MetaboLights

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ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS10846/m_MTBLS10846_MSImaging___metabolite_profiling_v2_maf.tsvftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS10846/a_MTBLS10846_MSImaging___metabolite_profiling.txtftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS10846/i_Investigation.txtftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS10846/s_MTBLS10846.txtftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS10846/FILES/DERIVED_FILES/Figure6a_HpStomach_E3B3S15_1wk_infected.imzMLftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS10846/FILES/RAW_FILES/Figure6e_coloreactaltumour.ibdftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS10846/FILES/DERIVED_FILES/Figure6e_coloreactaltumour.imzMLftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS10846/FILES/DERIVED_FILES/SIFigure9_jejunum.imzMLftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS10846/FILES/RAW_FILES/Figure6a_HpStomach_E3B3S15_1wk_infected.ibdftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS10846/FILES/RAW_FILES/SIFigure9_jejunum.ibdprimaryOK200ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS10846No metabolite identification has been performed.MetaboLightsPublicMS Imaging -Universal, untargeted detection of bacteria in human tissues using spatial metabolomics.James S McKenzieImperial College, Londoncolonstomachjejunummass spectrometryMus musculushttps://www.ebi.ac.uk/metabolights/MTBLS10846Wei Chen. Technische Universität München. chemie_wei.chen@tum.de.Nicole Strittmatter. Technische Universität München. nicole.strittmatter@tum.de.Min Qiu. Technische Universität München. min.qiu@tum.de.James McKenzie. Imperial College London. j.mckenzie@imperial.ac.uk.All Thermo raw mass spectrometric data were converted to mzML format first via MSConvertGUI and to imzML format via imzML Converter with centroid mode. Refs:[1] Holman, J. D., Tabb, D. L. & Mallick, P. Employing ProteoWizard to Convert Raw Mass Spectrometry Data. Curr Protoc Bioinformatics 46, 13.24.11-13.24.19 (2014). https://doi.org:10.1002/0471250953.bi1324s46[2] Race, A. M., Styles, I. B. & Bunch, J. Inclusive sharing of mass spectrometry imaging data requires a converter for all. J Proteomics 75, 5111-5112 (2012). https://doi.org:10.1016/j.jprot.2012.05.035Infectionj.mckenzie@imperial.ac.ukThe murine colorectal tumour tissue (compound transgenic strain Apc+/1638N on a C57/BL6N background) and murine jejunum tissue (BALB/c mouse) were offered by the Department of Surgery, School of Medicine, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany. Animal experiments were carried out following institutional and national guidelines and regulations. Helicobacter pylori-infected stomach tissue was offered by the Institute of Medical Microbiology, Immunology and Hygiene, Technische Universität München, Munich, Germany.MetabolomicsNo histology was performed on these samples.Fresh frozen tissues were embedded in hydroxypropyl methylcellulose (HPMC) and polyvinylpyrrolidone (PVP) mix (3:1, m/m) as described in the reference and cryosectioned with a thickness of 10 µm and thaw mounted onto Superfrost glass slides and stored under -80 °C until analysis.  Ref: [1] Dannhorn, A. et al. Universal Sample Preparation Unlocking Multimodal Molecular Tissue Imaging. Analytical Chemistry 92, 11080-11088 (2020). https://doi.org:10.1021/acs.analchem.0c00826colorectal cancermass spectrometryDesorption electrospray ionisation imaging mass spectrometrycolorectal cancermass spectrometryDesorption electrospray ionisation imaging mass spectrometryA home-built DESI ion source was used for imaging and the analysis was performed on a Q Exactive Orbitrap Mass Spectrometers (Thermo Fisher Scientific Inc., Bremen, Germany). The mass resolution used for all measurements was set to 70,000 at 200 m/z. The spatial resolution of the imaging experiments was set to 75 µm, except for the murine jejunum tissue at 80 µm. The height distance between the DESI sprayer and the sample surface was set to 4 mm; the distance between the sprayer and the inlet capillary was 7 mm. All presented spectra were recorded in negative ion mode. Mass spectra were recorded in the mass range of m/z = 200-1000 for the colorectal tumour tissue and jejunum tissue, and for the Helicobacter pylori-infected stomach tissue: m/z = 100-600. Methanol:water (95:5 v/v) was used as electrospray solvent at a flow rate of 1.3 µL/min and spray voltage of -4.5 kV with a spray angle of 80°. Nitrogen N4.8 was used as nebulising gas at a pressure of 7 bars. The inlet capillary temperature was 320 °C. S-lens RF level at 100.falseDESI mass spectrometry imaging of murine tissuesDESI-MS imaging results of a murine colorectal tumour tissue, a murine jejunum tissue and a Helicobacter pylori-infected murine stomach tissue are available. Data were all obtained under negative ion mode. Corresponding H&E staining results can be found in the associated publication2025-07-102024-08-21MTBLS10846