Metabolite identification was performed by matching accurate mass and MS/MS spectra against an in-house reference spectral library. The mass tolerance for precursor ions was set to < 25 ppm. Metabolite annotations were classified according to the Metabolomics Standards Initiative (MSI) levels: Level 2 annotation was assigned for metabolites confirmed by MS/MS spectral matching; Level 1 annotation was assigned only when authenticated chemical reference standards were analyzed under identical chromatographic conditions. Metabolite pathway classification was mapped to the Kyoto Encyclopedia of Genes and Genomes (KEGG) database.
"],"repository":["MetaboLights"],"study_status":["Public"],"ptm_modification":[""],"instrument_platform":["Liquid Chromatography MS - positive - hilic"],"chromatography_protocol":["Chromatographic separation was performed on an Agilent 1290 Infinity LC ultra-high performance liquid chromatography system using a Waters ACQUITY UPLC BEH Amide column (1.7 μm, 2.1 mm × 100 mm). The mobile phase consisted of (A) 25 mM ammonium acetate and 25 mM ammonium hydroxide in water and (B) acetonitrile. The gradient elution program was set as follows: 0–0.5 min, 95% B; 0.5–7 min, linear gradient from 95% B to 65% B; 7–9 min, linear gradient from 65% B to 40% B; 9–10 min, 40% B; 10–11.1 min, linear gradient from 40% B to 95% B; 11.1–16 min, 95% B for column re-equilibration. The flow rate was 0.3 mL/min, column temperature was maintained at 25 °C, and injection volume was 5 μL. The autosampler was kept at 4 °C throughout the analysis. No guard column was used.
"],"publication":["Histone H3K4me3 Demethylase RBP2 Transcriptionally Activates PPARγ to Drive Lipid Metabolic Reprogramming in Gastric Carcinoma."],"submitter_name":["Xize Li"],"submitter_affiliation":["University of Health and Rehabilitation Sciences"],"organism_part":["Stomach"],"technology_type":["mass spectrometry assay"],"disease":[""],"extraction_protocol":["Metabolites were extracted from cell pellets using a pre-cooled methanol/acetonitrile/water mixture (2:2:1, v/v/v). Briefly, 1 mL of extraction solvent was added to each cell pellet, followed by vigorous vortexing and ultrasonication on ice for 60 min. Samples were incubated at −20 °C for 1 h to precipitate proteins, then centrifuged at 14,000 × g for 20 min at 4 °C. The supernatant was collected and vacuum-dried. Dried extracts were reconstituted in 100 μL of acetonitrile/water (1:1, v/v), vortexed thoroughly, and centrifuged at 14,000 × g for 15 min at 4 °C. The resulting supernatant was used for subsequent LC-MS analysis. No derivatization step was performed.
"],"organism":["Homo sapiens"],"full_dataset_link":["https://www.ebi.ac.uk/metabolights/MTBLS15324"],"author":["Jiping Zeng. University of Health and Rehabilitation Sciences. zengjiping@uhrs.edu.cn.","Xize Li. University of Health and Rehabilitation Sciences. lixize@uhrs.edu.cn."],"data_transformation_protocol":["Raw mass spectrometry data were converted to mzXML format via ProteoWizard. Peak alignment, retention time correction, and peak area extraction were performed using the XCMS package. Features with missing values > 50% within each group were excluded from further analysis. The remaining intensity data were Pareto-scaled and imported into SIMCA-P 14.1 software for multivariate statistical analysis, including unsupervised principal component analysis (PCA), supervised partial least squares discriminant analysis (PLS-DA), and orthogonal partial least squares discriminant analysis (OPLS-DA). Differential metabolites were screened using the combined criteria of variable importance in projection (VIP) > 1 from the OPLS-DA model and P < 0.05 from Student’s two-tailed t-test. Pathway enrichment analysis was conducted based on the KEGG database.
"],"study_factor":["Treatment"],"submitter_email":["lixize@uhrs.edu.cn"],"sample_collection_protocol":["Human gastric adenocarcinoma AGS cells were cultured in Ham's F12 medium supplemented with 12% fetal bovine serum at 37°C with 5% carbon dioxide.Cells were transfected with negative control siRNA (si-NC) or RBP2-targeting siRNA (si-RBP2) at 30% confluence. At 48 h post-transfection, cells were harvested at ~80% confluence, washed twice with ice-cold phosphate-buffered saline (PBS), and cell pellets were collected by centrifugation. All samples were immediately snap-frozen in liquid nitrogen and stored at −80 °C until metabolite extraction. Pooled quality control (QC) samples were prepared by mixing equal volumes of supernatant from all individual samples. Solvent blank samples were prepared using the same extraction procedure without cell input.
"],"omics_type":["Metabolomics"],"study_design":["Stomach","Metabolomics","gastric cancer","untargeted analysis","AB SCIEX TripleTOF 5600+","Homo sapiens","experimental blank","Agilent 1290 Infinity LC","Lipid Metabolic Process","untargeted metabolite profiling"],"curator_keywords":["Stomach","Metabolomics","gastric cancer","untargeted analysis","AB SCIEX TripleTOF 5600+","Homo sapiens","experimental blank","Agilent 1290 Infinity LC","Lipid Metabolic Process","untargeted metabolite profiling"],"mass_spectrometry_protocol":["Mass spectrometric detection was performed on an AB SCIEX TripleTOF 5600+ mass spectrometer equipped with an electrospray ionization (ESI) source. Information-dependent acquisition (IDA) was used for MS/MS data collection in high-sensitivity mode. The ESI source parameters were set as follows: Ion Source Gas1 = 60, Ion Source Gas2 = 60, Curtain Gas = 30, source temperature = 600 °C, IonSpray Voltage Floating = ±5500 V. The TOF MS scan range was m/z 60–1200 Da with an accumulation time of 0.15 s per spectrum; the product ion scan range was m/z 25–1200 Da with an accumulation time of 0.03 s per spectrum. Declustering potential was set to ±60 V, and normalized collision energy was 30 eV. IDA settings excluded isotopes within 4 Da, and monitored 6 candidate ions per cycle.
"],"metabolite_name":["LysoPE(16:0/0:0)","Adenosine","N-Acetylglycine","Adenosine 5'-phosphosulfate","Adenosine 5'-diphosphate","FA 18:4+1O","beta-Nicotinamide adenine dinucleotide","Citrate","Erucamide","Linoleic acid","Caprylic acid","N-ACETYL-DL-SERINE","Malic acid","Oxypurinol","LysoPE(18:0/0:0)","Stearic acid"],"additional_accession":[]},"is_claimable":false,"name":"Histone H3K4me3 Demethylase RBP2 Transcriptionally Activates PPARγ to Drive Lipid Metabolic Reprogramming in Gastric Carcinoma","description":"This work investigates epigenetic driven lipid metabolic reprogramming in gastric carcinoma. We characterize that histone H3K4me3 demethylase RBP2 transcriptionally activates PPARgama by binding to its promoter region,thereby promoting lipogenic gene expression and intracellular lipid accumulation in gastric cancer cells. Correlative bioinformatic analyses from TCGA cohort and paired clinical specimens support the RBP2&PPARgama regulatory axis. Cellular rescue assays and xenograft models further verify that PPARgama serves as a critical downstream mediator for RBP2 mediated lipid metabolic rewiring and gastric tumor progression.
","dates":{"publication":"2026-08-14","submission":"2026-08-14"},"accession":"MTBLS15324","cross_references":{}}