A cheminformatics approach to characterize metabolomes in stable-isotope-labeled organisms

We report a computational approach (implemented in MS-DIAL 3.0; http://prime.psc.riken.jp/ ) for metabolite structure characterization using fully 13C-labeled and non-labeled plants and LC–MS/MS. Our approach facilitates carbon number determination and metabolite classification for unknown molecules. Applying our method to 31 tissues from 12 plant species, we assigned 1,092 structures and 344 formulae to 3,604 carbon-determined metabolite ions, 69 of which were found to represent structures currently not listed in metabolome databases. A computational approach facilitates molecular formula, metabolite class, and structure assignment for plant metabolites on the basis of LC–MS analysis of fully 13C-labeled and unlabeled plants.