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BREAKTHROUGH TECHNOLOGIES

Profiling of Arabidopsis Secondary Metabolites by Capillary Liquid Chromatography Coupled to Electrospray Ionization Quadrupole Time-of-Flight Mass Spectrometry¹

Department of Stress and Developmental Biology (E.R., M.Z., M.F., U.R., D.S., S.C.) and Department of Bioorganic Chemistry (T.D., L.W., J.S.), Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120 Halle/Saale, Germany

Large-scale metabolic profiling is expected to develop into an integral part of functional genomics and systems biology. The metabolome of a cell or an organism is chemically highly complex. Therefore, comprehensive biochemical phenotyping requires a multitude of analytical techniques. Here, we describe a profiling approach that combines separation by capillary liquid chromatography with the high resolution, high sensitivity, and high mass accuracy of quadrupole time-of-flight mass spectrometry. About 2,000 different mass signals can be detected in extracts of Arabidopsis roots and leaves. Many of these originate from Arabidopsis secondary metabolites. Detection based on retention times and exact masses is robust and reproducible. The dynamic range is sufficient for the quantification of metabolites. Assessment of the reproducibility of the analysis showed that biological variability exceeds technical variability. Tools were optimized or established for the automatic data deconvolution and data processing. Subtle differences between samples can be detected as tested with the chalcone synthase deficient tt4 mutant. The accuracy of time-of-flight mass analysis allows to calculate elemental compositions and to tentatively identify metabolites. In-source fragmentation and tandem mass spectrometry can be used to gain structural information. This approach has the potential to significantly contribute to establishing the metabolome of Arabidopsis and other model systems. The principles of separation and mass analysis of this technique, together with its sensitivity and resolving power, greatly expand the range of metabolic profiling.

¹ This project has been part of the German plant genome project, GABI, and was supported by the Ministry of Research and Education. This work was additionally supported by the Deutsche Forschungsgemeinschaft (grant no. SCHE 235/11–1) and by the Fonds der Chemischen Industrie.

^* Corresponding author; e-mail sclemens{at}ipb-halle.de; fax 49–345–5582–1409.

Received September 2, 2003; returned for revision October 8, 2003; accepted November 18, 2003.

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