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BREAKTHROUGH TECHNOLOGIES

Clarification of Pathway-Specific Inhibition by Fourier Transform Ion Cyclotron Resonance/Mass Spectrometry-Based Metabolic Phenotyping Studies^1,[W]

Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Sakai 599–8531, Japan (A.O., T.O., A.K., D.O.); Research Association for Biotechnology, Tokyo 105–0003, Japan (A.O., Y.S.); Department of Bioinformatics and Genomics, Nara Institute of Science and Technology, Ikoma 630–0192, Japan (Y.N., Y.S., S.K.); Ehime Women's College, Uwajima 798–0025, Japan (Y.N.); and Kazusa DNA Research Institute, Kisarazu 292–0818, Japan (Y.N., H.S., N.S., D.S.)

We have developed a metabolic profiling scheme based on direct-infusion Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR/MS). The scheme consists of: (1) reproducible data collection under optimized FT-ICR/MS analytical conditions; (2) automatic mass-error correction and multivariate analyses for metabolome characterization using a newly developed metabolomics tool (DMASS software); (3) identification of marker metabolite candidates by searching a species-metabolite relationship database, KNApSAcK; and (4) structural analyses by an MS/MS method. The scheme was applied to metabolic phenotyping of Arabidopsis (Arabidopsis thaliana) seedlings treated with different herbicidal chemical classes for pathway-specific inhibitions. Arabidopsis extracts were directly infused into an electrospray ionization source on an FT-ICR/MS system. Acquired metabolomics data were comprised of mass-to-charge ratio values with ion intensity information subjected to principal component analysis, and metabolic phenotypes from the herbicide treatments were clearly differentiated from those of the herbicide-free treatment. From each herbicide treatment, candidate metabolites representing such metabolic phenotypes were found through the KNApSAcK database search. The database search and MS/MS analyses suggested dose-dependent accumulation patterns of specific metabolites including several flavonoid glycosides. The metabolic phenotyping scheme on the basis of FT-ICR/MS coupled with the DMASS program is discussed as a general tool for high throughput metabolic phenotyping studies.

The author responsible for distribution of materials integral to the findings presented in this article in accordance with the policy described in the Instructions for Authors (www.plantphysiol.org) is: Daisaku Ohta (ohtad{at}bioinfo.osakafu-u.ac.jp).

^[W] The online version of this article contains Web-only data.

www.plantphysiol.org/cgi/doi/10.1104/pp.106.080317

^* Corresponding author; e-mail ohtad{at}bioinfo.osakafu-u.ac.jp; fax 81–72–254–9409.

Received March 15, 2006; accepted August 4, 2006; published August 11, 2006.

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