MAGE-TAB Version	1.1
Comment[MetaboBank accession]	MTBKS216
Study Title	Food lipidomics for 155 agricultural plant products
Study Description	Lipids exhibit functional bioactivities based on their polar and acyl chain properties; humans obtain lipids from dietary plant product intake. Therefore, the identification of different molecular species facilitates the evaluation of biological functions and nutrition levels and new phenotype-modulating lipid structures. As a rapid screening strategy, we performed untargeted lipidomics for 155 agricultural products in 58 species from 23 plant families, wherein product-specific lipid diversities were shown using computational mass spectrometry. We characterized 716 lipid species, for which the profiles revealed the National Center for Biotechnology Information-established organismal classification and unique plant tissue metabotypes. Moreover, we annotated unreported subclasses in plant lipidology; e.g., triacylglycerol estolide (TG-EST) was detected in rice seeds (Oryza sativa) and several plant species. TG-EST is known as the precursor molecule producing the fatty acid ester of hydroxy fatty acid, which lowers ambient glycemia and improves glucose tolerance. Hence, our method can identify agricultural plant products containing valuable lipid ingredients.

Experimental Design	species design
Experimental Factor Name	organism	cultivar	strain	tissue
Experimental Factor Type	organism	cultivar	strain	tissue

Person Last Name	Takahashi	Matsuzawa	Tsugawa
Person First Name	Mikiko	Yuki	Hiroshi
Person Mid Initials
Person Affiliation	RIKEN Center for Sustainable Resource Science	Tokyo University of Agriculture and Technology	Tokyo University of Agriculture and Technology; RIKEN Center for Sustainable Resource Science; RIKEN Center for Integrative Medical Sciences
Person Roles	submitter	submitter	submitter

