MAGE-TAB Version	1.1
Comment[MetaboBank accession]	MTBKS217
Study Title	A lipidome atlas in MS-DIAL 4 (Plants study)
Study Description	We present Mass Spectrometry-Data Independent Analysis software version 4 (MS-DIAL 4), a comprehensive lipidome atlas with retention time, collision cross-section and tandem mass spectrometry information. We formulated mass spectral fragmentations of lipids across 117 lipid subclasses and included ion mobility tandem mass spectrometry. Using human, murine, algal and plant biological samples, we annotated and semiquantified 8,051 lipids using MS-DIAL 4 with a 1-2% estimated false discovery rate. MS-DIAL 4 helps standardize lipidomics data and discover lipid pathways. This dataset describes experiments about plants lipid.

Experimental Design	software variation design
Experimental Factor Name	organism
Experimental Factor Type	organism

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

PubMed ID	32541957
Publication DOI

Protocol Name	Sample collection	Extraction	Chromatography	Mass spectrometry	Data processing	Metabolite identification
Protocol Type	Sample collection	Extraction	Chromatography	Mass spectrometry	Data processing	Metabolite identification
Protocol Description	Arabidopsis and eggplant were grown on soil (PROMIX BX (Premier Horticulture Inc., Quakertown, PA): vermiculite = 2:1) supplemented with fertilizer in a greenhouse at 22 degree C under fluorescent light (16 h light/8 h dark cycle, 55 micromol photons s-1 m-2 ) for 7 weeks and 37 days, respectively. Rice was grown on wet commercial soil (Bonsol II (Sumitomo Chemical, Tokyo, Japan)) in a greenhouse with sunlight under a 16-h fluorescent light (28 degree C)/8-h dark (20 degree C) cycle. Plants were kept under constant subirrigation conditions with tap water and fertilizer for 5 weeks. The entire aboveground (aerial) parts were harvested, immediately frozen in liquid nitrogen and lyophilized by the freeze dryer FDU-2200 (EYELA, Tokyo, Japan).	The freeze-dried plant material was milled by a blender (IFM-800DG, Iwatani, Tokyo, Japan), filtered with a screen (0.5 mm) and transferred into a 2.0-mL microcentrifuge tube containing a zirconia bead. Lipids were extracted from the freeze-dried powdered plant material with a 160-fold volume of extraction solvent (160 microliter mg-1 D.W. plant sample) (methyl tert-butyl ether/methanol = 3/1, (v/v) with 1 microM 1,2-didecanoyl-sn-glycero-3-phosphocholine, Sigma-Aldrich) as the internal standard (160 pmol mg-1 D.W. plant sample). After vigorous stirring on a vortex mixer, a 50-fold volume of water (50 microliter mg-1 D.W. 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 3,000 x g for 10 min. The upper layer (160 microliter) was transferred to a new 1.5-mL microcentrifuge tube. The organic phase was dried by the centrifugal concentrator (ThermoSavant SPD2010, Thermo Fisher Scientific) at room temperature. The dried lipid extract was dissolved in 200 microliter of ethanol, centrifuged at 14,000 x g for 10 min and transferred to a vial with a glass insert for LC-MS analysis.	The LC system consisted of a Waters Acquity UPLC system. Lipids were separated on an Acquity UPLC HSS T3 C18 column (50 x 1.0 mm; 1.8 micrometer) (Waters, Milford, MA, USA). The column was maintained at 55 degree C at a flow-rate of 0.15 mL/min. The mobile phases consisted of (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. A sample volume of 1 microliter was used for the injection. The separation was conducted under the 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). Sample temperature was maintained at 10 degree C.	Mass spectrometric detection of lipids was performed on a quadrupole/time-of-flight mass spectrometer Xevo G2 QTOF MS (Waters, Milford, MA, USA). MS2 analyses were performed at the sensitivity mode. Data dependent MS/MS acquisition (DDA) was used for MS2. The conditions for recording were as follows: source capillary, 3.0 (positive ion mode) and 2.5 kV (negative ion mode); sampling cone, 20 (positive) and 40 (negative); extraction cone, 4.0; source temperature, 120 degree C; desolvation temperature, 450 degree C; cone gas flow, 50 L/h; desolvation gas flow, 600 L/h; scan ranges, m/z 100-1600; MS1 scan time, 200 ms (centroid); MS2 scan time, 100 ms (centroid); collision energy, 20-50 eV (ramp mode). The other DDA parameters were event number, 6; scan repeat, 3; peak selection mode to trigger MS/MS, intensity-based detection; deisotope peak detection, yes; ionization mode, ESI; and correction by lock mass function, yes.	use MS-DIAL ver.4.0 (For parameters used: Supplementary Table S3e at https://doi.org/10.1038/s41587-020-0531-2).	use MS-DIAL ver.4.0
Protocol Parameters		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 ver.4.0	MS-DIAL ver.4.0

Public Release Date	2023-06-14

Term Source Name
Term Source File
Term Source Version

SDRF File	MTBKS217.sdrf.txt

Comment[Study type]	lipid profiling
Comment[Experiment type]	liquid chromatography-mass spectrometry	quadrupole mass spectrometer	time-of-flight mass spectrometry	tandem mass spectrometry	data-dependent acquisition
Comment[Submission type]	LC-MS
Comment[BioProject]	PRJDB15006
Comment[Related study]
Comment[Contributor]	Kazutaka Ikeda(Department of Applied Genomics, Kazusa DNA Research Institute; RIKEN Center for Integrative Medical Sciences), Masanori Arita(National Institute of Genetics; RIKEN Center for Sustainable Resource Science), Makoto Arita(RIKEN Center for Integrative Medical Sciences; Graduate School of Pharmaceutical Sciences, Keio University; Graduate School of Medical Life Science, Yokohama City University)
Comment[Submission Date]	2022-12-28
Comment[Last Update Date]	2023-06-14