MetaboLights

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ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS14374/m_MTBLS14374_LC-MS_negative_reverse-phase-2_v2_maf.tsvftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS14374/m_MTBLS14374_LC-MS_positive_reverse-phase_v2_maf.tsvftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS14374/m_MTBLS14374_LC-MS_negative_reverse-phase_v2_maf.tsvftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS14374/m_MTBLS14374_LC-MS_negative_reverse-phase-3_v2_maf.tsvftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS14374/m_MTBLS14374_LC-MS_alternating_hilic_v2_maf.tsvftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS14374/m_MTBLS14374_LC-MS_positive_reverse-phase-2_v2_maf.tsvftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS14374/m_MTBLS14374_LC-MS_negative_reverse-phase-1_v2_maf.tsvftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS14374/m_MTBLS14374_LC-MS_alternating_hilic-1_v2_maf.tsvftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS14374/m_MTBLS14374_LC-MS_positive_reverse-phase-1_v2_maf.tsvftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS14374/m_MTBLS14374_LC-MS_positive_reverse-phase-3_v2_maf.tsvftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS14374/a_MTBLS14374_LC-MS_positive_reverse-phase-2.txtftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS14374/a_MTBLS14374_LC-MS_positive_reverse-phase.txtftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS14374/a_MTBLS14374_LC-MS_negative_reverse-phase-2.txtftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS14374/a_MTBLS14374_LC-MS_alternating_hilic-1.txtftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS14374/a_MTBLS14374_LC-MS_alternating_hilic.txtftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS14374/a_MTBLS14374_LC-MS_negative_reverse-phase-3.txtftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS14374/i_Investigation.txtftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS14374/a_MTBLS14374_LC-MS_positive_reverse-phase-1.txtftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS14374/a_MTBLS14374_LC-MS_positive_reverse-phase-3.txtftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS14374/s_MTBLS14374.txtftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS14374/a_MTBLS14374_LC-MS_negative_reverse-phase-1.txtftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS14374/a_MTBLS14374_LC-MS_negative_reverse-phase.txtprimaryOK200ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS14374Post-processing of raw MS data was performed using MZmine version 4.9.14, generating a list of high-confidence annotated (Schymanski EL, et al. Identifying small molecules via high resolution mass spectrometry: communicating confidence. Environ Sci Technol. 2014) metabolites detected in more than 90% of samples.MetaboLightsPublicLiquid Chromatography MS - alternating - hilicLiquid Chromatography MS - negative - reverse-phaseLiquid Chromatography MS - positive - reverse-phaseBatches 1 & 2Dried samples were resuspended in 80 µL of a 20:80 acetonitrile-H2O mixture (high pressure liquid chromatography grade, Merck Millipore) and stored at −20 °C until use. Chromatographic analysis was performed with the DIONEX Ultimate 3000 HPLC system coupled to a chromatographic column (Phenomenex Synergi 4 u Hydro-RP 80A 250×3.0 mm) set at 40 °C and a flow rate of 0.9 mL/min. Gradients of mobile phases (mobile phase A: 0.1% formic acid in water and mobile phase B: 0.1% formic acid in acetonitrile) were performed over a total of 25 minutes. Batches 3 & 4Chromatographic separation was performed with the DIONEX UltiMate 3000 HPLC system coupled to two different columns to enrich metabolome coverage. For reverse-phase chromatography, samples were resuspended in 80 μL of a 90:10 Mili-Q water/acetonitrile (hypergrade for LC-MS, LiChrosolv, Supelco, Merck, Molsheim, France) mixture with 0.1% formic acid (Optima LC/MS, Fisher Chemical, Thermo Fisher Scientific). A Hypersil GOLD C18 100 × 2.1 mm × 1.9 µm (Thermo Fisher Scientific, France) was used with a mobile phase consisting of 0.1% formic acid in Mili-Q water (A) and 0.1% formic acid in acetonitrile (B) at a flow rate of 0.4 mL/min (40 °C) over 16 min. The gradient started at 0% (B) for 1 min, increased to 100% (B) over 10 min, was maintained at 100% (B) for 2 min, and then returned to 0% (B) in 1 min, and the column was equilibrated at 0% (B) for 2 min. For hydrophilic interaction liquid chromatography (HILIC), samples were resuspended in 80 μL of a 90:10 Acetonitrile/Mili-Q water mixture with 0.1% formic acid. A SeQuant ZIC-HILIC Peek Coated (150 × 2.1 mm × 5 µm) (Merck Millipore, Billerica, MA, USA) column was used with a mobile phase consisting of Mili-Q water plus 16 mM ammonium formate (A) and 0.1% formic acid in acetonitrile (B) at a flow rate of 0.4 mL/min (40 °C) over 27 min. The gradient started at 97% (B) for 2 min, decreased to 70% (B) over 8 min and to 10% (B) in 5 min, then was maintained at 10% (B) for 2 min, was returned to 97% (B) in 1 min and held at 97% (B) until the end of the gradient for column equilibration. Samples were randomly assigned to the injection (5 µL), and quality control samples (QC, a pool of all samples of a biological matrix) were injected several