Summary of Study ST001830

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	ST001830
Study Title	Exhaustive analysis of endogenous oxPCs in APAP-treated mice.
Study Summary	A single dose of APAP at 300 mg/kg body weight was intraperitoneally administered into eight-week-old C57BL/6J male mice. After extraction of hepatic lipids, oxPCs were analyzed by LC/HRMS/MS. 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, Fukuoka, Not USCanada, 812-8582, Japan
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:	SU001907
Subject Type:	Mammal
Subject Species:	Mus musculus
Taxonomy ID:	10090

Factors:

Subject type: Mammal; Subject species: Mus musculus (Factor headings shown in green)

mb_sample_id	local_sample_id	Treatments	Treatment times	Air conditions
SA170005	S2_0194	C57BL6J, APAP 300 mg/kg+MT 20 mg/kg	4h	normal air
SA170006	S2_0193	C57BL6J, APAP 300 mg/kg+MT 20 mg/kg	4h	normal air
SA170007	S2_0192	C57BL6J, APAP 300 mg/kg+MT 20 mg/kg	4h	normal air
SA170008	S2_0195	C57BL6J, APAP 300 mg/kg+MT 20 mg/kg	4h	normal air
SA170009	S2_0198	C57BL6J, APAP 300 mg/kg+MT 20 mg/kg	4h	normal air
SA170010	S2_0200	C57BL6J, APAP 300 mg/kg+MT 20 mg/kg	4h	normal air
SA170011	S2_0199	C57BL6J, APAP 300 mg/kg+MT 20 mg/kg	4h	normal air
SA170012	S2_0191	C57BL6J, APAP 300 mg/kg+MT 20 mg/kg	4h	normal air
SA170013	S2_0196	C57BL6J, APAP 300 mg/kg+MT 20 mg/kg	4h	normal air
SA170014	S2_0189	C57BL6J, APAP 300 mg/kg+MT 20 mg/kg	4h	normal air
SA170015	S2_0184	C57BL6J, APAP 300 mg/kg+MT 20 mg/kg	4h	normal air
SA170016	S2_0183	C57BL6J, APAP 300 mg/kg+MT 20 mg/kg	4h	normal air
SA170017	S2_0182	C57BL6J, APAP 300 mg/kg+MT 20 mg/kg	4h	normal air
SA170018	S2_0185	C57BL6J, APAP 300 mg/kg+MT 20 mg/kg	4h	normal air
SA170019	S2_0186	C57BL6J, APAP 300 mg/kg+MT 20 mg/kg	4h	normal air
SA170020	S2_0201	C57BL6J, APAP 300 mg/kg+MT 20 mg/kg	4h	normal air
SA170021	S2_0188	C57BL6J, APAP 300 mg/kg+MT 20 mg/kg	4h	normal air
SA170022	S2_0187	C57BL6J, APAP 300 mg/kg+MT 20 mg/kg	4h	normal air
SA170023	S2_0190	C57BL6J, APAP 300 mg/kg+MT 20 mg/kg	4h	normal air
SA170024	S2_0197	C57BL6J, APAP 300 mg/kg+MT 20 mg/kg	4h	normal air
SA170025	S2_0202	C57BL6J, APAP 300 mg/kg+MT 20 mg/kg	4h	normal air
SA170026	S2_0204	C57BL6J, APAP 300 mg/kg+MT 20 mg/kg	4h	normal air
SA170027	S2_0205	C57BL6J, APAP 300 mg/kg+MT 20 mg/kg	4h	normal air
SA170028	S2_0203	C57BL6J, APAP 300 mg/kg+MT 20 mg/kg	4h	normal air
SA170029	S2_0160	C57BL6J, APAP 300 mg/kg+NAC 300 mg/kg	4h	normal air
SA170030	S2_0159	C57BL6J, APAP 300 mg/kg+NAC 300 mg/kg	4h	normal air
SA170031	S2_0161	C57BL6J, APAP 300 mg/kg+NAC 300 mg/kg	4h	normal air
SA170032	S2_0168	C57BL6J, APAP 300 mg/kg+NAC 300 mg/kg	4h	normal air
SA170033	S2_0158	C57BL6J, APAP 300 mg/kg+NAC 300 mg/kg	4h	normal air
SA170034	S2_0162	C57BL6J, APAP 300 mg/kg+NAC 300 mg/kg	4h	normal air
SA170035	S2_0181	C57BL6J, APAP 300 mg/kg+NAC 300 mg/kg	4h	normal air
SA170036	S2_0178	C57BL6J, APAP 300 mg/kg+NAC 300 mg/kg	4h	normal air
SA170037	S2_0177	C57BL6J, APAP 300 mg/kg+NAC 300 mg/kg	4h	normal air
SA170038	S2_0179	C57BL6J, APAP 300 mg/kg+NAC 300 mg/kg	4h	normal air
SA170039	S2_0180	C57BL6J, APAP 300 mg/kg+NAC 300 mg/kg	4h	normal air
SA170040	S2_0169	C57BL6J, APAP 300 mg/kg+NAC 300 mg/kg	4h	normal air
SA170041	S2_0157	C57BL6J, APAP 300 mg/kg+NAC 300 mg/kg	4h	normal air
SA170042	S2_0171	C57BL6J, APAP 300 mg/kg+NAC 300 mg/kg	4h	normal air
SA170043	S2_0173	C57BL6J, APAP 300 mg/kg+NAC 300 mg/kg	4h	normal air
SA170044	S2_0174	C57BL6J, APAP 300 mg/kg+NAC 300 mg/kg	4h	normal air
