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1 Mass Spectrometry for the Novice John Greaves and John Roboz (^>, yc**' CRC Press J Taylor & Francis Group Boca Raton London New York CRC Press is an imprint of the Taylor & Francis Croup, an informa business

2 Contents List of Figures List of Tables Acknowledgments About the Authors Abbreviations To the Reader xiii xix xxi xxiii xxv xxix Chapter 1 An Overview A Brief History Definitions Concerning Instruments, Mass, m/z, and Ions Components of Instruments and Their Functions Sample Introduction Ion Sources Mass Analyzers Ion Current Detectors Vacuum Systems Data Systems Definitions Concerning Instrument Performance Definitions Concerning Applications Information from Mass Spectra Diversity and Scope of Applications 31 Chapter 2 Instrumentation Sample Introduction Pure Samples or Simple Mixtures Introduction of Gases and Volatile Liquids Using Batch Inlets Semipermeable Polymer Membrane Inlets Direct (Static) Insertion Probes Chromatographic Separation of Complex Mixtures Gas Chromatography-Mass Spectrometry (GC-MS) Liquid Chromatography-Mass Spectrometry (LC-MS) Capillary Electrophoresis (CE) Ion Sources and Methods of Ionization Electron Ionization (EI) Soft Ionization Chemical Ionization (CI) Electrospray Ionization (ESI) 56 vii

3 vjjj Contents Atmospheric Pressure Chemical Ionization (APCI) Atmospheric Pressure Photo-Ionization (APPI) Surface Ionization Methods Desorption Electrospray Ionization (DESI) Direct Analysis in Real Time (DART) Matrix-Assisted Laser Desorption/Ionization (MALDI) Surface-Enhanced Laser Desorption Ionization (SELDI) Alternative Ionization Methods Mass Analyzers Quadrupole (Q) Quadrupoles as Ion Guides (q) Ion Traps Quadrupole Ion Trap (QIT) Linear Ion Trap (LIT) Time-of-Flight (TOF) Analyzer Fourier Transform Ion Traps Orbitrap Fourier Transform-Ion Cyclotron Resonance (FT-ICR) Ion Mobility Analyzers High-Field Asymmetric Waveform Ion Mobility Spectrometer (FAIMS) Ion Mobility Separator (IMS) Magnetic Sector Analyzers Multianalyzer (MS/MS) Systems Tandem MS/MS Instruments Hybrid MS/MS Instruments Ion Current Detectors Electron Multipliers Daly Detector Image Currents Vacuum Systems Backing (Roughing) Pumps Rotary Pumps Scroll Pumps Turbomolecular Pumps Data Systems 107 Chapter 3 Methodologies and Strategies Ill 3.1 Measures of Instrument Performance Ill Instrument Tuning and Mass Scale Calibration Ill

4 Contents 'x Resolution Accurate Mass Measurement Interpretation of Mass Spectra What Is a Mass Spectrum? Isotope Patterns Electron Ionization Spectra of Small Molecules Spectra from Ionization by the Addition or Removal of Charges Electrospray Ionization Spectra of Large Molecules Atmospheric Pressure Ionization and Fragmentation Fragmentation and Quantification A Few Ions to Avoid (or at least recognize) Analytical Techniques and Strategies Techniques for Instruments with Single Analyzers Techn iques for Ion Activation Ion Activation and Fragment Formation in Single-Analyzer Instruments Mass Spectrometry/Mass Spectrometry (MS/MS) Collision-Induced Dissociation (CID) Infrared Multiphoton Dissociation (IRMPD) Electron Transfer Dissociation (ETD) and Electron Capture Dissociation (ECD) Photodissociation and Surface-Induced Dissociation Tandem-in-Space MS/MS MS/MS Techniques Using Triple Quadrupole (QqQ) Analyzers MS/MS Techniques Using Time-of- Flight/Time-of-Flight (TOF/TOF) Analyzers MS/MS Techniques Using Hybrid Instruments Data Dependent Acquisition (DDA) and CID Fragmentation by Voltage Switching (Data Independent Acquisition, DIA) MS/MS Techniques Using Tandem-in-Time (Trapped-Ion) Analyzers Quantification of Small Molecules Standard Deviations and Method Validation 157

5 x Contents 3.4 Omics Metabolomics Lipidomics Biopolymers Proteomics Peptide Sequencing Bottom-Up Protein Sequencing Top-Down Protein Sequencing De Novo Protein Sequencing Post-Translational Modification (PTM) Some Other Ions to Know About and Avoid Protein Conformation Hydrogen/Deuterium Exchange (HDX) Quantification of Proteins Nucleomics (Nucleic Acid Analysis) Glycomics Imaging Mass Spectrometry Bioinformatics Buying a Mass Spectrometer 198 Chapter 4 Examples from Representative Publications An Open-Access Mass Spectrometry Facility Environmental: Organochlorines in Fish Environmental: Pharmaceuticals in Surface and Wastewaters Pharmacology: Lipitor Metabolism New Techniques: Paper Spray of Pharmaceuticals Petroleomics: Crude Oil Characterization Metabolomics: Disease Markers for a Tropical Disease Metabolomics: Chemical Defense Lipidomics: Coronary Artery Disease Proteomics: Protein Identification in a Painting Proteomics: Protein Identification and Metastasis Proteomics: Noncovalent Interactions Tissue Imaging 235 Chapter 5 The Absolute Essentials General Instrument Components Performance Parameters Techniques and Strategies 250

6 Contents *' Chapter 6 Resources Books, Journals, Review Articles, Classical Publications General Formulas and Derivations Instrumentation and Techniques Applications General Protoeomics Other Omics Pharmaceutical, Medical, and Clinical Miscellaneous Journals Selected Review Articles General and Sample Preparation Instrumentation Quantification MS/MS Data Processing and Bioinformatics Applications Classic Publications Major Instrument Manufacturers Mass Spectrometry Societies, Blogs, and Discussion Groups The Mass Spectrometrist and the Internet Wikipedia Tutorials Databases Miscellaneous Resources 266 Index 267

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