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Mass values were calibrated using the sign … Mass values were calibrated using the signals of sodium formate detected at 16-17 min using Compass DataAnalysis software (ver. 4.2, Bruker Daltonik, GmbH). The calibrated mass chromatogram was converted to an mzXML-formatted file using the MSConvert function of the ProteoWizard software (ver. 3.0, http://proteowizard.sourceforge.net/, Kessner et al., Bioinformatics 24: 2534-2536, 2008).
The compound peaks were detected and characterized using the mzXML files and PowerGetBatch software (ver. 0.5.4, http://www.kazusa.or.jp/komics/software/PowerGetBatch, Sakurai and Shibata, Carotenoid Science 22: 16-22, 2017). Three different sets (Setting 1-3) of peak detection parameters were applied for each sample and a single set of parameters was used for the mock sample. The parameters were available at the Things Metabolome Repository website (http://metabolites.in/oryza/data/PGB_params.zip).
The peaks detected with all three parameters for a sample and not detected in two mock samples obtained in the same measurement batch were selected as valid peaks. The peaks with a retention time less than 1.5 min or greater than 15 min were omitted. The most intense and major pattern of the MS/MS spectrum was selected among the alignment results for each peak.
Compound database search and prediction of flavonoid aglycones were performed as described in AM1 (http://metabolonote.kazusa.or.jp/SE229:/AM1). p://metabolonote.kazusa.or.jp/SE229:/AM1).
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