Mass Spectrometry

With contributions from noted experts from Europe and North America, Mass Spectrometry Instrumentation, Interpretation, and Applications serves as a forum to introduce students to the whole world of mass spectrometry and to the many different perspectives that each scientific field brings to its use. The book emphasizes the use of this important analytical technique in many different fields, including applications for organic and inorganic chemistry, forensic science, biotechnology, and many other areas. After describing the history of mass spectrometry, the book moves on to discuss instrumentation, theory, and basic applications.

Foreword xiii

Contributors xv

Part I Instrumentation 1

1 Definitions and Explanations 3
Ann Westman-Brinkmalm and Gunnar Brinkmalm

References 13

2 A Mass Spectrometer’s Building Blocks 15
Ann Westman-Brinkmalm and Gunnar Brinkmalm

2.1. Ion Sources 15

2.1.1. Gas Discharge 16

2.1.2. Thermal Ionization 16

2.1.3. Spark Source 19

2.1.4. Glow Discharge 20

2.1.5. Inductively Coupled Plasma 21

2.1.6. Electron Ionization 23

2.1.7. Chemical Ionization 24

2.1.8. Atmospheric Pressure Chemical Ionization 24

2.1.9. Photoionization 25

2.1.10. Multiphoton Ionization 25

2.1.11. Atmospheric Pressure Photoionization 26

2.1.12. Field Ionization 26

2.1.13. Field Desorption 27

2.1.14. Thermospray Ionization 27

2.1.15. Electrospray Ionization 27

2.1.16. Desorption Electrospray Ionization 29

2.1.17. Direct Analysis in Real Time 30

2.1.18. Secondary Ion Mass Spectrometry 31

2.1.19. Fast Atom Bombardment 33

2.1.20. Plasma Desorption 34

2.1.21. Laser Desorption/Ionization 34

2.1.22. Matrix-Assisted Laser Desorption/Ionization 35

2.1.23. Atmospheric Pressure Matrix-Assisted Laser Desorption/Ionization 37

2.2. Mass Analyzers 38

2.2.1. Time-of-Flight 40

2.2.2. Magnetic/Electric Sector 45

2.2.3. Quadrupole Mass Filter 49

2.2.4. Quadrupole Ion Trap 51

2.2.5. Orbitrap 55

2.2.6. Fourier Transform Ion Cyclotron Resonance 58

2.2.7. Accelerator Mass Spectrometry 62

2.3. Detectors 65

2.3.1. Photoplate Detector 65

2.3.2. Faraday Detector 67

2.3.3. Electron Multipliers 67

2.3.4. Focal Plane Detector 69

2.3.5. Scintillation Detector 69

2.3.6. Cryogenic Detector 70

2.3.7. Solid-State Detector 70

2.3.8. Image Current Detection 70

References 71

3 Tandem Mass Spectrometry 89
Ann Westman-Brinkmalm and Gunnar Brinkmalm

3.1. Tandem MS Analyzer Combinations 91

3.1.1. Tandem-in-Space 91

3.1.2. Tandem-in-Time 95

3.1.3. Other Tandem MS Configurations 97

3.2. Ion Activation Methods 97

3.2.1. In-Source Decay 97

3.2.2. Post-Source Decay 98

3.2.3. Collision Induced/Activated Dissociation 98

3.2.4. Photodissociation 100

3.2.5. Blackbody Infrared Radiative Dissociation 100

3.2.6. Electron Capture Dissociation 101

