BOOK
Mass Spectrometry in Chemical Biology
Norberto Peporine Lopes | Ricardo Roberto da Silva
(2017)
Additional Information
Book Details
Abstract
Mass spectrometry is one of the most widespread technologies in chemistry and has been increasingly used in biology with the rise of omics sciences. This book summarizes some important methodological approaches in mass spectrometry and applications in the field of chemical biology.
The core chapters build on basic concepts introduced in the opening chapter and explore established fields such as high throughput screening, proteomics and metabolomics. Emerging applications of mass spectrometry in elucidating biosynthetic pathways, enzyme mechanisms and protein-protein interactions are then presented. Connections between these diverse research fields are highlighted throughout. The book concludes with a discussion of databases and future perspectives.
This book will be a useful tool to early chemical biology researchers wishing to incorporate mass spectrometry as a tool in their research.
Professor Norberto Peporine Lopes obtained B.Sc. and M.Sc. degrees in Pharmacy and a Ph.D. in Chemistry from the University of Sao Paulo. At present, he is Full Professor of Organic Chemistry at the University of Sao Paulo in Ribeirao Preto and head of the Physics and Chemistry Department of the School of Pharmaceutical Sciences at the Ribeirao Preto University of Sao Paulo and the Research Support Center in Natural and Synthetic Products (NPPNS). He is a board member of the Brazilian Chemical Society and the Brazilian Society of Mass Spectrometry. His research deals with organic chemistry, with an emphasis on multidisciplinary research into natural products chemistry using mass spectrometry.
Ricardo Roberto da Silva obtained his M.Sc. Degree in Genetics from the Federal University of Viçosa and a Ph.D. in Genetics/Bioinformatics from the University of Sao Paulo in Ribeirão Preto. Currently, Ricardo is a postdocoral researcher at the Research Support Center in Natural and Synthetic Products (NPPNS), working on the establishment of metabolomics analysis platforms.
Table of Contents
| Section Title | Page | Action | Price |
|---|---|---|---|
| Cover | Cover | ||
| Mass Spectrometry in Chemical Biology: Evolving Applications | i | ||
| Foreword | v | ||
| Contents | ix | ||
| Acknowledgments | xiv | ||
| Chapter 1 - Introduction | 1 | ||
| References | 15 | ||
| Chapter 2 - Introduction to Mass Spectrometry Instrumentation and Methods Used in Chemical Biology | 17 | ||
| 2.1 Introduction to Mass Spectrometry (MS) | 17 | ||
| 2.1.1 The MS | 18 | ||
| 2.2 Sample Introduction and Separation Methods for Coupling to MS | 19 | ||
| 2.2.1 LC | 19 | ||
| 2.2.2 GC | 21 | ||
| 2.2.3 Capillary Electrophoresis (CE) | 23 | ||
| 2.3 Ionization Methods | 23 | ||
| 2.3.1 EI | 24 | ||
| 2.3.2 CI | 25 | ||
| 2.3.3 ESI | 26 | ||
| 2.3.4 APCI | 28 | ||
| 2.3.5 MALDI | 29 | ||
| 2.3.6 Other Ionization Techniques | 30 | ||
| 2.4 Mass Analysers | 30 | ||
| 2.4.1 TOF Mass Analysers | 31 | ||
| 2.4.2 Magnetic Sector Mass Analysers | 33 | ||
| 2.4.3 Quadrupole | 34 | ||
| 2.4.4 Ion Traps (ITs) | 34 | ||
| 2.4.5 Orbitrap | 35 | ||
| 2.4.6 Ion Cyclotron Resonance (ICR) | 36 | ||
| 2.5 Detectors | 36 | ||
| 2.5.1 Faraday Cup | 36 | ||
| 2.5.2 EM Detectors | 37 | ||
| 2.5.3 Scintillator Detectors | 37 | ||
| 2.5.4 FT | 38 | ||
| 2.6 Tandem MS (MS/MS) | 38 | ||
| 2.6.1 Hybrid Instruments | 39 | ||
| 2.6.1.1 QqQ | 40 | ||
| 2.6.1.2 Quadrupole Time-Of-Flight (QqTOF) Analyser | 40 | ||
| 2.6.1.3 Tandem TOF (TOF–TOF) | 41 | ||
| 2.6.1.4 Quadrupole Ion Trap (QqIT) | 41 | ||
| 2.6.1.5 Orbitrap-based Hybrid Analysers | 41 | ||
| 2.6.1.6 Other Hybrid Mass Analysers | 42 | ||
