Table of Contents. Contents...IX

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1 Table of Contents Contents...IX 1 Introduction Aims and Scope What Is Mass Spectrometry? Mass Spectrometry Mass Spectrometer Mass Spectrum Filling the Black Box Terminology Units, Physical Quantities, and Physical Constants...9 Reference List Gas Phase Ion Chemistry Quasi-Equilibrium Theory Basic Assumptions of QET Ionization Electron Ionization Ionization Energy Vertical Transitions Ionization Efficiency and Ionization Cross Section Internal Energy and the Further Fate of Ions Degrees of Freedom Appearance Energy Bond Dissociation Energies and Heats of Formation Randomization of Energy Rate Constants from QET Meaning of the Rate Constant Typical k (E) Functions Description of Reacting Ions Using k (E) Functions Direct Cleavages and Rearrangement Fragmentations Practical Consequences of Internal Energy...31

2 X Table of Contents 2.7 Time Scale of Events Stable, Metastable, and Unstable Ions Kinetic Shift Activation Energy of the Reverse Reaction and Kinetic Energy Release Activation Energy of the Reverse Reaction Kinetic Energy Release Isotope Effects Kinetic Isotope Effects Determination of Ionization Energies and Appearance Energies Conventional Determination of Ionization Energies Experimental Improvements of IE Accuracy Photoelectron Spectroscopy and Derived Modern Methods Determination of Appearance Energies Breakdown Graphs Gas Phase Basicity and Proton Affinity Tandem Mass Spectrometry Collision-Induced Dissociation Other Methods of Ion Activation Reactive Collisions Reference List Isotopes Isotopic Classification of the Elements Monoisotopic Elements Di-isotopic Elements Polyisotopic Elements Calculation of Atomic, Molecular, and Ionic Mass Natural Variations in Relative Atomic Mass Calculation of Isotopic Distributions X+1 Element Carbon Binomial Approach Halogens Combinations of Carbon and Halogens Polynomial Approach Oxygen, Silicon and Sulfur Polyisotopic Elements Practical Aspects of Isotopic Patterns Isotopic Enrichment and Isotopic Labeling High-Resolution and Accurate Mass Exact Mass Deviations from Nominal Mass Mass Accuracy Resolution Mass Calibration Interaction of Resolution and Isotopic Patterns Multiple Isotopic Compositions at Very High Resolution

3 XI Multiple Isotopic Compositions and Accurate Mass Isotopic Patterns of Large Molecules Interaction of Charge State and Isotopic Patterns Reference List Instrumentation Creating a Beam of Ions Time-of-Flight Instruments Introduction to Time-of-Flight Basic Principle of TOF Instruments Linear Time-of-Flight Analyzer Reflector Time-of-Flight Analyzer Further Improvement of Resolution Orthogonal Acceleration TOF Tandem MS on TOF Instruments Magnetic Sector Instruments Introduction to Magnetic Sector Instruments Principle of the Magnetic Sector Double-Focusing Sector Instruments Setting the Resolution of a Sector Instrument Further Improvement of Sector Instruments Tandem MS with Magnetic Sector Instruments Linear Quadrupole Instruments Introduction to the Linear Quadrupole Principle of the Linear Quadrupole Resolving Power of Linear Quadrupoles RF-Only Quadrupoles Tandem MS with Quadrupole Analyzers Linear Quadrupole Ion Traps Three-Dimensional Quadrupole Ion Trap Introduction to the Quadrupole Ion Trap Principle of the Quadrupole Ion Trap Operation of the Quadrupole Ion Trap External Ion Sources for the Quadrupole Ion Trap Tandem MS with the Quadrupole Ion Trap Fourier Transform Ion Cyclotron Resonance Introduction to Ion Cyclotron Resonance Principle of Ion Cyclotron Resonance Fourier Transform Ion Cyclotron Resonance Experimental Setup of FT-ICR-MS Excitation Modes in FT-ICR-MS Detection in FT-ICR-MS External Ion Sources for FT-ICR-MS Tandem MS with FT-ICR Instruments Hybrid Instruments Detectors...175