SA170045	S2_0175	C57BL6J, APAP 300 mg/kg+NAC 300 mg/kg	4h	normal air
SA170046	S2_0176	C57BL6J, APAP 300 mg/kg+NAC 300 mg/kg	4h	normal air
SA170047	S2_0170	C57BL6J, APAP 300 mg/kg+NAC 300 mg/kg	4h	normal air
SA170048	S2_0163	C57BL6J, APAP 300 mg/kg+NAC 300 mg/kg	4h	normal air
SA170049	S2_0172	C57BL6J, APAP 300 mg/kg+NAC 300 mg/kg	4h	normal air
SA170050	S2_0164	C57BL6J, APAP 300 mg/kg+NAC 300 mg/kg	4h	normal air
SA170051	S2_0167	C57BL6J, APAP 300 mg/kg+NAC 300 mg/kg	4h	normal air
SA170052	S2_0166	C57BL6J, APAP 300 mg/kg+NAC 300 mg/kg	4h	normal air
SA170053	S2_0165	C57BL6J, APAP 300 mg/kg+NAC 300 mg/kg	4h	normal air
SA170054	S2_0054	C57BL6J, APAP 300 mg/kg	1h	normal air
SA170055	S2_0053	C57BL6J, APAP 300 mg/kg	1h	normal air
SA170056	S2_0050	C57BL6J, APAP 300 mg/kg	1h	normal air
SA170057	S2_0036	C57BL6J, APAP 300 mg/kg	1h	normal air
SA170058	S2_0038	C57BL6J, APAP 300 mg/kg	1h	normal air
SA170059	S2_0039	C57BL6J, APAP 300 mg/kg	1h	normal air
SA170060	S2_0040	C57BL6J, APAP 300 mg/kg	1h	normal air
SA170061	S2_0052	C57BL6J, APAP 300 mg/kg	1h	normal air
SA170062	S2_0035	C57BL6J, APAP 300 mg/kg	1h	normal air
SA170063	S2_0031	C57BL6J, APAP 300 mg/kg	1h	normal air
SA170064	S2_0032	C57BL6J, APAP 300 mg/kg	1h	normal air
SA170065	S2_0033	C57BL6J, APAP 300 mg/kg	1h	normal air
SA170066	S2_0034	C57BL6J, APAP 300 mg/kg	1h	normal air
SA170067	S2_0041	C57BL6J, APAP 300 mg/kg	1h	normal air
SA170068	S2_0037	C57BL6J, APAP 300 mg/kg	1h	normal air
SA170069	S2_0047	C57BL6J, APAP 300 mg/kg	1h	normal air
SA170070	S2_0051	C57BL6J, APAP 300 mg/kg	1h	normal air
SA170071	S2_0042	C57BL6J, APAP 300 mg/kg	1h	normal air
SA170072	S2_0045	C57BL6J, APAP 300 mg/kg	1h	normal air
SA170073	S2_0046	C57BL6J, APAP 300 mg/kg	1h	normal air
SA170074	S2_0043	C57BL6J, APAP 300 mg/kg	1h	normal air
SA170075	S2_0044	C57BL6J, APAP 300 mg/kg	1h	normal air
SA170076	S2_0048	C57BL6J, APAP 300 mg/kg	1h	normal air
SA170077	S2_0049	C57BL6J, APAP 300 mg/kg	1h	normal air
SA170078	S2_0155	C57BL6J, APAP 300 mg/kg	24h	normal air
SA170079	S2_0137	C57BL6J, APAP 300 mg/kg	24h	normal air
SA170080	S2_0156	C57BL6J, APAP 300 mg/kg	24h	normal air
SA170081	S2_0147	C57BL6J, APAP 300 mg/kg	24h	normal air
SA170082	S2_0153	C57BL6J, APAP 300 mg/kg	24h	normal air
SA170083	S2_0136	C57BL6J, APAP 300 mg/kg	24h	normal air
SA170084	S2_0148	C57BL6J, APAP 300 mg/kg	24h	normal air
SA170085	S2_0149	C57BL6J, APAP 300 mg/kg	24h	normal air
SA170086	S2_0150	C57BL6J, APAP 300 mg/kg	24h	normal air
SA170087	S2_0152	C57BL6J, APAP 300 mg/kg	24h	normal air
SA170088	S2_0151	C57BL6J, APAP 300 mg/kg	24h	normal air
SA170089	S2_0154	C57BL6J, APAP 300 mg/kg	24h	normal air
SA170090	S2_0144	C57BL6J, APAP 300 mg/kg	24h	normal air
SA170091	S2_0140	C57BL6J, APAP 300 mg/kg	24h	normal air
SA170092	S2_0141	C57BL6J, APAP 300 mg/kg	24h	normal air
SA170093	S2_0139	C57BL6J, APAP 300 mg/kg	24h	normal air
SA170094	S2_0138	C57BL6J, APAP 300 mg/kg	24h	normal air
SA170095	S2_0146	C57BL6J, APAP 300 mg/kg	24h	normal air
SA170096	S2_0142	C57BL6J, APAP 300 mg/kg	24h	normal air
SA170097	S2_0143	C57BL6J, APAP 300 mg/kg	24h	normal air
SA170098	S2_0134	C57BL6J, APAP 300 mg/kg	24h	normal air
SA170099	S2_0135	C57BL6J, APAP 300 mg/kg	24h	normal air
SA170100	S2_0133	C57BL6J, APAP 300 mg/kg	24h	normal air
SA170101	S2_0145	C57BL6J, APAP 300 mg/kg	24h	normal air
SA170102	S2_0231	C57BL6J, APAP 300 mg/kg	2h	18O2 air
SA170103	S2_0232	C57BL6J, APAP 300 mg/kg	2h	18O2 air
SA170104	S2_0069	C57BL6J, APAP 300 mg/kg	2h	normal air

