Characterization of Metabolites From Medicago truncatula Using Gas Chromatography Mass Spectrometry—Addressing the Knowns and Unknowns Using High Resolution Time-of-Flight

One of the principle challenges to metabolomic analyses is the identification of unknown analytes. Many studies report in excess of 60% of the analytes as unknown. Gas chromatography with mass spectrometry (GC-MS) has been a standard for metabolite analysis and historically relies on established databases for analyte identification. Nominal mass information, poor spectral quality, and limited databases have left many metabolites as poorly identified or unidentified. Here, metabolites from M. truncatula extracts are characterized using GC with high resolution time-of-flight (HRT) mass spectral detection. The combination of high resolution/accurate mass with either EI-MS (library matching and classification) or CI-MS (molecular formula assignment) was used to elucidate or confirm metabolite identities. This ultimately improves the biological context of the metabolomics experiments and provides the key information to determine what else is in your samples.