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E-grāmata: Lipidomics - Technologies and Applications: Technologies and Applications [Wiley Online]

Edited by (Zora Biosciences, Espoo, Finland)
  • Formāts: 356 pages
  • Izdošanas datums: 24-Oct-2012
  • Izdevniecība: Blackwell Verlag GmbH
  • ISBN-10: 3527655948
  • ISBN-13: 9783527655946
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Lipidomics - Technologies and Applications: Technologies and ApplicationsPalielināt
  • Formāts: 356 pages
  • Izdošanas datums: 24-Oct-2012
  • Izdevniecība: Blackwell Verlag GmbH
  • ISBN-10: 3527655948
  • ISBN-13: 9783527655946
Citas grāmatas par šo tēmu:
Wiley Online E-booksMore info about Wiley Online
Rokasgrāmatas mājas lapa: https://onlinelibrary.wiley.com/doi/book/10.1002/9783527655946
For students and scientists studying lipids, lipoproteins, membranes, and lipid-related diseases, specialists summarize the current status of using a lipidomic approach in which all the lipid elements and processes are considered a single complex system within a larger biological organism. Their topics include lipids in cells, multidimensional mass spectrometry-based shotgun lipidomics, lipids in human diseases, lipidomics for elucidating metabolic syndrome and related lipid metabolic disorder, and the tumor mitochondrial lipidome and respiratory bioenergic insufficiency. Annotation ©2013 Book News, Inc., Portland, OR (booknews.com)

Focusing on the practical applications, this user-oriented guide presents current technologies and strategies for systems-level lipid analysis, going beyond basic research to concentrate on commercial uses of lipidomics in biomarker and diagnostic development, as well as within pharmaceutical drug discovery and development.
The editor and authors have experience of the most recent analytical instruments and techniques, allowing them to provide here first-hand practical experience for newcomers to the field. The first half of the book covers current methodologies, ranging from global to targeted lipidomics and shotgun approaches, while the second part discusses the role of lipidomics in biomedical and pharmaceutical research, covering such diverse fields as inflammation, metabolic syndrome, cardiovascular and neurological disease. Both small and large-scale, high-throughput approaches are discussed, resulting in an invaluable source for academic and industrial research and development.
Preface xiii
List of Contributors
xv
1 Lipidomics Perspective: From Molecular Lipidomics to Validated Clinical Diagnostics
1(20)
Kim Ekroos
1.1 Introduction
1(1)
1.2 Hierarchical Categorization of the Analytical Lipid Outputs
2(5)
1.2.1 Lipid Class
3(1)
1.2.2 Sum Compositions
4(1)
1.2.3 Molecular Lipids
5(1)
1.2.4 Structurally Defined Molecular Lipids
6(1)
1.3 The Type of Lipid Information Delivers Different Biological Knowledge
7(2)
1.4 Untying New Biological Evidences through Molecular Lipidomic Applications
9(2)
1.5 Molecular Lipidomics Approaches Clinical Diagnostics
11(3)
1.6 Current Roadblocks in Lipidomics
