategies and data basing for efficient data storage. Metabolomics rely heavily upon bioinformatics for the storage, retrieval, and analysis of large data sets. Basic tools align, visualize, and differentiate components in large data sets. Individual components are then correlated and placed in metabolic networks or pathways and used to model and simulate pathways for a better understanding of biological and biochemical phenomena and functional genomics in an ecosystem and systems biology as well.
