Imaging Mass Spectrometry (eBook)

Preface 5
Contents 6
Contributors 8
Part I: Innovation of Imaging Mass Spectrometry 10
Chapter 1 11
IMS as an Historical Innovation 11
References 15
Part II: Planning the Sample Preparation 16
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
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 < 1,000 Region
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
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
Chapter 9 111
Ion Image Reconstruction Using BioMap Software 111
9.1 Introduction 111
9.2 Required Environment for Installation 112
9.3 Setup of BioMap (in Windows XP Operating System) 113
9.4 Example of Ion Image Reconstruction from IMS Data 115
9.5 Comparison Analysis of Mass Spectra in Each ROI 120
References 124
Chapter 10 125
Statistical Procedure for IMS Data Analysis 125
10.1 Introduction 125
10.2 IMS Linked to Multivariate Analysis 126
10.3 IMS-PCA on the Genetically Manipulated Mouse Brain 129
10.4 IMS of WT and Scr-KO Mouse Brain Sections 130
10.4.1 Materials Used and Measurement Conditions 131
10.4.2 IMS-PCA of WT and Scr-KO Mouse Brains 133
10.4.3 Data Interpretation of PCA 133
10.4.3.1 Interpretation of Component Scores 133
10.4.3.2 Interpretation of Factor Loading 135
10.5 Conclusion 139
References 139
Chapter 11 141
Statistical Analysis of IMS Dataset with ClinproTool Software 141
11.1 PCA of IMS Dataset with ClinProTools Software 141
11.1.1 PCA Protocol 142
11.2 Biomarker Discovery from IMS Dataset with ClinProTools 145
11.2.1 Biomarker Discovery by Comparing Two Groups 146
11.2.2 Procedure for Biomarker Discovery 147
11.2.3 Correlations Between Peaks 151
11.2.4 Correlation Matrix View 151
11.2.5 Correlation List View 153
Part VI: Applications of MALDI-IMS 154
Chapter 12 155
Imaging of Cultured Cells by Mass Spectrometry 155
12.1 Introduction 155
12.2 Preparation of Cultured Cells for IMS 158
12.2.1 Coating of ITO-Glass Slide 159
12.2.2 Preparation of SCG Cell Culture 159
12.3 MALDI-IMS of SCG Neuron 161
12.4 Supplemental: SIMS-IMS of SCG Neuron 163
References 163
Chapter 13 165
TLC-Blot-MALDI-IMS 165
13.1 Introduction 165
13.2 TLC Analysis 166
13.2.1 Materials 166
13.2.2 Reagents 166
13.2.3 TLC Method 166
13.3 Primuline Staining 167
13.3.1 Materials 167
13.3.2 Reagents 167
13.3.3 Primuline Staining Method 167
13.4 TLC-Blot 168
13.4.1 Materials 168
13.4.2 Reagents 168
13.4.3 TLC-Blot Method 168
13.5 Preparation for MS Analysis 169
13.5.1 Materials 169
13.5.2 Reagents 169
13.5.3 Method of Preparing for MS Analysis 169
13.6 Imaging Analysis 170
References 172
Part VII: IMS Applications Provided by Manufacturers 174
Chapter 14 175
Applied Biosystems 175
14.1 Introduction 175
14.2 Imaging of Rat Brain Sections on the 4800 MALDI-TOF/TOF Analyzer 176
14.2.1 Experimental Methods 177
14.2.2 Results 177
14.2.3 Conclusion 178
14.3 Multiplexing MALDI-MS Imaging Using DPI 180
14.3.1 Materials and Methods 180
14.3.1.1 Instrumentation 180
14.3.1.2 Software 180
14.3.1.3 Sample Preparation 180
14.3.1.4 Acquisition Parameters 181
14.3.2 Data Acquisition 182
14.3.3 Results 183
14.3.4 Summary 186
14.4 High-Resolution MALDI-MS Imaging 186
14.4.1 Materials and Methods 186
14.4.1.1 Instrument 186
14.4.1.2 Software 186
14.4.1.3 Sample Preparation 187
14.4.1.4 Method 187
14.4.2 Results 189
14.4.3 Summary 190
References 192
Chapter 15 193
Bruker Daltonics 193
15.1 Preparing Instrument Parameters for MALDI Imaging Experiments 193
15.1.1 Laser Diameter Settings 194
15.2 Data Acquisition and Processing with the Bruker Daltonics MALDI Imaging Solution 194
15.2.1 The Primary Image 194
15.2.2 Creating a New Imaging Sequence 195
15.3 Evaluation of the Results 197
15.3.1 Distribution of Mass Signals 197
15.4 Statistical Analysis 199
15.4.1 Statistical Analysis of Single Imaging Datasets 199
15.4.1.1 Principal Component Analysis 199
15.4.1.2 Hierarchical Clustering 200
15.4.1.3 Statistical Analysis on Many Datasets 200
15.4.2 Supervised Classification 201
Chapter 16 203
Imaging and Molecular Identification of Biomolecules on Tissue Sections with AXIMA-QIT: Shimadzu Corporation 203
16.1 Introduction 203
16.2 Imaging and Identification of Lipids in Negative Ion Detection Mode 205
16.3 Imaging of Positively Charged Lipids Within the Minute Structure of a Mouse Retina 205
16.4 Visualization of Heme B localization in Colon Cancer Liver Metastasis 208
16.5 Imaging and Identification of Peptides in Mouse Brain Sections 210
16.6 High-Performance MS n on the Tissue Surface with AXIMA-QIT 210
16.7 Conclusions 212
References 212
Chapter 17 214
MALDI Imaging with Ion-Mobility MS: Waters Corporation 214
17.1 Introduction 214
17.1.1 Physical Properties of Tissue Samples 216
17.1.2 Sample Complexity 216
17.1.3 Abundance of Compound of Interest 216
17.2 Methods 217
17.2.1 Selection of Area for Mass Analysis 217
17.2.2 Automated HDMS or MS Imaging Experiments 218
17.2.3 Ion-Mobility Data Conversion to Imaging Format 218
17.3 Results and Discussion 219
17.4 Conclusions 223
References 223
Part VIII: Comparison of SIMS and MALDI for Mass Spectrometric Imaging 225
Chapter 18 226
Comparison of SIMS and MALDI for Mass Spectrometric Imaging 226
18.1 Introduction 227
18.2 SIMS Overview 227
18.2.1 Analytical Overview 227
18.2.2 Primary Ion Sources and Ion Creation 228
18.2.3 SIMS Analyzers 231
18.2.4 Two-Dimensional Analyses 232
18.2.5 Depth Profile Analysis and 3D Analyses 235
18.2.6 Sample Preparation 238
18.3 Applications of TOF-SIMS Imaging 240
18.3.1 Tissue Cross-Section Analyses 240
18.3.2 Imaging of Disease Biomarkers 243
18.3.3 Imaging of Drugs with Controlled Drug-Release Coatings 245
18.4 Comparison of MALDI and TOF-SIMS 247
18.5 Future Developments for TOF-SIMS 247
References 248
Index 249