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Preface XIII
List of Contributors XV
1 Lipidomics Perspective: From Molecular Lipidomics to Validated Clinical Diagnostics 1
Kim Ekroos
1.1 Introduction 1
1.2 Hierarchical Categorization of the Analytical Lipid Outputs 2
1.2.1 Lipid Class 3
1.2.2 Sum Compositions 4
1.2.3 Molecular Lipids 5
1.2.4 Structurally Defined Molecular Lipids 6
1.3 The Type of Lipid Information Delivers Different Biological Knowledge 7
1.4 Untying New Biological Evidences through Molecular Lipidomic Applications 9
1.5 Molecular Lipidomics Approaches Clinical Diagnostics 11
1.6 Current Roadblocks in Lipidomics 14
1.7 Conclusions 16
References 16
2 Lipids in Cells 21
Kai Simons, Christian Klose, and Michal Surma
2.1 Introduction 21
2.2 Basis of Cellular Lipid Distribution 22
2.3 Lipid Distribution by Nonvesicular Routes 23
2.4 Lipids in Different Cell Types 24
2.5 Functional Implications of Membrane Lipid Composition 26
2.6 Outlook: Collectives and Phase Separation 29
References 30
3 High-Throughput Molecular Lipidomics 35
Marcus Stahlman, Jan Boren, and Kim Ekroos
3.1 Introduction 35
3.2 Lipid Diversity 35
3.3 Function of Molecular Lipids 38
3.4 Automated Sample Preparation 39
3.5 Different Approaches to Molecular Lipidomics 41
3.5.1 Untargeted versus Targeted Approaches 41
3.5.2 Shotgun Lipidomics 42
3.5.3 Analytical Validation of the Shotgun Approach 44
3.5.4 Targeted LC-MS Lipidomics 45
3.6 Data Processing and Evaluation 46
3.7 Lipidomic Workflows 47
3.8 Conclusions and Future Perspectives 48
References 49
4 Multidimensional Mass Spectrometry-Based Shotgun Lipidomics 53
Hui Jiang, Michael A. Kiebish, Daniel A. Kirschner, and Xianlin Han
4.1 Introduction 53
4.2 Multidimensional Mass Spectrometry-Based Shotgun Lipidomics 53
4.2.1 Intrasource Separation 54
4.2.2 The Principle of Multidimensional Mass Spectrometry 55
4.2.3 Variables in Multidimensional Mass Spectrometry 57
4.2.3.1 Variables in Fragment Monitoring by Tandem MS Scans 57
4.2.3.2 Variables Related to the Infusion Conditions 57
4.2.3.3 Variables under Ionization Conditions 57
4.2.3.4 Variables under Collision Conditions 58
4.2.3.5 Variables Related to the Sample Preparations 58
4.3 Application of Multidimensional Mass Spectrometry-Based Shotgun Lipidomics for Lipidomic Analysis 59
4.3.1 Identification of Lipid Molecular Species by 2D Mass Spectrometry 59
4.3.1.1 Identification of Anionic Lipids 59
4.3.1.2 Identification of Weakly Anionic Lipids 59
4.3.1.3 Identification of Charge Neutral but Polar Lipids 59
4.3.1.4 Identification of Sphingolipids 59
4.3.1.5 The Concerns of the MDMS-Based Shotgun Lipidomics for Identification of Lipid Species 61
4.3.2 Quantification of Lipid Molecular Species by MDMS-Based Shotgun Lipidomics 61
4.3.2.1 The Principle of Quantification of Individual Lipid Species by MS 62
4.3.2.2 Quantification by Using a Two-Step Procedure in MDMS-Based Shotgun Lipidomics 62
4.3.2.3 Quantitative Analysis of PEX7 Mouse Brain Lipidome by MDMS-Based Shotgun Lipidomics 63
4.4 Conclusions 66
References 68
5 Targeted Lipidomics: Sphingolipidomics 73
Ying Liu, Yanfeng Chen, and M. Cameron Sullards
5.1 Introduction 73
5.2 Sphingolipids Description and Nomenclature 75
5.3 Sphingolipids Analysis via Targeted LC-MS/MS 76
5.3.1 Sphingolipid Internal Standards 77
5.3.2 Biological Sample Preparation and Storage 78
5.3.3 Sphingolipid Extraction Protocol 79
5.3.4 Liquid Chromatography 81
5.3.4.1 LCBs and Cer1P 83
5.3.4.2 Cer, HexCer, LacCer, SM, ST, and Cer1P 84
5.3.4.3 Separation of GlcCer and GalCer 85
5.3.5 Mass Spectrometry 85
5.3.5.1 Electrospray Ionization 85
5.3.5.2 Tandem Mass Spectrometry 86
5.3.5.3 Multiple Reaction Monitoring 88
5.3.6 Generation of Standard Curves 89
5.3.7 Data Analysis 90
5.3.8 Quality Control 90
