Candidate metabolites were annotated by matching accurate mass, retention time and MS/MS fragment spectra against HMDB, Metlin and mzCloud databases. Compound Discoverer 3.3 was adopted for spectrum matching and metabolite identification; mass tolerance was set within 5 ppm for precursor ions and 0.02 Da for fragment ions.
"],"repository":["MetaboLights"],"study_status":["Public"],"ptm_modification":[""],"instrument_platform":["Liquid Chromatography MS - negative - reverse-phase","Liquid Chromatography MS - positive - reverse-phase"],"chromatography_protocol":["Chromatographic separation was performed using a Waters ACQUITY Premier HSS T3 column (particle size 1.8 µm, inner diameter 2.1 mm, length 100 mm). Mobile phase A consisted of water containing 0.1% formic acid, and mobile phase B was acetonitrile supplemented with 0.1% formic acid. The column temperature was maintained at 40 °C with a flow rate of 0.4 mL/min, and the injection volume was set to 3 μL.The gradient elution schedule was configured as described below: the initial mobile phase composition was 95% phase A and 5% phase B at 0 min. The proportion of phase A was linearly reduced to 80% while phase B increased to 20% at 2 min, followed by a further decrease of phase A to 40% together with an increase of phase B to 60% at 5 min. At 6 min, phase A was lowered to 1% and phase B raised to 99%, and this mobile phase ratio was held constant until 7.5 min. The mobile phase composition was instantly returned to the initial ratio (95% A, 5% B) at 7.6 min and kept stable until the whole 10 min elution procedure was completed.
"],"publication":["Study on Structural Modification of Panaxadiol and Its Anti-Gastric Cancer Activity."],"submitter_name":["Duo Keai"],"submitter_affiliation":["Peking University"],"organism_part":["cells"],"technology_type":["mass spectrometry assay"],"disease":[""],"extraction_protocol":["Subsequently, 500 μL of 80% aqueous methanol solution containing internal standard was added to the cell pellet. The mixture was vortexed for 3 min to achieve complete cell resuspension. The centrifuge tubes were snap-frozen in liquid nitrogen for 5 min, thawed on dry ice for 5 min, and further thawed on ice for another 5 min, followed by vortexing for 2 min to homogenize the contents. This freeze–thaw–vortex cycle was repeated three times in total.The mixture was centrifuged at 12000 r/min for 10 min at 4 °C, and 300 μL of the supernatant was transferred into correspondingly labeled centrifuge tubes. The collected supernatant was incubated at 20 °C for 30 min and re-centrifuged at 12000 r/min for 3 min at 4 °C. Finally, 200 μL of the resultant supernatant was transferred into the inner liner of matched sample vials for subsequent LC-MS detection.
"],"organism":["Homo sapiens"],"full_dataset_link":["https://www.ebi.ac.uk/metabolights/MTBLS15239"],"author":["Yun Zhou. Shandong Academy of Agricultural Sciences. zysass2021@163.com.","Yueru Zhang. Shandong University of Traditional Chinese Medicine. 13553169667@163.com."],"data_transformation_protocol":["Raw LC-MS .raw files acquired by Thermo mass spectrometer were converted into standard mzML format using ProteoWizard MSConvert (v3.0) with default parameters for metabolomics data transformation. Peak alignment, peak picking, feature detection and peak intensity matrix extraction were performed with Compound Discoverer 3.3 software.
