Mass Spectrometry

Professor Edmond de Hoffmann, Universit Catholique de Louvain, Belgium.Dr Vincent Stroobant, Ludwig Institute for Cancer Research, ?Brussels, Belgium.

Contents Preface Introduction Principles Diagram of a Mass Spectrometer History Ion Free Path 1 Ion Sources 1.1 Electron Ionization 1.2 Chemical Ionization 1.2.1 Proton transfer 1.2.2 Adduct formation 1.2.3 Charge-transfer chemical ionization 1.2.4 Reagent gas 1.2.5 Negative ion formation 1.2.6 Desorption chemical ionization (DCI) 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 1.8.1 Principle of MALDI 1.8.2 Practical considerations 1.8.3 Fragmentations 1.8.4 Atmospheric pressure matrix-assisted laser desorption ionization 1.9 Thermospray 1.10 Atmospheric Pressure Ionization 1.11 Electrospray 1.11.1 Multiply charged ions 1.11.2 Electrochemistry and electric field as origins of multiply charged ions 1.11.3 Sensitivity to concentration 1.11.4 Limitation of ion current from the source by the electrochemical process 1.11.5 Practical considerations 1.12 Atmospheric Pressure Chemical Ionization 1.13 Atmospheric Pressure Photoionization (APPI) 1.14 Atmospheric Pressure Secondary Ion Mass Spectrometry (APSIMS) 1.14.1 Desorption electrospray ionization (DESI) 1.14.2 Direct analysis in real time (DART) 1.15 Inorganic Ionization Sources 1.15.1 Thermal ionization source 1.15.2 Spark source 1.15.3 Glow discharge source 1.15.4 Inductively coupled plasma source 1.15.5 Practical considerations 1.16 Gas-Phase Ion-Molecule Reactions 1.17 Formation and Fragmentation of Ions: Basic Rules 1.17.1 Electron ionization and photoionization under vacuum 1.17.2 Ionization at low pressure or at atmospheric pressure 1.17.3 Proton transfer 1.17.4 Adduct formation 1.17.5 Formation of aggregates or clusters 1.17.6 Reactions at the interface between source and analyzer 2 Mass Analyzers 2.1 Quadrupole Analyzers 2.1.1 Description 2.1.2 Equations of motion 2.1.3 Ion guide and collision cell 2.1.4 Spectrometers with several quadrupoles in tandem 2.2 Ion Trap Analyzers 2.2.1 Three-dimensional ion trap 2.2.2 Two-dimensional ion trap 2.3 The Electrostatic Trap or "Orbitrap" 2.4 Time-of-Flight Analyzers 2.4.1 Linear time-of-flight mass spectrometer 2.4.2 Delayed pulsed extraction 2.4.3 Reflectrons 2.4.4 Tandem mass spectrometry with time-of-flight analyzer 2.4.5 Orthogonal acceleration time-of-flight instruments 2.5 Magnetic and Electromagnetic Analyzers 2.5.1 Action of the magnetic field 2.5.2 Electrostatic field 2.5.3 Dispersion and resolution 2.5.4 Practical considerations 2.5.5 Tandem mass spectrometry in electromagnetic analyzers 2.6 Ion Cyclotron Resonance and Fourier Transform Mass Spectrometry 2.6.1 General principle 2.6.2 Ion cyclotron resonance 2.6.3 Fourier transform mass spectrometry 2.6.4 MSn in ICR/FTMS instruments 2.7 Hybrid Instruments 2.7.1 Electromagnetic analyzers coupled to quadrupoles or ion trap 2.7.2 Ion trap analyzer combined with time-of-flight or ion cyclotron resonance 2.7.3 Hybrids including a time-of-flight with orthogonal acceleration 3 Detectors and Computers 3.1 Detectors 3.1.1 Photographic plate 3.1.2 Faraday cup 3.1.3 Electron multipliers 3.1.4 Electro-optical ion detectors 3.2 Computers 3.2.1 Functions 3.2.2 Instrumentation 3.2.3 Data acquisition 3.2.4 Data conversion 3.2.5 Data reduction 3.2.6 Library search 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) 4.3.1 Collision energy conversion to internal energy 4.3.2 High-energy collision (keV) 4.3.3 Low-energy collision (between 1 and 100 eV) 4.4 Other Methods of Ion Activation 4.5 Reactions Studied in MS/MS 4.6 Tandem Mass Spectrometry Applications 4.6.1 Structure elucidation 4.6.2 Selective detection of target compound class 4.6.3 Ion-molecule reaction 4.6.4 The kinetic method 5 Mass Spectrometry/Chromatography Coupling 5.1 Elution Chromatography Coupling Techniques 5.1.1 Gas chromatography/mass spectrometry (GC/MS) 5.1.2 Liquid chromatography/mass spectrometry (LC/MS) 5.1.3 Capillary electrophoresis/mass spectrometry (CE/MS) 5.2 Chromatography Data Acquisition Modes 5.3 Data Recording and Treatment 5.3.1. Data recording 5.3.2 Instrument control and treatment of results 6 Analytical Information 6.1 Mass Spectrometry Spectral Collections 6.2 High Resolution 6.2.1 Information at different resolving powers 6.2.2 Determination of the elemental composition 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 6.6.1 Electron parity 6.6.2 Mass parity 6.6.3 Relationship between mass and electron parity 6.7 Quantitative Data 6.7.1 Specificity 6.7.2 Sensitivity and detection limit 6.7.3 External standard method 6.7.4 Sources of error 6.7.5 Internal standard method 6.7.6 Isotopic dilution method 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 7.4.1 Fragmentation of odd-electron cations or radical cations (OE.+) 7.4.2 Fragmentation of cations with an even number of electrons (EE+) 7.4.3 Fragmentations obeying the parity rule 7.4.4 Fragmentations not obeying the parity rule 7.5 Fragmentation Reactions of Negative Ions 7.5.1 Fragmentation mechanisms of even electron anions (EE-) 7.5.2 Fragmentation mechanisms of radical anions (OE. -) 7.6 Charge Remote Fragmentation (CRF) 7.7 Spectrum Interpretation 7.7.1 Typical ions 7.7.2 Presence of the molecular ion 7.7.3 Typical neutrals 7.7.4 A few examples of the interpretation of mass spectra 8 Analysis of Biomolecules 8.1 Biomolecules and Mass Spectrometry 8.2 Proteins and Peptides 8.2.1 ESI and MALDI 8.2.2 Structure and sequence determination using fragmentation 8.2.3. Applications 8.3. Oligonucleotides 8.3.1. Mass Spectra of Oligonucleotides 8.3.2. Applications of Mass Spectrometry to Oligonucleotides 8.3.3. Fragmentation of Oligonucleotides 8.3.4. Characterization of Modified Oligonucleotides 8.4. Oligosaccharides 8.4.1. Mass Spectra of Oligosaccharides 8.4.2. Fragmentation of Oligosaccharides 8.4.3. Degradation of Oligosaccharides Coupled with Mass Spectrometry 8.5. Lipids 8.5.1. Fatty Acids 8.5.2 Acylglycerols 8.5.3. Bile Acids 8.6 Metabolomics 8.6.1 Mass spectrometry in metabolomics 8.6.2 Applications 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 Radicals Appendix 8. Literature on Mass Spectrometry Appendix 9. Mass Spectrometry on Internet Index