PubMed ID	33570932
Publication DOI

Protocol Name	Sample collection	Extraction1	Extraction2	Extraction3	Chromatography	Mass spectrometry	Data processing	Metabolite identification
Protocol Type	Sample collection	Extraction	Extraction	Extraction	Chromatography	Mass spectrometry	Data processing	Metabolite identification
Protocol Description	All plant resources were obtained in Japan. Details of the biological resources are summarized in Supplementary Table 2 of the Supporting Information. (https://doi.org/10.1021/acs.jafc.0c07356)	The freeze-dried plant material was milled using a blender (IFM-800DG, Iwatani, Tokyo, Japan) and filtered with a sieve (0.5 mm). The powdered plant material (8 mg) was transferred to a 2.0 mL microcentrifuge tube containing a zirconia bead. Lipids were extracted from the powdered plant material using a 160-fold volume of extraction solvent [methyl tert-butyl ether/methanol = 3:1 (v/v), containing 1 microM 1,2-didecanoyl-sn-glycero-3-phosphocholine, Sigma-Aldrich; 160 microliter of the extraction solvent with 160 pmol of the internal standard (IS) per milligramof dry weight of the plant sample]. After vigorous stirring on a vortex mixer, a 50-fold volume of water (50 microliter/mg of dry weight of the plant sample) was added to the homogenate. After vigorous stirring on a vortex mixer and dark incubation on ice for 15 min, the homogenate was centrifuged at 3000g for 10 min. The upper layer (160 microliter) was transferred to a new 1.5 mL microcentrifuge tube. The organic phase was evaporated to dryness using a centrifugal concentrator (ThermoSavant SPD2010, Thermo Fisher Scientific) at room temperature. The residue was dissolved in 200 microliter of ethanol, centrifuged at 14000g for 10 min, and transferred to a vial with a glass insert, for performing LC-MS/MS analysis.PC 10:0_10:0	Dry grain material was milled using a blender (IFM-800DG, Iwatani, Tokyo, Japan) and filtered with a sieve (0.5 mm). The powdered grain material (50 mg) was transferred to a 2.0 mL microcentrifuge tube containing a zirconia bead. Lipids were extracted from the powdered grain material using a 16-fold volume of extraction solvent [methyl tert-butyl ether/methanol = 3:1 (v/v) containing 10 microM1,2-didecanoyl-sn-glycero-3-phosphocholine, Sigma- Aldrich; 16 microliter of the extraction solvent with 160 pmol of the IS per milligram of the plant sample]. After vigorous stirring on a vortex mixer, a 5-fold volume of water (5 microliter/mg of the plant sample) was added to the homogenate. After vigorous stirring on a vortex mixer and dark incubation on ice for 15 min, the homogenate was centrifuged at 3000g for 10 min. The upper layer (50 microliter) was transferred to a new 1.5 mL microcentrifuge tube. The organic phase was evaporated to dryness using a centrifugal concentrator (ThermoSavant SPD2010, Thermo Fisher Scientific) at room temperature. The residue was dissolved in 625 microliter of ethanol and centrifuged at 14000g for 10 min. A total of 200 microliter of the supernatant was transferred to a vial with a glass insert, for performing LC-MS/MS analysis.	Mature seeds (approximately 100 mg) placed in a 13 mL centrifuge tube were milled by shaking at 1200 rpm for 10 min on Shake Master Neo (BMS, Tokyo, Japan) using zirconia beads and then mixed with 1mL of extraction solvent [methyl tert-butyl ether/methanol = 3:1 (v/v) containing 20 microM 1,2-didecanoyl-sn-glycero-3-phosphocholine, Sigma-Aldrich]. The homogenate was diluted with the extraction solvent to an 80-fold volume, including the initial volume (i.e., 80 microliter of the extraction solvent with 1.6 nmol of the IS per milligram of the plant sample in total). After vigorous stirring on a vortex mixer, a 20-fold volume of water (20 microliter/mg of the plant sample) was added to the homogenate. After vigorous stirring on a vortex mixer and dark incubation for 15 min on ice, the homogenate was centrifuged at 3000g for 10 min. The upper layer (50 microliter) was transferred to a new 2.0 mL microcentrifuge tube. The organic phase was evaporated to dryness using a centrifugal concentrator (ThermoSavant SPD2010, Thermo Fisher Scientific) at room temperature. The residue was dissolved in 1.25 mL of ethanol and centrifuged at 14000g for 10 min. A total of 200 microliter of the supernatant was transferred to a vial with a glass insert, for performing LC-MS/MS analysis.	Analytical time: 15.0; Column name: Acquity UPLC HSS T3 C18 column (50 x 1.0 mm; 1.8 mictometer) (Waters, Milford, MA, USA); Column temperature: 55.0 degree C; Column type: ODS; Flow gradient: following gradient: 0 min 35% (B); 3 min 70% (B); 7 min 85% (B); 10 min 90% (B); 12 min 90% (B); 12.5 min 35% (B); and 15 min 35% (B); Flow rate: 0.15 ml/min; Instrument: Waters Acquity UPLC system; Solvent: (A) 200:800:10:1 (v/v/v/v) acetonitrile:water:1 M ammonium acetate:formic acid and (B) 100:900:10:1 (v/v/v/v) acetonitrile:isopropanol:1 M ammonium acetate:formic acid;	Mass spectrometric detection of lipids were performed on a quadrupole/time-of-flight mass spectrometer Xevo G2 QTOF MS (Waters, Milford, MA, U.S.A.). MS2 analyses were performed in the sensitivity mode. DDA was used for MS2. The recording conditions were as follows: source capillary, 3.0 kV (positive ion mode) and 2.5 kV (negative ion mode); sampling cone, 20 (positive) and 40 (negative); extraction cone, 4.0; source temperature, 120 degreeC; desolvation temperature, 450 degreeC; cone gas flow, 50 L/h; desolvation gas flow, 600 L/h; scan range, m/z 100-1600; MS1 scan time, 200 ms (centroid); MS2 scan time, 100 ms (centroid); and collision energy, 20-50 eV (ramp mode). The other DDA parameters were as follows: event number, 6; scan repeat, 3; peak selection mode to trigger MS/MS, intensity-based detection; deisotope peak detection, yes; ionization mode, electrospray ionization (ESI); and correction by lock mass function, yes.	The MS-DIAL program, version 4.38 (http://prime.psc.riken.jp/compms/msdial/main.html) was used for the analysis of untargeted lipidomics data. The parameters were set as follows: retention time begin, 0 min; retention time end, 100 min; mass range (MS1) begin, 0 Da; mass range (MS1) end, 2000 Da; mass range (MS2) begin, 0 Da, mass range (MS2) end, 2000 Da; accurate mass tolerance (MS1), 0.01 Da; accurate mass tolerance (MS2), 0.025 Da; maximum charge number, 2; consider Cl and Br elements, false; execute retention time corrections, false; smoothing method, linear weighted moving average; smoothing level, 3 scan; minimum peak width, 5 scan; minimum peak height, 1000 amplitude; mass slice width, 0.1 Da; sigma window value, 0.5; MS2Dec amplitude cut-off, 30 amplitude; exclude after precursor, true; keep isotopic ions until, 0.5 Da; keep the isotopic ions w/o MS2Dec, false; retention time tolerance for identification, 100 min; accurate mass tolerance (MS1) for identification, 0.01 Da; accurate mass tolerance (MS2) for identification, 0.05 Da; identification score cut-off, 80%; using retention time for scoring, false; using retention time for filtering, false; relative abundance cut-off, 0%; top candidate report, false; retention time tolerance for alignment, 0.2 min; MS1 tolerance for alignment, 0.015 Da; peak count filter, 0%; remove features based on blank information, false. The annotations and peak picking results were manually confirmed.	The MS-DIAL program, version 4.38 (http://prime.psc.riken.jp/compms/msdial/main.html) was used for the analysis of untargeted lipidomics data.
Protocol Parameters		Post extraction;Derivatization	Post extraction;Derivatization	Post extraction;Derivatization	Chromatography instrument;Autosampler model;Column model;Column type;Guard column	Scan polarity;Scan m/z range;Instrument;Ion source;Mass analyzer
Protocol Hardware
Protocol Software							MS-DIAL version 4.38	MS-DIAL version 4.38

Public Release Date	2023-02-08

Term Source Name
Term Source File
Term Source Version

SDRF File	MTBKS216.sdrf.txt

Comment[Study type]	lipid profiling
Comment[Experiment type]	data-dependent acquisition	liquid chromatography-mass spectrometry	quadrupole mass spectrometer	tandem mass spectrometry	time-of-flight mass spectrometry
Comment[Submission type]	LC-MS
Comment[BioProject]	PRJDB14912
Comment[Related study]
Comment[Contributor]	Yasuhiro Higashi (RIKEN Center for Sustainable Resource Science)
Comment[Submission Date]	2022-12-14
Comment[Last Update Date]	2023-02-08