MetaboLights

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_FILES/CE_OP2_QC07.lcdftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS15755/FILES/RAW_FILES/LI_OP2_ND_1.lcdftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS15755/FILES/RAW_FILES/PL_OP1_N4.lcdftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS15755/FILES/RAW_FILES/PL_OP2_QC02.lcdftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS15755/FILES/RAW_FILES/PL_OP1_H6.lcdftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS15755/FILES/RAW_FILES/PL_OP2_O4.lcdftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS15755/FILES/RAW_FILES/PL_OP1_QC08.lcdftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS15755/FILES/RAW_FILES/CE_OP2_05.lcdftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS15755/FILES/RAW_FILES/LI_OP2_ND_5.lcdftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS15755/FILES/RAW_FILES/PL_OP2_N6.lcdftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS15755/FILES/RAW_FILES/CE_OP1_QC08.lcdftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS15755/FILES/RAW_FILES/PL_OP2_O8.lcdftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS15755/FILES/RAW_FILES/PL_OP2_QC05.lcdftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS15755/FILES/RAW_FILES/PL_OP1_QC04.lcdftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS15755/FILES/RAW_FILES/LI_OP1_QC02.lcdftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS15755/FILES/RAW_FILES/CE_OP2_QC03.lcdftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS15755/FILES/RAW_FILES/PL_OP2_N3.lcdftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS15755/FILES/RAW_FILES/CE_OP1_QC01.lcdftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS15755/FILES/RAW_FILES/LI_OP2_QC04.lcdftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS15755/FILES/RAW_FILES/PL_OP2_O1.lcdftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS15755/FILES/RAW_FILES/LI_OP1_ND_3.lcdftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS15755/FILES/RAW_FILES/CE_OP2_01.lcdftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS15755/FILES/RAW_FILES/PL_OP1_N1.lcdftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS15755/FILES/RAW_FILES/PL_OP1_H2.lcdprimaryOK200ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS15755Lipids were tentatively identified by comparing the experimental data against Lipid Maps databases (www.lipidmaps.org). Fragment patterns (MS/MS spectra) were also used to identify lipid metabolites.  MetaboLightsPublicLiquid Chromatography MS - positive - reverse-phaseAll samples were analyzed on a Shimadzu LCMS-8060 triple-quadrupole liquid chromatography–tandem mass spectrometry (LC-MS/MS) system (Shimadzu, Kyoto, Japan). Separation was carried out with a Kinetex C18 column (100 × 2.1 mm, 2.6 μm particle size, Phenomenex, Torrance, CA, USA). Mobile phase A consisted of 10 mM ammonium acetate in water/methanol (1/9, v/v), while mobile phase B was 10 mM ammonium acetate in methanol/isopropanol (1/1, v/v). The gradient elution condition was as follows: 30% B at 0 min, 95% B at 15 min, 95% B at 20 min, and 30% B at 25 min. The sample injection volume was 1 μL for cell and liver samples and 5 μL for plasma samples. The injection volume was set for each matrix according to its endogenous lipid concentration and signal response to keep the signals within the optimal detection range. As the same internal-standard mixture was added to every sample and the datasets were evaluated on a matrix-specific basis rather than compared quantitatively across matrices, this does not affect within-matrix comparability. The flow rate was maintained at 0.2 mL/min.A Multi-Matrix Targeted Lipidomics Dataset for Quality-Control Guideline Development and Validation.subin baeKyungpook National UniversityPlasmaCell culturetissuemass spectrometry assayLipid extraction was conducted according to the Matyash method with a minor modification. For tissue and cell samples, 400 μL of 75% methanol containing 0.1% butylated hydroxytoluene was added. For plasma samples, 300 μL of 100% methanol containing 0.1% butylated hydroxytoluene and 90 μL of water were added. Following this, 1 mL of MTBE was added to all samples. The mixture was shaken for 1 h at room temperature, then 250 μL of water was added, and the mixture was vortexed for 10 min. Phase separation was performed by centrifugation at 14,000 xg for 15 min at 4°C.Mus musculusHomo sapienshttps://www.ebi.ac.uk/metabolights/MTBLS15755Kwang-Hyeon Liu. Kyungpook National University. dstlkh@knu.ac.kr.Subin Bae. Kyungpook National University. bsb960908@naver.com.Quantitative analysis was performed using a Nexera2 LC system (Shimadzu Corporation, Kyoto, Japan).Factorsbsb960908@naver.com1.     