SE196:/MS10

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.

Analytical Method Details Information

ID	MS10
Title	Method 10: Agilent 6546 LC-QTOF/MS DDA for NIST SRM 1950 human plasma
Instrument	LC, Agilent 1290 Infinity II; MS, Agilent 6546 Q-TOF
Instrument Type	UPLC-QTOF-MS
Ionization	ESI
Ion Mode	Positive and Negative
Description	Ultrapure water was produced with a Milli-Q Integral system equipped with a LC-Pak Polisher and a 0.22 μm point of use membrane filter cartridge (EMD Millipore, Billerica, MA, USA). Ammonium fluoride and LC/MS grade ammonium acetate were purchased from Millipore Sigma (St. Louis, MO, USA). Isopropanol of LC/MS grade “LiChrosolv” was purchased from Sigma Aldrich. HPLC-grade acetonitrile and methanol were purchased from Honeywell (Morristown, NJ, USA). SPLASH lipidomics I used as internal standards were purchased from Avanti Polar Lipids. Chloroform was purchased from Honeywell (Charlotte, North Carolina). <LC Method> The LC system consisted of an Agilent 1290 Infinity II (Agilent Technologies, Santa Clara, CA, USA) with a pump, a column oven and an autosampler. Lipids were separated on an Agilent InfinityLab Poroshell 120 EC-C18 column (100 x 3.0 mm; 2.7 µm) coupled to an Agilent InfinityLab Poroshell 120 EC-C18 column precolumn (5 x 3.0 mm; 2.7 µm). The column was maintained at 50°C at a flow-rate of 0.6 mL/min. The mobile phases consisted of (A) 9:1 (v/v) water:methanol with ammonium acetate (10 mM) and ammonium fluoride (0.2 mM) and (B) 2:3:5 (v/v/v) acetonitrile:methanol/isopropanol with ammonium formate (10 mM) and ammonium fluoride (0.2 mM). A sample volume of 5 µL was used for tinjections in ESI(+) and ESI(-). Separation was conducted under the following gradient: 0 min 70% (B); 1 min 70% (B); 3.5 min 86% (B); 10.0 min 86% (B); 11.0 min 100% (B); 17.0 min 100% (B); 17.1 min 70% (B); 19.0 min 70% (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 6546 Q-TOF (Agilent Technologies, Santa Clara, CA, USA). Simultaneous MS1 and MS/MS (data-dependent MS/MS) acquisition was used. The parameters were as follows: gas temperature, 200°C; gas flow, 10 L/min; nebulizer (psig), 50; sheath gas temperature, 300°C; sheath gas flow, 12 L/min; VCap, 3.5 kV and -3.0 kV for ESI(+) and ESI(-), respectively; nozzle voltage, 0 V; fragmentor, 150 V; skimmer, 65 V; octupole RF Vpp, 750 V; MS1 and MS2 mass range, m/z 40-1700; min MS and MS/MS acquisition rate: 3 spectra/s; isolation width, narrow (~1.3 m/z); max precursors per cycle, 3; precursor abundance-based scan speed, target 25,000 counts/spectrum; use MS/MS accumulation time limit, yes; reject precursors that cannot reach target TIC, no; threshold for MS/MS, 5,000 counts and 0.001%; active exclusion enabled, one repeat, then exclude for 0.05 minutes; purity, stringency 70%, cut off 0%; isotope model, common organic molecules; sort precursors, 1,2,unknown; static exclusion ranges, m/z 40 to 151 for ESI(+) and m/z 40 to 210 for ESI(-); collision energy, 20 eV for ESI(+) and 25 eV for ESI(-). The instrument was tuned using a reference mass m/z 121.050873, m/z 1221.990637 (+) and m/z 119.03632, m/z 980.016375 (-).
Comment_of_details