MASS SPECTROMETRY -- CONTENTS -- FOREWORD -- CONTRIBUTORS -- PART I INSTRUMENTATION -- 1 DEFINITIONS AND EXPLANATIONS -- References -- 2 A MASS SPECTROMETER'S BUILDING BLOCKS -- 2.1. Ion Sources -- 2.1.1. Gas Discharge -- 2.1.2. Thermal Ionization -- 2.1.3. Spark Source -- 2.1.4. Glow Discharge -- 2.1.5. Inductively Coupled Plasma -- 2.1.6. Electron Ionization -- 2.1.7. Chemical Ionization -- 2.1.8. Atmospheric Pressure Chemical Ionization -- 2.1.9. Photoionization -- 2.1.10. Multiphoton Ionization -- 2.1.11. Atmospheric Pressure Photoionization -- 2.1.12. Field Ionization -- 2.1.13. Field Desorption -- 2.1.14. Thermospray Ionization -- 2.1.15. Electrospray Ionization -- 2.1.16. Desorption Electrospray Ionization -- 2.1.17. Direct Analysis in Real Time -- 2.1.18. Secondary Ion Mass Spectrometry -- 2.1.19. Fast Atom Bombardment -- 2.1.20. Plasma Desorption -- 2.1.21. Laser Desorption/Ionization -- 2.1.22. Matrix-Assisted Laser Desorption/Ionization -- 2.1.23. Atmospheric Pressure Matrix-Assisted Laser Desorption/Ionization -- 2.2. Mass Analyzers -- 2.2.1. Time-of-Flight -- 2.2.2. Magnetic/Electric Sector -- 2.2.3. Quadrupole Mass Filter -- 2.2.4. Quadrupole Ion Trap -- 2.2.5. Orbitrap -- 2.2.6. Fourier Transform Ion Cyclotron Resonance -- 2.2.7. Accelerator Mass Spectrometry -- 2.3. Detectors -- 2.3.1. Photoplate Detector -- 2.3.2. Faraday Detector -- 2.3.3. Electron Multipliers -- 2.3.4. Focal Plane Detector -- 2.3.5. Scintillation Detector -- 2.3.6. Cryogenic Detector -- 2.3.7. Solid-State Detector -- 2.3.8. Image Current Detection -- References -- 3 TANDEM MASS SPECTROMETRY -- 3.1. Tandem MS Analyzer Combinations -- 3.1.1. Tandem-in-Space -- 3.1.2. Tandem-in-Time -- 3.1.3. Other Tandem MS Configurations -- 3.2. Ion Activation Methods -- 3.2.1. In-Source Decay -- 3.2.2. Post-Source Decay -- 3.2.3. Collision Induced/Activated Dissociation.

3.2.4. Photodissociation -- 3.2.5. Blackbody Infrared Radiative Dissociation -- 3.2.6. Electron Capture Dissociation -- 3.2.7. Electron Transfer Dissociation -- 3.2.8. Surface-Induced Dissociation -- References -- 4 SEPARATION METHODS -- 4.1. Chromatography -- 4.1.1. Gas Chromatography -- 4.1.2. Liquid Chromatography -- 4.1.3. Supercritical Fluid Chromatography -- 4.2. Electric-Field Driven Separations -- 4.2.1. Ion Mobility -- 4.2.2. Electrophoresis -- References -- PART II INTERPRETATION -- 5 INTRODUCTION TO MASS SPECTRA INTERPRETATION: ORGANIC CHEMISTRY -- 5.1. Basic Concepts -- 5.2. Inlet Systems -- 5.2.1. Direct Inlet -- 5.2.2. Chromatography-Mass Spectrometry -- 5.3. Physical Bases of Mass Spectrometry -- 5.3.1. Electron Ionization -- 5.3.2. Basics of Fragmentation Processes in Mass Spectrometry -- 5.3.3. Metastable Ions -- 5.4. Theoretical Rules and Approaches to Interpret Mass Spectra -- 5.4.1. Stability of Charged and Neutral Particles -- 5.4.2. The Concept of Charge and Unpaired Electron Localization -- 5.4.3. Charge Remote Fragmentation -- 5.5. Practical Approaches to Interpret Mass Spectra -- 5.5.1. Molecular Ion -- 5.5.2. High Resolution Mass Spectrometry -- 5.5.3. Determination of the Elemental Composition of Ions on the Basis of Isotopic Peaks -- 5.5.4. The Nitrogen Rule -- 5.5.5. Establishing the (13)C Isotope Content in Natural Samples -- 5.5.6. Calculation of the Isotopic Purity of Samples -- 5.5.7. Fragment Ions -- 5.5.8. Mass Spectral Libraries -- 5.5.9. Additional Mass Spectral Information -- 5.5.10. Fragmentation Scheme -- References -- 6 SEQUENCING OF PEPTIDES AND PROTEINS -- 6.1. Basic Concepts -- 6.2. Tandem Mass Spectrometry of Peptides and Proteins -- 6.3. Peptide Fragmentation Nomenclature -- 6.3.1. Roepstorff's Nomenclature -- 6.3.2. Biemann's Nomenclature -- 6.3.3. Cyclic Peptides.

