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Non-processed MS data from GC-TOF/MS analy … Non-processed MS data from GC-TOF/MS analysis were exported in NetCDF format generated by chromatography processing and mass spectral deconvolution software, Leco ChromaTOF version 3.22 (LECO, St. Joseph, MI, USA) to MATLAB 6.5 (Mathworks, Natick, MA, USA), where all data-pretreatment procedures, such as smoothing, alignment, time-window setting, and peak deconvolution, were carried out by using hyphenated data analysis (HDA) (Jonsson et al., 2004; Jonsson et al., 2006). The resolved MS spectra were matched against reference mass spectra using the NIST mass spectral search program for the NIST/EPA/NIH mass spectral library (version 2.0) and our custom software for peak annotation written in JAVA. Peaks were identified or annotated based on their RIs and a reference mass spectra comparison to the Golm Metabolome Database (GMD) and our in-house spectral library. The metabolites were identified by comparison with the RIs from library databases (GMD and our own library) and with the mass spectra of authentic standards, and the metabolites were defined as annotated metabolites upon comparison with the mass spectra and RIs from these two libraries. The 5 batches of metabolite profiles were combined using the HDA method (Jonsson et al., 2004; Jonsson et al., 2006). To correct the “batch effect” we applied COMBAT normalization (Johnson et al., 2007) to our quality samples consisting of Col-0 wild-type plants for each batch. Data were normalized using the CCMN algorithm (Redestig et al., 2009). he CCMN algorithm (Redestig et al., 2009).
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