Contents

Preface

Introduction

Principles

Diagram of a Mass Spectrometer

History

Ion Free Path

1 Ion Sources

1.1 Electron Ionization

1.2 Chemical Ionization

1.3 Field Ionization

1.4 Fast Atom Bombardment and Liquid Secondary Ion Mass Spectrometry

1.5 Field Desorption

1.6 Plasma Desorption

1.7 Laser Desorption

1.8 Matrix-Assisted Laser Desorption Ionization

1.9 Thermospray

1.10 Atmospheric Pressure Ionization

1.11 Electrospray

1.12 Atmospheric Pressure Chemical Ionization

1.13 Atmospheric Pressure Photoionization (APPI)

1.14 Atmospheric Pressure Secondary Ion Mass Spectrometry (APSIMS)

1.15 Inorganic Ionization Sources

1.16 Gas-Phase Ion-Molecule Reactions

1.17 Formation and Fragmentation of Ions: Basic Rules

2 Mass Analyzers

2.1 Quadrupole Analyzers

2.2 Ion Trap Analyzers

2.3 The Electrostatic Trap or "Orbitrap"

2.4 Time-of-Flight Analyzers

2.5 Magnetic and Electromagnetic Analyzers

2.6 Ion Cyclotron Resonance and Fourier Transform Mass Spectrometry

2.7 Hybrid Instruments

3 Detectors and Computers

3.1 Detectors

3.2 Computers

4 Tandem Mass Spectrometry (MS/MS)

4.1 Tandem Mass Spectrometry in Space or in Time

4.2 Tandem Mass Spectrometry Scan Modes

4.3 Collision-activated or Collision-induced Dissociation (CAD or CID)

4.4 Other Methods of Ion Activation

4.5 Reactions Studied in MS/MS

4.6 Tandem Mass Spectrometry Applications

5 Mass Spectrometry/Chromatography Coupling

5.1 Elution Chromatography Coupling Techniques

5.2 Chromatography Data Acquisition Modes

5.3 Data Recording and Treatment

6 Analytical Information

6.1 Mass Spectrometry Spectral Collections

6.2 High Resolution

6.3 Isotopic Abundances

6.4 Low-mass Fragments and Lost Neutrals

6.5 Number of Rings or Unsaturations

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

6.7 Quantitative Data

7 Fragmentation Reactions

7.1 Electron Ionization and Fragmentation Rates

7.2 Quasi-equilibrium and RRKM Theory

7.3 Ionization and Appearance Energies

7.4 Fragmentation Reactions of Positive Ions

7.5 Fragmentation Reactions of Negative Ions

7.6 Charge Remote Fragmentation (CRF)

7.7 Spectrum Interpretation

8 Analysis of Biomolecules

8.1 Biomolecules and Mass Spectrometry

8.2 Proteins and Peptides

8.3. Oligonucleotides

8.4. Oligosaccharides

8.5. Lipids

8.6 Metabolomics

9 Exercises

A. Questions

B. Answers

Appendices

Appendix 1. Nomenclature

1.1. Units

1.2. Definitions

1.3. Analyzers

1.4. Detection

1.5. Ionization

1.6 Ion Types

1.7. Ion-molecule Reaction

1.8. Fragmentation

Appendix 2. Abbreviations

Appendix 3. Fundamental Physical Constants

Appendix 4A . Table of Isotopes in Ascending Mass Order

Appendix 4B. Table of Isotopes in Alphabetical Order

Appendix 5. Isotopic Abundances in % for Various Elemental Compositions CHON (M = 100%)

Appendix 6. Gas-Phase Ion Thermochemical Data of Molecules

Appendix 7. Gas-Phase Ion Thermochemical Data of