Abstract
Metabolomics has grown greatly as a functional genomics tool, and has become an invaluable diagnostic tool for biochemical phenotyping of biological systems. Over the past decades, a number of databases involving information related to mass spectra, compound names and structures, statistical/mathematical models and metabolic pathways, and metabolite profile data have been developed. Such databases complement each other and support efficient growth in this area, although the data resources remain scattered across the World Wide Web. Here, we review available metabolome databases and summarize the present status of development of related tools, particularly focusing on the plant metabolome. Data sharing discussed here will pave way for the robust interpretation of metabolomic data and advances in plant systems biology.
Highlights
Metabolomics, i.e., the measurement of the full suite of metabolites in a living tissue, has expanded greatly over the last decade, especially in the context of biochemical phenotyping
MASS SPECTRUM-ORIENTED INFORMATION Since non-targeted metabolite profiling using GC-mass spectrometry (MS) for plant extracts was established in the early 2000s (Fiehn, 2001; Lisec et al, 2006), many software packages and databases for electron impact (EI) mass spectra and retention indices (RIs) of compounds analyzed by gas chromatography–mass spectrometry (GC-MS) have been created (Table 1)
Mass spectra based on GC-MS, LC-MS, MS2, etc MSn spectrum collection of literature [LC-specific] Spectral database for organic compounds
Summary
Metabolomics, i.e., the measurement of the full suite of metabolites in a living tissue, has expanded greatly over the last decade, especially in the context of biochemical phenotyping. MASS SPECTRUM-ORIENTED INFORMATION Since non-targeted metabolite profiling using GC-MS for plant extracts was established in the early 2000s (Fiehn, 2001; Lisec et al, 2006), many software packages and databases for electron impact (EI) mass spectra and RIs of compounds analyzed by GC-MS have been created (Table 1). The glycan mass spectral database (GMDB) The MetabolomeExpress http://riodb01.ibase.aist.go.jp/sdbs /cgi-bin/cre_index.cgi?lang = eng http://fiehnlab.ucdavis.edu/projects /FiehnLib/:8080/m1/ http://riodb.ibase.aist.go.jp/rcmg /glycodb/Ms_ResultSearch https://www.metabolome-express.org/ Mass spectral database for LC-MS, MS2 A software tool for metabolite identification
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