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Published on August 11, 2006; 10.1104/pp.106.080317

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Received March 15, 2006
Accepted August 4, 2006

Clarification of Pathway Specific Inhibition by FT-ICR/MS-Based Metabolic Phenotyping Studies

Akira Oikawa , Yukiko Nakamura , Tomonori Ogura , Atsuko Kimura , Hideyuki Suzuki , Nozomu Sakurai , Yoko Shinbo , Daisuke Shibata , Shigehiko Kanaya , and Daisaku Ohta *

Graduate School of Life and Environmental Sciences, Osaka Prefecture University; Research Association for Biotechnology
Department of Bioinformatics and Genomics, NAIST; Ehime Women's College
Graduate School of Life and Environmental Sciences, Osaka Prefecture University
Kazusa DNA Research Institute
Research Association for Biotechnology; Department of Bioinformatics and Genomics, NAIST
Department of Bioinformatics and Genomics, NAIST

* Corresponding author; email: ohtad{at}bioinfo.osakafu-u.ac.jp.

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 MSMS method. The scheme was applied to metabolic phenotyping of Arabidopsis 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 m/z 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 MSMS 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.




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