Edmond de Hoffmann, Université Catholique de Louvain, Belgium & Ludwig Institute for Cancer Research, Brussels, Belgium.

Vincent Stroobant, Ludwig Institute for Cancer Research, Brussels, Belgium.

Preface xi

Introduction 1

Principles 1

Diagram of a Mass Spectrometer 4

History 5

Ion Free Path 10

1 Ion Sources 15

1.1 Electron Ionization 15

1.2 Chemical Ionization 17

1.2.1 Proton transfer 19

1.2.2 Adduct formation 21

1.2.3 Charge-transfer chemical ionization 21

1.2.4 Reagent gas 22

1.2.5 Negative ion formation 25

1.2.6 Desorption chemical ionization 27

1.3 Field Ionization 28

1.4 Fast Atom Bombardment and Liquid Secondary Ion Mass Spectrometry 29

1.5 Field Desorption 31

1.6 Plasma Desorption 32

1.7 Laser Desorption 33

1.8 Matrix-Assisted Laser Desorption Ionization 33

1.8.1 Principle of MALDI 33

1.8.2 Practical considerations 36

1.8.3 Fragmentations 39

1.8.4 Atmospheric pressure matrix-assisted laser desorption ionization 39

1.9 Thermospray 41

1.10 Atmospheric Pressure Ionization 42

1.11 Electrospray 43

1.11.1 Multiply charged ions 46

1.11.2 Electrochemistry and electric field as origins of multiply charged ions 48

1.11.3 Sensitivity to concentration 50

1.11.4 Limitation of ion current from the source by the electrochemical process 51

1.11.5 Practical considerations 54

1.12 Atmospheric Pressure Chemical Ionization 55

1.13 Atmospheric Pressure Photoionization 56

1.14 Atmospheric Pressure Secondary Ion Mass Spectrometry 61

1.14.1 Desorption electrospray ionization 61

1.14.2 Direct analysis in real time 62

1.15 Inorganic Ionization Sources 65

1.15.1 Thermal ionization source 65

1.15.2 Spark source 67

1.15.3 Glow discharge source 68

1.15.4 Inductively coupled plasma source 69

1.15.5 Practical considerations 71

1.16 Gas-Phase Ion-Molecule Reactions 72

1.17 Formation and Fragmentation of Ions: Basic Rules 76

1.17.1 Electron ionization and photoionization under vacuum 77

1.17.2 Ionization at low pressure or at atmospheric pressure 77

1.17.3 Proton transfer 77

1.17.4 Adduct formation 78

1.17.5 Formation of aggregates or clusters 79

1.17.6 Reactions at the interface between source and analyser 79

2 Mass Analysers 85

2.1 Quadrupole Analysers 88

2.1.1 Description 88

2.1.2 Equations of motion 91

2.1.3 Ion guide and collision cell 96

2.1.4 Spectrometers with several quadrupoles in tandem 98

2.2 Ion Trap Analysers 100

2.2.1 The 3D ion trap 100

2.2.2 The 2D ion trap 117

2.3 The Electrostatic Trap or 'Orbitrap' 122

2.4 Time-of-Flight Analysers 126

2.4.1 Linear time-of-flight mass spectrometer 126

2.4.2 Delayed pulsed extraction 129

2.4.3 Reflectrons 131

2.4.4 Tandem mass spectrometry with time-of-flight analyser 134

2.4.5 Orthogonal acceleration time-of-flight instruments 139

2.5 Magnetic and Electromagnetic Analysers 143

2.5.1 Action of the magnetic field 143

2.5.2 Electrostatic field 144

2.5.3 Dispersion and resolution 145

2.5.4 Practical considerations 146

2.5.5 Tandem mass spectrometry in electromagnetic analysers 149

2.6 Ion Cyclotron Resonance and Fourier Transform Mass Spectrometry 157

2.6.1 General principle 157

2.6.2 Ion cyclotron resonance 159

2.6.3 Fourier transform mass spectrometry 159

2.6.4 MSn in ICR/FTMS instruments 164

2.7 Hybrid Instruments 164

2.7.1 Electromagnetic analysers coupled to quadrupoles or ion trap 165

2.7.2 Ion trap analyser combined with time-of-flight or ion cyclotron resonance 166

2.7.3 Hybrids including time-of-flight with orthogonal acceleration 167

3 Detectors and Computers 175

3.1 Detectors 175

3.1.1 Photographic plate 176

3.1.2 Faraday cup 176

3.1.3 Electron multipliers 177

3.1.4 Electro-optical ion detectors 181

3.2 Computers 182

3.2.1 Functions 183

3.2.2 Instrumentation 183

3.2.3 Data acquisition 183

3.2.4 Data conversion 186

3.2.5 Data reduction 186

3.2.6 Library search 186

4 Tandem Mass Spectrometry 189

4.1 Tandem Mass Spectrometry in Space or in Time 189

4.2 Tandem Mass Spectrometry Scan Modes 192

