Study design

Description
Male mice, were fed control (chow) or corn oil-based high-fat diet (HFD) for 2 months (chow-2m, HFD-2m) and 10 months (HDF-10m).
Urine, plasma, feces, and 18 different tissues were collected from each animal for metabolomics and lipidomics analysis. These matrices cover digestive, excretory, respiratory, reproductive, endocrine, muscular, cardiovascular and nervous systems. In addition, chow and HFD feed was analyzed along with quality control human plasma/serum materials (NIST SRM 1950 plasma, Merck S1-100ML serum, Sigma 7023 serum). In total, 408 samples were included in this study.
Animals
Male C57BL/6N mice, ages 6–7 weeks, were housed in a temperature and humidity controlled room on a 12 h light:dark cycle and provided free access to food and water.
Diets
Chow and HFD were also collected for analysis.
Methodology
An LC−MS workflow LIMeX (LIpids, Metabolites and eXposome compounds) was used for the simultaneous extraction of complex lipids, polar metabolites, and exposome compounds that combines LC–MS-based untargeted and targeted analysis.
Samples were extracted using a biphasic solvent system of cold methanol, methyl tert-butyl ether (MTBE), and water. In total, 65 internal standards were added during extraction covering main lipid classes and polar metabolites.
The upper (organic) phase was used for lipidomics profiling using reversed-phase liquid chromatography (RPLC) while the bottom (polar) phase was used for metabolomics analysis using RPLC and hydrophilic interaction chromatography (HILIC). The bottom (polar) phase was also used for profiling of short-chain fatty acids after derivatization using RPLC.
Overall, biofluids and non-fat matrices were analyzed using LIMeX-7D, while for adipose tissues a separate analysis of high abundant triacylglycerols was included (LIMeX-8D).
  • For lipidomics profiling, two RPLC (ACQUITY UPLC BEH C18 column) methods with acetonitrile/water (3:2) and propan-2-ol/acetonitrile (9:1) as mobile phases were used with different mobile-phase modifiers based on electrospray ionization (ESI) polarity used. Specifically, RPLC lipidomic method in ESI(+) used ammonium formate (10 mM) and formic acid (0.1%), while RPLC lipidomic method in ESI(–) worked with ammonium acetate (10 mM) and acetic acid (0.1%). In case of adipose tissues (eWAT, BAT, scWAT) separate ESI(+) analyses were conducted for minor and major lipid species.
  • For metabolomics profiling, HILIC (ACQUITY UPLC BEH Amide column) with acetonitrile/water (95:5) and water as mobile phases, both with ammonium formate (10 mM) and formic acid (0.125%) operated in ESI(+) and ESI(–) were used followed by RPLC (ACQUITY UPLC HSS T3 column) with water and methanol as mobile phases, both with formic acid (0.2 and 0.1%, respectively) in ESI(+) and ESI(–).
  • For profiling short-chain fatty acids (FA 1:0–FA 6:0) after derivatization using O-benzoylhydroxylamine, RPLC (ACQUITY UPLC BEH C18 column) method with water/0.1% formic acid and methanol as mobile phases and operated in ESI(+) was used.
The dimension of all columns used was 50 mm × 2.1 mm id with 1.7–1.8 μm particle size. Each column was connected to a VanGuard pre-column (5 mm × 2.1 mm id with 1.7–1.8 μm particle size).
Matrices were analyzed in blocks. Each block consisted of randomized samples, QC samples injected between actual samples, blank, serial dilution of QC sample, and spikes for external quantification. Between each block, a composite sample of all QC samples (super-QC) was injected to monitor instrumental drift.
Data acquisition
Data sets were acquired using a Vanquish UHPLC System (Thermo Fisher Scientific) coupled to a Q Exactive Plus mass spectrometer. Simultaneous acquisition of MS1 data at 35,000 FWHM (m/z 200) and 3 data-dependent scans at 17,500 FWHM (m/z 200) was used for all platforms.
For lipidomics platforms, normalized collision energy (NCE) 20% for ESI(+) and 10, 20, 30% for ESI(–) was used. For metabolomics platforms, NCE 20, 30, 40% was used for both ESI(+) and ESI(–).
Processing
MS-DIAL software was used for peak alignment followed by automated annotation using in-house retention time–MS/MS libraries and compilation of MS/MS libraries (NIST20, MassBank, MoNA) for polar metabolites, and LipidBlast MS/MS library accommodated in MS-DIAL and covering 117 lipid subclasses.
Analysis
Samples with more than 50% of zero values are excluded from the analysis. Remaining zero values are replaced by half of the minimum value calculated from non-zero values from the sample.