"],"study_factor":["Group"],"submitter_email":["keaiduoduo998@126.com"],"sample_collection_protocol":["Three experimental groups were established for AGS gastric cancer cells: a Control group treated with culture medium only, Treat 1 group cultured in medium supplemented with 5 μM Compound 7, and Treat 2 group cultured in medium supplemented with 8 μM Compound 7. After 48 h of drug intervention, the cell culture medium was aspirated, and the cell monolayers were rapidly rinsed 2–3 times with pre-cooled PBS solution. A small volume of PBS was added to the culture plates, and adherent cells were gently scraped off using a cell scraper before being transferred into centrifuge tubes.The cell suspension was centrifuged at 300–500 × g for 5 min at 4 °C, and the supernatant was discarded. The cell pellet was washed with pre-cooled PBS followed by another centrifugation at 1000 × g for 5 min at 4 °C, after which the supernatant was removed again. The PBS-resuspended cells were counted, and a suspension containing 1 × 10000000 cells was transferred into a 2 mL sterile centrifuge tube. After centrifugation at 1000 × g for 10 min at 4 °C, the supernatant was discarded.
"],"omics_type":["Metabolomics"],"study_design":["Metabolomics","Ultra Performance Liquid Chromatography","Anti-gastric cancer","cells","untargeted analysis","Thermo Scientific Q Exactive HF-X","Modification of key sites","AGS cells","Homo sapiens","Combined transcriptomics and metabolomics analysis","Panaxadiol derivatives"],"curator_keywords":["Metabolomics","Ultra Performance Liquid Chromatography","Anti-gastric cancer","cells","untargeted analysis","Thermo Scientific Q Exactive HF-X","Modification of key sites","AGS cells","Homo sapiens","Combined transcriptomics and metabolomics analysis","Panaxadiol derivatives"],"mass_spectrometry_protocol":["Mass spectrometric parameters were optimized under both positive electrospray ionization (ESI+) and negative electrospray ionization (ESI-) modes. The resolution of the full scan MS¹ was set to 60000 with an automatic gain control (AGC) target of 3.00×1000000, and the mass scan range was fixed at 70–1000 Da for both ionization modes. For data-dependent MS² acquisition, the resolution was 15000 and the AGC target was adjusted to 1.00×100000, while the MS² mass scanning range was maintained as 70–1000 Da. Up to 10 precursor ions were selected for fragmented analysis with a dynamic exclusion duration of 3 s, and the signal intensity threshold was defined as 1.00×1000000 cps. Normalized collision energies were set at 30, 40 and 50 V with a collision energy step of 50 V. The ion transfer tube temperature was kept at 320 °C for both modes. The spray voltage was set to 3800 V in ESI+ mode and 3400 V in ESI- mode. The auxiliary gas flow rate was 20 Arb, the sheath gas flow rate was 60 Arb, and the auxiliary gas heater temperature was configured at 350 °C for positive ion mode and 650 °C for negative ion mode.
"],"metabolite_name":["LPC(18:0_0:0)","gammLinolenic Acid","Pantetheine","Azelaic acid","Uridine-5'-monophosphate","Myristic acid","2,4-Dtert-butylphenol","Pyroglutamic acid","Uridine","4-Methyloctanoic acid","3,4-Dimethylbenzoic acid","Glyceric acid"],"additional_accession":[]},"is_claimable":false,"name":"Study on Structural Modification of Panaxadiol and Its Anti-Gastric Cancer Activity","description":"In this study, untargeted metabolomic sequencing was performed to investigate the metabolic alterations induced by protopanaxadiol derivatives in gastric cancer cells. All cellular samples were collected from control and treatment groups to explore differentially expressed metabolites and key metabolic pathways associated with the anti-gastric cancer effects of protopanaxadiol derivatives.","dates":{"publication":"2026-08-03","submission":"2026-08-03"},"accession":"MTBLS15239","cross_references":{"HMDB":["HMDB0000050","HMDB0061822","HMDB0010384","HMDB0031641","HMDB0001406","HMDB0000159","HMDB0001065","HMDB0013302","HMDB0254199","HMDB0000034","HMDB0000123","HMDB0010382","HMDB0000806","HMDB0000296","HMDB0002237","HMDB0013816","HMDB0000784","HMDB0003073","HMDB0031557","HMDB0006372","HMDB0000288","HMDB0000267","HMDB0003426"]}}