14(2)
1.7 Conclusions
16(5)
References
16(5)
2 Lipids in Cells
21(14)
Kai Simons
Christian Klose
Michal Surma
2.1 Introduction
21(1)
2.2 Basis of Cellular Lipid Distribution
22(1)
2.3 Lipid Distribution by Nonvesicular Routes
23(1)
2.4 Lipids in Different Cell Types
24(2)
2.5 Functional Implications of Membrane Lipid Composition
26(3)
2.6 Outlook: Collectives and Phase Separation
29(6)
References
30(5)
3 High-Throughput Molecular Lipidomics
35(18)
Marcus Stahlman
Jan Boren
Kim Ekroos
3.1 Introduction
35(1)
3.2 Lipid Diversity
35(3)
3.3 Function of Molecular Lipids
38(1)
3.4 Automated Sample Preparation
39(2)
3.5 Different Approaches to Molecular Lipidomics
41(5)
3.5.1 Untargeted versus Targeted Approaches
41(1)
3.5.2 Shotgun Lipidomics
42(2)
3.5.3 Analytical Validation of the Shotgun Approach
44(1)
3.5.4 Targeted LC-MS Lipidomics
45(1)
3.6 Data Processing and Evaluation
46(1)
3.7 Lipidomic Workflows
47(1)
3.8 Conclusions and Future Perspectives
48(5)
References
49(4)
4 Multidimensional Mass Spectrometry-Based Shotgun Lipidomics
53(20)
Hui Jiang
Michael A. Kiebish
Daniel A. Kirschner
Xianlin Han
4.1 Introduction
53(1)
4.2 Multidimensional Mass Spectrometry-Based Shotgun Lipidomics
53(6)
4.2.1 Intrasource Separation
54(1)
4.2.2 The Principle of Multidimensional Mass Spectrometry
55(2)
4.2.3 Variables in Multidimensional Mass Spectrometry
57(1)
4.2.3.1 Variables in Fragment Monitoring by Tandem MS Scans
57(1)
4.2.3.2 Variables Related to the Infusion Conditions
57(1)
4.2.3.3 Variables under Ionization Conditions
57(1)
4.2.3.4 Variables under Collision Conditions
58(1)
4.2.3.5 Variables Related to the Sample Preparations
58(1)
4.3 Application of Multidimensional Mass Spectrometry-Based Shotgun Lipidomics for Lipidomic Analysis
59(7)
4.3.1 Identification of Lipid Molecular Species by 2D Mass Spectrometry
59(1)
4.3.1.1 Identification of Anionic Lipids
59(1)
4.3.1.2 Identification of Weakly Anionic Lipids
59(1)
4.3.1.3 Identification of Charge Neutral but Polar Lipids
59(1)
4.3.1.4 Identification of Sphingolipids
59(2)
4.3.1.5 The Concerns of the MDMS-Based Shotgun Lipidomics for Identification of Lipid Species
61(1)
4.3.2 Quantification of Lipid Molecular Species by MDMS-Based Shotgun Lipidomics
61(1)
4.3.2.1 The Principle of Quantification of Individual Lipid Species by MS
62(1)
4.3.2.2 Quantification by Using a Two-Step Procedure in MDMS-Based Shotgun Lipidomics
62(1)
4.3.2.3 Quantitative Analysis of PEX7 Mouse Brain Lipidome by MDMS-Based Shotgun Lipidomics
63(3)
4.4 Conclusions
66(7)
References
68(5)
5 Targeted Lipidomics: Sphingolipidomics
73(26)
Ying Liu
Yanfeng Chen
M. Cameron Sullards
5.1 Introduction
73(2)
5.2 Sphingolipids Description and Nomenclature
75(1)
5.3 Sphingolipids Analysis via Targeted LC-MS/MS
76(15)
5.3.1 Sphingolipid Internal Standards
77(1)
5.3.2 Biological Sample Preparation and Storage
78(1)
5.3.3 Sphingolipid Extraction Protocol
79(2)
5.3.4 Liquid Chromatography
81(2)
5.3.4.1 LCBs and Cer1P
83(1)
5.3.4.2 Cer, HexCer, LacCer, SM, ST, and Cer1P
84(1)
5.3.4.3 Separation of GlcCer and GalCer
