Summary of Study ST001829

This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench, https://www.metabolomicsworkbench.org, where it has been assigned Project ID PR001156. The data can be accessed directly via it's Project DOI: 10.21228/M88T3S This work is supported by NIH grant, U2C- DK119886.

See: https://www.metabolomicsworkbench.org/about/howtocite.php

This study contains a large results data set and is not available in the mwTab file. It is only available for download via FTP as data file(s) here.

Study ID	ST001829
Study Title	Analysis and annotation of oxidized PCs generated in vitro.
Study Summary	Oxidized PC16:0/PUFA (18:2, 20:4 and 22:6) generated in vitro were analyzed by LC/HRMS/MS analysis.All mass spectrometry raw data obtained in this study were deposited.
Institute	Kyushu university
Last Name	Matsuoka
First Name	Yuta
Address	3-1-1 Maidashi Higashi-ku
Email	ymatsu1205@gmail.com
Phone	+81-92-642-6624
Submit Date	2021-06-13
Raw Data Available	Yes
Raw Data File Type(s)	mzML
Analysis Type Detail	LC-MS
Release Date	2021-10-14
Release Version	1

Select appropriate tab below to view additional metadata details:

Project:

Project ID:	PR001156
Project DOI:	doi: 10.21228/M88T3S
Project Title:	Structural Library and Visualization of Endogenously Oxidized Phosphatidylcholines Using Mass Spectrometry-based Techniques
Project Summary:	Although oxidized phosphatidylcholines (oxPCs) play critical roles in numerous pathological events, the type and production site(s) of endogenous oxPCs remain unknown because of the lack of related structural information and analytical methods. Herein, a library of 465 oxPCs was constructed using high-resolution mass spectrometry (HRMS)-based analytical methods and employed to detect 70 oxPCs in mice with acetaminophen-induced acute liver failure.
Institute:	Kyushu university
Last Name:	Matsuoka
First Name:	Yuta
Address:	3-1-1 Maidashi Higashi-ku
Email:	ymatsu1205@gmail.com
Phone:	+81-92-642-6624

Subject:

Subject ID:	SU001906
Subject Type:	Synthetic sample

Factors:

Subject type: Synthetic sample; Subject species: - (Factor headings shown in green)

