Elsevier S & T

Lipidomics and Bioactive Lipids: Mass Spectrometry Based Lipid Analysis: Mass Spectrometry Based Lipid Analysis

Brown, H. Alex

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Table of contents
  • Contentsv
  • Contributorsxi
  • Prefacexvii
  • Volumes in Seriesxix
  • Chapter 1: Qualitative Analysis and Quantitative Assessment of Changes in Neutral Glycerol Lipid Mol1
  • 1. Introduction2
  • 2. Reagents3
  • 2.1. Cell culture3
  • 2.2. Standards3
  • 2.3. Extraction and purification3
  • 3. Methods4
  • 3.1. Cell culture4
  • 4. Results7
  • 4.1. Qualitative analysis7
  • 4.2. Quantitative analysis11
  • 5. Conclusions19
  • Acknowledgments19
  • References19
  • Chapter 2: Glycerophospholipid Identification and Quantitation by Electrospray Ionization Mass Spect21
  • 1. Introduction22
  • 2. Nomenclature25
  • 3. Mass Spectrometry26
  • 4. General Strategy for Phospholipid Isolation and Mass Spectral Analysis27
  • 5. Extraction and Mass Spectral Analysis of Global Glycerophospholipids28
  • 5.1. Phospholipid extraction from cultured cells29
  • 5.2. Phospholipid extraction from tissue30
  • 5.3. Direct infusion mass spectrometry of phospholipid extracts30
  • 5.4. LC-MS analysis (quantitation) of phospholipid extracts33
  • 6. Polyphosphoinositide Extraction and Mass Spectral Analysis35
  • 6.1. Extraction of polyphosphoinositides from cultured cells37
  • 6.2. Extraction of polyphosphoinositides from tissue37
  • 6.3. Direct-infusion mass spectral analysis of polyphosphoinositides38
  • 6.4. Deacylation of GPInsPn lipids39
  • 6.5. LC-MS analysis of deacylated GPInsPn compounds39
  • 7. Computational Analysis of Mass Spectral Data41
  • 7.1. Direct infusion (intra-source separation)43
  • 7.2. LC-MS data analysis47
  • Acknowledgments54
  • References54
  • Chapter 3: Detection and Quantitation of Eicosanoids via High Performance Liquid Chromatography-Elec59
  • 1. Introduction60
  • 2. Methods62
  • 2.1. Sample collection62
  • 2.2. Eicosanoid isolation62
  • 2.3. Reverse-phase liquid chromatography62
  • 2.4. Chiral chromatography63
  • 2.5. Mass spectrometry63
  • 2.6. Quantitation63
  • 3. Results and Discussion74
  • 3.1. MRM transition selection74
  • 3.2. Stereoisomer detection77
  • 3.3. Lower limit of detection78
  • 3.4. Recoveries79
  • 3.5. Miscellany79
  • 3.6. Summary80
  • Acknowledgments80
  • References81
  • Chapter 4: Structure-Specific, Quantitative Methods for Analysis of Sphingolipids by Liquid Chromato83
  • 1. Introduction: An Overview of Sphingolipid Structures and Nomenclature86
  • 2. Analysis of Sphingolipids by Mass Spectrometry89
  • 2.1. Electron ionization-mass spectrometry89
  • 2.2. Fast atom bombardment and liquid secondary ionization mass spectrometry90
  • 2.3. Electrospray ionization90
  • 2.4. Liquid chromatography, electrospray ionization, mass spectrometry and tandem mass spectrometry91
  • 2.5. MALDI, mass spectrometry, and tandem mass spectrometry91
  • 3. Analysis of Sphingolipids by ‘‘OMIC’’ Approaches92
  • 4. Materials and Methods95
  • 5. Materials98
  • 5.1. Biological samples98
  • 6. Extraction98
  • 6.1. Preparation of samples for LC-MS/MS99
  • 7. Identification of the Molecular Species by Tandem Mass Spectrometry100
  • 7.1. Materials for infusion and LC-ESI-MS/MS100
  • 7.2. Sphingolipid subspecies characterization prior to quantitative LC-MS/MS analysis100
  • 8. Quantitation by LC-ESI-MS/MS Using Multireaction Monitoring101
  • 8.1. Analysis of sphingoid bases and sphingoid base 1-phosphates in positive ion mode102
  • 9. Analysis of (Dihydro)Ceramides, (Dihydro)Sphingomyelins, and (Dihydro)Monohexosyl-Ceramides in Po104