4.3 Collision-Activated Decomposition or Collision-Induced Dissociation 195

4.3.1 Collision energy conversion to internal energy 196

4.3.2 High-energy collision (keV) 198

4.3.3 Low-energy collision (between 1 and 100 eV) 199

4.4 Other Methods of Ion Activation 199

4.5 Reactions Studied in MS/MS 202

4.6 Tandem Mass Spectrometry Applications 204

4.6.1 Structure elucidation 205

4.6.2 Selective detection of target compound class 207

4.6.3 Ion-molecule reaction 210

4.6.4 The kinetic method 211

5 Mass Spectrometry/Chromatography Coupling 217

5.1 Elution Chromatography Coupling Techniques 218

5.1.1 Gas chromatography/mass spectrometry 219

5.1.2 Liquid chromatography/mass spectrometry 221

5.1.3 Capillary electrophoresis/mass spectrometry 228

5.2 Chromatography Data Acquisition Modes 228

5.3 Data Recording and Treatment 230

5.3.1 Data recording 230

5.3.2 Instrument control and treatment of results 232

6 Analytical Information 243

6.1 Mass Spectrometry Spectral Collections 243

6.2 High Resolution 245

6.2.1 Information at different resolving powers 249

6.2.2 Determination of the elemental composition 251

6.3 Isotopic Abundances 251

6.4 Low-mass Fragments and Lost Neutrals 257

6.5 Number of Rings or Unsaturations 258

6.6 Mass and Electron Parities, Closed-shell Ions and Open-shell Ions 259

6.6.1 Electron parity 259

6.6.2 Mass parity 259

6.6.3 Relationship between mass and electron parity 260

6.7 Quantitative Data 260

6.7.1 Specificity 260

6.7.2 Sensitivity and detection limit 262

6.7.3 External standard method 264

6.7.4 Sources of error 265

6.7.5 Internal standard method 266

6.7.6 Isotopic dilution method 268

7 Fragmentation Reactions 273

7.1 Electron Ionization and Fragmentation Rates 273

7.2 Quasi-Equilibrium and RRKM Theory 275

7.3 Ionization and Appearance Energies 279

7.4 Fragmentation Reactions of Positive Ions 280

7.4.1 Fragmentation of odd-electron cations or radical cations (OE¿+) 280

7.4.2 Fragmentation of cations with an even number of electrons (EE+) 286

7.4.3 Fragmentations obeying the parity rule 288

7.4.4 Fragmentations not obeying the parity rule 291

7.5 Fragmentation Reactions of Negative Ions 291

7.5.1 Fragmentation mechanisms of even electron anions (EE-) 292

7.5.2 Fragmentation mechanisms of radical anions (OE¿¿) 293

7.6 Charge Remote Fragmentation 293

7.7 Spectrum Interpretation 294

7.7.1 Typical ions 296

7.7.2 Presence of the molecular ion 296

7.7.3 Typical neutrals 296

7.7.4 A few examples of the interpretation of mass spectra 298

8 Analysis of Biomolecules 305

8.1 Biomolecules and Mass Spectrometry 305

8.2 Proteins and Peptides 306

8.2.1 ESI and MALDI 307

8.2.2 Structure and sequence determination using fragmentation 309

8.2.3 Applications 324

8.3 Oligonucleotides 342

8.3.1 Mass spectra of oligonucleotides 343

8.3.2 Applications of mass spectrometry to oligonucleotides 346

8.3.3 Fragmentation of oligonucleotides 351

8.3.4 Characterization of modified oligonucleotides 355

8.4 Oligosaccharides 357

8.4.1 Mass spectra of oligosaccharides 358

8.4.2 Fragmentation of oligosaccharides 360

8.4.3 Degradation of oligosaccharides coupled with mass spectrometry 367

8.5 Lipids 371

8.5.1 Fatty acids 373

8.5.2 Acylglycerols 376

8.5.3 Bile acids 382

8.6 Metabolomics 386

8.6.1 Mass spectrometry in metabolomics 387

8.6.2 Applications 388

9 Exercises 403

Questions 403

Answers 415

Appendices 437

1 Nomenclature 437

1.1 Units 437

1.2 Definitions 437

1.3 Analysers 438

1.4 Detection 439

1.5 Ionization 440

1.6 Ion types 441

1.7 Ion-molecule reaction 442

1.8 Fragmentation 442

2 Acronyms and abbreviations 442

3 Fundamental Physical Constants 446

4A Table of Isotopes in Ascending Mass Order 447

4B Table of Isotopes in Alphabetical Order 452

5 Isotopic Abundances (in %) for Various Elemental Compositions CHON 457

6 Gas-Phase Ion Thermochemical Data of Molecules 467

7 Gas-Phase Ion Thermochemical Data of Radicals 469

8 Literature on Mass Spectrometry 470

9 Mass Spectrometry on Internet 476

Index 479