Human Plasma: The study protocol was approved by the Institutional Review Board of Kyungpook National University Hospital (KNUH 2022-09-016-001) and the study was conducted in accordance with the Declaration of Helsinki. The clinical study was registered with the Clinical Research Information Service (KCT0007864). Written informed consent was obtained from all participants before enrollment and sample collection. The consent materials specified that collected biospecimens would be used for endogenous metabolite analysis; therefore, the targeted lipidomics analysis performed in the present study was considered to fall within the consented scope of metabolomic analysis. The consent form permitted the use and sharing of participants’ health information but did not explicitly mention public deposition of derived or raw analytical data. Detailed procedures for participant recruitment and the clinical study design, including inclusion/exclusion criteria, have been previously described by Kim et al. (2025)8. A total of 14 plasma samples from 14 participants were included, with one sample analyzed per participant. The dataset comprised seven participants in the normal-BMI group and seven participants in the high-BMI group. The present study was not designed to characterize the complete longitudinal lipidomic response to dapagliflozin. Rather, plasma samples collected on day 6 following administration of a single 10 mg dose of dapagliflozin were selected as a defined human plasma dataset for evaluating the applicability and reproducibility of the targeted lipidomics workflow under a consistent sampling condition. Samples from the remaining time points were outside the scope of the present methodological validation. Participants were categorized according to baseline BMI as the normal-BMI group (BMI 18.0–25.0 kg/m2) and the high-BMI group (BMI ≥ 25.0 kg/m2). Whole blood was collected in heparinized tubes, centrifuged at 1900 xg for 10 min at 4°C, and the resulting plasma was stored at -80°C until targeted lipidomic analysis.2.     Cell Culture: SNU-484 human gastric cancer cells were purchased from the Korean Cell Line Bank (KCLB, Seoul, Korea) and were used from a stock maintained in our laboratory until the time of sample preparation. A total of nine technical replicate samples were prepared from the same cell culture batch. Cell line authentication and mycoplasma testing were not performed for these samples. Cells were cultured in RPMI-1640 medium (Corning, NY, USA) supplemented with 10% fetal bovine serum (Gibco, MA, USA) and 1% penicillin–streptomycin solution (Gibco). Cells were maintained at 37 °C in a humidified atmosphere containing 5% CO2. For sample collection, cultured cells were washed twice with phosphate-buffered saline (PBS) and collected in 1,000 μL of methanol (80:20, v/v). The collected cell samples were stored at −80 °C until analysis.3.     Mouse liver tissue: Liver tissue samples were obtained commercially from SMC Laboratories, Inc. (Tokyo, Japan). The samples were derived from five individual normal-diet control mice from a diet-induced MASH study. All animal procedures—including animal housing, dietary treatment, euthanasia, and tissue collection—were conducted at the SMC Laboratories Animal Research Facility in accordance with an animal protocol approved by the SMC Laboratories Institutional Animal Care and Use Committee (Approval No. S250). Tissue collection and handling were performed by the supplier in accordance with its institutional guidelines for animal care and use. The authors used only commercially supplied tissue samples, and no additional animal experiments were performed as part of this study; any additional institutional ethical review or exemption was determined in accordance with the policies of the authors' institution. One liver sample from each of the five mice was included as an independent biological sample. Upon receipt, the liver samples were stored at −80 °C until lipid extraction and LC-MS/MS analysis.Metabolomicsmulti-matrix studyPlasmaCell cultureMus musculustandem mass spectrometrytargeted analysisShimadzu Nexera UHPLC systemHomo sapiensLipidomicstissueShimadzu 8060 MS (triple quadrupole)multi-matrix studyPlasmaCell cultureMus musculustandem mass spectrometrytargeted analysisShimadzu Nexera UHPLC systemHomo sapiensLipidomicstissueShimadzu 8060 MS (triple quadrupole)The mass operating conditions were as follows: desolvation temperature, 250°C; heat block temperature, 400°C; spray voltage, 4 kV; drying gas (N2) flow rate, 10 L/min; collision gas, argon; nebulizing gas (N2) flow rate, 3 L/min; collision gas pressure, 230 kPa; and detector voltage, 1.90 kV. A total of 306 targeted lipid species were analyzed in the selected reaction monitoring mode (SRM), with one SRM transition assigned to each targeted lipid species.falseDevelopment and verification of quality control guidelines for the utilization of lipidomic dataMetabolome data has been accumulating exponentially like other omics fields as the metabolomics field has grown and expanded to a remarkable level worldwide in the past 10 years. In line with this situation, it is necessary to establish a metabolomic data center and build and operate a global open platform to accumulate and share metabolite big data worldwide. In this study, guidelines for the collection of targeted lipid metabolite data from plasma, cells, and tissues were developed and validated. Lipids in each sample were extracted using a liquid-liquid extraction method using methyl-tert butyl ester (MTBE), and lipid metabolites were analyzed using LC-MS/MS. For the validation of the guideline, independent experiments were conducted by different experimenters using identical samples and the same lipid extraction method. For quantitative comparison, the incurred sample reanalysis (ISR) method was used to secure the reliability of clinical sample analysis results according to FDA guidance. The verification of the analysis method was completed by confirming that 70% of the samples repeatedly analyzed were within 30% of the initial analysis results.2026-09-212026-09-21MTBLS15755