5.4 Applications of Sphingolipidomics in Biology and Disease 91
5.4.1 LC-MS/MS 91
5.4.2 Transcriptomic Guided Tissue Imaging Mass Spectrometry 92
5.5 Conclusions 94
References 94
6 Structural Lipidomics 99
Todd W. Mitchell, Simon H.J. Brown, and Stephen J. Blanksby
6.1 Introduction 99
6.2 Lipid Structure 100
6.3 Structural Analysis of Lipids by Mass Spectrometry 100
6.4 sn Position 105
6.5 Double Bond Position 107
6.5.1 Untargeted Fragmentation 108
6.5.2 Targeted Fragmentation 115
6.6 Double Bond Stereochemistry 122
6.7 Conclusions 123
References 124
7 Imaging Lipids in Tissues by Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry 129
Robert M. Barkley, Joseph A. Hankin, Karin A. Zemski Berry, and Robert C. Murphy
7.1 Introduction 129
7.2 Sample Preparation 130
7.3 Matrix 131
7.3.1 Techniques for Matrix Application 131
7.3.2 Matrix Compounds 133
7.4 Instrumentation 134
7.4.1 Lasers and Rastering 134
7.4.2 Ion Formation 136
7.4.3 Mass Analyzers and Ion Detection 137
7.5 Data Processing 139
7.6 Conclusions 141
References 142
8 Lipid Informatics: From a Mass Spectrum to Interactomics 147
Christer S. Ejsing, Peter Husen, and Kirill Tarasov
8.1 Introduction 147
8.2 Lipid Nomenclature 148
8.3 Basic Properties of Lipid Mass Spectrometric Data 151
8.3.1 Mass Spectrum 152
8.3.2 Mass Accuracy and Reproducibility 154
8.3.3 Isotopes, Deisotoping, and Isotope Correction 154
8.4 Data Processing 158
8.4.1 De Novo Lipid Identification 159
8.4.2 Targeted Export of Lipidomic Data 161
8.4.3 Normalization of Lipidomic Data 162
8.5 Lipidomic Data Mining and Visualization 165
8.5.1 Comparative Lipidomics 165
8.5.2 Multivariate Data Analysis 166
8.5.3 Lipidomics in Biomarker Research 166
8.6 Lipidomic Data Integration 168
8.7 Conclusions and Future Perspectives 169
References 170
9 Lipids in Human Diseases 175
M. Mobin Siddique and Scott A. Summers
9.1 Introduction 175
9.2 Obesity 176
9.3 Dyslipidemia 177
9.4 Diabetes 177
9.5 Cardiovascular Disorders 179
9.6 Hereditary Sensory Neuropathy 181
9.7 Neurodegeneration 182
9.8 Cancer 184
9.9 Lysosomal Storage Disorders 186
9.10 Cystic Fibrosis 187
9.11 Anti-Inflammatory Lipid Mediators 188
9.12 Conclusions 188
References 189
10 Lipidomics in Lipoprotein Biology 197
Marie C. Lhomme, Laurent Camont, M. John Chapman, and Anatol Kontush
10.1 Introduction 197
10.2 Metabolism of Lipoproteins 198
10.3 Lipoproteinomics in Normolipidemic Subjects 200
10.3.1 Phospholipids 202
10.3.1.1 Phosphatidylcholine 202
10.3.1.2 Lysophosphatidylcholine 202
10.3.1.3 Phosphatidylethanolamine 203
10.3.1.4 Phosphatidylethanolamine Plasmalogens 203
10.3.1.5 Phosphatidylinositol, Phosphatidylserine, Phosphatidylglycerol, and Phosphatidic Acid 203
10.3.1.6 Cardiolipin 203
10.3.1.7 Isoprostane-Containing PC 203
10.3.2 Sphingolipids 203
10.3.2.1 Sphingomyelin 204
10.3.2.2 Lysosphingolipids 204
10.3.2.3 Ceramide 204
10.3.2.4 Minor Sphingolipids 204
10.3.3 Sterols 205
10.3.4 Cholesteryl Esters 205
10.3.5 Triacylglycerides 205
10.3.6 Minor Lipids 205
10.4 Altered Lipoproteinomics in Dyslipidemia 206
10.4.1 Phospholipids 206
10.4.1.1 Phosphatidylcholine 206
10.4.1.2 Lysophosphatidylcholine 207
10.4.1.3 Phosphatidylethanolamine 208
10.4.1.4 Phosphatidylethanolamine Plasmalogens 208
10.4.1.5 Phosphatidylinositol 208
10.4.1.6 Isoprostane-Containing PC 208
10.4.2 Sphingolipids 209
10.4.2.1 Sphingomyelin 209
10.4.2.2 Lysosphingolipids: S1P and Dihydro S1P 209
10.4.2.3 Ceramide 210
10.4.3 Free Cholesterol 210
10.4.4 Cholesteryl Esters 210
10.4.5 Triacylglycerides 210
10.4.6 Minor Lipids 211
10.4.6.1 Nonesterified Fatty Acids 211
10.4.6.2 Ganglioside GM1 211
10.4.6.3 Oxidized Lipids 211
10.5 Conclusions 211
References 212
11 Mediator Lipidomics in Inflammation Research 219
Makoto Arita, Ryo Iwamoto, and Yosuke Isobe