mb_sample_id	local_sample_id	Treatments	Treatment times	Air conditions
SA169881	S1_0087	PC15;0/18;1-d7	no treatment	-
SA169882	S1_0088	PC15;0/18;1-d7	no treatment	-
SA169883	S1_0089	PC15;0/18;1-d7	no treatment	-
SA169884	S1_0090	PC15;0/18;1-d7	no treatment	-
SA169885	S1_0086	PC15;0/18;1-d7	no treatment	-
SA169886	S1_0085	PC15;0/18;1-d7	no treatment	-
SA169887	S1_0080	PC15;0/18;1-d7	no treatment	-
SA169888	S1_0081	PC15;0/18;1-d7	no treatment	-
SA169889	S1_0083	PC15;0/18;1-d7	no treatment	-
SA169890	S1_0084	PC15;0/18;1-d7	no treatment	-
SA169891	S1_0091	PC15;0/18;1-d7	no treatment	-
SA169892	S1_0082	PC15;0/18;1-d7	no treatment	-
SA169893	S1_0094	PC15;0/18;1-d7	no treatment	-
SA169894	S1_0092	PC15;0/18;1-d7	no treatment	-
SA169895	S1_0093	PC15;0/18;1-d7	no treatment	-
SA169896	S1_0079	PC16;0/18;2, AAPH+hemin	4h	18O2 air
SA169897	S1_0076	PC16;0/18;2, AAPH+hemin	4h	18O2 air
SA169898	S1_0070	PC16;0/18;2, AAPH+hemin	4h	normal air
SA169899	S1_0069	PC16;0/18;2, AAPH+hemin	4h	normal air
SA169900	S1_0071	PC16;0/18;2, AAPH+hemin	4h	normal air
SA169901	S1_0055	PC16;0/18;2, AAPH+hemin	4h	normal air
SA169902	S1_0040	PC16;0/18;2, AAPH+hemin	4h	normal air
SA169903	S1_0041	PC16;0/18;2, AAPH+hemin	4h	normal air
SA169904	S1_0039	PC16;0/18;2, AAPH+hemin	4h	normal air
SA169905	S1_0054	PC16;0/18;2, AAPH+hemin	4h	normal air
SA169906	S1_0075	PC16;0/18;2, AAPH+hemin	4h	normal air
SA169907	S1_0056	PC16;0/18;2, AAPH+hemin	4h	normal air
SA169908	S1_0028	PC16;0/18;2, AAPH+hemin	4h	normal air
SA169909	S1_0029	PC16;0/18;2, AAPH+hemin	4h	normal air
SA169910	S1_0004	PC16;0/18;2, AAPH+hemin	4h	normal air
SA169911	S1_0005	PC16;0/18;2, AAPH+hemin	4h	normal air
SA169912	S1_0008	PC16;0/18;2, AAPH+hemin	4h	normal air
SA169913	S1_0007	PC16;0/18;2, AAPH+hemin	4h	normal air
SA169914	S1_0078	PC16;0/18;2, AAPH+hemin	4h	normal air
SA169915	S1_0002	PC16;0/18;2, AAPH+hemin	4h	normal air
SA169916	S1_0003	PC16;0/18;2, AAPH+hemin	4h	normal air
SA169917	S1_0006	PC16;0/18;2, AAPH+hemin	4h	normal air
SA169918	S1_0050	PC16;0/18;2, AAPH	4h	normal air
SA169919	S1_0049	PC16;0/18;2, AAPH	4h	normal air
SA169920	S1_0048	PC16;0/18;2, AAPH	4h	normal air
SA169921	S1_0065	PC16;0/18;2, AAPH	4h	normal air
SA169922	S1_0064	PC16;0/18;2, AAPH	4h	normal air
SA169923	S1_0063	PC16;0/18;2, AAPH	4h	normal air
SA169924	S1_0033	PC16;0/18;2, AAPH	4h	normal air
SA169925	S1_0035	PC16;0/18;2, AAPH	4h	normal air
SA169926	S1_0034	PC16;0/18;2, AAPH	4h	normal air
SA169927	S1_0037	PC16;0/18;2, Autoxidation	24h	normal air
SA169928	S1_0036	PC16;0/18;2, Autoxidation	24h	normal air
SA169929	S1_0067	PC16;0/18;2, Autoxidation	24h	normal air
SA169930	S1_0068	PC16;0/18;2, Autoxidation	24h	normal air
SA169931	S1_0038	PC16;0/18;2, Autoxidation	24h	normal air
SA169932	S1_0066	PC16;0/18;2, Autoxidation	24h	normal air
SA169933	S1_0053	PC16;0/18;2, Autoxidation	24h	normal air
SA169934	S1_0051	PC16;0/18;2, Autoxidation	24h	normal air
SA169935	S1_0052	PC16;0/18;2, Autoxidation	24h	normal air
SA169945	S1_0077	PC16;0/18;2, control	no treatment	-
SA169946	S1_0045	PC16;0/18;2, control	no treatment	-
SA169947	S1_0031	PC16;0/18;2, control	no treatment	-
SA169948	S1_0030	PC16;0/18;2, control	no treatment	-
SA169949	S1_0046	PC16;0/18;2, control	no treatment	-
SA169950	S1_0061	PC16;0/18;2, control	no treatment	-
SA169951	S1_0032	PC16;0/18;2, control	no treatment	-
SA169952	S1_0001	PC16;0/18;2, control	no treatment	-
SA169953	S1_0062	PC16;0/18;2, control	no treatment	-
SA169954	S1_0060	PC16;0/18;2, control	no treatment	-
SA169955	S1_0047	PC16;0/18;2, control	no treatment	-
SA169936	S1_0074	PC16;0/18;2, CuSO4+AsA	72h	normal air
SA169937	S1_0072	PC16;0/18;2, CuSO4+AsA	72h	normal air
SA169938	S1_0042	PC16;0/18;2, CuSO4+AsA	72h	normal air
SA169939	S1_0073	PC16;0/18;2, CuSO4+AsA	72h	normal air
SA169940	S1_0059	PC16;0/18;2, CuSO4+AsA	72h	normal air
SA169941	S1_0057	PC16;0/18;2, CuSO4+AsA	72h	normal air
SA169942	S1_0058	PC16;0/18;2, CuSO4+AsA	72h	normal air
SA169943	S1_0044	PC16;0/18;2, CuSO4+AsA	72h	normal air
SA169944	S1_0043	PC16;0/18;2, CuSO4+AsA	72h	normal air
SA169956	S1_0014	PC16;0/20;4, AAPH+hemin	4h	normal air
SA169957	S1_0015	PC16;0/20;4, AAPH+hemin	4h	normal air
SA169958	S1_0016	PC16;0/20;4, AAPH+hemin	4h	normal air
SA169959	S1_0013	PC16;0/20;4, AAPH+hemin	4h	normal air
SA169960	S1_0010	PC16;0/20;4, AAPH+hemin	4h	normal air
SA169961	S1_0017	PC16;0/20;4, AAPH+hemin	4h	normal air
SA169962	S1_0011	PC16;0/20;4, AAPH+hemin	4h	normal air
SA169963	S1_0012	PC16;0/20;4, AAPH+hemin	4h	normal air
SA169964	S1_0009	PC16;0/20;4, control	no treatment	-
SA169965	S1_0019	PC16;0/22;6, AAPH+hemin	4h	normal air
SA169966	S1_0024	PC16;0/22;6, AAPH+hemin	4h	normal air
SA169967	S1_0025	PC16;0/22;6, AAPH+hemin	4h	normal air
SA169968	S1_0027	PC16;0/22;6, AAPH+hemin	4h	normal air
SA169969	S1_0023	PC16;0/22;6, AAPH+hemin	4h	normal air
SA169970	S1_0026	PC16;0/22;6, AAPH+hemin	4h	normal air
SA169971	S1_0022	PC16;0/22;6, AAPH+hemin	4h	normal air
SA169972	S1_0021	PC16;0/22;6, AAPH+hemin	4h	normal air
SA169973	S1_0020	PC16;0/22;6, AAPH+hemin	4h	normal air
SA169974	S1_0018	PC16;0/22;6, control	no treatment	-
SA169990	S1_0121	Standard oxPCs	no treatment	-
SA169991	S1_0119	Standard oxPCs	no treatment	-
SA169992	S1_0120	Standard oxPCs	no treatment	-
SA169993	S1_0123	Standard oxPCs	no treatment	-
SA169994	S1_0118	Standard oxPCs	no treatment	-
SA169995	S1_0124	Standard oxPCs	no treatment	-

