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Data processing for GC-TOF-MS data:<br … Data processing for GC-TOF-MS data:<br />
Nonprocessed MS data from GC-TOF-MS analysis were exported in NetCDF format generated by chromatography processing and mass spectral deconvolutionsoftware, 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 H-MCR, were carried out (Jonsson et al., 2005). 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 RIs and the reference mass spectra comparison to the Golm Metabolome Database (GMD; http://csbdb.mpimp-golm.mpg.de/csbdb/gmd/msri/gmd_msri.html) released from CSB.DB (Kopka et al., 2004) and our in-house spectral library. The metabolites were identified by comparison with RIs from the library databases (GMD and our own library) and with those of authentic standards, and the metabolites were defined as annotated metabolites on comparison with mass spectra and RIs from these two libraries. The normalized response for the calculation of the signal intensity of each metabolite from the mass-detector response was obtained by each selected ion current that was unique in each metabolite MS spectrum to normalize the peak response. The normalized responses are peak areas corrected using the CCMN method (Redestig et al., 2009). g the CCMN method (Redestig et al., 2009).
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