PXD027776

PXD027776 is an original dataset announced via ProteomeXchange.

Title	Qualification of PtdCho species extracted from the hXkr8-hBSGD complex
Description	PtdCho species extracted from the hXkr8-hBSGD complex were identified by LC-MS/MS analysis. 5 µl of the hXkr8-hBSGΔ complex (5 mg/ml) was mixed with 1 ml of methanol/chloroform/water (10:5:3, v/v/v) and vortexed at the maximum setting for 143 min. The mixture was sonicated at 4°C with a Bioruptor II (Cosmo Bio) at maximum power for 30 s for five times with 30 s intervals, and span at 16,000 x g for 5 min at 4°C. An aliquot (700 µl) of the supernatant was transferred to a clean tube. After adding 195 µl of chloroform and 195 µl of water, the aqueous and organic layers were separated by centrifugation at 16,000 x g for 3 min at 4°C. The 200 µl of the organic layer was evaporated in a SpeedVac concentrator and re-dissolved in 100 µl of 10 mM ammonium formate containing 25% (v/v) isopropanol and 25% (v/v) acetonitrile. LC-MS/MS analysis was performed using an UltiMate 3000 HPLC system coupled with a Q Exactive hybrid quadrupole Orbitrap mass spectrometer (Thermo Fisher Scientific). The mass spectrometer was equipped with an electrospray ionization (ESI) source. The LC-MS conditions with Phenomenex Kinetex C8 column (Shimadzu GLC) were as follows: injection volume, 1 or 2 µl; mobile phase A, 20 mM ammonium formate; mobile phase B, isopropanol/acetonitrile (1:1, v/v); flow rate of mobile phase, 0.2 ml/min; modifier (B) gradient; 0 min, 20%: 1 min, 20%: 2 min, 45%: 25 min, 92.5%: 26 min, 100%: 35 min, 100%: 35.1 min, 20%: 41 min, 20%; column temperature, 45°C. The following MS tune conditions were used. Ionization mode, positive and negative; capillary voltage, 3.5 kV for both positive and negative ionization; capillary temperature, 350°C. The following full mass scan/data-dependent MS/MS (Full MS/dd-MS2) mode was used for phospholipid analysis. Scan range, 500–1,100 m/z; mass resolution, 70,000; AGC target, 3e6; maximum injection time, 100 ms. The parameters for data-dependent product ion scanning were: mass resolution, 17,500; AGC target, 1e5; maximum injection time, 100 ms; loop count, 5; isolation width, 2.0 m/z; stepped normalized collision energy (NCE), 15, 25 and 35. The LC-MS/MS system was controlled by Chromeleon 6.8 and Xcalibur 4.0 softwares (Thermo Fisher Scientific). Phospholipid species were analyzed by Xcalibur Qual Browser 4.3 software.
HostingRepository	jPOST
AnnounceDate	2021-08-06
AnnouncementXML	Submission_2022-09-18_03:23:13.300.xml
DigitalObjectIdentifier
ReviewLevel	Non peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Kohei Nishino
SpeciesList	scientific name: cellular organisms; NCBI TaxID: 131567;
ModificationList	unknown modification
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2021-08-05 23:25:31	ID requested
1	2021-08-05 23:55:15	announced
⏵ 2	2022-09-18 03:23:13	announced	2022-09-18: Updated FTP location.

Dataset with its publication pending

submitter keyword: PtdCho, Xkr8

Hidetaka Kosako
lab head
Kohei Nishino
contact affiliation	Tokushima University
dataset submitter

jPOST dataset URI

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