11.1 Introduction 219
11.2 PUFA-Derived Lipid Mediators: Formation and Action 219
11.3 LC-ESI-MS/MS-Based Lipidomics 222
11.3.1 Sample Preparation 222
11.3.2 LC-ESI-MS/MS Analysis 223
11.4 Mediator Lipidomics in Inflammation and Resolution 226
11.5 Conclusion and Future Perspective 230
References 230
12 Lipidomics for Elucidation of Metabolic Syndrome and Related Lipid Metabolic Disorder 233
Ryo Taguchi, Kazutaka Ikeda, and Hiroki Nakanishi
12.1 Introduction 233
12.2 Basic Strategy of Lipidomics for Elucidating Metabolic Changes of Lipids at the Level of their Molecular Species in Metabolic Syndrome and Related Diseases 234
12.3 Analytical Systems by Mass Spectrometry in Lipidomics 235
12.3.1 LC-MS and LC-MS/MS Analyses for Global Detection of Phospholipids and Triglycerides 235
12.3.2 Infusion Analysis with Precursor Ion and Neutral Loss Scanning 236
12.3.3 Targeted Analysis by Multiple Reaction Monitoring for Oxidized Lipids and Lipid Mediators by LC-MS/MS on Triple-Stage Quadrupole Mass Spectrometers 236
12.4 Lipidomic Data Processing 236
12.4.1 Strategy of Lipid Search 236
12.4.2 Application and Identification Results of “Lipid Search” 237
12.5 Analysis of Lipids as Markers of Metabolic Syndrome 239
12.5.1 Oxidized Phospholipids 239
12.5.1.1 Application for Myocardial Ischemia-Reperfusion Model 239
12.5.2 Bioactive Acidic Phospholipids 240
12.5.2.1 Lysophosphatidic Acid 240
12.5.2.2 Phosphoinositides 241
12.5.3 Oxidative Triglycerides 241
12.5.3.1 Application for Mouse White Adipose Tissue 242
12.5.4 Sphingolipids 244
12.5.4.1 Application for Sphinogolipid Metabolism 244
12.6 Direct Detection of Lipid Molecular Species in Specific Tissue Domains by Disease-Specific Changes 245
12.7 Conclusions 245
References 246
13 Lipidomics in Atherosclerotic Vascular Disease 251
Minna T. J€anis and Reijo Laaksonen
13.1 Introduction 251
13.2 Lipids and Atherosclerotic Vascular Disease 253
13.2.1 Lipoproteins 254
13.2.2 Atherosclerotic Plaque 255
13.2.3 Molecular Lipids 256
13.2.3.1 Eicosanoids 256
13.2.3.2 Sphingolipids and Cholesterol 257
13.2.3.3 Phospholipids 258
13.2.4 Animal Models of Atherosclerotic Research 259
13.3 Diagnostics and Treatment 260
13.3.1 Diagnostic Biomarkers of Atherosclerosis 260
13.3.2 Lipidomics in Efficacy and Safety Measurements 261
13.4 Conclusions 262
References 263
14 Lipid Metabolism in Neurodegenerative Diseases 269
Lynette Lim, Guanghou Shui, and Markus R. Wenk
14.1 Introduction 269
14.1.1 Brain Lipids 270
14.1.2 Mass Spectrometry of Brain Lipids 272
14.2 Alzheimer’s Disease 275
14.2.1 Cholesterol and Cholesterol Esters 276
14.2.2 Sulfatides 277
14.2.3 Plasmalogen Ethanolamines 277
14.2.4 Phospholipases 278
14.2.4.1 Phospholipase A2 278
14.2.4.2 Phospholipase C and Phospholipase D 279
14.3 Parkinson’s Disease 281
14.3.1 Cerebrosides 283
14.3.2 Coenzyme Q 284
14.3.3 Endocannabinoids 285
14.4 Conclusions 287
References 288
15 The Tumor Mitochondrial Lipidome and Respiratory Bioenergetic Insufficiency 297
Thomas N. Seyfried, Jeffrey H. Chuang, Lu Zhang, Xianlin Han, and Michael A. Kiebish
15.1 Introduction 297
15.1.1 Lipidomic Abnormalities in Tumor Mitochondria 298
15.2 Cardiolipin and Electron Transport Chain Abnormalities in Mouse Brain Tumor Mitochondria 299
15.3 Complicating Influence of the in vitro Growth Environment on Cardiolipin Composition and Energy Metabolism 307
15.4 Bioinformatic Methods to Interpret Alterations in the Mitochondrial Lipidome 311
15.5 Conclusions 314
References 314
16 Lipidomics for Pharmaceutical Research 319
Yoshinori Satomi
16.1 Introduction 319
16.2 Biomarkers for Pharmaceutical Research 320
16.3 Strategy for Biomarker Discovery 321
16.4 Conclusions 326
References 326
Index 329
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