SE196:/S80/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	S80
Title	80_Human_Plasma (SRM1950) (Agilent 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	Agilent SRM1950 plasma: Plasma (SRM1950) (Human) LC-ESI-MS analysis
Method Details ID	MS10
Sample Amount	Positive mode: 5 microLiter; Negative mode: 5 microLiter
Comment

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