SE196:/S67/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	S67
Title	67_Algae_Chlamydomonas reinhardtii (UC Davis Sciex Algaes)
Organism - Scientific Name	Chlamydomonas reinhardtii (Algae)
Organism - ID	NCBI taxonomy 3055
Compound - ID
Compound - Source
Preparation
Sample Preparation Details ID
Comment

Analytical Method Information

ID	M01
Title	UC Davis Sciex Algaes: Chlamydomonas reinhardtii (Algae) LC-ESI-MS analysis
Method Details ID	MS08
Sample Amount	Positive mode: 3 microLiter; Negative mode: 5 microLiter
Comment

Analytical Method Details Information

ID	MS08
Title	Method 8: SCIEX TripleTOF 6600 SWATH for NIST SRM 1950 human plasma
Instrument	LC, Agilent 1290 system; MS, AB Sciex TripleTOF 6600 system
Instrument Type	UPLC-QTOF-MS
Ionization	ESI
Ion Mode	Positive and Negative
Description	Water, isopropanol, and acetonitrile were purchased from Fisher Optima. Methanol was purchased from J.T. Baker. Ammonium formate, ammonium acetate, formic acid, and methyl tert-butyl ether (MTBE) were purchased from Sigma-Aldrich. Odd chain and deuterated lipids used as internal standards were purchased from Avanti Polar Lipids, CDN Isotopes, Cayman Chemical, and Sigma-Aldrich. <LC Method> The LC system consisted of an Agilent 1290 system (Agilent Technologies Inc.) with a pump (G4220A), a column oven (G1316C), and an autosampler (G4226A). Lipids were separated on an Acquity UPLC CSH C18 column (100 x 2.1 mm; 1.7 µm) coupled to an Acquity UPLC CSH 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) as mobile-phase modifier. A sample volume of 3 µL was used for the injection in both ESI(+) and ESI(-). The separation was conducted under the following gradient in ESI(+): 0 min 15% (B); 0-2 min 30% (B); 2-2.5 min 48% (B); 2.5-11 min 82% (B); 11-11.5 min 99% (B); 11.5-12 min 99% (B); 12-12.1 min 15% (B); and 12.1-15 min 15% (B). The separation was conducted under the following gradient in ESI(-): 0 min 15% (B); 0-2 min 30% (B); 2-2.5 min 48% (B); 2.5-9.5 min 76%; 9.5-9.6 min 99% (B); 9.6-10.5 min 99% (B); 10.5-10.6 min 15% (B); 10.6-13.5 min 15% (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 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 (~15,000 FWHM) in MS2. For ESI(+), the SWATH parameters were MS1 accumulation time, 100 ms; MS1 mass range, m/z 100-1700; MS2 accumulation time, 10 ms; collision energy, 45 eV; collision energy spread, 15 eV; cycle time, 550 ms; Q1 window, 20 Da; SWATH mass range, m/z 300-1100; number of SWATH experiments, 40; MS2 mass range: m/z 80-1100. Other parameters were curtain gas, 35; ion source gas 1, 60; ion source gas 2, 60; temperature, 350°C; ion spray voltage floating, 4.5 kV; declustering potential, 80 V. For ESI(-), the SWATH parameters were MS1 accumulation time, 100 ms; MS1 mass range, m/z 100-1700; MS2 accumulation time, 10 ms; collision energy, -50 eV; collision energy spread, 10 eV; cycle time, 550 ms; Q1 window, 15 Da; SWATH mass range, m/z 400-1000; number of SWATH experiments, 40; MS2 mass range: m/z 80-1000. Other parameters were curtain gas, 35; ion source gas 1, 60; ion source gas 2, 60; temperature, 350°C; ion spray voltage floating, -4.5 kV; declustering potential, -80 V. The mass calibration was automatically performed using an APCI positive/negative calibration solution via a calibration delivery system (CDS).
Comment_of_details