MAGE-TAB Version	1.1
Comment[MetaboBank accession]	MTBKS221
Study Title	A lipidome atlas in MS-DIAL 4 (Mouse tissues 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 on mouse tissues.

Experimental Design	software variation design
Experimental Factor Name	tissue	genetic_modification
Experimental Factor Type	tissue	genetic_modification

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	Mouse samples: The adrenal gland, brain, brown adipose tissue, eye, feces, heart, kidney, large intestine, liver, lung, pancreas, skeletal muscle, skin (ear), small intestine, spleen, testis, and white adipose tissues of 8-10 weeks male mice (C57BL/6 J background, CLEA Japan, Tokyo, Japan) were harvested according to the ethical protocol approved by the RIKEN Center for Integrative Medical Sciences (2019-015(2)). Normal and fads2 knockout mouse were used in this experiment.	The tissues were homogenized by a multi-beads shocker (YASUI KIKAI, Japan) with a metal cone (YASUI KIKAI, Japan) at 1500 x g for 15 s x 2, and MeOH was added to the homogenate according to the tissue weight. After the solvent was homogenized again by the same condition, the appropriate amount of MeOH (<100 microliter) solving 10 mg tissue weight was transferred to a 2-mL glass tube. After the solvent was messed up to 175 microliter by MeOH, 25 microliter of MeOH containing internal standards was added to the solvent, and vortexed for 10 s. After the solvent was incubated for 2 hours on ice, 100 microliter of chloroform was added, and vortexed for 10 s. After the solvent was incubated for 1 hour on ice, 20 microliter of Milli-Q water was added, and vortexed for 10 s. After 10 min incubation on ice, the solvent was centrifugated at 2000 x g for 10 min at 4 degree C, and the supernatant was transferred to the LC-MS vial.	The LC system consisted of a Waters Acquity UPLC system. Lipids were separated on an Acquity UPLC Peptide BEH C18 column (50 x 2.1 mm; 1.7 micrometer) (Waters, Milford, MA, USA). The column was maintained at 45 degree C at a flow-rate of 0.3 mL/min. The mobile phases consisted of (A) 1:1:3 (v/v/v) acetonitrile:methanol:water with ammonium formate (5 mM) and 10 nM EDTA and (B) 100% isopropanol with ammonium formate (5 mM) and 10 nM EDTA. A sample volume of 0.5-3 microliter, which depended on biological samples, was used for the injection. The separation was conducted under the following gradient: 0 min 0% (B); 1 min 0% (B); 5 min 40% (B); 7.5 min 64% (B); 12 min 64% (B); 12.5 min 82.5% (B); 19 min 85% (B); 20 min 95% (B); 20.1 min 0% (B); and 25 min 0% (B). Sample temperature was maintained at 4 degree C.	Mass spectrometric detection of lipids was performed on a quadrupole/time-of-flight mass spectrometer TripleTOF 6600 (SCIEX, Framingham, MA, USA). All analyses were performed at the high resolution mode in MS1 (~35,000 full width at half maximum (FWHM)) and at the high sensitivity mode (~20,000 FWHM) in MS2. Data dependent MS/MS acquisition (DDA) was used. The parameters were MS1 and MS2 mass ranges, m/z 70-1750; MS1 accumulation time, 200 ms; MS2 accumulation time, 70 ms; collision energy, +40/-42 eV; collision energy spread, 15 eV; cycle time, 1370 ms; curtain gas, 30; ion source gas 1, 40(+)/50(-); ion source gas 2, 80(+)/50(-); temperature, 250 degree C(+)/300 degree C(-); ion spray voltage floating, +5.5/-4.5 kV; declustering potential, 80 V. The other DDA parameters were dependent product ion scan number, 16; intensity threshold, 100 cps; exclusion time of precursor ion, 0s; mass tolerance, 20 ppm; ignore peaks, within m/z 200; and dynamic background subtraction, True. The mass calibration was automatically performed using an APCI positive/negative calibration solution via a calibration delivery system (CDS).	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	MTBKS221.sdrf.txt

Comment[Study type]	lipid profiling
Comment[Experiment type]	liquid chromatography-mass spectrometry	time-of-flight mass spectrometry	tandem mass spectrometry	data-dependent acquisition	quadrupole mass spectrometer
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