6.4. Technical Aspects and Fragmentation Rules -- 6.5. Why Peptide Sequencing? -- 6.6. De Novo Sequencing -- 6.6.1. Data Acquisition -- 6.6.2. Sequencing Procedure Examples -- 6.6.3. Tips and Tricks -- 6.7. Peptide Derivatization Prior to Fragmentation -- 6.7.1. Simplification of Fragmentation Patterns -- 6.7.2. Stable Isotopes Labeling -- Acknowledgments -- References -- Online Tutorials -- 7 OPTIMIZING SENSITIVITY AND SPECIFICITY IN MASS SPECTROMETRIC PROTEOME ANALYSIS -- 7.1. Quantitation -- 7.2. Peptide and Protein Identification -- 7.3. Success Rate and Relative Dynamic Range -- 7.4. Summary -- References -- PART III APPLICATIONS -- 8 DOPING CONTROL -- References -- 9 OCEANOGRAPHY -- References -- 10 "OMICS" APPLICATIONS -- 10.1. Introduction -- 10.2. Genomics and Transcriptomics -- 10.3. Proteomics -- 10.4. Metabolomics -- 11 SPACE SCIENCES -- 11.1. Introduction -- 11.2. Origins -- 11.3. Dynamics -- 11.4. The Space MS Paradox -- 11.5. A Brief History of Space MS -- 11.5.1. Beginnings -- 11.5.2. Linear TOF-MS -- 11.5.3. Isochronous TOF-MS -- 11.6. GENESIS and the Future -- References -- 12 BIOTERRORISM -- 12.1. What is Bioterrorism? -- 12.2. Some Historical Accounts of Bioterrorism -- 12.3. Geneva Protocol of 1925 and Biological Weapons Convention of 1972 -- 12.4. Categories of Biothreat Agents -- 12.5. Challenges -- 12.6. MS Identification of Biomarker Proteins -- 12.7. Development of New Therapeutics and Vaccines Using Immunoproteomics -- References -- 13 IMAGING OF SMALL MOLECULES -- 13.1. SIMS Imaging -- 13.2. Biological Applications (Cells, Tissues, and Pharmaceuticals) -- 13.3. Catalysis -- 13.4. Forensics -- 13.5. Semiconductors -- 13.6. The Future -- References -- 14 UTILIZATION OF MASS SPECTROMETRY IN CLINICAL CHEMISTRY -- 14.1. Introduction -- 14.2. Where are Mass Spectrometers Utilized in Clinical Applications?.

14.3. Most Common Analytes Detected by Mass Spectrometers -- 14.4. Multianalyte Detection of Clinical Biomarkers, The Real Success Story -- 14.5. Quantitative Profiling -- 14.6. A Clinical Example of the Use of Mass Spectrometry -- 14.7. Demonstrations of Concepts of Quantification in Clinical Chemistry -- 14.7.1. Tandem Mass Spectrometry and Sorting (Pocket Change) -- 14.7.2. Isotope Dilution and Quantification (the Jelly Bean Experiment) -- 15 POLYMERS -- 15.1. Introduction -- 15.2. Instrumentation, Sample Preparation, and Matrices -- 15.3. Analysis of Ultrapure Polymer Samples -- 15.4. Analysis of Polymer Samples in which all Chains Possess the Same Backbone -- 15.5. Analysis of Polymer Mixtures with Different Backbones -- 15.6. Determination of Average Molar Masses -- References -- 16 FORENSIC SCIENCES -- 16.1. Introduction -- 16.2. Materials Examined and Goals of Analysis -- 16.3. Sample Preparation -- 16.4. Systematic Toxicological Analysis -- 16.4.1. GC-MS Procedures -- 16.4.2. LC-MS Procedures -- 16.5. Quantitative Analysis -- 16.6. Identification of Arsons -- References -- 17 NEW APPROACHES TO NEUROCHEMISTRY -- 17.1. Introduction -- 17.2. Why is there so Little Research in this Area? -- 17.3. Proteomics and Neurochemistry -- 17.3.1. The Synapse -- 17.3.2. Learning and Memory -- 17.3.3. The Brain and the Immune System -- 17.3.4. Stress and Anxiety -- 17.3.5. Psychiatric Diseases and Disorders -- 17.3.6. Chronic Fatigue Syndrome -- 17.3.7. Addiction -- 17.3.8. Pain -- 17.3.9. Neurodegenerative Diseases -- 17.4. Conclusions -- Acknowledgments -- References -- PART IV APPENDIX -- INDEX.