SE189:/DS1

Sample Set Information

ID	SE189
Title	Clarification of pathway-specific inhibition by Fourier transform ion cyclotron resonance/mass spectrometry-based metabolic phenotyping studies.
Description	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.
Authors	Oikawa, A., Nakamura, Y., Ogura, T., Kimura, A., Suzuki, H., Sakurai, N., Shinbo, Y., Shibata, D., Kanaya, S. and Ohta, D.
Reference	Plant Physiol. 2006 Oct;142(2):398-413
Comment

PubMed

Data Analysis Details Information

ID	DS1
Title	Data analysis
Description	Species-Metabolite Relationship Database For systematic and comprehensive understanding of species-specific metabolic diversities, we have designed a database system, KNApSAcK, for searching relationships between metabolites and species (Shinbo et al., 2006). The database has incorporated a tool for analyzing datasets acquired by FT-ICR/MS. KNApSAcK consists of information about metabolite names, molecular formulas, structural formulas, species names, Chemical Abstract Service (CAS) registration numbers, and biological activities. All the KNApSAcK data were collected from published literature. Metabolites are checked for the accuracy of both molecular formulas and structural formulas using the CAS database, and the CAS registration numbers are obtained from the same database. Species names were checked for the accuracy of spelling using the National Center for Biotechnology Information Taxonomy Browser (http://www.ncbi.nlm.nih.gov/Taxonomy/), the Plants Database (http://plants.usda.gov/index.html), and the Integrated Taxonomic Information System (http://www.itis.usda.gov/). A total of 25,930 metabolite-species pairs encompassing 11,075 metabolites and 8,557 species were obtained from about 7,600 published references (January 19, 2006). These data have been stored on a server, which is located in the Nara Institute of Science and Technology. The database system is freely available at http://kanaya.naist.jp/KNApSAcK/ on the Java 1.4.2.
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