A Novel Integrated Method for Large-Scale Detection, Identification, and Quantification of Widely Targeted Metabolites: Application in the Study of Rice Metabolomics

Abstract

Liquid chromatography-mass spectrometry (LC-MS)-based metabolomics has been facilitated by the construction of MS(2) spectral tag (MS2T) library from the total scan ESI MS/MS data, and the development of widely targeted metabolomics method using MS/MS data gathered from authentic standards. In this report, a novel strategy called stepwise multiple ion monitoring-enhanced product ions (stepwise MIM-EPI) was developed to construct the MS2T library, in which stepwise MIM was used as survey scans to trigger the acquisition of EPI. A total number of 698 (almost) non-redundant metabolites with MS(2) spectra were obtained, of which 135 metabolites were identified/annotated. Integrating the data gathered from our MS2T library and other available multiple reaction monitoring (MRM) information, a widely targeted metabolomics method was developed to quantify 277 metabolites, including some phytohormones. Evaluation of the dehydration responses and natural variations of these metabolites in rice leaf not only suggested the coordinated regulation of abscisic acid (ABA) with metabolites such as serotonin derivative(s), polyamine conjugates under drought stress, but also revealed some C-glycosylated flavones as the potential markers for the discrimination of indica and japonica rice subspecies. The new MS2T library construction and widely targeted metabolomics strategy could be used as a tool for rice functional genomics.

Metabolome Analysis of <i>Oryza sativa</i> (Rice) Using Liquid Chromatography-Mass Spectrometry for Characterizing Organ Specificity of Flavonoids with Anti-inflammatory and Anti-oxidant Activity

“…It has been reported that the Indica rice variety exhibits higher C-glycosylflavonoid production than the Japonica variety. 19,24,25,29) Principal component analysis (PCA) using the metabolome data characterized the accumulation patterns of the metabolites in the samples and showed the organ specificity of the metabolites (Fig. 3).…”

“…[15][16][17][18][19][20] Such metabolites exhibit properties beneficial to humans, including anti-tumor, 21) anti-inflammatory, 22) and anti-oxidant activities. 8) To improve the quality of rice plants, the organ-specific metabolic networks of primary and specialized metabolites were recently investigated using metabolite profiling based on liquid chromatography (LC)-MS.…”

“…[15][16][17][18][19][20] Such metabolites exhibit properties beneficial to humans, including anti-tumor, 21) anti-inflammatory, 22) and anti-oxidant activities. 8) To improve the quality of rice plants, the organ-specific metabolic networks of primary and specialized metabolites were recently investigated using metabolite profiling based on liquid chromatography (LC)-MS. 19,[23][24][25][26][27][28] Metabolome-genome-wide association studies on rice have been increasingly attracting attention. 25,29) There are two primary types of rice grown in the world (i.e., the Indica and Japonica varieties).…”

Genetic analysis of the metabolome exemplified using a rice population

“…described previously (12,14) (Dataset S1). A data matrix was generated, consisting a total of 1,000 metabolites including 683 in flag leaf and 317 germinating seed, with 100 metabolites were detected in both tissues ( Fig.…”

“…Here, we report a genetic analysis of rice metabolome combining metabolic profiling (12) with an ultrahigh-density genetic map (13) using a recombinant inbred line (RIL) population. We demonstrated that the high-resolution mapping of the large number of mQTLs may greatly accelerate gene identification and pathway elucidation for metabolites, which will enhance our understanding of the genetic and biochemical basis of the metabolome and also be valuable for crop genetic improvement through metabolomics-assisted breeding.…”