In addition to the essential theoretical background and fundamental principles, this unique reference presents a detailed, step-by-step methodology for interpreting even electron mass spectrometry results. Specific chapters are devoted to: proteomics; biomolecule spectral interpretation of small molecules; biomolecule spectral interpretation of biological macromolecules; and MALDI-TOF-Postsource Decay (PSD). Chapters feature detailed examples, questions, and problems to help readers solidify their understanding of the concepts and techniques.

Bryan M. Ham, PhD, is a member of the American Society for Mass Spectrometry, the American Chemical Society, the Tear Film and Ocular Surface Society, and the Association for Research in Vision and Ophthalmology. He is currently conducting proteomics research at Pacific Northwest National Laboratory in Richland WA. His research interests include biomolecule analysis in the areas of proteomics, lipidomics, and metabolomics.

Preface	p. xiii
Acknowledgments	p. xiv
Introduction and Basic Definitions	p. 1
Definition and Description of Mass Spectrometry	p. 1
Basic Design of Mass Analyzer Instrumentation	p. 2
Mass Spectrometry of Protein, Metabolite, and Lipid Biomolecules	p. 5
Proteomics	p. 5
Metabolomics	p. 8
Lipidomics	p. 8
Fundamental Studies of Biological Compound Interactions	p. 11
Mass-to-Charge Ratio (m/z): How the Mass Spectrometer Separates Ions	p. 13
Exact Mass versus Nominal Mass	p. 16
Mass Accuracy and Resolution	p. 18
High-Resolution Mass Measurements	p. 20
Rings Plus Double Bonds (r + db)	p. 23
Nitrogen Rule in Mass Spectrometry	p. 24
Problems	p. 25
References	p. 27
Ionization in Mass Spectrometry	p. 29
Ionization Techniques and Sources	p. 29
Electron Ionization (EI)	p. 30
Chemical Ionization (CI)	p. 32
Positive Chemical Ionization	p. 34
Negative Chemical Ionization	p. 39
Atmospheric Pressure Chemical Ionization (APCI)	p. 40
Electrospray Ionization (ESI)	p. 42
Nanoelectrospray Ionization (Nano-ESI)	p. 46
Atmospheric Pressure Photoionization (APPI)	p. 50
APPI Mechanism	p. 51
APPI VUV Lamps	p. 52
APPI Sources	p. 52
Comparison of ESI and APPI	p. 53
Matrix-Assisted Laser Desorption Ionization (MALDI)	p. 57
Fast Atom Bombardment (FAB)	p. 64
Application of FAB versus EI	p. 66
Problems	p. 68
References	p. 69
Mass Analyzers in Mass Spectrometry	p. 72
Mass Analyzers	p. 72
Magnetic and Electric Sector Mass Analyzer	p. 74
Time-of-Flight Mass Analyzer (TOF/MS)	p. 79
Time-of-Flight/Time-of-Flight Mass Analyzer (TOF-TOF/MS)	p. 83
Quadrupole Mass Filter	p. 86
Triple Quadrupole Mass Analyzer (QQQ/MS)	p. 91
Three-Dimensional Quadrupole Ion Trap Mass Analyzer (QIT/MS)	p. 93
Linear Quadrupole Ion Trap Mass Analyzer (LTQ/MS)	p. 98
Quadrupole Time-of-Flight Mass Analyzer (Q-TOF/MS)	p. 101
Fourier Transform Ion Cyclotron Resonance Mass Analyzer (FTICR/MS)	p. 103
Introduction	p. 103
FTICR Mass Analyzer	p. 105
FTICR Trapped Ion Behavior	p. 106
Cyclotron and Magnetron Ion Motion	p. 112
Basic Experimental Sequence	p. 115
Linear Ion Trap Fourier Transform Mass Analyzer (LTQ-FT/MS)	p. 118
Linear Ion Trap Orbitrap Mass Analyzer (LTQ-Orbitrap/MS)	p. 121
Problems	p. 134
References	p. 135
Collision and Unimolecular Reaction Rate Theory	p. 137
Introduction to Collision Theory	p. 137
Noncovalent Bond Dissociation Energy	p. 142
Low-Molecular-Weight BDE Predictive Model	p. 148
Computer Modeling of BDE Values	p. 149
High-Molecular-Weight BDE Predictive Model	p. 152
Noncovalent BDE of Li[superscript +] Adduct of Monopentadecanoin	p. 153
Practice Problems	p. 155
Problem 1	p. 155
Problem 2	p. 155
Problem 3	p. 157
Problem 4	p. 157
Problem 5	p. 159
BDE Determination of Li[superscript +] Lipid Dimer Adducts	p. 160
Covalent Apparent Threshold Energies of Li[superscript +] Adducted Acylglycerols	p. 164
Apparent Threshold Energy Predictive Model	p. 165
