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This volume explores lipidomics through protocols that focus on areas of utility, techniques, and bioinformatics advancements. The protocols in this book cover topics such as isolation of specific membranes and specialized fractionation of subcellular compartments, and computational and functional analysis of lipid metabolizing enzymes. Each protocol also discusses methods of dealing with fractionated organelles-cells to whole organisms. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls.

Cutting-edge and comprehensive, Lipidomics: Methods and Protocols is a useful and valuable resource for biochemists, molecular biologists, and neuroscientists interested in neurology, ophthalmology and vision sciences, as well as mass spectrometrists with interest in disease discovery.

Lipidomics: Methods and Protocols

Preface...
Table of Contents...
Contributing Authors...

1. Lipid Sample Preparation for Biomedical Research
Ravin Sajnani and Katyayini Aribindi

2. Lipid Extraction Techniques for Stable Isotope Analysis and Ecological Assays
Kyle H. Elliot, James D. Roth, and Kevin Crook

3. Isolation of Lipid Raft Proteins from CD133+ Cancer Stem Cells
Vineet K. Gupta and Sulagna Banerjee

4. Isolation of Neuronal Synaptic Membranes by Sucrose Gradient Centrifugation
Blake E. Hopiavuori, Dustin E. Masser, Joseph L. Wilkerson, Richard S. Brush, Nawajes A. Mandal, Robert E. Anderson, and Willard M. Freeman

5. Sample Preparation and Analysis for Imaging Mass Spectrometry
Genea Edwards, Annia Mesa, Robert I. Vazquez-Padron, Paul Kowalski, and Sanjoy K. Bhattacharya

6. Direct Measurement of Free and Esterified Cholesterol Mass in Differentiated Human Podocytes: A TLC and Enzymatic Assay Based Method
Christopher E. Pedigo, Sandra M. Merscher, and Alessia Fornoni

7. High-Performance Chromatographic Separation of Cerebrosides
Renaud Sicard and Ralf Landgraf              

8. Lipid Identification by Untargeted Tandem Mass Spectrometry Coupled with Ultra-High-Pressure Liquid Chromatography
Gabriel B. Gugiu

9. Utility of Moderate and High Resolution Mass Spectrometry for Class-Specific Lipid Identification and Quantification
Maria del Carmen Piqueras

10. A Robust Lipidomics Workflow for Mammalian Cells, Plasma, and Tissue using Liquid-Chromatography High-Resolution Tandem Mass Spectrometry
Candice Z. Ulmer, Rainey Patterson, Jeremy Koelmel, Timothy J. Garrett, and Richard A. Yost

11. Combined Use of MALDI-TOF Mass Spectrometry and ³¹PNMR Spectrometry for Analysis of Phospholipids
Jenny Schröter, Yulia Popkova, Rosmarie Süß, and Jürgen Schiller

12. Global Monitoring of Mammalian Lipidome by Quantitative Shotgun Lipodomics
Inger Odum Nielsen, Kenji Maeda, and Mesut Bilgin

13. Bioinformatics Pertinent to Lipid Analysis in Biological Samples
Justin Ma, Ulises Arbelo, Yenifer Guerra, Katyayini Aribindi, Sanjoy K. Bhattacharya, and Daniel Pelaez

14. LC-MS-Based Lipidomics and Automated Identification of Lipids using the LipidBlast In-Silico MS/MS Library
Tomas Cajka and Oliver Fiehn

15. Single-Step Capture and Targeted Metabolomics of Alkyl-Quinolones in Outer Membrane Vesicles of Pseudomonas aeruginosa
Pallavi Lahiri and Dipankar Ghosh

16. Analysis of Fatty Acid and Cholesterol Content from Detergent-Resistant and Detergent-Free Membrane Microdomains
Mark E. McClellan and Michael H. Elliott

17. Computational Functional Analysis of Lipid Metabolic Enzymes
Carolina Bagnato, Arjen Ten Have, María B. Prados, and María B. Beligni

18. Isoprenylation of Monomeric GTPases in Human Trabecular Meshwork Cells
Evan B. Stubbs, Jr.

19. Purification and Validation of Lipid Transfer Proteins
Matti A. Kjellberg, Anders P.E. Backman, Anna Möuts, and Peter Mattjus

20. Incorporation of Artificial Lipid-Anchored Proteins into Cultured Mammalian Cells
Rania Leventis and John R. Silvius

21. Sonication-Based Basic Protocol for Liposome Synthesis
Roberto Mendez and Santanu Banerjee

22. On Electrochemical Methods for Determination of Protein-Lipid Interaction
Zhiping Hu and Yanli Mao

23. Angiogenesis Model of Cornea to Understand the Role of Sphingosine 1-Phosphate
Joseph L. Wilkerson and Nawajes A. Mandal