Showing page 1 of 2 Results: 1 2 Next Showing results 1 to 100 of 124

Collection:

Collection ID:	CO001899
Collection Summary:	PC16:0/18:2, PC16:0/20:4, and PC16:0/22:6 were purchased from Avanti Polar Lipids (Albaster, AL). Each PC was oxidized by using several LPO systems, such as AAPH, autoxidation, AAPH+hemin and CuSO4+AsA.
Sample Type:	Standard phosphadylcholines

Treatment:

Treatment ID:	TR001919
Treatment Summary:	For in vitro experiments, a mixture containing 500 µM PC16:0/PUFAs (PC16:0/18:2, PC16:0/20:4, and PC16:0/22:6), 0.5% ethanol, and either 50 mM AAPH or 50 mM AAPH + 10 µM hemin was incubated in phosphate-buffered saline (PBS; pH 7.4) at 37 °C under normal or 18O2 air. For autoxidation, a solution of 500 nmol of PC16:0/18:2 in chloroform (1 mL) was immediately dried using nitrogen gas in a glass tube. The dried samples were incubated at 37 °C for 24 h and then resuspended in methanol (200 µL). For CuSO4 + AsA–induced peroxidation, a solution containing 500 µM PC16:0/18:2 and 500 µM CuSO4 + 1 mM AsA was incubated in PBS (pH 7.4) at 37 °C for 72 h.

Treatment ID:

TR001919

Treatment Summary:

For in vitro experiments, a mixture containing 500 µM PC16:0/PUFAs (PC16:0/18:2, PC16:0/20:4, and PC16:0/22:6), 0.5% ethanol, and either 50 mM AAPH or 50 mM AAPH + 10 µM hemin was incubated in phosphate-buffered saline (PBS; pH 7.4) at 37 °C under normal or 18O2 air. For autoxidation, a solution of 500 nmol of PC16:0/18:2 in chloroform (1 mL) was immediately dried using nitrogen gas in a glass tube. The dried samples were incubated at 37 °C for 24 h and then resuspended in methanol (200 µL). For CuSO4 + AsA–induced peroxidation, a solution containing 500 µM PC16:0/18:2 and 500 µM CuSO4 + 1 mM AsA was incubated in PBS (pH 7.4) at 37 °C for 72 h.

Sample Preparation:

Sampleprep ID:	SP001912
Sampleprep Summary:	For in vitro experiments, the reaction solutions were extracted using the modified Bligh and Dyer method. Briefly, a mixed solution of 1 mL methanol and 1 mL chloroform, containing 100 μM dibutylhydroxytoluene and ethylenediaminetetraacetic acid as antioxidants, and 100 nM PC15:0/18:1-d7 as an internal standard was added to the reaction solution. After 1 min vortex, the organic layer was collected in a glass tube. The extracted solution was dried under a stream of nitrogen gas, and the residue was dissolved in methanol (200 µL) and stored at −80 °C before injection into the HPLC column.