85(1)
5.3.5 Mass Spectrometry
85(1)
5.3.5.1 Electrospray Ionization
85(1)
5.3.5.2 Tandem Mass Spectrometry
86(2)
5.3.5.3 Multiple Reaction Monitoring
88(1)
5.3.6 Generation of Standard Curves
89(1)
5.3.7 Data Analysis
90(1)
5.3.8 Quality Control
90(1)
5.4 Applications of Sphingolipidomics in Biology and Disease
91(3)
5.4.1 LC-MS/MS
91(1)
5.4.2 Transcriptomic Guided Tissue Imaging Mass Spectrometry
92(2)
5.5 Conclusions
94(5)
References
94(5)
6 Structural Lipidomics
99(30)
Todd W. Mitchell
Simon H.J. Brown
Stephen J. Blanksby
6.1 Introduction
99(1)
6.2 Lipid Structure
100(1)
6.3 Structural Analysis of Lipids by Mass Spectrometry
100(5)
6.4 sn Position
105(2)
6.5 Double Bond Position
107(15)
6.5.1 Untargeted Fragmentation
108(7)
6.5.2 Targeted Fragmentation
115(7)
6.6 Double Bond Stereochemistry
122(1)
6.7 Conclusions
123(6)
References
124(5)
7 Imaging Lipids in Tissues by Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry
129(18)
Robert M. Barkley
Joseph A. Hankin
Karin A. Zemski Berry
Robert C. Murphy
7.1 Introduction
129(1)
7.2 Sample Preparation
130(2)
7.3 Matrix
132(2)
7.3.1 Techniques for Matrix Application
131(2)
7.3.2 Matrix Compounds
133(1)
7.4 Instrumentation
134(5)
7.4.1 Lasers and Rastering
134(2)
7.4.2 Ion Formation
136(1)
7.4.3 Mass Analyzers and Ion Detection
137(2)
7.5 Data Processing
139(2)
7.6 Conclusions
141(6)
References
142(5)
8 Lipid Informatics: From a Mass Spectrum to Interactomics
147(28)
Christer S. Ejsing
Peter Husen
Kirill Tarasov
8.1 Introduction
147(1)
8.2 Lipid Nomenclature
148(3)
8.3 Basic Properties of Lipid Mass spectrometric Data
151(7)
8.3.1 Mass Spectrum
152(2)
8.3.2 Mass Accuracy and Reproducibility
154(1)
8.3.3 Isotopes, Deisotoping, and Isotope Correction
154(4)
8.4 Data Processing
158(7)
8.4.1 De Novo Lipid Identification
159(2)
8.4.2 Targeted Export of Lipidomic Data
161(1)
8.4.3 Normalization of lipidomic Data
162(3)
8.5 Lipidomic Data Mining and Visualization
165(3)
8.5.1 Comparative Lipidomics
165(1)
8.5.2 Multivariate Data Analysis
166(1)
8.5.3 Lipidomics in Biomarker Research
166(2)
8.6 Lipidomic Data Integration
168(1)
8.7 Conclusions and Future Perspectives
169(6)
References
170(5)
9 Lipids in Human Diseases
175(22)
M. Mobin Siddique
Scott A. Summers
9.1 Introduction
175(1)
9.2 Obesity
176(1)
9.3 Dyslipidemia
177(1)
9.4 Diabetes
177(2)
9.5 Cardiovascular Disorders
179(2)
9.6 Hereditary Sensory Neuropathy
181(1)
9.7 Neurodegeneration
182(2)
9.8 Cancer
184(2)
9.9 Lysosomal Storage Disorders
186(1)
9.10 Cystic Fibrosis
187(1)
9.11 Anti-Inflammatory Lipid Mediators
188(1)
9.12 Conclusions
188(9)
References
189(8)
10 Lipidomics in Lipoprotein Biology
197(22)
Marie C. Lhomme
Laurent Camont
M. John Chapman
Anatol Kontush
10.1 Introduction
197(1)
10.2 Metabolism of Lipoproteins
198(2)
10.3 Lipoproteinomics in Normolipidemic Subjects
200(6)
10.3.1 Phospholipids
202(1)
10.3.1.1 Phosphatidylcholine
202(1)
10.3.1.2 Lysophosphatidylcholine
202(1)
10.3.1.3 Phosphatidylethanolamine
203(1)
10.3.1.4 Phosphatidylethanolamine Plasmalogens
203(1)