3.2.7. Electron Transfer Dissociation 101

3.2.8. Surface-Induced Dissociation 101

References 102

4 Separation Methods 105
Ann Westman-Brinkmalm, Jerzy Silberring, and Gunnar Brinkmalm

4.1. Chromatography 106

4.1.1. Gas Chromatography 106

4.1.2. Liquid Chromatography 107

4.1.3. Supercritical Fluid Chromatography 109

4.2. Electric-Field Driven Separations 110

4.2.1. Ion Mobility 110

4.2.2. Electrophoresis 111

References 113

Part II Interpretation 117

5 Introduction to Mass Spectra Interpretation: Organic Chemistry 119
Albert T. Lebedev

5.1. Basic Concepts 119

5.2. Inlet Systems 121

5.2.1. Direct Inlet 121

5.2.2. Chromatography-Mass Spectrometry 121

5.3. Physical Bases of Mass Spectrometry 128

5.3.1. Electron Ionization 129

5.3.2. Basics of Fragmentation Processes in Mass Spectrometry 130

5.3.3. Metastable Ions 135

5.4. Theoretical Rules and Approaches to Interpret Mass Spectra 137

5.4.1. Stability of Charged and Neutral Particles 137

5.4.2. The Concept of Charge and Unpaired Electron Localization 148

5.4.3. Charge Remote Fragmentation 151

5.5. Practical Approaches to Interpret Mass Spectra 152

5.5.1. Molecular Ion 152

5.5.2. High Resolution Mass Spectrometry 155

5.5.3. Determination of the Elemental Composition of Ions on the Basis of Isotopic Peaks 158

5.5.4. The Nitrogen Rule 164

5.5.5. Establishing the 13 C Isotope Content in Natural Samples 166

5.5.6. Calculation of the Isotopic Purity of Samples 166

5.5.7. Fragment Ions 168

5.5.8. Mass Spectral Libraries 173

5.5.9. Additional Mass Spectral Information 173

5.5.10. Fragmentation Scheme 175

References 177

6 Sequencing of Peptides and Proteins 179
Marek Noga, Tomasz Dylag, and Jerzy Silberring

6.1. Basic Concepts 179

6.2. Tandem Mass Spectrometry of Peptides and Proteins 181

6.3. Peptide Fragmentation Nomenclature 183

6.3.1. Roepstorff’s Nomenclature 183

6.3.2. Biemann’s Nomenclature 185

6.3.3. Cyclic Peptides 187

6.4. Technical Aspects and Fragmentation Rules 188

6.5. Why Peptide Sequencing? 190

6.6. De Novo Sequencing 192

6.6.1. Data Acquisition 193

6.6.2. Sequencing Procedure Examples 194

6.6.3. Tips and Tricks 205

6.7. Peptide Derivatization Prior to Fragmentation 207

6.7.1. Simplification of Fragmentation Patterns 208

6.7.2. Stable Isotopes Labeling 209

Acknowledgments 210

References 210

Online Tutorials 210

7 Optimizing Sensitivity and Specificity in Mass Spectrometric Proteome Analysis 211
Jan Eriksson and David Fenyö

7.1. Quantitation 212

7.2. Peptide and Protein Identification 213

7.3. Success Rate and Relative Dynamic Range 218

7.4. Summary 220

References 220

Part III Applications 223

8 Doping Control 225
Graham Trout

References 233

9 Oceanography 235
R. Timothy Short, Robert H. Byrne, David Hollander, Johan Schijf, Strawn K. Toler, and Edward S. VanVleet