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Collection:

Collection ID:	CO001900
Collection Summary:	The animals were anesthetized with a solution of hydrochloric acid medetomidine (Kyoritsu Seiyaku Corporation, Tokyo, Japan), midazolam (Sandoz K.K., Tokyo, Japan), and butorphanol (Meiji Seika Pharma Co., Ltd., Tokyo, Japan) 1, 2, 4, 8, or 24 h after APAP administration. Mouse liver samples were collected, and the liver samples were immediately frozen in liquid nitrogen.
Sample Type:	Liver

Treatment:

Treatment ID:	TR001920
Treatment Summary:	A single dose of APAP at 300 mg/kg body weight was intraperitoneally administered into eight-week-old C57BL/6J male mice. To suppress LPO induction by APAP administration, either 300 mg/kg body weight of NAC or 20 mg/kg body weight of MT in saline was intraperitoneally injected 1 h after APAP administration.

Sample Preparation:

Sampleprep ID:	SP001913
Sampleprep Summary:	Hepatic lipids were extracted from the liver samples according to the modified Bligh and Dyer method. Briefly, 1 mL of extraction solution (methanol:chloroform:water = 5:2:2) containing 100 μM dibutylhydroxytoluene, 100 μM ethylenediaminetetraacetic acid, and 100 nM PC15:0/18:1-d7 was added to a frozen tissue sample (wet weight: approx. 50 mg), and then, the sample was homogenized using a Macro Smash homogenizer. Subsequently, the extraction solutions were sonicated on ice bath for 5 min. After centrifugation (6,000 g, 10 min, 4°C), 700 µL of the supernatant was collected, and then, 235 µL chloroform and 155 µL water were added to the supernatant. The organic layer was collected in a glass tube and dried under a stream of nitrogen gas; the dried residue was dissolved in methanol (200 µL) and stored at −80 °C before performing the LC/HRMS/MS experiments.

Sampleprep ID:

SP001913

Sampleprep Summary:

Hepatic lipids were extracted from the liver samples according to the modified Bligh and Dyer method. Briefly, 1 mL of extraction solution (methanol:chloroform:water = 5:2:2) containing 100 μM dibutylhydroxytoluene, 100 μM ethylenediaminetetraacetic acid, and 100 nM PC15:0/18:1-d7 was added to a frozen tissue sample (wet weight: approx. 50 mg), and then, the sample was homogenized using a Macro Smash homogenizer. Subsequently, the extraction solutions were sonicated on ice bath for 5 min. After centrifugation (6,000 g, 10 min, 4°C), 700 µL of the supernatant was collected, and then, 235 µL chloroform and 155 µL water were added to the supernatant. The organic layer was collected in a glass tube and dried under a stream of nitrogen gas; the dried residue was dissolved in methanol (200 µL) and stored at −80 °C before performing the LC/HRMS/MS experiments.

Combined analysis:

Analysis ID	AN002970	AN002971
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:	CH002200
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:	MS002760
Analysis ID:	AN002970
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. The inclusion list contained 465 precursor ions (m/z) of oxPCs for MS/MS analysis. LC/HRMS/MS analysis was controlled using Xcalibur 4.2.47 software (Thermo Fisher Scientific).
Ion Mode:	POSITIVE

MS ID:	MS002761
Analysis ID:	AN002971
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. The inclusion list contained 465 precursor ions (m/z) of oxPCs for MS/MS analysis. LC/HRMS/MS analysis was controlled using Xcalibur 4.2.47 software (Thermo Fisher Scientific).
Ion Mode:	NEGATIVE