10.3.1.5 Phosphatidylinositol, Phosphatidylserine, Phosphatidylglycerol, and Phosphatidic Acid
203(1)
10.3.1.6 Cardiolipin
203(1)
10.3.1.7 Isoprostane-Containing PC
203(1)
10.3.2 Sphingolipids
203(1)
10.3.2.1 Sphingomyelin
204(1)
10.3.2.2 Lysosphingolipids
204(1)
10.3.2.3 Ceramide
204(1)
10.3.2.4 Minor Sphingolipids
204(1)
10.3.3 Sterols
205(1)
10.3.4 Cholesteryl Esters
205(1)
10.3.5 Triacylglycerides
205(1)
10.3.6 Minor Lipids
205(1)
10.4 Altered Lipoproteinomics in Dyslipidemia
206(5)
10.4.1 Phospholipids
206(1)
10.4.1.1 Phosphatidylcholine
206(1)
10.4.1.2 Lysophosphatidylcholine
207(1)
10.4.1.3 Phosphatidylethanolamine
208(1)
10.4.1.4 Phosphatidylethanolamine Plasmalogens
208(1)
10.4.1.5 Phosphatidylinositol
208(1)
10.4.1.6 Isoprostane-Containing PC
208(1)
10.4.2 Sphingolipids
209(1)
10.4.2.1 Sphingomyelin
209(1)
10.4.2.2 Lysosphingolipids: S1P and Dihydro S1P
209(1)
10.4.2.3 Ceramide
210(1)
10.4.3 Free Cholesterol
210(1)
10.4.4 Cholesteryl Esters
210(1)
10.4.5 Triacylglycerides
210(1)
10.4.6 Minor Lipids
211(1)
10.4.6.1 Nonesterified Fatty Acids
211(1)
10.4.6.2 Ganglioside GM1
211(1)
10.4.6.3 Oxidized Lipids
211(1)
10.5 Conclusions
211(8)
References
212(7)
11 Mediator Lipidomics in Inflammation Research
219(14)
Makoto Arita
Ryo Iwamoto
Yosuke Isobe
11.1 Introduction
219(1)
11.2 PUFA-Derived Lipid Mediators: Formation and Action
219(3)
11.3 LC-ESI-MS/MS-Based Lipidomics
222(4)
11.3.1 Sample Preparation
222(1)
11.3.2 LC-ESI-MS/MS Analysis
223(3)
11.4 Mediator Lipidomics in Inflammation and Resolution
226(4)
11.5 Conclusion and Future Perspective
230(3)
References
230(3)
12 Lipidomics for Elucidation of Metabolic Syndrome and Related Lipid Metabolic Disorder
233(18)
Ryo Taguchi
Kazutaka Ikeda
Hiroki Nakanishi
12.1 Introduction
233(1)
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(1)
12.3 Analytical Systems by Mass Spectrometry in Lipidomics
235(1)
12.3.1 LC-MS and LC-MS/MS Analyses for Global Detection of Phospholipids and Triglycerides
235(1)
12.3.2 Infusion Analysis with Precursor Ion and Neutral Loss Scanning
236(1)
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(1)
12.4 Lipidomic Data Processing
236(3)
12.4.1 Strategy of Lipid Search
236(1)
12.4.2 Application and Identification Results of "Lipid Search"
237(2)
12.5 Analysis of Lipids as Markers of Metabolic Syndrome
239(6)
12.5.1 Oxidized Phospholipids
239(1)
12.5.1.1 Application for Myocardial Ischemia-Reperfusion Model
239(1)
12.5.2 Bioactive Acidic Phospholipids
240(1)
12.5.2.1 Lysophosphatidic Acid
240(1)
12.5.2.2 Phosphoinositides
241(1)
12.5.3 Oxidative Triglycerides
241(1)
12.5.3.1 Application for Mouse White Adipose Tissue
242(2)
12.5.4 Sphingolipids
244(1)
12.5.4.1 Application for Sphinogolipid Metabolism
244(1)
12.6 Direct Detection of Lipid Molecular Species in Specific Tissue Domains by Disease-Specific Changes
245(1)
12.7 Conclusions
245(6)
References
246(5)
13 Lipidomics in Atherosclerotic Vascular Disease
251(18)
Minna T. Janis
Reijo Laaksonen
13.1 Introduction
251(2)
13.2 Lipids and Atherosclerotic Vascular Disease
253(7)
