SE196:/S36/M02

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	S36
Title	36_52_Mouse_Kidney (Bruker Mouse tissues)
Organism - Scientific Name	Kidney (Mouse)
Organism - ID	NCBI taxonomy 10090
Compound - ID
Compound - Source
Preparation
Sample Preparation Details ID
Comment

Analytical Method Information

ID	M02
Title	52_Bruker Mouse tissues: Kidney (Mouse) LC-ESI-MS analysis (PASEF)
Method Details ID	MS06
Sample Amount	Positive mode: 1 microLiter; Negative mode: 2 microLiter
Comment

Analytical Method Details Information

ID	MS06
Title	Method 6: Bruker timsTOF Pro PASEF for mouse tissue lipidomics
Instrument	LC, Bruker Elute UHPLC system; MS, Bruker timsTOF Pro
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 and EDTA were purchased from Wako and Dojindo, respectively. Milli-Q water was purchased from Millipore. <LC Method> The LC system consisted of a Bruker Elute UHPLC system. Lipids were separated on an Acquity UPLC Peptide BEH C18 column (50 x 2.1 mm; 1.7 µm) (Waters, Milford, MA, USA). The column was maintained at 45°C at a flow-rate of 0.3 mL/min. The mobile phases consisted of (A) 1:1:3 (v/v/v) acetonitrile:methanol:water with ammonium formate (5 mM) and 10 nM EDTA and (B) 100% isopropanol with ammonium formate (5 mM) and 10 nM EDTA. A sample volume of 0.5-3 µL, which depended on biological samples, was used for the injection. The separation was conducted under the following gradient: 0 min 0% (B); 1 min 0% (B); 5 min 40% (B); 7.5 min 64% (B); 12 min 64% (B); 12.5 min 82.5% (B); 19 min 85% (B); 20 min 95% (B); 20.1 min 0% (B); and 25 min 0% (B). Sample temperature was maintained at 4°C. <MS Method> Mass spectrometric detection of lipids was performed on a hybrid trapped ion mobility-quadrupole time-of-flight mass spectrometer (timsTOF Pro, Bruker Daltonics, Bremen, Germany). Data dependent MS/MS acquisition (DDA) was used. The parameters were MS1 and MS2 mass ranges, m/z 50-2500; MS1 and MS2 accumulation time, 100 ms; mobility range, 0.55-1.90; collision energy 30 eV; end plate offset, 500 V; capillary voltage, +4.5 kV/-4.2 kV; nebulizer pressure, 2 bar; dry gas, 10.0 L/min; dry temperature, 220°C; funnel 1 RF, 300 Vpp; funnel 2 RF, 200 Vpp/250 Vpp; multipole RF, 200 Vpp; deflection delta, 70 V/-70 V; quadrupole ion energy, 6 eV/5 eV; collision transfer energy, 14 eV/15 eV; collision RF, 1500 Vpp/1100 Vpp; transfer time 75 µs/54 µs; pre-pulse storage, 10 µs/5 µs; tims transfer Δ1, -20 V/20 V; tims transfer Δ2, -120 V/120 V; tims transfer Δ3, 70 V/-70 V; tims transfer Δ4, 100 V/-100 V; tims transfer Δ5, 0 V; tims transfer Δ6, 100 V/-100 V; intensity threshold, 250 cts.; target intensity, 4000 cts; exclusion time of precursor ion, 0.1 min. The mass calibration was automatically performed using 5 mM sodium acetate calibration solution. For the confirmation of ESI(+)-MS/MS spectra for phosphatidylcholine, the positive ion mode data was acquired with the following setting. The parameters were dry temperature, 200°C; funnel 2 RF, 250 Vpp; quadrupole ion energy, 5 eV; collision transfer energy, 15 eV; collision RF, 1100 Vpp; and transfer time 54 µs; pre-pulse storage, 5 µs. The other parameters were the same as above.
Comment_of_details