  • 9.1. Modifications for analysis of glucosylceramides and galactosylceramides105
  • 9.2. Analysis of ceramide 1-phosphates by positive and negative ion modes106
  • 9.3. Analytical methods for additional analytes106
  • 10. Other Methods109
  • Acknowledgments111
  • References112
  • Chapter 5: Analysis of Ubiquinones, Dolichols, and Dolichol Diphosphate-Oligosaccharides by Liquid C117
  • 1. Introduction118
  • 2. Materials121
  • 3. Liquid Chromatography-Mass Spectrometry122
  • 4. Preparation of Lipid Extracts122
  • 5. LC-MS Detection and Quantification of Coenzyme Q123
  • 6. LC-MS Detection and Quantification of Dolichol130
  • 7. LC-MS and LC-MS/MS Characterization of Dolichol Diphosphate-Linked Oligosaccharides136
  • Acknowledgment140
  • References140
  • Chapter 6: Extraction and Analysis of Sterols in Biological Matrices by High Performance Liquid Chro145
  • 1. Introduction146
  • 2. Supplies and Reagents148
  • 3. Extraction of Lipids from Cultured Cells and Tissues149
  • 4. Saponification of Lipid Extracts151
  • 5. Solid-Phase Extraction152
  • 6. Analysis by HPLC-ESI-MS153
  • 6.1. High performance liquid chromatography153
  • 6.2. Electrospray ionization mass spectrometry153
  • 7. Quantitation156
  • 8. Data157
  • 9. Discussion, Nuances, Caveats, and Pitfalls162
  • 9.1. Quantitation162
  • 9.2. Availability and purity of primary and deuterated standards163
  • 9.3. Resolving related sterols by HPLC164
  • 9.4. Acetonitrile and signal intensity165
  • 9.5. Auto-oxidation and use of SPE columns165
  • 9.6. Sample clean-up166
  • 9.7. Residual insoluble material167
  • 9.8. Comparing relative peak areas168
  • 9.9. Electrospray using other instrumental platforms168
  • Acknowledgments168
  • References169
  • Chapter 7: The Lipid Maps Initiative in Lipidomics171
  • 1. Introduction172
  • 2. Building Infrastructure in Lipidomics173
  • 3. Classification, Nomenclature, and Structural Representation of Lipids174
  • 4. Mass Spectrometry as a Platform for Lipid Molecular Species177
  • 5. Future Plans180
  • Acknowledgments182
  • References182
  • Chapter 8: Basic Analytical Systems for Lipidomics by Mass Spectrometry in Japan185
  • 1. Introduction186
  • 2. Lipid Bank and Related Databases187
  • 3. Strategies for Lipid Identification and Quantitative Analysis by Mass Spectrometry188
  • 3.1. Accurate mass value of molecular weight-related ions188
  • 3.2. Characteristic fragment ions189
  • 3.3. Good separation and reproducible retention time in liquid chromatography189
  • 4. Several Practical Lipidomics Methods by Mass Spectrometry190
  • 4.1. Global and untargeted190
  • 4.2. Focused191
  • 4.3. Targeted192
  • 5. Strategies for Identification of Individual Molecular Species in Glycerolipids and Glycerophospho192
  • 5.1. Theoretical database and search engine for identification of phospholipid molecular species and193
  • 6. Quantitative Analysis or Profiling of Lipid Molecular Species197
  • 6.1. Compensation by a few selected internal standards for correcting relative ionization efficiency198
  • 6.2. Compensation with limited number of proper internal standards198
  • 6.3. Compensation with stable isotope-labeled standard198
  • 7. Application of Several Different Methods in Lipidomics199
  • 7.1. Global and comprehensive analyses in lipidomics under non-targeted strategies199
  • 7.2. Application of focused methods by mass spectrometry for lipidomics200
  • 7.3. Application of targeted method using expanded MRM for oxidized phospholipids207
  • 8. Future Program for Lipidomics208
