SE143:/DS1

Sample Set Information

ID	SE143
Title	Application of a metabolomic method combining one-dimensional and two-dimensional gas chromatography-time-of-flight/mass spectrometry to metabolic phenotyping of natural variants in rice.
Description	We have developed a comprehensive method combining analytical techniques of one-dimensional (1D) and two-dimensional (GC × GC) gas chromatography-time-of-flight (TOF)–mass spectrometry. This method was applied to the metabolic phenotyping of natural variants in rice for the 68 world rice core collection (WRC) and two other varieties. Ten metabolites were selected as metabolite representatives, and the selected ion current of each metabolite peak obtained from both techniques were statistically compared. Our method of combining 1D- and GC × GC-TOF/MS is useful for the metabolic phenotyping of natural variants in rice for further studies in breeding programs.
Authors	Kusano M, Fukushima A, Kobayashi M, Hayashi N, Jonsson P, Moritz T, Ebana K, Saito K.
Reference	J Chromatogr B Analyt Technol Biomed Life Sci. 2007 Aug;855(1):71-9. Epub 2007 May 16.
Comment

PubMed

Data Analysis Details Information

ID	DS1
Title	Mass spectral data processing
Description	To compare the response of the metabolite peaks with the same algorithm, the Leco ChromaTOF optimized for Pegasus 4D software version 2.32 (Leco, St. Joseph, MI, USA) was used. Data, including baseline correction, peak deconvolution, and peak annotation for 1D- and GC × GC-TOF/MS were processed. In parallel, non-processed MS data from the 1D-GC-TOF/MS analysis were exported in the NetCDF format to MATLAB software 6.5 (Mathworks, Natick, MA, USA), where all data-pretreatment procedures such as data normalization, baseline correction, and the subsequent data treatments were performed using custom scripts to perform multivariate statistical analysis for metabolite phenotype clustering. The resolved MS spectra obtained from the custom scripts were matched against reference mass spectra by using the National Institute of Standards and Technology (NIST) mass spectral search program for the NIST/EPA/NIH mass spectral library (version 2.0) and our custom mass spectral search software written in JAVA (http://www.metabolome.jp/). Two mass spectral libraries – an in-house metabolite library in PRIMe (Platform for RIKEN Metabolomics, http://prime.psc.riken.jp) and the library in the Golm Metabolome Database (GMD) at CSB.DB – were used for the collection of mass spectra obtained by analysis. The extracted MS spectra were finally identified or annotated according to their RI and comparison with the reference mass spectra in the libraries.
Comment_of_details