Sampleprep ID:

SP001912

Sampleprep Summary:

For in vitro experiments, the reaction solutions were extracted using the modified Bligh and Dyer method. Briefly, a mixed solution of 1 mL methanol and 1 mL chloroform, containing 100 μM dibutylhydroxytoluene and ethylenediaminetetraacetic acid as antioxidants, and 100 nM PC15:0/18:1-d7 as an internal standard was added to the reaction solution. After 1 min vortex, the organic layer was collected in a glass tube. The extracted solution was dried under a stream of nitrogen gas, and the residue was dissolved in methanol (200 µL) and stored at −80 °C before injection into the HPLC column.

Combined analysis:

Analysis ID	AN002968	AN002969
Analysis type	MS	MS
Chromatography type	Reversed phase	Reversed phase
Chromatography system	Nexera LC system (Shimadzu Co., Kyoto, Japan)	Nexera LC system (Shimadzu Co., Kyoto, Japan)
Column	Inertsil ODS-P (150 x 2.1mm,3um)	Inertsil ODS-P (150 x 2.1mm,3um)
MS Type	ESI	ESI
MS instrument type	Orbitrap	Orbitrap
MS instrument name	Thermo Q Exactive Orbitrap	Thermo Q Exactive Orbitrap
Ion Mode	POSITIVE	NEGATIVE
Units	Normalized amount	Normalized amount

Chromatography:

Chromatography ID:	CH002199
Instrument Name:	Nexera LC system (Shimadzu Co., Kyoto, Japan)
Column Name:	Inertsil ODS-P (150 x 2.1mm,3um)
Chromatography Type:	Reversed phase

MS:

MS ID:	MS002758
Analysis ID:	AN002968
Instrument Name:	Thermo Q Exactive Orbitrap
Instrument Type:	Orbitrap
MS Type:	ESI
MS Comments:	Individual oxPCs were identified by full-scan MS/data-dependent MS/MS or parallel reaction monitoring (PRM). The ionization conditions were as follows: ionization mode = positive, sheath gas flow rate = 40 arbitrary units, auxiliary gas flow rate = 10 arbitrary units, spray voltage = 2000 V, capillary temperature = 265 °C, S-lens level = 50, and heater temperature = 425 °C. The experimental conditions for full-scan MS were as follows: resolving power = 70000, automatic gain control target = 1 × 106, trap fill time = 100 ms, scan range = m/z 120–1500. The experimental conditions for MS/MS and PRM were as follows: resolving power = 17500, automatic gain control target = 1 × 106, trap fill time = 80 ms, isolation width = ±0.6 Da, fixed first mass = m/z 80, normalized collision energy = 20 or 35 eV, intensity threshold of precursor ions for MS/MS analysis = 3100, apex trigger = 2–4 s, and dynamic exclusion = 2 s. The intensity threshold of precursor ions for MS/MS analysis and the dynamic exclusion were set to 1 × 104 and 1 s, respectively. LC/HRMS/MS analysis was controlled using Xcalibur 4.2.47 software (Thermo Fisher Scientific).
Ion Mode:	POSITIVE

MS ID:	MS002759
Analysis ID:	AN002969
Instrument Name:	Thermo Q Exactive Orbitrap
Instrument Type:	Orbitrap
MS Type:	ESI
MS Comments:	Individual oxPCs were identified by full-scan MS/data-dependent MS/MS or parallel reaction monitoring (PRM). The ionization conditions were as follows: ionization mode = negative, sheath gas flow rate = 40 arbitrary units, auxiliary gas flow rate = 10 arbitrary units, spray voltage = 2000 V, capillary temperature = 265 °C, S-lens level = 50, and heater temperature = 425 °C. The experimental conditions for full-scan MS were as follows: resolving power = 70000, automatic gain control target = 1 × 106, trap fill time = 100 ms, scan range = m/z 120–1500. The experimental conditions for MS/MS and PRM were as follows: resolving power = 17500, automatic gain control target = 1 × 106, trap fill time = 80 ms, isolation width = ±0.6 Da, fixed first mass = m/z 80, normalized collision energy = 20 or 35 eV, intensity threshold of precursor ions for MS/MS analysis = 3100, apex trigger = 2–4 s, and dynamic exclusion = 2 s. The intensity threshold of precursor ions for MS/MS analysis and the dynamic exclusion were set to 1 × 104 and 1 s, respectively. LC/HRMS/MS analysis was controlled using Xcalibur 4.2.47 software (Thermo Fisher Scientific).
Ion Mode:	NEGATIVE