Preface xiii Acknowledgments xiv 1 Introduction and Basic Definitions 1 1.1 Definition and Description of Mass Spectrometry 1 1.2 Basic Design of Mass Analyzer Instrumentation 2 1.3 Mass Spectrometry of Protein, Metabolite, and Lipid Biomolecules 5 1.3.1 Proteomics 5 1.3.2 Metabolomics 8 1.

3.3 Lipidomics 8 1.4 Fundamental Studies of Biological Compound Interactions 11 1.5 Mass-to-Charge Ratio ( m / z ): How the Mass Spectrometer Separates Ions 13 1.6 Exact Mass versus Nominal Mass 16 1.7 Mass Accuracy and Resolution 18 1.8 High-Resolution Mass Measurements 20 1.9 Rings Plus Double Bonds (r + db) 23 1.

10 Nitrogen Rule in Mass Spectrometry 24 1.11 Problems 25 References 27 2 Ionization in Mass Spectrometry 29 2.1 Ionization Techniques and Sources 29 2.2 Electron Ionization (EI) 30 2.3 Chemical Ionization (CI) 32 2.3.1 Positive Chemical Ionization 34 2.3.

2 Negative Chemical Ionization 39 2.4 Atmospheric Pressure Chemical Ionization (APCI) 40 2.5 Electrospray Ionization (ESI) 42 2.6 Nanoelectrospray Ionization (Nano-ESI) 6 2.7 Atmospheric Pressure Photoionization (APPI) 50 2.7.1 APPI Mechanism 51 2.7.

2 APPI VUV Lamps 52 2.7.3 APPI Sources 52 2.7.4 Comparison of ESI and APPI 53 2.8 Matrix-Assisted Laser Desorption Ionization (MALDI) 57 2.9 Fast Atom Bombardment (FAB) 64 2.9.

1 Application of FAB versus EI 66 2.10 Problems 68 References 69 3 Mass Analyzers in Mass Spectrometry 72 3.1 Mass Analyzers 72 3.2 Magnetic and Electric Sector Mass Analyzer 74 3.3 Time-of-Flight Mass Analyzer (TOF/MS) 79 3.4 Time-of-Flight/Time-of-Flight Mass Analyzer (TOF-TOF/MS) 83 3.5 Quadrupole Mass Filter 86 3.6 Triple Quadrupole Mass Analyzer (QQQ/MS) 91 3.

7 Three-Dimensional Quadrupole Ion Trap Mass Analyzer (QIT/MS) 93 3.8 Linear Quadrupole Ion Trap Mass Analyzer (LTQ/MS) 98 3.9 Quadrupole Time-of-Flight Mass Analyzer (Q-TOF/MS) 101 3.10 Fourier Transform Ion Cyclotron Resonance Mass Analyzer (FTICR/MS) 103 3.10.1 Introduction 103 3.10.2 FTICR Mass Analyzer 105 3.

10.3 FTICR Trapped Ion Behavior 106 3.10.4 Cyclotron and Magnetron Ion Motion 112 3.10.5 Basic Experimental Sequence 115 3.11 Linear Ion Trap Fourier Transform Mass Analyzer (LTQ-FT/MS) 118 3.12 Linear Ion Trap Orbitrap Mass Analyzer (LTQ-Orbitrap/MS) 121 3.

13 Problems 134 References 135 4 Collision and Unimolecular Reaction Rate Theory 137 4.1 Introduction to Collision Theory 137 4.2 Noncovalent Bond Dissociation Energy 142 4.3 Low-Molecular-Weight BDE Predictive Model 148 4.4 Computer Modeling of BDE Values 149 4.5 High-Molecular-Weight BDE Predictive Model 152 4.6 Noncovalent BDE of Li+ Adduct of Monopentadecanoin 153 4.7 Practice Problems 155 4.

7.1 Problem 1 155 4.7.2 Problem 2 155 4.7.3 Problem 3 157 4.7.4 Problem 4 157 4.

7.5 Problem 5 159 4.8 BDE Determination of Li+ Lipid Dimer Adducts 160 4.9 Covalent Apparent Threshold Energies of Li+ Adducted Acylglycerols 164 4.9.1 Apparent Threshold Energy Predictive Model 165 4.9.2 Apparent Threshold Energies for Lithiated Monopentadecanoin 167 4.

9.3 Apparent Threshold Energies for Lithiated 1-Stearin,2-Palmitin 170 4.9.4 Apparent Threshold Energies for Lithiated 1,3-Dipentadecanoin 175 4.10 Computational Reaction Enthalpies and Predicted Apparent Threshold Energies 177 4.11 Conclusions 182 References 183 5 the Mass Spectrum: Odd Electron Molecular Ion versus Even Electron Precursor Ion Mass Spectra 186 5.1 Electron Ionization Odd Electron Processes 186 5.2 Oleamide Fragmentation Pathways--Odd Electron M+ by Gas Chromatography/Electron Ionization-Mass Spectrometry (GC/EI-MS) 190 5.

