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Molecular Imaging of Mouse Brain Tissue Using Cluster Time-Of-Flight

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Molecular Imaging of Mouse Brain Tissue Using Cluster Time-Of-Flight Molecular imaging of mouse brain tissue using Cluster Time-of-Flight Secondary Ion Mass Spectrometry A thesis submitted to The University of Manchester for the degree of Doctor of Philosophy in the Faculty of Engineering and Physical Sciences Irma Berrueta Razo 2015 The University of Manchester Faculty of Engineering and Physical Sciences School of Chemistry Contents Contents ............................................................................................................................................................................... 2 List of Figures ..................................................................................................................................................................... 7 List of Tables .................................................................................................................................................................... 22 List of Equations ............................................................................................................................................................. 23 Abbreviations ................................................................................................................................................................... 24 Abstract .............................................................................................................................................................................. 26 Declaration ........................................................................................................................................................................ 27 Copyright Statement ..................................................................................................................................................... 27 Acknowledgements ....................................................................................................................................................... 28 1 Introduction ............................................................................................................................................................ 29 1.1 Aim of the study ............................................................................................................................................ 30 2 Literature review .................................................................................................................................................. 31 2.1 Secondary ion mass spectrometry (SIMS) ......................................................................................... 31 2.1.1 SIMS basic experimental parameters ......................................................................................... 31 2.1.2 Damage cross section ....................................................................................................................... 32 2.2 SIMS methodologies .................................................................................................................................... 33 2.2.1 Static SIMS ............................................................................................................................................. 33 2.2.2 Dynamic SIMS ...................................................................................................................................... 34 2.2.3 Molecular imaging with SIMS ........................................................................................................ 34 2.3 ToF-SIMS .......................................................................................................................................................... 36 2.3.1 Analysis beams used in ToF-SIMS ............................................................................................... 36 2.3.2 Physics of polyatomic projectiles ................................................................................................ 37 2.3.3 Time-of-Flight mass analysers ...................................................................................................... 39 2.4 Data processing for ToF-SIMS................................................................................................................. 41 2.4.1 Multivariate analysis ......................................................................................................................... 41 2.5 ToF-SIMS imaging of biological systems ............................................................................................ 44 2.5.1 Complementary techniques in mass spectrometry imaging for the analysis of biological systems ........................................................................................................................... 45 2 2.5.2 Targeted and untargeted metabolomic studies with MSI ................................................. 52 2.5.3 ToF-SIMS imaging of mouse brain tissue ................................................................................. 57 2.5.4 Sample preparation workflow for mouse brain imaging with ToF-SIMS ................... 61 2.5.5 Bio-medical applications of ToF-SIMS imaging ..................................................................... 63 2.5.6 Challenges of analysis of bio-systems with ToF-SIMS......................................................... 66 2.5.7 Water cluster primary ion beams ................................................................................................ 68 2.5.8 Sputtering studies .............................................................................................................................. 69 2.6 Summary .......................................................................................................................................................... 70 2.7 References ....................................................................................................................................................... 70 3 Instrumentation .................................................................................................................................................... 92 3.1 Mass resolution ............................................................................................................................................. 92 3.1.1 Obtainable mass resolution with different ToF-SIMS configurations .......................... 93 3.2 Mass accuracy ................................................................................................................................................ 94 3.3 The duty cycle ................................................................................................................................................ 94 3.4 The J105-3D Chemical imager ................................................................................................................ 94 3.4.1 Operation of the J105 instrument................................................................................................ 95 3.5 Analysis beams in the J105-3D Chemical Imager ........................................................................... 97 3.5.1 40 keV C60 ion gun .............................................................................................................................. 98 3.5.2 20 keV Gas cluster ion beam ....................................................................................................... 101 3.6 References .................................................................................................................................................... 105 4 Materials and methods .................................................................................................................................... 109 4.1 Analysis of biomolecules ........................................................................................................................ 109 4.1.1 Studied biomolecular standards ............................................................................................... 109 4.1.2 Preparation of spin-coated films for ToF-SIMS analysis ................................................. 113 4.2 Sample preparation of mouse brain tissue and brain total lipid extract ........................... 116 4.2.1 Preparation of brain total lipid extract................................................................................... 116 4.2.2 Preparing mouse brain tissue sections for ToF-SIMS analysis ..................................... 116 4.2.3 Lipid standards for ion suppression/enhancement studies ......................................... 118 3 4.3 Methodology for correlation of multi-modal imaging techniques: ToF-SIMS imaging and fluorescence microscopy ............................................................................................................ 119 4.3.1 Sample preparation of 3xTg-AD brain tissue....................................................................... 120 4.3.2 Thioflavin S staining protocol .................................................................................................... 121 4.3.3 Fluorescence microscopy imaging ........................................................................................... 123 4.3.4 Handling brain sections for ToF-SIMS imaging .................................................................. 123 4.3.5 Synthetic Amyloid-β peptide (1-40) ........................................................................................ 123 4.4 References ...................................................................................................................................................
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