| 2.6.2 Fragmentation Devices | 42 | ||
| 2.6.2.1 Collision Induced Dissociation (CID) | 42 | ||
| 2.6.2.2 Electron Capture Dissociation (ECD) | 43 | ||
| 2.6.2.3 Electron Transfer Dissociation (ETD) | 43 | ||
| 2.6.2.4 Photodissociation (PD) | 43 | ||
| 2.7 Application of MS to Chemical Biology | 44 | ||
| 2.7.1 Types of Biomolecules Analysed by MS | 44 | ||
| 2.7.1.1 Analysis of Oligonucleotides: Genomics | 44 | ||
| 2.7.1.2 Analysis of Proteins: Proteomics | 45 | ||
| 2.7.1.3 Analysis of Metabolites: Metabolomics | 46 | ||
| 2.7.1.4 Analysis of Lipids: Lipidomics | 46 | ||
| 2.7.1.5 Analysis of Glycans: Glycomics | 47 | ||
| 2.7.2 Other MS Applications: Imaging MS and Microorganism Identification | 48 | ||
| Abbreviations | 48 | ||
| Acknowledgements | 49 | ||
| References | 50 | ||
| Chapter 3 - Metabolomics | 57 | ||
| 3.1 Introduction | 57 | ||
| 3.2 Experimental Design | 59 | ||
| 3.3 Sample Preparation | 63 | ||
| 3.4 Analytical Platforms—Hyphenated Methods | 66 | ||
| 3.5 Data Acquisition | 68 | ||
| 3.6 Data Processing | 70 | ||
| References | 75 | ||
| Chapter 4 - Proteomics | 82 | ||
| 4.1 Introduction to Proteomics | 82 | ||
| 4.2 Sample Preparation for Proteomics Studies and Proteolysis | 85 | ||
| 4.3 Approaches for Protein Separation | 87 | ||
| 4.3.1 Gel-based Proteomics Approaches | 87 | ||
| 4.3.1.1 1-DGE | 87 | ||
| 4.3.1.2 2-DGE | 88 | ||
| 4.3.1.3 Electrophoretic Separation of Native Proteins | 89 | ||
| 4.3.2 Gel-free Proteomics Approaches | 89 | ||
| 4.3.2.1 Affinity Chromatography | 90 | ||
| 4.3.2.2 Gel Filtration Chromatography | 90 | ||
| 4.3.2.3 Reverse Phase Liquid Chromatography (RPLC) | 90 | ||
| 4.3.2.4 Hydrophilic Interaction Liquid Chromatography (HILIC) | 91 | ||
| 4.3.2.5 Ion Exchange Chromatography | 91 | ||
| 4.3.2.6 In-solution IEF: Offgel Fractionation | 92 | ||
| 4.4 Multidimensional Protein Identification Technology (MudPIT) | 92 | ||
| 4.5 MS for Proteomics | 93 | ||
| 4.5.1 Ionization | 93 | ||
| 4.5.1.1 MALDI | 93 | ||
| 4.5.1.2 ESI | 94 | ||
| 4.5.2 Mass Analyzers | 94 | ||
| 4.6 Tandem MS (MS/MS) | 95 | ||
| 4.7 Approaches in Proteomics | 95 | ||
| 4.7.1 Top-down Proteomics Approach | 95 | ||
| 4.7.2 Bottom-up Proteomics Approach | 98 | ||
| 4.7.3 Directed Proteomics Approach | 99 | ||
| 4.7.4 Targeted Proteomics Approach | 100 | ||
| 4.8 Quantitative Proteomics | 100 | ||
| 4.8.1 2D Difference GE (2D-DIGE) | 101 | ||
| 4.8.2 Labeled Quantification or Stable Isotope Labeling | 102 | ||
| 4.8.2.1 In vivo Methods of Metabolic Labeling | 102 | ||
| 4.8.2.2 In vitro Methods: Enzymatic and Chemical Labeling | 104 | ||
| 4.8.2.2.1\rEnzymatic Labeling.In this method, the C-terminal carboxyl groups of peptides are labeled with 18O in the presence of trypsin or... | 104 | ||
| 4.8.2.2.2\rChemical Labeling.Chemical labeling is the most widely used method for relative quantification. In this peptides are tagged with... | 104 | ||
| 4.8.2.2.3\rChemical Labeling by Isobaric Tagging.This is the most widely used method of quantification as it enables efficient multiplexing... | 107 | ||
| 4.8.3 Label-free Quantification | 108 | ||
| 4.8.3.1 Spectral Counting | 108 | ||
| 4.8.3.2 Extracted Ion Current (XIC) | 110 | ||
| 4.8.3.3 Data-independent Acquisition (DIA) | 111 | ||
| 4.8.4 Absolute Quantification | 111 | ||
| 4.8.4.1 Absolute Quantification Using the Targeted Proteomics Method (MRM, SRM, PRM) | 111 | ||
| 4.8.4.2 AQUA Signal Based Quantification | 112 | ||
| 4.9 Computational Methods of Proteomics Data Analysis | 113 | ||
| 4.10 Applications of Proteomics | 118 | ||
| Acknowledgement | 119 | ||
| References | 119 | ||
| Chapter 5 - Mass Spectrometry for Discovering Natural Products | 144 | ||
