SE196:/S29/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	S29
Title	29_30_Plant_Arabidopsis thaliana (Bruker Plants)
Organism - Scientific Name	Arabidopsis thaliana (Plant)
Organism - ID	NCBI taxonomy 3702
Compound - ID
Compound - Source
Preparation
Sample Preparation Details ID
Comment

Analytical Method Information

ID	M02
Title	30_Bruker Plants: Arabidopsis thaliana (Plant) LC-ESI-MS analysis (PASEF)
Method Details ID	MS04
Sample Amount	Positive mode: 1 microLiter; Negative mode: 1 microLiter
Comment

Analytical Method Details Information

ID	MS04
Title	Method 4: Bruker timsTOF Pro PASEF for plant 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 formate and formic acid were purchased from Wako. Water was purchased from Millipore. <LC Method> The LC system consisted of a Bruker Elute UHPLC system. Lipids were separated on an Acquity UPLC HSS T3 C18 column (50 x 1.0 mm; 1.8 µm) (Waters, Milford, MA, USA). The column was maintained at 55°C at a flow-rate of 0.15 mL/min. The mobile phases consisted of (A) 200:800:10:1 (v/v/v/v) acetonitrile:water:1M ammonium formate:formic acid and (B) 100:900:10:1 (v/v/v/v) acetonitrile:isopropanol:1M ammonium formate:formic acid. A sample volume of 2 µL was used for the injection. The separation was conducted under the following gradient: 0 min 35% (B); 3 min 70% (B); 7 min 85% (B); 10 min 90% (B); 12 min 90% (B); 12.5 min 35% (B); and 15 min 35% (B). Sample temperature was maintained at 10°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). The PASEF mode acquisition, i.e. data dependent MS/MS acquisition with the ion mobility separation, was performed by the following parameters. The parameters were MS1 mass ranges, m/z 200-1600 and MS2 mass ranges, m/z 50-1600; MS1 and MS2 accumulation time, 148.5 ms; mobility range 0.55-1.9; collision energy 30 eV; end plate offset, 500 V; capillary voltage, +4.2/-4.2 kV; nebulizer pressure, 2 bar; dry gas, 8.0 l/min; dry temperature, 200°C; funnel 1 RF (radio frequency), 300 Vpp; funnel 2 RF, 250 Vpp; multipole RF, 200 Vpp; deflection delta, 70 V; quadrupole ion energy, 5 eV; collision transfer energy, 15 eV; collision RF, 1100 Vpp; transfer time 54 µs; pre-pulse storage, 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, 2500 cts; target intensity, 20000 cts; exclusion time of precursor ion, 0.1 min. The mass calibration was automatically performed using 5 mM sodium formate calibration solution.
Comment_of_details