4 XII Table of Contents Discrete Dynode Electron Multipliers Channel Electron Multipliers Microchannel Plates Post-Acceleration and Conversion Dynode Focal Plane Detectors Vacuum Technology Basic Mass Spectrometer Vacuum System High Vacuum Pumps Buying an Instrument Reference List Electron Ionization Behavior of Neutrals Upon Electron Impact Formation of Ions Processes Accompanying Electron Ionization Efficiency of Electron Ionization Practical Consequences of Internal Energy Low-Energy Electron Ionization Mass Spectra Electron Ionization Ion Sources Layout of an Electron Ionization Ion Source Generation of Primary Electrons Overall Efficiency of an Electron Ionization Ion Source Optimization of Ion Beam Geometry Sample Introduction Direct Insertion Probe Direct Exposure Probe Reference Inlet System Gas Chromatograph Liquid Chromatograph Ion Chromatograms Total Ion Current Reconstructed Ion Chromatogram Mass Analyzers for EI Analytes for EI Mass Spectral Databases for EI Reference List Fragmentation of Organic Ions and Interpretation of EI Mass Spectra Cleavage of a Sigma-Bond Writing Conventions for Molecular Ions σ-bond Cleavage in Small Non-Functionalized Molecules 'Even-Electron Rule' σ-bond Cleavage in Small Functionalized Molecules Alpha-Cleavage α-cleavage of Acetone Molecular Ion Stevenson's Rule

5 XIII α-cleavage of Non-Symmetrical Aliphatic Ketones Acylium Ions and Carbenium Ions α-cleavage of Amines, Ethers, and Alcohols α-cleavage of Halogenated Hydrocarbons Double α-cleavage Distonic Ions Definition of Distonic Ions Formation and Properties of Distonic Ions Distonic Ions as Intermediates Benzylic Bond Cleavage Cleavage of the Benzylic Bond in Phenylalkanes The Further Fate of [C 6 H 5 ] + and [C 7 H 7 ] Isomerization of [C 7 H 8 ] + and [C 8 H 8 ] + Ions Rings Plus Double Bonds Allylic Bond Cleavage Cleavage of the Allylic Bond in Aliphatic Alkenes Methods for the Localization of the Double Bond Cleavage of Non-Activated Bonds Saturated Hydrocarbons Carbenium Ions Very Large Hydrocarbons Recognition of the Molecular Ion Peak McLafferty Rearrangement McLafferty Rearrangement of Aldehydes and Ketones Fragmentation of Carboxylic Acids and Their Derivatives McLafferty Rearrangement of Aromatic Hydrocarbons McLafferty Rearrangement with Double Hydrogen Transfer Retro-Diels-Alder Reaction Properties of the Retro-Diels-Alder Reaction Influence of Positional Isomerism on the RDA Reaction Is the RDA Reaction Stepwise or Concerted? RDA Reaction in Natural Products Widespread Occurrence of the RDA Reaction Elimination of Carbon Monoxide CO Loss from Phenols CO and C 2 H 2 Loss from Quinones Fragmentation of Arylalkylethers CO Loss from Transition Metal Carbonyl Complexes CO Loss from Carbonyl Compounds Differentiation Between Loss of CO, N 2, and C 2 H Thermal Degradation Versus Ion Fragmentation Decarbonylation and Decarboxylation Retro-Diels-Alder Reaction Loss of H 2 O from Alkanols EI Mass Spectra of Organic Salts Alkene Loss from Onium Ions...292

6 XIV Table of Contents McLafferty Rearrangement of Onium Ions Onium Reaction Ion-Neutral Complexes Ortho Elimination (Ortho Effect) Ortho Elimination from Molecular Ions Ortho Elimination from Even-Electron Ions Ortho Elimination in the Fragmentation of Nitroarenes Heterocyclic Compounds Saturated Heterocyclic Compounds Aromatic Heterocyclic Compounds Guidelines for the Interpretation of Mass Spectra Summary of Rules Systematic Approach to Mass Spectra Reference List Chemical Ionization Basics of Chemical Ionization Formation of Ions in Chemical Ionization Chemical Ionization Ion Sources Sensitivity of Chemical Ionization Chemical Ionization by Protonation Source of Protons Methane Reagent Gas Plasma Energetics of Protonation Methane Reagent Gas PICI Spectra Other Reagent Gases in PICI Charge Exchange Chemical Ionization Energetics of CE Reagent Gases for CE-CI Compound Class-Selective CE-CI Regio- and Stereoselectivity in CE-CI Electron Capture Ion Formation by Electron Capture Energetics of EC Creating Thermal Electrons Appearance of EC Spectra Applications of EC Sample Introduction in CI Desorption Chemical Ionization Analytes for CI Mass Analyzers for CI Reference List Field Ionization and Field Desorption Field Ionization Process FI and FD Ion Source