  • 8.1. MassBank: Mass fragment database for metabolomics in Japan’s BIRD project208
  • 8.2. Flux analysis by stable isotope labeling208
  • 8.3. Mass imaging of lipids by MALDI-MS and TOF-SIMS208
  • Acknowledgments209
  • References209
  • Chapter 9: The European Lipidomics Initiative: Enabling Technologies213
  • 1. Introduction214
  • 2. Methods of Lipidomics: Quantitative Analysis in Time215
  • 2.1. Ongoing technology development215
  • 2.2. Need for further technology development217
  • 3. Imaging Lipids218
  • 4. Methods to Study the Physical Properties of Lipids219
  • 4.1. Lipids as amphiphiles220
  • 4.2. Lipid–lipid interactions and mesomorphism220
  • 4.3. Lipid structural functions220
  • 4.4. Lipid signaling functions223
  • 5. Data Handling and Standardization224
  • 5.1. Software requirements224
  • 5.2. Existing lipid-related databases224
  • 5.3. Lipidomics expertise platform226
  • 6. Perspectives226
  • Acknowledgments227
  • References227
  • Chapter 10: Lipidomic Analysis of Signaling Pathways233
  • 1. General Considerations235
  • 2. Lipid Extraction235
  • 2.1. General lipid extraction (Folch procedure)235
  • 2.2. Acidified phosphoinositide/lysolipid extraction236
  • 3. HPLC-MS Analysis237
  • 4. General Phospholipid HPLC237
  • 5. Ceramide, Diradylglycerol, and Monoradylglycerol Separation239
  • 6. Phosphoinositide Separation240
  • 7. Analysis of Phospholipid Synthesis by ESI-MS/MS Using Stable Isotopes241
  • 8. Labeling Protocols242
  • 8.1. In vivo242
  • 8.2. In cultured cells242
  • 9. Lipid Extraction for ESI-MS/MS243
  • 10. LC-MS Analysis (methyl-d9 )-Choline243
  • 11. MRM Analysis of (methyl-d9 )-Choline Enrichment in Cell and Tissue Phosphorylcholine244
  • 12. ESI-MS/MS Analysis of Native and Newly Synthesized Phospholipids244
  • 13. Data Analysis245
  • References246
  • Chapter 11: Bioinformatics for Lipidomics247
  • 1. Introduction248
  • 2. Lipid Structure Databases249
  • 2.1. Ontology, classification, and nomenclature249
  • 2.2. Lipid structure databases251
  • 2.3. Lipid structure representation253
  • 3. Lipid-Associated Protein/Gene Databases254
  • 3.1. LIPID MAPS genome/proteome database254
  • 3.2. Extracting lipid genes and proteins from databases and legacy knowledge255
  • 4. Tools for Lipidomics256
  • 4.1. LIPID MAPS website and user interface256
  • 4.2. Tools for automated drawing and naming of lipids260
  • 4.3. Tools for prediction of lipid mass spectra262
  • 4.4. Tools for managing lipidomic metadata263
  • 4.5. Tools for collection, display, and analysis of experimental lipidomic data264
  • 4.6. Tools for lipid profiling267
  • 5. Lipid Pathways268
  • 5.1. Bioinformatics resources for lipid-related pathways268
  • 5.2. Tools for drawing pathways269
  • 6. Challenges for Future Lipid Informatics270
  • Acknowledgments272
  • References272
  • Chapter 12: Mediator Lipidomics: Search Algorithms for Eicosanoids, Resolvins, and Protectins275
  • 1. Introduction: Metabolomics and Mediator Lipidomics–Informatics276
  • 2. Engineered Animals and Human Tissues278
  • 3. New Chemical Mediator Pathways in Resolution of Inflammation279
  • 4. Logic Diagram to Identify PUFA-Derived Lipid Mediators: Eicosanoids, Resolvins, and Protectins284
  • 4.1. Databases286
  • 5. Cognoscitive-Contrast-Angle Algorithm286
  • 5.1. Identification of mass spectral ions286
  • 5.2. Modification of MS/MS ion intensities according to identities289
  • 5.3. Cognoscitive-contrast-angle algorithm and databases contrast angle290
  • 5.4. Integrating MS/MS spectra with UV spectra and chromatograms in COCAD to identify LMs291
