SE196:/S29/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.
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 | M01 |
|---|---|
| Title | 29_Bruker Plants: Arabidopsis thaliana (Plant) LC-ESI-MS analysis (DDA) |
| Method Details ID | MS03 |
| Sample Amount | Positive mode: 1 microLiter; Negative mode: 1 microLiter |
| Comment |
Analytical Method Details Information
| ID | MS03 |
|---|---|
| Title | Method 3: Bruker timsTOF Pro DDA 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). Data dependent MS/MS acquisition (DDA) was used. The parameters were MS1 mass ranges, m/z 200-1600 and MS2 mass ranges, m/z 50-1600; MS1 cycle time time, 0.5 sec; MS2 accumulation, 14 Hz ; 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, 8 eV; collision RF, 1100 Vpp; transfer time, 54 µs; pre-pulse Storage, 5 µs; intensity threshold, 31cts.; exclusion time of precursor ion, 0.2 min. The mass calibration was automatically performed using 5 mM sodium formate calibration solution. |
| Comment_of_details |
