MetaboLights

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s/metabolights/studies/public/MTBLS15127/FILES/MCF4278_2/WV060_MCF4278_WV76.rawprimaryOK200ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS15127Annotation of metabolites was performed by comparing exact mass and isotopic configurations. The database used for annotation was the Human Metabolome DatabaseMetaboLightsPublicSamples were run on Lumos MS using the AcquireX method. A blank sample (80% MeOH) was used to create an exclusion list (background signal). A quality control (QC) sample containing an aliquot of each sample, was used to for both quality measurement throughout the run and to create an inclusion list for metabolite identification (using fragmentation strategies). The individual samples were run in full scan mode with the range 70 - 750 m/z.Flow injection analysis MS - negativePhenomic and multiomic characterisation of microsatellite-stable colorectal cancer reveals novel biology and targets of vulnerability.Marco GiampàVIB -KU LeuvenA total of 25 µL of the aforementioned samples were analysed using an Infinity II autosampler and pump (Agilent Technologies, Santa Clara, CA, USA) coupled to a Orbitrap Lumos (Thermo Scientific) operating in both positive and negative ion mode. Both polar and apolar fractions were analysed in randomised order, and each sample was measured in triplicate. QC samples were injected every 15 runs to monitor batch effects and instrument stability. Samples were introduced to the MS by a continuous flow of 80% 2-Propanol (80:20 LC-MS grade isopropanol:H2O). The MS was operated in full scan mode over an m/z range of 107–800, with a resolution of approximately 1M, 500k, 100k in the low-, mid- and high-mass ranges, respectively.Tissuemass spectrometry assayTissue sections were homogenised in 650 µL of 60% methanol in RiboLyser tubes. The samples were stored overnight in a -80 ultrafreezer and were centrifuged the next day for 15 min at 15,000 x g at 4 °C. The protein pellets were used to normalise metabolite data and were quantified using the BCA protein assay (Thermo Fisher Scientific). Next, 500 µL of the supernatant was transferred to a fresh microfuge tube, and 500 µL of chloroform was added. This mixture was left to shake on a thermoshaker (28 °C, 1,000 rpm) for 2 hours. Subsequently, 200 µL of the upper polar phase was transferred to a liquid chromatography mass spectrometry (LC-MS vial). The lower apolar phase (450 µL) was dried in a SpeedVac concentrator, resuspended in 200 µL of 100% ethanol, and transferred to an LC-MS vial. For each phase (polar/apolar), a QC sample was generated by collecting 10 µL from each sample. Tumouroid pellets were processed using a similar extraction workflow. Pellets were resuspended in 1,000 μL of 100% methanol, stored overnight at −80 °C, and centrifuged the next day for 15 minutes at 15,000 × g at 4 °C. Next, 300 μL of the methanol extract was transferred to a fresh microcentrifuge tube, and 300 μL of chloroform was added. The mixture was vortexed for 30 seconds, followed by addition of 200 μL of molecular-grade water to induce phase separation. After vortexing for 30 seconds, samples were centrifuged for 5 minutes at 5,000 × g at 4 °C. Subsequently, 44 μL of the upper polar phase was diluted with 176 μL of methanol and transferred to an LC–MS vial.Homo sapienshttps://www.ebi.ac.uk/metabolights/MTBLS15127Bart Ghesquière. KU Leuven - Laboratory of Applied Mass Soectrometry. bart.ghesquiere@kuleuven.be.The raw were uploaded in Compound Discoverer softwareMultiomicsCancermarco.giampa@kuleuven.beTissues from a total of 317 individuals diagnosed with MSS RAS mt CRC were accessed and analysed as part of the COLOSSUS study. MetabolomicsTissueOrbitrap Fusion Lumoscolorectal cancerThermo Scientific Orbitrap Fusion Lumos Tribriduntargeted analysismetabolomicsHomo sapiensMultiomicsexperimental sampleTissueOrbitrap Fusion Lumoscolorectal cancerThermo Scientific Orbitrap Fusion Lumos Tribriduntargeted analysismetabolomicsHomo sapiensMultiomicsexperimental sampleSamples were run on Lumos MS using the AcquireX method. A blank sample (80% MeOH) was used to create an exclusion list (background signal). A quality control (QC) sample containing an aliquot of each sample, was used to for both quality measurement throughout the run and to create an inclusion list for metabolite identification (using fragmentation strategies). The individual samples were run in full scan mode with the range 70 - 750 m/z.falsePhenomic and multiomic characterisation of microsatellite-stable colorectal cancer reveals novel biology and targets of vulnerabilityIntegrating data from approximately 2,000 tumour samples, corresponding to ~4,500 platform-specific multiomic sample profiles, and 195,246 single cells/nuclei from diverse in-house and publicly available datasets, single-to-integrated multiomic and clinical phenome data fusion analysis uncovers the mechanistic and molecular complexity of microsatellite-stable colorectal cancer (MSS CRC). Nevertheless, we identify potentially actionable vulnerability targets validated in state-of-the-art patient-derived tumouroid and xenograft models. Overall, we propose FAK, PDK1/2 (PIK3CA/AKT/mTOR), and proteasomal inhibitors, combined with trametinib, as translatable combinatorial treatment strategies.2026-09-152026-07-22MTBLS15127