SE196:/S63/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	S63
Title	63_Plant_Arabidopsis thaliana (Waters Plants)
Organism - Scientific Name	Arabidopsis thaliana (Plant)
Organism - ID	NCBI taxonomy 3702
Compound - ID
Compound - Source
Preparation
Sample Preparation Details ID
Comment

Analytical Method Information

ID	M01
Title	Waters Plants: Arabidopsis thaliana (Plant) LC-ESI-MS analysis
Method Details ID	MS07
Sample Amount	Positive mode: 1 microLiter; Negative mode: 1 microLiter
Comment

Analytical Method Details Information

ID	MS07
Title	Method 7: Waters XevoG2 QTOF DDA for plant lipidomics
Instrument	LC, Waters Acquity UPLC system; MS, Waters Xevo G2 QTOF MS
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, formic acid, methyl tert-butyl ether (MTBE), and water were also purchased from Wako. 1,2-Didecanoyl-sn-glycero-3-phosphocholine used for the internal standard was purchased from Sigma-Aldrich. <LC Method> The LC system consisted of a Waters Acquity UPLC system. Lipids were separated on the mostly same condition as described in Method 3 except for using ammonium acetate instead of ammonium formate. 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 µm) (Waters, Milford, MA, USA). The column was maintained at 55°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 µL 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°C. <MS Method> 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°C; desolvation temperature, 450°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.
Comment_of_details