SE199:/S41/M90/D9

Sample Set Information

ID	SE199
Title	Untargeted metabolome analysis of rice using LC-MS / LC-MSを用いたイネのノンターゲットメタボローム解析
Description	Untargeted metabolome analyses of rice using liquid chromatography-mass spectrometry (LC-MS). Two rice cultivars, Koshichikar and Nipponbare, were used. The information on the peaks detected in rice was available at the Plant Metabolome Repository website (http://metabolites.in/plants). 液体クロマトグラフィー-質量分析（LC）を用いたイネのノンターゲットメタボローム解析です。試料として、二種類のレタス（コシヒカリとニッポンバレ）を用いました。 検出されたピークは、植物メタボロームレポジトリ (http://metabolites.in/plants) から公開されています。
Authors	Sakurai N1,2, Suda K1, Keiichi Kanno3, Soichi Kojima3, Akimoto N1, Hoshi K1, Osawa S1, Ikeda C1, Ozawa K1, Yamada M1, Muneto R1, Shibata D1 (1 Kazusa DNA Research Institute, 2 National Institute of Genetics), Contact: sakurai AT nig.ac.jp (replace AT with @) 櫻井望1,2、須田邦裕1、菅野圭一3、小島創一3、秋元奈弓1、星久美1、大澤祥子1、池田千晶1、小澤馨史1、山田学1、宗藤玲子1、柴田大輔1（1 かずさDNA研究所, 2 国立遺伝学研究所、3 東北大学農学研究科）
Reference
Comment

Sample Information

ID	S41
Title	Rice (Nipponbare), leaf
Organism - Scientific Name	Oryza sativa
Organism - ID	NCBI taxonomy: 4530
Compound - ID
Compound - Source
Preparation
Sample Preparation Details ID	SS1
Comment

Sample Preparation Details Information

ID	SS1
Title	Preparation of the samples
Description	The rice seeds were provided by Dr. Keiichi Kanno and Dr. Soichi Kojima (Tohoku University). The rice plants were grown in a greenhouse. The brown rice and the leaf blades were harvested, immediately frozen in liquid nitrogen, and stored at -80C. The sample was homogenated using mortar and pestle under liquid nitrogen into a fine powder and stored at -80C until use.
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Analytical Method Information

ID	M90
Title	PSEUDO: Positive, A set of analyses for valid peak selection
Method Details ID
Sample Amount
Comment	This metadata represents a set of data obtained below for the convenience of the subsequent data analysis, including peak alignment between the data. SE199_S41_M011 (http://metabolonote.kazusa.or.jp/SE199:/S41/M011) SE199_S41_M012 (http://metabolonote.kazusa.or.jp/SE199:/S41/M012) SE199_S41_M041 (http://metabolonote.kazusa.or.jp/SE199:/S41/M041) SE199_S41_M021 (http://metabolonote.kazusa.or.jp/SE199:/S41/M021) SE199_S41_M031 (http://metabolonote.kazusa.or.jp/SE199:/S41/M031) SE199_S41_M051 (http://metabolonote.kazusa.or.jp/SE199:/S41/M051) SE199_S95_M01 (http://metabolonote.kazusa.or.jp/SE199:/S95/M01) SE199_S95_M02 (http://metabolonote.kazusa.or.jp/SE199:/S95/M02)

Data Analysis Information

ID	D9
Title	Valid peak selection by alignment and characterization
Data Analysis Details ID	DS1
Recommended decimal places of m/z	default
Comment

Data Analysis Details Information

ID	DS1
Title	Peak detection, alignment and characterization using PowerGetBatch
Description	The PowerGetBach software (version 0.5.4, http://www.kazusa.or.jp/komics/software/PowerGetBatch) was used for peak detection. In the case of the sample with more than three biological or technical replications, a single parameter setting for high resolution (Method 1-4) was applied for peak detection. In the case of the sample without replications, a single raw datum was processed using three different parameter settings for high resolution (Method 1-4). The data obtained in low-resolution settings (Method 5 and 7) was processed with a single parameter setting. The detailed peak detection parameters for PowerGetBatch are available at the Plant Metabolome Repository website (http://metabolites.in/plants/data/PGB_params.zip). The detected peaks in the samples with high- and low-resolution analyses and in the mock samples were aligned using PowerGetBatch software for each positive and negative mode. The reproducibly detected peaks in the samples and absent in the mock samples were selected as valid peaks. The selection was performed manually using Microsoft Excel with consideration of the analytical replications of the sample. The most intense and major patterns of the MS2 and MS3 spectra were selected among the alignment results for each peak. Searching candidate compounds in compound databases and prediction of flavonoid aglycones using FlavonoidSearch system for valid peaks were performed as described in the annotation details AM1.
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