| 5.1 Introduction | 144 | ||
| 5.2 GC-MS | 146 | ||
| 5.3 Dereplication | 149 | ||
| 5.4 Imaging MS | 152 | ||
| 5.5 MS and Quality Control of Herbal Medicines | 154 | ||
| Acknowledgements | 155 | ||
| References | 155 | ||
| Chapter 6 - Applications of Mass Spectrometry in Synthetic Biology | 159 | ||
| 6.1 Introduction | 159 | ||
| 6.2 MS as Emerging Tool for Synthetic Biology | 161 | ||
| 6.2.1 Prospecting for Target Molecules | 161 | ||
| 6.2.2 Pathway Design and Optimization | 163 | ||
| 6.3 MS Contribution to the Classic Example of the Semi-synthesis of the Anti-malarial Drug Artemisinin | 168 | ||
| 6.4 Conclusion | 170 | ||
| Acknowledgements | 171 | ||
| References | 171 | ||
| Chapter 7 - Studying Enzyme Mechanisms Using Mass Spectrometry, Part 1: Introduction | 173 | ||
| 7.1 Introduction | 173 | ||
| 7.2 Methods for Studying Enzyme Mechanisms | 177 | ||
| 7.2.1 X-Ray Crystallography | 177 | ||
| 7.2.2 Site-directed Mutagenesis | 178 | ||
| 7.2.3 Optical Methods | 178 | ||
| 7.2.4 Isothermal Titration Calorimetry (ITC) | 179 | ||
| 7.2.5 Two-dimensional Nuclear Magnetic Resonance (2D NMR) Spectroscopy | 180 | ||
| 7.2.6 Mass Spectrometry (MS) | 181 | ||
| 7.2.6.1 Time-resolved ESI MS (TRESI-MS) | 182 | ||
| 7.2.6.2 Determination of Binding Constants and Allostery in Multimeric Enzymes | 184 | ||
| 7.2.6.3 Hydrogen–Deuterium Exchange Coupled to MS for Studying Catalysis-linked Dynamics | 185 | ||
| 7.3 Conclusion and Future Directions | 188 | ||
| References | 189 | ||
| Chapter 8 - Studying Enzyme Mechanisms Using Mass Spectrometry, Part 2: Applications | 197 | ||
| 8.1 Introduction | 197 | ||
| 8.2 Enzyme Mechanisms | 198 | ||
| 8.2.1 Complex, Multistep Enzymatic Mechanisms | 198 | ||
| 8.2.2 Time-resolved Electrospray Ionization (TRESI) for the Detection of Enzymatic Intermediates | 198 | ||
| 8.2.3 Combination With Isotopic Labeling | 201 | ||
| 8.2.4 Pre-steady-state Kinetic Isotope Effects (KIEs) Using TRESI-MS | 202 | ||
| 8.3 Steady-state Kinetics | 204 | ||
| 8.3.1 Steady-state Kinetics for Drug Development Assays | 204 | ||
| 8.3.2 Quantitative Assays on Challenging Analytes | 205 | ||
| 8.4 Pre-steady-state Kinetics | 208 | ||
| 8.5 Binding Constants | 208 | ||
| 8.6 Allosteric Regulation | 211 | ||
| 8.7 Catalysis-linked Dynamics | 212 | ||
| 8.8 Conclusions and Future Directions (MS: Is It One-size Fits All for Studying Enzyme Mechanisms) | 212 | ||
| References | 216 | ||
| Chapter 9 - Chemical Biology Databases | 221 | ||
| 9.1 Introduction | 221 | ||
| 9.2 General Biological Databases | 224 | ||
| 9.3 Databases in Proteomics | 226 | ||
| 9.3.1 Integrating the Omics Cascade from Transcripts to Proteins: A Successful Case in Plant Science | 229 | ||
| 9.4 Databases in Metabolomics | 231 | ||
| 9.4.1 Spectral Reference Databases | 233 | ||
| 9.4.2 Compound-centric Databases (Metabolic Class-, Species- and Tissue-specific) | 241 | ||
| 9.4.3 Databases of Metabolic Pathways | 243 | ||
| 9.4.4 Metabolomics Laboratory Information Management System (LIMS) Databases | 245 | ||
| 9.5 Databases for Drug Discovery and Natural Products | 247 | ||
| 9.5.1 Databases for Drug Discovery | 248 | ||
| 9.5.2 Natural Product Databases | 250 | ||
| 9.6 Conclusions | 254 | ||
| References | 254 | ||
| Chapter 10 - Perspectives for the Future | 264 | ||
| 10.1 Introduction | 264 | ||
| 10.2 MS Imaging (MSI) | 266 | ||
| 10.3 Ion Mobility | 267 | ||
| 10.4 Microfluidics | 268 | ||
| 10.5 Single-cell Metabolomics | 272 | ||
| 10.6 Mass Spectrometry in Surgery | 277 | ||
| 10.7 Synthetic Ecology | 280 | ||
| 10.8 Final Considerations | 281 | ||
| Acknowledgements | 281 | ||
| References | 282 | ||
| Subject Index | 288 |