7 XV 8.3 Field Emitters Blank Metal Wires as Emitters Activated Emitters Emitter Temperature Handling of Activated Emitters Liquid Injection Field Desorption Ionization FI Spectra Origin of [M+H] + Ions in FI-MS Field-Induced Dissociation Multiply-Charged Ions in FI-MS FD Spectra Ion Formation in FD-MS Cluster Ion Formation in FD-MS FD-MS of Ionic Analytes Best Anode Temperature and Thermal Decomposition FD-MS of Polymers Sensitivity of FI-MS and FD-MS Types of Ions in FD-MS Analytes for FI and FD Mass Analyzers for FI and FD Reference List Fast Atom Bombardment Ion Sources for FAB and LSIMS FAB Ion Sources LSIMS Ion Sources FAB Probes Ion Formation in FAB and LSIMS Ion Formation from Inorganic Samples Ion Formation from Organic Samples FAB Matrices The Role of the Liquid Matrix Characteristics of FAB Matrix Spectra Unwanted Reactions in FAB-MS Applications of FAB-MS FAB-MS of Analytes of Low to Medium Polarity FAB-MS of Ionic Analytes High-Mass Analytes in FAB-MS Accurate Mass Measurements in FAB Continuous-Flow FAB Low-Temperature FAB FAB-MS and Peptide Sequencing Massive Cluster Impact Californium Plasma Desorption General Characteristics of FAB and LSIMS Sensitivity of FAB-MS...402

8 XVI Table of Contents Types of Ions in FAB-MS Analytes for FAB-MS Mass Analyzers for FAB-MS Reference List Matrix-Assisted Laser Desorption/Ionization Ion Sources for LDI and MALDI Ion Formation Ion Yield and Laser Fluence Effect of Laser Irradiation on the Surface Temporal Evolution of a Laser Desorption Plume Ion Formation in MALDI MALDI Matrices Role of the Solid Matrix Matrices in UV-MALDI Characteristics of MALDI Matrix Spectra Sample Preparation Standard Sample Preparation Cationization and Cation Removal Solvent-Free Sample Preparation Sample Introduction Additional Methods of Sample Supply Applications of LDI Applications of MALDI MALDI-MS of Synthetic Polymers Fingerprints by MALDI-MS Carbohydrates by MALDI-MS Structure Elucidation of Carbohydrates by MALDI Oligonucleotides in MALDI Desorption/Ionization on Silicon Atmospheric Pressure MALDI General Characteristics of MALDI Sample Consumption and Detection Limit Analytes for MALDI Types of Ions in LDI and MALDI-MS Mass Analyzers for MALDI-MS Reference List Electrospray Ionization Development of ESI and Related Methods Atmospheric Pressure Ionization Thermospray Electrohydrodynamic Ionization Electrospray Ionization Ion Sources for ESI Basic Design Considerations

9 XVII ESI with Modified Sprayers Nano-Electrospray ESI with Modified Spray Geometries Skimmer CID Ion Formation Formation of an Electrospray Disintegration of Charged Droplets Formation of Ions from Charged Droplets Charge Deconvolution Problem of Multiple Charging Mathematical Charge Deconvolution Hardware Charge Deconvolution Controlled Charge Reduction in ESI Applications of ESI ESI of Small Molecules ESI of Metal Complexes ESI of Surfactants Oligonucleotides, DNA, and RNA ESI of Oligosaccharides Atmospheric Pressure Chemical Ionization Atmospheric Pressure Photoionization General Characteristics of ESI Sample Consumption Types of Ions in ESI Mass Analyzers for ESI Reference List Hyphenated Methods General Properties of Chromatography-Mass Spectrometry Coupling Chromatograms and Spectra Selected Ion Monitoring Quantitation Gas Chromatography-Mass Spectrometry GC-MS Interfaces Volatility and Derivatization Column Bleed Fast GC-MS Liquid Chromatography-Mass Spectrometry LC-MS Interfaces Multiplexed Electrospray Inlet Systems Tandem Mass Spectrometry Ultrahigh-Resolution Mass Spectrometry Reference List...491

10 XVIII Table of Contents Appendix Isotopic Composition of the Elements Carbon Isotopic Patterns Silicon and Sulfur Isotopic Patterns Chlorine and Bromine Isotopic Patterns Characteristic Ions Frequent Impurities Subject Index