  • 6. Theoretical Database for Novel LM and Search Algorithm292
  • 6.1. RvD1, O,O,O,O-d4-RvD1, and 21,21,22,22,22-d5-RvD1301
  • 6.2. PD1, O,O,O-d3-PD1, 21,21,22,22,22-d5-PD1, and O,O,O, 21,21,22,22,22-d8-PD1306
  • 7. Discussion308
  • 7.1. Impact of a functional group and enes on MS/MS fragmentation of various lipid mediators308
  • 8. Conclusions and Next Steps311
  • 8.1. Materials and sample preparation312
  • 8.2. Instrumentation313
  • Acknowledgments313
  • References313
  • Chapter 13: A Guide to Biochemical Systems Modeling of Sphingolipids for the Biochemist319
  • 1. Introduction320
  • 2. System Map: Specifying the Model322
  • 2.1. Creation of the system’s parts list322
  • 2.2. Determination of dependent and independent variables322
  • 2.3. Graphical representation of the system’s parts list323
  • 2.4. Specific example: dihydro- and phyto-ceramide dynamics323
  • 3. Symbolic Equations: From Words and Pictures to Equations327
  • 4. Numerical Equations: From the Symbolic to a Computational Model331
  • 4.1. Ceramide synthase332
  • 4.2. Dihydroceramidase334
  • 4.3. Inositol phosphorylceramide synthase336
  • 4.4. Inositol phosphosphingolipid phospholipase C338
  • 4.5. Hydroxylase339
  • 4.6. Other parameter calculations340
  • 5. Model Analysis: Steady State, Stability, and Sensitivity341
  • 6. Simulation: What Happens If...?345
  • 7. Conclusion346
  • 8. Epilogue346
  • Acknowledgments348
  • References348
  • Chapter 14: Quantitation and Standardization of Lipid Internal Standards for Mass Spectroscopy351
  • 1. Introduction352
  • 2. Lipid Handling Guidelines352
  • 3. Chemical Characterization of Lipid Stocks353
  • 4. Preparation of Working Lipid Standards355
  • 5. Packaging of Lipid Standards359
  • 6. Quality Control and Stability Testing361
  • 6.1. Ceramide/sphingoid base internal standard mixture361
  • 6.2. Triglyceride-d5 internal standard mixture363
  • 7. Discussion364
  • References366
  • Author Index369
  • Subject Index381
Book details
  • Vendor Elsevier S & T
  • SKU 9780123738950
  • ISBN-13 9780080554884
  • Author Brown, H. Alex
  • Category Medical
  • Subject Biochemistry

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This volume in the well-established Methods in Enzymology series features methods for the study of lipids using mass spectrometry techniques. Articles in this volume cover topics such as Qualitative Analysis and Quantitative Assessment of Changes in Neutral Glycerol Lipid Molecular Species within Cells; Glycerophospholipid identification and quantitation by electrospray ionization mass spectrometry; Detection and Quantitation of Eicosanoids via High Performance Liquid Chromatography/Electrospray Ionization Mass Spectrometry; Structure-specific, quantitative methods for "lipidomic" analysis of sphingolipids by tandem mass spectrometry; Analysis of Ubiquinones, Dolichols and Dolichol Diphosphate-Oligosaccharides by Liquid Chromatography Electrospray Ionization Mass Spectrometry; Extraction and Analysis of Sterols in Biological Matrices by High-Performance Liquid Chromatography Electrospray Ionization Mass Spectrometry; The Lipid Maps Initiative in Lipidomics; Basic analytical systems for lipidomics by mass spectrometry in Japan; The European Lipidomics Initiative Enabling technologies; Lipidomic analysis of Signaling Pathways; Bioinformatics for Lipidomics; Mediator Lipidomics: Search Algorithms for Eicosanoids, Resolvins and Protectins; A guide to biochemical systems modeling of sphingolipids for the biochemist; and Quantitation and Standardization of Lipid Internal Standards for Mass Spectroscopy.