Apparent Threshold Energies for Lithiated Monopentadecanoin	p. 167
Apparent Threshold Energies for Lithiated 1-Stearin,2-Palmitin	p. 170
Apparent Threshold Energies for Lithiated 1,3-Dipentadecanoin	p. 175
Computational Reaction Enthalpies and Predicted Apparent Threshold Energies	p. 177
Conclusions	p. 182
References	p. 183
The Mass Spectrum: Odd Electron Molecular Ion Versus Even Electron Precursor Ion Mass Spectra	p. 186
Electron Ionization Odd Electron Processes	p. 186
Oleamide Fragmentation Pathways-Odd Electron M[superscript + middle dot] by Gas Chromatography/Electron Ionization-Mass Spectrometry (GC/EI-MS)	p. 190
Oleamide Fragmentation Pathways-Even Electron [M + H superscript +] by Electrospray Ionization/Ion Trap Mass Spectrometry (ESI/IT-MS)	p. 194
Problem: Methyl Oleate EI Mass Spectrum	p. 200
References	p. 200
Product Ion Spectral Interpretation	p. 201
Introduction to Product Ion Spectral Interpretation	p. 201
Structural Elucidation of 1,3-Dipentadecanoin	p. 203
Problem: Lithiated Monopentadecanoin Product Ion Spectrum	p. 213
Biomolecule Spectral Interpretation: Proteins	p. 214
Introduction to Proteomics	p. 214
Protein Structure and Chemistry	p. 215
Bottom-Up Proteomics-Mass Spectrometry of Peptides	p. 217
History and Strategy	p. 217
Protein Identification Through Product Ion Spectra	p. 221
High-Energy Product Ions	p. 226
De Novo Sequencing	p. 228
Electron Capture Dissociation	p. 230
Top-Down Proteomics: Mass Spectrometry of Intact Proteins	p. 231
Background	p. 231
Gas-Phase Basicity and Protein Charging	p. 232
Calculation of Charge State and Molecular Weight	p. 234
Top-Down Protein Sequencing	p. 236
Posttranslational Modification of Proteins (PTM)	p. 239
Three Main Types of PTM	p. 239
Glycosylation of Proteins	p. 239
Phosphorylation of Proteins	p. 244
Sulfation of Proteins	p. 262
Systems Biology and Bioinformatics	p. 272
Biomarkers in Cancer	p. 277
Problems	p. 279
References	p. 280
Biomolecule Spectral Interpretation-Small Molecules	p. 284
Introduction	p. 284
Ionization Efficiency of Lipids	p. 285
Fatty Acids	p. 287
Negative Ion Mode Electrospray Behavior of Fatty Acids	p. 289
Quantitative Analysis by GC/EI Mass Spectrometry	p. 295
Wax Esters	p. 300
Oxidized Wax Esters	p. 302
Oxidation of Monounsaturated Wax Esters by Fenton Reaction	p. 302
Sterols	p. 305
Synthesis of Cholesteryl Phosphate	p. 308
Single-Stage and High-Resolution Mass Spectrometry	p. 309
Proton Nuclear Magnetic Resonance	p. 310
Theoretical NMR Spectroscopy	p. 310
Structure Elucidation	p. 310
Acylglycerols	p. 315
Analysis of Monopentadecanoin	p. 316
Analysis of 1,3-Dipentadecanoin	p. 317
Analysis of Triheptadecanoin	p. 318
ESI/MS of Phosphorylated Lipids	p. 319
Electrospray Ionization Behavior of Phosphorylated Lipids	p. 322
Positive Ion Mode ESI of Phosphorylated Lipids	p. 323
Negative Ion Mode ESI of Phosphorylated Lipids	p. 326
Problems	p. 327
References	p. 328
Biomolecule Spectral Interpretation: Biological Macromolecules	p. 331
Introduction	p. 331
Carbohydrates	p. 332
Ionization of Oligosaccharides	p. 334
Carbohydrate Fragmentation	p. 335
Complex Oligosaccharide Structural Elucidation	p. 338
Nucleic Acids	p. 340
Negative Ion Mode ESI of a Yeast 76-mer tRNA[superscript Phe]	p. 346
Positive Ion Mode MALDI Analysis	p. 348
Problems	p. 353
References	p. 353
Maldi-Tof-Postsource Decay (PSD)	p. 355
Introduction	p. 355
Metastable Decay	p. 356
Ion Mirror Ratio Measurement of PSD Spectra	p. 358
Postsource Decay of Phosphatidylserine	p. 358
Problem 10.1	p. 364
Postsource Decay of Phosphatidylcholines	p. 365
Problem 10.2	p. 367
Problem 10.3	p. 369
Postsource Decay of Phosphatidylglycerol	p. 369
Problem 10.4	p. 373
Problem 10.5	p. 373
Atomic Weights and Isotopic Compositions	p. 375
Solutions to Chapter Problems	p. 383
Fundamental Physical Constants	p. 401
Glossary	p. 402
Index	p. 415
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