SE199:/S41/M131

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.
Comment_of_details

Analytical Method Information

ID	M131
Title	ESI Negative (Method 3)
Method Details ID	MS11
Sample Amount	5 mg FW / 20 uL injection
Comment

Analytical Method Details Information

ID	MS11
Title	LC-FT-MS, ESI, Negative
Instrument	Agilent1100 HPLC (Agilent), LTQ-FT (Thermo Fisher Scientific)
Instrument Type	LC-FTICR-MS
Ionization	ESI
Ion Mode	Negative
Description	Metabolite extraction 300 mg of powdered sample was mixed with 900 uL of 100% methanol solution containing 25 uM of 7-hydroxy-5-methylflavone as internal standard (IS). The sample was homogenized using Mixer Mill MM 300 (QIAGEN) at 25 Hz for 2 min, twice. The homogenate was centrifuged under 17,400 x g for 5 min at 4 C. A supernatant was passed through a Polytetrafluoroethylene (PTFE) filter (pore size 0.2 um, Millipore), and the filtrate was applied to a C18 silica column (MonoSpin C18, GL Science) to remove highly-hydrophobic contaminants. The filtrate passed through the C18 column was used for LC-MS analyses. The same extraction procedure with 75% methanol was performed without a sample to prepare mock samples and used as negative controls. Liquid chromatography (LC)-mass spectrometry (MS) analysis Agilent 1100 system (Agilent) and Finnigan LTQ-FT (Thermo Fisher Scientific) were used. Aliquots (5 uL) of the methanol extract were applied to a TSK-gel ODS-100V column (4.6 x 250 mm, 5 um, TOSO) and separated by water containing 0.1%(v/v) formic acid (Solvent A) and acetonitrile containing 0.1%(v/v) formic acid (Solvent B). The gradient program was as follows: 3% B (0 min), 97% B (90 min), 97% B (100 min), 3% B (100.1 min), and 3% B (107 min). The flow rate was set at 0.25 mL/min for 0-100 min and 0.5 mL/min for 100.1-107 min. The conditions of mass spectrometry were as below: - Method 1: This method is used for measuring the accurate mass of the peaks and obtaining MS/MS spectra. [Full scan] resolution, 100,000 by FT; m/z range, 100-1500 [MS2 scan] data-dependent scan by IT for the most intense 5 ions in the full scan. [Dynamic exclusion setting for MS2 scan] repeat count, 3; repeat duration, 30 s; exclusion list size, 500; margin, 10 ppm; exclusion duration, 20 s. - Method 2: Same as Method 1 except below: [Dynamic exclusion setting for MS2 scan] exclusion duration, 30 s. - Method 3: Same as Method 1 except below: [Dynamic exclusion setting for MS2 scan] repeat count, 2; exclusion duration, 30 s. - Method 4: Same as Method 1 except below: [Dynamic exclusion setting for MS2 scan] off. - Method 5: This method is used for obtaining MS3 spectra. [Full scan] resolution, 12,500 by FT; m/z range, 100-1500. [MS2 scan] data-dependent scan by IT for the most intense 5 ions in the full scan. [Dynamic exclusion setting for MS2 scan] same as Method 1. [MS3 scan] data-dependent scan by IT for the most intense 2 ions in the MS2 scan - Method 6: This method is used for obtaining MS2 spectra in high-resolution: [Full scan] resolution, 12,500 by FT; m/z range, 100-1500. [MS2 scan] data-dependent scan by FT for the most intense 5 ions in the full scan. resolution, 12,500. [Dynamic exclusion setting for MS2 scan] repeat count, 1; repeat duration, 30 s; exclusion list size, 500; margin, 10 ppm; exclusion duration, 40 s. - Method 7: Same as Method 5 except below: [Dynamic exclusion setting for MS2 scan] same as Method 2 ESI: electrospray ionization, FT: Fourier transformation ion cyclotron resonance type mass spectrometry, IT: ion trap type mass spectrometry. The mass analyses with electrospray ionization (ESI) in positive or negative modes were performed. The combinations of Methods 1-7 and ionization polarity are different between the samples, but at least one method for accurate mass measurement (Method 1-4) was applied for each sample. The raw data were acquired using Xcalibur software (Thermo Fisher Scientific).
Comment_of_details	[column] TSK-gel ODS-100V (4.6 x 250 mm, 5 micrometer; TOSOH) [gradient] Solvent A: water containing 0.1% v/v formic acid; Solvent B: acetonitrile containing 0.1% v/v formic acid; Gradient: 3% B (0 min), 97% B (90 min), 97% B (100 min), 3% B (100.1 min), and 3% B (107 min) [total separation time] 107 min