13.2.1 Lipoproteins
254(1)
13.2.2 Atherosclerotic Plaque
255(1)
13.2.3 Molecular Lipids
256(1)
13.2.3.1 Eicosanoids
256(1)
13.2.3.2 Sphingolipids and Cholesterol
257(1)
13.2.3.3 Phospholipids
258(1)
13.2.4 Animal Models of Atherosclerotic Research
259(1)
13.3 Diagnostics and Treatment
260(2)
13.3.1 Diagnostic Biomarkers of Atherosclerosis
260(1)
13.3.2 Lipidomics in Efficacy and Safety Measurements
261(1)
13.4 Conclusions
262(7)
References
263(6)
14 Lipid Metabolism in Neurodegenerative Diseases
269(28)
Lynette Lim
Guanghou Shui
Markus R. Wenk
14.1 Introduction
269(6)
14.1.1 Brain Lipids
270(2)
14.1.2 Mass Spectrometry of Brain Lipids
272(3)
14.2 Alzheimer's Disease
275(6)
14.2.1 Cholesterol and Cholesterol Esters
276(1)
14.2.2 Sulfatides
277(1)
14.2.3 Plasmalogen Ethanolamines
277(1)
14.2.4 Phospholipases
278(1)
14.2.4.1 Phospholipase A2
278(1)
14.2.4.2 Phospholipase C and Phospholipase D
279(2)
14.3 Parkinson's Disease
281(6)
14.3.1 Cerebrosides
283(1)
14.3.2 Coenzyme Q
284(1)
14.3.3 Endocannabinoids
285(2)
14.4 Conclusions
287(10)
References
288(9)
15 The Tumor Mitochondrial Lipidome and Respiratory Bioenergetic Insufficiency
297(22)
Thomas N. Seyfried
Jeffrey H. Chuang
Lu Zhang
Xianlin Han
Michael A. Kiebish
15.1 Introduction
297(2)
15.1.1 Lipidomic Abnormalities in Tumor Mitochondria
298(1)
15.2 Cardiolipin and Electron Transport Chain Abnormalities in Mouse Brain Tumor Mitochondria
299(8)
15.3 Complicating Influence of the in vitro Growth Environment on Cardiolipin Composition and Energy Metabolism
307(4)
15.4 Bioinformatic Methods to Interpret Alterations in the Mitochondrial Lipidome
311(3)
15.5 Conclusions
314(5)
References
314(5)
16 Lipidomics for Pharmaceutical Research
319(7)
Yoshinori Satomi
16.1 Introduction
319(1)
16.2 Biomarkers for Pharmaceutical Research
320(1)
16.3 Strategy for Biomarker Discovery
321(5)
16.4 Conclusions
326(1)
References 326(3)
Index 329
Kim Ekroos currently heads the bioanalytics division at Zora Biosciences in Espoo (Finland). He holds a Ph.D. from the Technical University of Dresden (Germany) and has conducted research in the group of Professor Kai Simons and Dr. Andrej Shevchenko at the Max-Planck Institute of Molecular Cell Biology and Genetics in Dresden. Dr. Ekroos has also worked at the European Molecular Biology Laboratory in Heidelberg (Germany). He has made major contributions to the advancement of basic research on lipids and their study with advanced mass spectroscopy methods and software tools. In addition, he has pharmaceutical industry experience from Astra Zeneca where he spent three years successfully developing and utilizing high-throughput molecular lipidomics methods. Today he is focusing on applied molecular lipidomics for unscrambling the mechanistic details by which alterations in tissue-specific lipid metabolism are directly linked to the etiology of lipid-mediated disorders for the benefit of basic science, drug target and lipid biomarker discovery, and development of clinical diagnostics.
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