SE196:/S22/M01

Sample Set Information

ID	SE196
Title	A lipidome atlas in MS-DIAL 4
Description	We formulated mass spectral fragmentations of lipids across 117 lipid subclasses and included ion mobility tandem mass spectrometry (MS/MS) to provide a comprehensive lipidome atlas with retention time, collision cross section and MS/MS information. Using human, murine, algal, and plant biological samples, we annotated and semi-quantified 8,051 lipids by MS-DIAL 4 (http://prime.psc.riken.jp/) with a 1–2% estimated false discovery rate, using the lipidomics standards initiative level 2 or 3 definitions.
Authors	Hiroshi Tsugawa, Kazutaka Ikeda, Mikiko Takahashi, Aya Satoh, Yoshifumi Mori, Haruki Uchino, Nobuyuki Okahashi, Yutaka Yamada, Ipputa Tada, Paolo Bonini, Yasuhiro Higashi, Yozo Okazaki, Zhiwei Zhou, Zheng-Jiang Zhu, Jeremy Koelmel, Tomas Cajka, Oliver Fiehn, Kazuki Saito, Masanori Arita, and Makoto Arita
Reference	Tsugawa, H. et al. A lipidome atlas in MS-DIAL 4. Nat Biotechnol (2020). https://doi.org/10.1038/s41587-020-0531-2
Comment

The raw data files are available at DROP Met web site in PRIMe database of RIKEN.

The original paper is available at PubMed.

Sample Information

ID	S22
Title	22_Mouse_Lung (RIKEN IMS Sciex Mouse tissues)
Organism - Scientific Name	Lung (Mouse)
Organism - ID	NCBI taxonomy 10090
Compound - ID
Compound - Source
Preparation
Sample Preparation Details ID
Comment

Analytical Method Information

ID	M01
Title	RIKEN IMS Sciex Mouse tissues: Lung (Mouse) LC-ESI-MS analysis
Method Details ID	MS02
Sample Amount	Positive mode: 1 microLiter; Negative mode: 2 microLiter
Comment

Analytical Method Details Information

ID	MS02
Title	Method 2: SCIEX TripleTOF DDA normal mass range method
Instrument	LC, Waters Acquity UPLC system; MS, AB Sciex TripleTOF 5600+ or 6600 system
Instrument Type	UPLC-QTOF-MS
Ionization	ESI
Ion Mode	Positive and Negative
Description	Methanol, isopropanol, and acetonitrile of LC-MS grade were purchased from Wako. Ammonium acetate and EDTA were purchased from Wako and Dojindo, respectively. Milli-Q water was purchased from Millipore. SPLASH Lipidomics I or EquiSPLASH used as internal standards were purchased from Avanti Polar Lipids. <LC Method> 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 µm) (Waters, Milford, MA, USA). The column was maintained at 45°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 µL, 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°C. <MS Method> Mass spectrometric detection of lipids was performed on a quadrupole/time-of-flight mass spectrometer TripleTOF 5600 or 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 70-1250; MS1 accumulation time, 250 ms; MS2 accumulation time, 100 ms; collision energy, +40/-42 eV; collision energy spread, 15 eV; cycle time, 1300 ms; curtain gas, 30; ion source gas 1, 40(+)/50(-); ion source gas 2, 80(+)/50(-); temperature, 250°C(+)/300°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).
Comment_of_details