| Preface | 5 |
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| Contents | 6 |
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| Contributors | 8 |
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| Part I: Innovation of Imaging Mass Spectrometry | 10 |
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| Chapter 1 | 11 |
| IMS as an Historical Innovation | 11 |
| References | 15 |
| Part II: Planning the Sample Preparation | 16 |
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| Chapter 2 | 17 |
| Guide to Planning the Sample Preparation Step | 17 |
| 2.1 Introduction | 17 |
| 2.2 Characteristics of MALDI in Direct Tissue Mass Spectrometry | 18 |
| 2.3 IMS for Proteins and Peptides | 20 |
| 2.3.1 On-Tissue Digestion Method | 24 |
| 2.3.2 Application to Protein Studies | 24 |
| 2.4 IMS for Small Organic Compounds | 25 |
| 2.4.1 IMS for Endogenous Metabolites | 29 |
| 2.4.2 Application to Lipid Studies | 30 |
| 2.4.3 Imaging of Administered Drugs | 30 |
| 2.5 Conclusion | 34 |
| References | 35 |
| Part III: Sample Preparation | 37 |
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| Chapter 3 | 38 |
| Animal Care and Tissue Sample Extraction for IMS | 38 |
| 3.1 Methods of Mouse Euthanasia | 38 |
| 3.1.1 Euthanasia by Anesthetics | 38 |
| 3.1.2 Cervical Dislocation | 39 |
| 3.1.3 Decapitation | 39 |
| 3.2 Anatomy of the Mouse | 39 |
| 3.3 Freezing of the Mouse Brain | 40 |
| 3.3.1 Materials | 40 |
| 3.3.2 Procedure | 41 |
| 3.4 Samples Other Than Mouse Brain | 42 |
| 3.5 Evaluation of the Time Elapsed After Death in Animals | 43 |
| Chapter 4 | 45 |
| Preparing Biological Tissue Sections for Imaging Mass Spectrometry | 45 |
| 4.1 Introduction | 45 |
| 4.2 Embedding | 47 |
| 4.3 Excision of Thin Slices | 48 |
| 4.4 Section Support Materials | 49 |
| 4.5 Postmortem Degradation | 50 |
| 4.6 Rinsing of Tissue Sections with Organic Solvents | 53 |
| 4.7 Staining of Tissue Sections Before IMS Measurement | 55 |
| 4.8 A Standard Procedure for Preparing Frozen Sections | 56 |
| 4.8.1 Materials | 56 |
| 4.8.2 Methods | 56 |
| 4.8.3 Notes | 56 |
| 4.9 Conclusion | 57 |
| References | 57 |
| Chapter 5 | 59 |
| Matrix Choice | 59 |
| 5.1 Principle of Molecular Ionization | 59 |
| 5.2 Choice of Matrices | 60 |
| 5.2.1 Ionic Matrices | 61 |
| 5.2.2 Challenges for Imaging of Primary Metabolites in m / z | 61 |
| 62 | 61 |
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| 5.2.3 Nanoparticle-Based IMS | 63 |
| 5.3 Composition of Matrix Solvent | 66 |
| References | 72 |
| Chapter 6 | 74 |
| Methods of Matrix Application | 74 |
| 6.1 Introduction | 74 |
| 6.2 Manual Spray-Coating | 75 |
| 6.2.1 Protocol of Spraying Operation with an Artistic Air-Brush | 76 |
| 6.2.2 Preparation of Matrix Solution | 77 |
| 6.2.3 Matrix Application with an Artistic Air-Brush | 77 |
| Note | 77 |
| 6.2.4 Other Notes | 79 |
| 6.3 Automatic Dispensing of Small Droplets by the ChiP Instrument | 79 |
| 6.3.1 On-Tissue Digestion and Matrix Application with the ChIP-1000 Instrument | 80 |
| 6.3.1.1 Preparation of Trypsin Stock Solution | 81 |
| 6.3.2.1 Matrix Application Using the ChIP-1000 | 81 |
| 6.4 Spray-Droplet Method | 82 |
| 6.4.1 Protocol | 83 |
| 6.4.2 Notes Regarding the Spray-Droplet Method | 86 |
| 6.5 Matrix Sublimation Method | 86 |
| References | 88 |
| Chapter 7 | 89 |
| Matrix Applicadtion with ImagePrep | 89 |
| 7.1 Introduction | 89 |
| 7.2 The Simple GUI | 91 |
| 7.3 The Operation | 91 |
| 7.4 The Optical Sensor | 91 |
| 7.5 The Method Development GUI | 92 |
| Part IV: Instrumental Operation for IMS | 94 |
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| Chapter 8 | 95 |
| Method of Operating AXIMA-QIT as Imaging Instrument | 95 |
| 8.1 Outline of AXIMA-QIT-TOF-MS | 95 |
| 8.2 IMS by AXIMA-QIT-TOF-MS | 96 |
| 8.2.1 Acquisition of Position Information by ChIP-1000 | 96 |
| 8.2.2 Settings in AXIMA-QIT-TOF-MS | 100 |
| 8.2.3 Achieving Settings in AXIMA-QIT-TOF-MS | 102 |
| 8.2.4 Calibration | 102 |
| 8.2.5 Setting of Measurement Area | 103 |
| 8.2.6 IMS Measurement | 104 |
| 8.3 Tandem MS by AXIMA-QIT-TOF-MS | 105 |
| 8.3.1 Selection of Peak | 106 |
| 8.3.2 MS 2 Measurement | 107 |
| 8.3.3 Identification of Peptide | 108 |
| Part V: Analysis of Measurement Data | 110 |
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