times at the beginning for column equilibration and interspersed every set of five samples throughout the experimental sequence to evaluate the data quality. The extraction blank of the solvent mixture was analyzed at the beginning of the experimental batch sequence. Metabolome of 334 cerebral thrombi (in four batches) retrieved by mechanical thrombectomy after ischemic stroke due to large vessel occlusion (Retro-MATISSE study).Laurent SUISSAC2VN - Aix-Marseille UniversityBlood Clotmass spectrometry assayFor the metabolomic analysis, a volume of supernatant corresponding to 80 µg of protein was mixed with 5 volumes of methanol (high pressure liquid chromatography grade, Merck Millipore) and incubated overnight at −20 °C for protein precipitation. After centrifugation (13,000 × g for 15 minutes at 4 °C), the supernatant was collected and dried using a SpeedVac concentrator (SVC100H, Savant, Thermo Fisher Scientific, Illkirch, France) for batches 1 and 2, or a nitrogen evaporator for batches 3 and 4.Homo sapienshttps://www.ebi.ac.uk/metabolights/MTBLS14374Laurent SUISSA. Aix-Marseille Université. laurent.suissa@univ-amu.fr.Emilie DOCHE. Aix-Marseille Université. emilie.doche@ap-hm.fr.Metabolomic data were log-transformed and normalized using autoscaling.RTPA usedlaurent.suissa@univ-amu.frEach thrombus, in single or multiple fragments, was rinsed with cold saline solution after extraction by mechanical thrombectomy and stored at −80 °C. Initial processing of cerebral thrombi. The frozen thrombotic material was briefly rinsed in ice-cold saline solution and then crushed manually for 90 seconds in lysis buffer (7 mol/L urea, 2 mol/L thiourea, 4% n-dodecyl-β-D-maltoside, 50 mmol/L dithiothreitol) at 4 °C to break up the clots. After incubation for 20 minutes at 4 °C, the material was again homogenized for 90 seconds to obtain homogenates of similar consistency for all samples. For thrombi in batch 3, samples were processed exclusively by mechanical grinding using a metal homogenizer under liquid nitrogen. No lysis buffer was used in this batch. After centrifugation of the homogenates (13 000 g for 15 minutes at 4 °C), the supernatants were collected and the Bradford assay (Bio-Rad Protein Assay; Bio-Rad) was used to determine the protein concentrations. Metabolomicspositive ionization polaritypooled quality control sampleMetabolomicsuntargeted analysisThrombusnegative ionization polarityHomo sapiensHydrophilic interaction chromatography (HILIC)Thermo Scientific Dionex Ultimate 3000 HPLC systemThermo Scientific Q Exactive Plusexperimental sampleThrombectomy of arteryBatch#3reverse phase chromatographyBatch#4experimental blankBatch#1Batch#2ischemic strokeBlood Clotpositive ionization polaritypooled quality control sampleMetabolomicsuntargeted analysisThrombusnegative ionization polarityHomo sapiensHydrophilic interaction chromatography (HILIC)Thermo Scientific Dionex Ultimate 3000 HPLC systemThermo Scientific Q Exactive Plusexperimental sampleThrombectomy of arteryBatch#3reverse phase chromatographyBatch#4experimental blankBatch#1Batch#2ischemic strokeBlood ClotMS analysis was performed on a Thermo Scientific Exactive Plus Benchtop Orbitrap mass spectrometer. The heated electrospray ionization source was used in positive and negative ion modes. Full-scan data-dependent MS/MS (ddMS²) acquisition was performed in both positive and negative ionization modes over an m/z range of 80–1000 with a mass resolving power of 35,000 full width at half maximum (FWHM). SorbitolTaurineCitrateTetradecanedioic acidGlucoseHistidine16-Hydroxyhexadecanoic acidGlutamic_acidMalic acidGlyceric acidGluconic acidPhosphoric acidN-AcetylglycineThreonineAMPIle-LeuFA 18:1+3O2'.4'-DIHYDROXYACETOPHENONEGLUCOSE 6-PHOSPHATESALICYLATEN-UndecanoylglycineCitrullineUndecanedioic acidUrocanic acidSebacic acidFERULATESuccinic acidGlutamic acidSuberic acid5-OXO-L-PROLINEPyruvic acidAuraptenInosine monophosphateGuanosine monophosphateArginineProstaglandin F2aAZELAIC ACIDCanrenoneAspartatePimelic acidThreonic acidUric acidN-Acetylneuraminic Acid12,13-DiHOMEDodecylbenzenesulfonic acidQuinic acidFumaric acidGingerolAsparagine3-Oxohexadecanoic acidLactic acidGlutaminefalseMetabolome of 334 cerebral thrombi (in four batches) retrieved by mechanical thrombectomy after ischemic stroke due to large vessel occlusion (Retro-MATISSE study)The Retro-MATISSE study (Molecular Analysis of Thrombus for Ischemic Stroke prognosiS and Etiology) aimed to characterize the metabolome of 334 thrombi retrieved by mechanical thrombectomy after ischemic stroke due to large vessel occlusion. LC–MS analysis of the thrombi was performed in four batches: • Batch 1: NCE1 to NCE60 (59 samples) • Batch 2: MAR1 to MAR47 (47 samples) • Batch 3: MAR50 to MAR157 (103 samples) • Batch 4: MAR158 to MAR282 (125 samples) Some patients received intravenous thrombolytic therapy with rt-PA prior to mechanical thrombectomy, in accordance with current guidelines. The objective of this study was to identify molecular signatures of thrombi associated with different clinical outcomes, including resistance to thrombolytic therapy, arterial recanalization rate, functional outcome, and the etiology of cerebral infarction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