References 241

10 “omics” Applications 243
Simone König

10.1. Introduction 243

10.2. Genomics and Transcriptomics 246

10.3. Proteomics 248

10.4. Metabolomics 251

11 Space Sciences 253
Robert Sheldon

11.1. Introduction 253

11.2. Origins 254

11.3. Dynamics 256

11.4. The Space MS Paradox 257

11.5. A Brief History of Space MS 259

11.5.1. Beginnings 259

11.5.2. Linear TOF-MS 260

11.5.3. Isochronous TOF-MS 262

11.6. GENESIS and the Future 264

References 264

12 Bioterrorism 267
Vito G. DelVecchio and Cesar V. Mujer

12.1. What is Bioterrorism? 267

12.2. Some Historical Accounts of Bioterrorism 267

12.3. Geneva Protocol of 1925 and Biological Weapons Convention of 1972 268

12.4. Categories of Biothreat Agents 268

12.5. Challenges 269

12.6. MS Identification of Biomarker Proteins 270

12.7. Development of New Therapeutics and Vaccines Using Immunoproteomics 271

References 272

13 Imaging of Small Molecules 275
Małgorzata Iwona Szynkowska

13.1. SIMS Imaging 277

13.2. Biological Applications (Cells, Tissues, and Pharmaceuticals) 278

13.3. Catalysis 280

13.4. Forensics 281

13.5. Semiconductors 282

13.6. The Future 283

References 285

14 Utilization of Mass Spectrometry In Clinical Chemistry 287
Donald H. Chace

14.1. Introduction 287

14.2. Where are Mass Spectrometers Utilized in Clinical Applications? 288

14.3. Most Common Analytes Detected by Mass Spectrometers 288

14.4. Multianalyte Detection of Clinical Biomarkers, The Real Success Story 289

14.5. Quantitative Profiling 291

14.6. A Clinical Example of the Use of Mass Spectrometry 292

14.7. Demonstrations of Concepts of Quantification in Clinical Chemistry 294

14.7.1. Tandem Mass Spectrometry and Sorting (Pocket Change) 294

14.7.2. Isotope Dilution and Quantification (the Jelly Bean Experiment) 295

15 Polymers 299
Maurizio S. Montaudo

15.1. Introduction 299

15.2. Instrumentation, Sample Preparation, and Matrices 300

15.3. Analysis of Ultrapure Polymer Samples 301

15.4. Analysis of Polymer Samples in which all Chains Possess the Same Backbone 301

15.5. Analysis of Polymer Mixtures with Different Backbones 303

15.6. Determination of Average Molar Masses 303

References 306

16 Forensic Sciences 309
Maria Kala

16.1. Introduction 309

16.2. Materials Examined and Goals of Analysis 311

16.3. Sample Preparation 312

16.4. Systematic Toxicological Analysis 312

16.4.1. GC-MS Procedures 315

16.4.2. LC-MS Procedures 315

16.5. Quantitative Analysis 317

16.6. Identification of Arsons 319

References 319

17 New Approaches to Neurochemistry 321
Jonas Bergquist, Jerzy Silberring, and Rolf Ekman

17.1. Introduction 321

17.2. Why is there so Little Research in this Area? 322

17.3. Proteomics and Neurochemistry 323

17.3.1. The Synapse 324

17.3.2. Learning and Memory 324

17.3.3. The Brain and the Immune System 325

17.3.4. Stress and Anxiety 327

17.3.5. Psychiatric Diseases and Disorders 329

17.3.6. Chronic Fatigue Syndrome 329

17.3.7. Addiction 330

17.3.8. Pain 331

17.3.9. Neurodegenerative Diseases 331

17.4. Conclusions 333

Acknowledgments 333

References 334

Part IV Appendix 337

Index 353

"It was my great pleasure to read this clearly written and well organized mass spectrometry (MS) book. In view, it can serve as an excellent textbook for both undergraduate and graduate students who major in analytical, biological, forensic, or environmental chemistry, as well as a valuable resource to those researchers who are interested in the MS-based chemical analysis." (J Am Soc Mass Spectrom, 2011)

"The book is particularly designed for graduate students, with the assumption being made that most of them will not become mass spectrometry specialists. Instead, it focuses on how they can use the technique to support and advance research across a broad range of disciplines." (Chemistry Journals, 11 April 2011)

Rolf Ekman, PhD, is a Professor of Neurochemistry at University of Gothenburg in Sweden.

JERZY SILBERRING, PhD, is the Head of the Department of Neurobiochemistry in the Department of Chemistry and the former deputy head of the Regional Laboratory of Physicochemical Analyses at Jagiellonian University in Krakow, Poland.

Ann M. Westman-Brinkmalm, PhD, is a Junior Research Fellow at the Sahlgrenska Academy at University of Gothenburg in Sweden.

Agnieszka Kraj, PhD, is an Assistant Professor in the Department of Neurobiochemistry, Faculty of Chemistry at Jagiellonian University in Krakow, Poland.

Helps students fully leverage mass spectrometry in whichever field of research they choose

Mass Spectrometry: Instrumentation, Interpretation, and Applications enables students to become fully versed in the principles and uses of mass spectrometry. Featuring contributions from international experts, the text introduces the many perspectives and approaches that different scientific fields bring to mass spectrometry, including applications for organic and inorganic chemistry, forensic science, biotechnology, and much more. This multidisciplinary approach enables students to apply their knowledge in their chosen fields of research in order to identify, quantify, and determine the structures and chemical properties of compounds.

This text is divided into three parts that guide students from basic principles to applications:

• Part One, Instrumentation, begins with basic definitions and explanations followed by a discussion of the mass spectrometer and its building blocks. Next, the text describes fragmentation methods and tandem MS analyzer configurations, ending with a short summary of separation methods used in conjunction with mass spectrometry.

• Part Two, Interpretation, explains basic concepts in mass spectra interpretation and then demonstrates how these concepts are used to interpret mass spectra in organic chemistry. Students also learn how to use mass spectrometry as a tool for peptide sequencing and how to optimize sensitivity and specificity in mass spectrometric proteome analysis.

• Part Three, Applications, features ten researchers and research groups from different fields describing how they use mass spectrometry in their own work.

Designed for graduate-level students, this textbook assumes that most students will not become mass spectrometry specialists. Instead, it focuses on how they can use the mass spectrometer to support and advance research across a broad range of disciplines.