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MB Sample ID: SA170060
| Local Sample ID: | S2_0040 |
| Subject ID: | SU001907 |
| Subject Type: | Mammal |
| Subject Species: | Mus musculus |
| Taxonomy ID: | 10090 |
Select appropriate tab below to view additional metadata details:
Subject:
| Subject ID: | SU001907 |
| Subject Type: | Mammal |
| Subject Species: | Mus musculus |
| Taxonomy ID: | 10090 |
Factors:
| Local Sample ID | MB Sample ID | Factor Level ID | Level Value | Factor Name |
|---|---|---|---|---|
| S2_0040 | SA170060 | FL020247 | C57BL6J, APAP 300 mg/kg | Treatments |
| S2_0040 | SA170060 | FL020247 | 1h | Treatment times |
| S2_0040 | SA170060 | FL020247 | normal air | Air conditions |
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. |
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 |
