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Plant Physiology 141:1205-1218 (2006) © 2006 American Society of Plant Biologists A Liquid Chromatography-Mass Spectrometry-Based Metabolome Database for Tomato1Laboratory of Biochemistry, Wageningen University, 6703 HA Wageningen, The Netherlands (S.M., J.V.); Plant Research International, 6700 AA Wageningen, The Netherlands (S.M., R.J.B., O.V., H.A.V., J.d.G., C.H.R.d.V.); Centre for BioSystems Genomics, 6700 AB Wageningen, The Netherlands (S.M., R.J.B., O.V., H.A.V., C.H.R.d.V.); Laboratory of Organic Chemistry, Wageningen University, 6703 HB Wageningen, The Netherlands (T.A.v.B.); and Laboratory of Plant Physiology, Wageningen University, 6703 BD Wageningen, The Netherlands (R.J.B.)
For the description of the metabolome of an organism, the development of common metabolite databases is of utmost importance. Here we present the Metabolome Tomato Database (MoTo DB), a metabolite database dedicated to liquid chromatography-mass spectrometry (LC-MS)- based metabolomics of tomato fruit (Solanum lycopersicum). A reproducible analytical approach consisting of reversed-phase LC coupled to quadrupole time-of-flight MS and photodiode array detection (PDA) was developed for large-scale detection and identification of mainly semipolar metabolites in plants and for the incorporation of the tomato fruit metabolite data into the MoTo DB. Chromatograms were processed using software tools for mass signal extraction and alignment, and intensity-dependent accurate mass calculation. The detected masses were assigned by matching their accurate mass signals with tomato compounds reported in literature and complemented, as much as possible, by PDA and MS/MS information, as well as by using reference compounds. Several novel compounds not previously reported for tomato fruit were identified in this manner and added to the database. The MoTo DB is available at http://appliedbioinformatics.wur.nl and contains all information so far assembled using this LC-PDA-quadrupole time-of-flight MS platform, including retention times, calculated accurate masses, PDA spectra, MS/MS fragments, and literature references. Unbiased metabolic profiling and comparison of peel and flesh tissues from tomato fruits validated the applicability of the MoTo DB, revealing that all flavonoids and
1 This work was supported by the European Community-Access to Research Infrastructure action of the Improving Human Potential Program (grant no. HPRI–CT–1999–00085), the EU RTD project Capillary NMR (grant no. HPRI–CT–1999–50018), and the research programme of the Centre of BioSystems Genomics that is a part of The Netherlands Genomics Initiative/Netherlands Organization for Scientific Research. 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: Sofia Moco (sofia.moco@wur.nl). www.plantphysiol.org/cgi/doi/10.1104/pp.106.078428. * Corresponding author; e-mail sofia.moco{at}wur.nl; fax 31–317–484801. Received February 1, 2006; returned for revision May 8, 2006; accepted May 9, 2006. This article has been cited by other articles:
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-tomatine were specifically present in the peel, while several other alkaloids and some particular phenylpropanoids were mainly present in the flesh tissue. 
