SE196:/S79/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	S79
Title	79_Human_Plasma (SRM1950) (Thermo SRM1950 plasma)
Organism - Scientific Name	Plasma (SRM1950) (Human)
Organism - ID	NCBI taxonomy 9606
Compound - ID
Compound - Source
Preparation
Sample Preparation Details ID
Comment

Analytical Method Information

ID	M01
Title	Thermo SRM1950 plasma: Plasma (SRM1950) (Human) LC-ESI-MS analysis
Method Details ID	MS09
Sample Amount	Positive mode: 2 microLiter; Negative mode: 3 microLiter
Comment

Analytical Method Details Information

ID	MS09
Title	Method 9: Thermo Q Exactive Plus DDA for NIST SRM 1950 human plasma
Instrument	LC, Thermo Fisher Scientific Vanquish UHPLC system; MS, Thermo Fisher Scientific Q Exactive Plus with a HESI-II ion source
Instrument Type	LC-Orbitrap-MS
Ionization	ESI
Ion Mode	Positive and Negative
Description	Water was purchased from VWR International, isopropanol from Merck, and acetonitrile from Honeywell. MTBE, ammonium formate, ammonium acetate, formic acid, and acetic acid were purchased from Sigma-Aldrich. Odd chain and deuterated lipids used as internal standards were purchased from Avanti Polar Lipids, Chromsystems, Cayman Chemical, and Sigma-Aldrich. <LC Method> The LC system consisted of a Vanquish UHPLC system (Thermo Fisher Scientific, Bremen, Germany) with a pump, a column oven and an autosampler. Lipids were separated on an Acquity UPLC BEH C18 column (50 x 2.1 mm; 1.7 µm) coupled to an Acquity UPLC BEH C18 VanGuard precolumn (5 x 2.1 mm; 1.7 µm) (Waters, Milford, MA, USA). The column was maintained at 65°C at a flow-rate of 0.6 mL/min. For LC-ESI(+)-MS analysis the mobile phases consisted of (A) 60:40 (v/v) acetonitrile:water with ammonium formate (10 mM) and formic acid (0.1%) and (B) 90:10:0.1 (v/v/v) isopropanol:acetonitrile:water with ammonium formate (10 mM) and formic acid (0.1%). For LC-ESI(-)-MS analysis the organic solvents for mobile phases were the same with the exception of using ammonium acetate (10 mM) and acetic acid (0.1%) as mobile-phase modifiers. A sample volume of 2 µL and 3 µL was used for the injection in ESI(+) and ESI(-), respectively. Separation was conducted under the following gradient for LC-ESI(+): 0 min 15% (B); 0-1 min 30% (B); 1-1.3 min from 30% to 48% (B); 1.3-5.5 min from 48% to 82% (B); 5.5-5.8 min from 82% to 99% (B); 5.8-6 min 99% (B); 6-6.1 min from 99% to 15% (B); 6.1-7.5 min 15% (B). For LC-ESI(-), the following gradient was used: 0 min 15% (B); 0-1 min 30% (B); 1-1.3 min from 30% to 48% (B); 1.3-4.8 min from 48% to 76% (B); 4.8-4.9 min from 76% to 99% (B); 4.9-5.3 min 99% (B); 5.3-5.4 min from 99% to 15% (B); 5.4-6.8 min 15% (B). Sample temperature was maintained at 4°C. <MS Method> Mass spectrometric detection of lipids was performed on a quadrupole/orbital ion trap mass spectrometer Q Exactive Plus with a HESI-II ion source (Thermo Fisher Scientific, Bremen, Germany). Simultaneous MS1 and MS/MS (data-dependent MS/MS) acquisition was used. The parameters were as follows: sheath gas pressure, 60; aux gas flow, 25; sweep gas flow, 2; spray voltage, 3.6 kV and -3.0 kV for ESI(+) and ESI(-), respectively; capillary temperature, 300°C; aux gas heater temperature, 370°C; MS1 mass range, m/z 200-1700; MS1 resolving power, 35,000 FWHM (m/z 200); number of data-dependent scans per cycle: 3; MS/MS resolving power, 17,500 FWHM (m/z 200); MS1 ion time: 100 ms; MS2 ion time: 50 ms; normalized collision energy, 20% for ESI(+) and 10, 20, 30% for ESI(-). The instrument was tuned using a Thermo positive and negative ion mode calibration solutions.
Comment_of_details