3 Oleamide Fragmentation Pathways--Even Electron [M + H]+ by Electrospray Ionization/Ion Trap Mass Spectrometry (ESI/IT-MS) 194 5.4 Problem: Methyl Oleate EI Mass Spectrum 200 References 200 6 Product Ion Spectral Interpretation 201 6.1 Introduction to Product Ion Spectral Interpretation 201 6.2 Structural Elucidation of 1,3-Dipentadecanoin 203 6.3 Problem: Lithiated Monopentadecanoin Product Ion Spectrum 213 7 Biomolecule Spectral Interpretation: Proteins 214 7.1 Introduction to Proteomics 214 7.2 Protein Structure and Chemistry 215 7.3 Bottom-Up Proteomics--Mass Spectrometry of Peptides 217 7.

3.1 History and Strategy 217 7.3.2 Protein Identification Through Product Ion Spectra 221 7.3.3 High-Energy Product Ions 226 7.3.4 De Novo Sequencing 228 7.

3.5 Electron Capture Dissociation 230 7.4 Top-Down Proteomics: Mass Spectrometry of Intact Proteins 231 7.4.1 Background 231 7.4.2 Gas-Phase Basicity and Protein Charging 232 7.4.

3 Calculation of Charge State and Molecular Weight 234 7.4.4 Top-Down Protein Sequencing 236 7.5 Posttranslational Modification of Proteins (PTM) 239 7.5.1 Three Main Types of PTM 239 7.5.2 Glycosylation of Proteins 239 7.

5.3 Phosphorylation of Proteins 244 7.5.4 Sulfation of Proteins 262 7.6 Systems Biology and Bioinformatics 272 7.6.1 Biomarkers in Cancer 277 7.7 Problems 279 References 280 8 Biomolecule Spectral Interpretation--small Molecules 284 8.

1 Introduction 284 8.2 Ionization Efficiency of Lipids 285 8.3 Fatty Acids 287 8.3.1 Negative Ion Mode Electrospray Behavior of Fatty Acids 289 8.4 Quantitative Analysis by GCEI Mass Spectrometry 295 8.5 Wax Esters 300 8.5.

1 Oxidized Wax Esters 302 8.5.2 Oxidation of Monounsaturated Wax Esters by Fenton Reaction 302 8.6 Sterols 305 8.6.1 Synthesis of Cholesteryl Phosphate 308 8.6.2 Single-Stage and High-Resolution Mass Spectrometry 309 8.

6.3 Proton Nuclear Magnetic Resonance 310 8.6.4 Theoretical NMR Spectroscopy 310 8.6.5 Structure Elucidation 310 8.7 Acylglycerols 315 8.7.

1 Analysis of Monopentadecanoin 316 8.7.2 Analysis of 1,3-Dipentadecanoin 317 8.7.3 Analysis of Triheptadecanoin 318 8.8 ESIMS of Phosphorylated Lipids 319 8.8.1 Electrospray Ionization Behavior of Phosphorylated Lipids 322 8.

8.2 Positive Ion Mode ESI of Phosphorylated Lipids 323 8.8.3 Negative Ion Mode ESI of Phosphorylated Lipids 326 8.9 Problems 327 References 328 9 Biomolecule Spectral Interpretation: Biological Macromolecules 331 9.1 Introduction 331 9.2 Carbohydrates 332 9.2.

1 Ionization of Oligosaccharides 334 9.2.2 Carbohydrate Fragmentation 335 9.2.3 Complex Oligosaccharide Structural Elucidation 338 9.3 Nucleic Acids 340 9.3.1 Negative Ion Mode ESI of a Yeast 76-mer tRNAPhe 346 9.

3.2 Positive Ion Mode MALDI Analysis 348 9.4 Problems 353 References 353 10 Maldi-ToF-postsource Decay (PSD) 355 10.1 Introduction 355 10.2 Metastable Decay 356 10.3 Ion Mirror Ratio Measurement of PSD Spectra 358 10.4 Postsource Decay of Phosphatidylserine 358 10.4.

1 Problem 10.1 364 10.5 Postsource Decay of Phosphatidylcholines 365 10.5.1 Problem 10.2 367 10.5.2 Problem 10.

3 369 10.6 Postsource Decay of Phosphatidylglycerol 369 10.6.1 Problem 10.4 373 10.6.2 Problem 10.5 373 Appendix 1 Atomic Weights and Isotopic Compositions 375 Appendix 2 Solutions to Chapter Problems 383 Appendix 3 Fundamental Physical Constants 401 Glossary 402 Index 415.