Data were processed in Compound Discoverer 3.3 (Thermo Fisher Scientific). Alignment tolerances were 0.2 min for RP and 1 min for HILIC; mass tolerance was set to 5 ppm. Compound annotation was performed using mzCloud™, mzVault, ChemSpider, and mass lisrs (Thermo Fisher Scientific). After preprocessing, features were manually reviewed by inspecting chromatograms and matching MS/MS spectra.
"],"repository":["MetaboLights"],"study_status":["Public"],"ptm_modification":[""],"instrument_platform":["Liquid Chromatography MS - negative - reverse-phase","Liquid Chromatography MS - positive - hilic","Liquid Chromatography MS - positive - reverse-phase","Liquid Chromatography MS - negative - hilic"],"chromatography_protocol":["RP separations used an Acquity UPLC BEH C18 column (1.7 µm, 2.1 × 100 mm) with a matching guard column. Mobile phase A consisted of water with 0.1% formic acid, and mobile phase B of methanol with 0.1% formic acid. The gradient started at 0.5% B, increased to 98% B over 11 min, held until 15 min, and then returned to initial conditions by 20 min. HILIC runs employed an Acquity UPLC BEH Amide column (1.7 µm, 2.1 × 100 mm) and guard column. Mobile phase A was 10 mM ammonium formate with 0.1% formic acid; mobile phase B contained 10 mM ammonium formate in 95% ACN/5% water with 0.1% formic acid. The gradient began at 100% B, decreased to 50% B by 10 min, and returned to 100% B by 15.5 min.
For both chromatographic methods, the column temperature was consistently maintained at 40°C, the flow rate was set at 0.35 mL/ min and the injection volume was 5 µL.
"],"publication":["Aromatic amino acid metabolism shapes autophagy-mediated adaptation to iron deprivation in glioblastoma cells. 10.1007/s10534-026-00809-7."],"submitter_affiliation":["Uni Marburg"],"submitter_name":["Lena Ludwig-Radtke"],"organism_part":["blank","cell"],"technology_type":["mass spectrometry assay"],"disease":[""],"extraction_protocol":["Cells were washed three times with pre-warmed PBS (37°C), put on dry ice, and lysed. Metabolites were extracted by scraping the cells in 1 mL of pre-cooled (−20 °C) 80% methanol. The extracts were transferred to 1.5 mL Eppendorf tubes and centrifuged at 16,000 rpm for 5 min at 4 °C. Supernatants were aliquoted (350 µL each) for reverse-phase (RP) and hydrophilic interaction chromatography (HILIC) analysis, and an additional aliquot (250 µL) was set aside to prepare a pooled QC sample processed in parallel with all other samples. All aliquots were dried overnight in a speed vacuum concentrator and reconstituted in the appropriate RP or HILIC solvents prior to analysis.
"],"organism":["blank","Homo sapiens"],"full_dataset_link":["https://www.ebi.ac.uk/metabolights/MTBLS15394"],"author":["Jörg Bartsch. Philipps University of Marburg. Baldingerstrasse, 35043 Marburg, Germany. jbartsch@med.uni-marburg.de."],"data_transformation_protocol":["Peak areas were normalized to cell counts and corrected using QC-based adjustments. Peak lists from the four analytical modes (HILIC positive/negative and RP positive/negative) were merged in R. When the same compound appeared in more than one mode, the signal with the highest abundance was retained. The final merged dataset was used for downstream bioinformatic analysis.
"],"study_factor":["Treatment"],"submitter_email":["ludwigle@staff.uni-marburg.de"],"sample_collection_protocol":["
U87 and U251 human glioma cell lines were maintained under standard adherent culture conditions. Cells were cultured in Dulbecco’s Modified Eagle Medium (DMEM, 41965039, Gibco, USA) supplemented with 10% fetal bovine serum (FBS, FBS-16A, Capricorn, Germany), 1% sodium pyruvate (12539059, Gibco, USA), 1% penicillin/streptomycin (FS-B, Capricorn, Germany), and 1% non-essential amino acids (NEAA, 12084947, Gibco, USA). All cells were incubated at 37°C under 5% CO2 humidified incubator. Cells were regularly tested to be mycoplasma-free.
"],"omics_type":["Metabolomics"],"study_design":["cell lysate","ultra-performance liquid chromatography-mass spectrometry","Thermo Scientific Vanquish UHPLC System","blank","untargeted analysis","untargeted metabolites","Homo sapiens","cancer","cell","Orbitrap Exploris 480"],"curator_keywords":["cell lysate","ultra-performance liquid chromatography-mass spectrometry","Thermo Scientific Vanquish UHPLC System","blank","untargeted analysis","untargeted metabolites","Homo sapiens","cancer","cell","Orbitrap Exploris 480"],"mass_spectrometry_protocol":["The Orbitrap Exploris 480 was operated at 3.5 kV in positive mode and −3 kV in negative mode. Vaporizer temperatures were 320 °C for HILIC and 250 °C for RP. The ion transfer tube temperature was 275 °C for all runs. Sheath, auxiliary, and sweep gases were set to 40, 8, and 1 a.u., respectively, using nitrogen 5.0. Spectra were acquired from m/z 70–800.
For MS1 scans, the resolution was 90,000, with standard AGC and maximum injection times of 100 ms (HILIC) or 384 ms (RP). In ddMS2 mode, resolution was set to 30,000 with standard AGC and an injection time of 54 ms.
Data were processed in Compound Discoverer 3.3 (Thermo Fisher Scientific). Alignment tolerances were 0.2 min for RP and 1 min for HILIC; mass tolerance was set to 5 ppm.
"],"additional_accession":[]},"is_claimable":false,"name":"Aromatic amino acids metabolism shapes autophagy mediated adaptation to iron deprivation in glioma","description":"GBM displays profound iron dependence and metabolic plasticity, yet how iron deprivation interfaces with stress-response pathways and amino acid metabolism in glioma remains incompletely understood. DFO, an iron chelator and hypoxia mimetic, is widely used experimentally, but the integration of autophagy, apoptosis, and ferroptosis under DFO-induced stress is unclear. This study aims to clarify how iron chelation reshapes stress signaling and metabolism in glioma cells and to define the role of aromatic amino acid metabolism in autophagy-mediated adaptation to iron deprivation.
","dates":{"publication":"2026-08-20","submission":"2026-08-19"},"accession":"MTBLS15394","cross_references":{}}