Table of Contents. Contents...IX

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Transcript:

Table of Contents Contents...IX 1 Introduction...1 1.1 Aims and Scope...1 1.2 What Is Mass Spectrometry?...2 1.2.1 Mass Spectrometry...3 1.2.2 Mass Spectrometer...3 1.2.3 Mass Spectrum...4 1.3 Filling the Black Box...7 1.4 Terminology...7 1.5 Units, Physical Quantities, and Physical Constants...9 Reference List...10 2 Gas Phase Ion Chemistry...13 2.1 Quasi-Equilibrium Theory...13 2.1.1 Basic Assumptions of QET...14 2.2 Ionization...14 2.2.1 Electron Ionization...15 2.2.2 Ionization Energy...16 2.3 Vertical Transitions...18 2.4 Ionization Efficiency and Ionization Cross Section...20 2.5 Internal Energy and the Further Fate of Ions...21 2.5.1 Degrees of Freedom...21 2.5.2 Appearance Energy...22 2.5.3 Bond Dissociation Energies and Heats of Formation...24 2.5.4 Randomization of Energy...26 2.6 Rate Constants from QET...27 2.6.1 Meaning of the Rate Constant...28 2.6.2 Typical k (E) Functions...29 2.6.3 Description of Reacting Ions Using k (E) Functions...29 2.6.4 Direct Cleavages and Rearrangement Fragmentations...30 2.6.5 Practical Consequences of Internal Energy...31

X Table of Contents 2.7 Time Scale of Events... 32 2.7.1 Stable, Metastable, and Unstable Ions... 33 2.7.2 Kinetic Shift... 35 2.8 Activation Energy of the Reverse Reaction and Kinetic Energy Release.. 36 2.8.1 Activation Energy of the Reverse Reaction... 36 2.8.2 Kinetic Energy Release... 37 2.9 Isotope Effects... 40 2.9.1 Kinetic Isotope Effects... 40 2.10 Determination of Ionization Energies and Appearance Energies... 44 2.10.1 Conventional Determination of Ionization Energies... 44 2.10.2 Experimental Improvements of IE Accuracy... 45 2.10.3 Photoelectron Spectroscopy and Derived Modern Methods... 46 2.10.4 Determination of Appearance Energies... 48 2.10.5 Breakdown Graphs... 49 2.11 Gas Phase Basicity and Proton Affinity... 50 2.12 Tandem Mass Spectrometry... 53 2.12.1 Collision-Induced Dissociation... 53 2.12.2 Other Methods of Ion Activation... 57 2.12.3 Reactive Collisions... 59 Reference List... 61 3 Isotopes... 67 3.1 Isotopic Classification of the Elements... 67 3.1.1. Monoisotopic Elements... 68 3.1.2 Di-isotopic Elements... 68 3.1.3 Polyisotopic Elements... 69 3.1.4 Calculation of Atomic, Molecular, and Ionic Mass... 71 3.1.5 Natural Variations in Relative Atomic Mass... 73 3.2 Calculation of Isotopic Distributions... 74 3.2.1 X+1 Element Carbon... 74 3.2.2 Binomial Approach... 77 3.2.3 Halogens... 78 3.2.4 Combinations of Carbon and Halogens... 79 3.2.5 Polynomial Approach... 80 3.2.6 Oxygen, Silicon and Sulfur... 81 3.2.7 Polyisotopic Elements... 83 3.2.8 Practical Aspects of Isotopic Patterns... 84 3.2.9 Isotopic Enrichment and Isotopic Labeling... 87 3.3 High-Resolution and Accurate Mass... 88 3.3.1 Exact Mass... 88 3.3.2 Deviations from Nominal Mass... 89 3.3.3 Mass Accuracy... 92 3.3.4 Resolution... 96 3.3.5 Mass Calibration... 99 3.4 Interaction of Resolution and Isotopic Patterns... 104 3.4.1 Multiple Isotopic Compositions at Very High Resolution... 104

XI 3.4.2 Multiple Isotopic Compositions and Accurate Mass...106 3.4.3 Isotopic Patterns of Large Molecules...106 3.5 Interaction of Charge State and Isotopic Patterns...108 Reference List...109 4 Instrumentation...111 4.1 Creating a Beam of Ions...112 4.2 Time-of-Flight Instruments...113 4.2.1 Introduction to Time-of-Flight...113 4.2.2 Basic Principle of TOF Instruments...114 4.2.3 Linear Time-of-Flight Analyzer...117 4.2.4 Reflector Time-of-Flight Analyzer...119 4.2.5 Further Improvement of Resolution...122 4.2.6 Orthogonal Acceleration TOF...125 4.2.7 Tandem MS on TOF Instruments...128 4.3 Magnetic Sector Instruments...130 4.3.1 Introduction to Magnetic Sector Instruments...130 4.3.2 Principle of the Magnetic Sector...131 4.3.3 Double-Focusing Sector Instruments...134 4.3.4 Setting the Resolution of a Sector Instrument...138 4.3.5 Further Improvement of Sector Instruments...139 4.3.6 Tandem MS with Magnetic Sector Instruments...140 4.4 Linear Quadrupole Instruments...145 4.4.1 Introduction to the Linear Quadrupole...145 4.4.2 Principle of the Linear Quadrupole...146 4.4.3 Resolving Power of Linear Quadrupoles...150 4.4.4 RF-Only Quadrupoles...151 4.4.5 Tandem MS with Quadrupole Analyzers...152 4.4.6 Linear Quadrupole Ion Traps...153 4.5 Three-Dimensional Quadrupole Ion Trap...154 4.5.1 Introduction to the Quadrupole Ion Trap...154 4.5.2 Principle of the Quadrupole Ion Trap...155 4.5.3 Operation of the Quadrupole Ion Trap...157 4.5.4 External Ion Sources for the Quadrupole Ion Trap...162 4.5.6 Tandem MS with the Quadrupole Ion Trap...163 4.6 Fourier Transform Ion Cyclotron Resonance...164 4.6.1 Introduction to Ion Cyclotron Resonance...164 4.6.2 Principle of Ion Cyclotron Resonance...165 4.6.3 Fourier Transform Ion Cyclotron Resonance...166 4.6.4 Experimental Setup of FT-ICR-MS...167 4.6.5 Excitation Modes in FT-ICR-MS...168 4.6.6 Detection in FT-ICR-MS...169 4.6.7 External Ion Sources for FT-ICR-MS...171 4.6.8 Tandem MS with FT-ICR Instruments...172 4.7 Hybrid Instruments...173 4.8 Detectors...175

XII Table of Contents 4.8.1 Discrete Dynode Electron Multipliers... 175 4.8.2 Channel Electron Multipliers... 176 4.8.3 Microchannel Plates... 177 4.8.4 Post-Acceleration and Conversion Dynode... 178 4.8.5 Focal Plane Detectors... 179 4.9 Vacuum Technology... 180 4.9.1 Basic Mass Spectrometer Vacuum System... 180 4.9.2 High Vacuum Pumps... 181 4.10 Buying an Instrument... 182 Reference List... 182 5 Electron Ionization... 193 5.1 Behavior of Neutrals Upon Electron Impact... 193 5.1.1 Formation of Ions... 193 5.1.2 Processes Accompanying Electron Ionization... 195 5.1.3 Efficiency of Electron Ionization... 196 5.1.4 Practical Consequences of Internal Energy... 197 5.1.5 Low-Energy Electron Ionization Mass Spectra... 198 5.2 Electron Ionization Ion Sources... 200 5.2.1 Layout of an Electron Ionization Ion Source... 200 5.2.2 Generation of Primary Electrons... 202 5.2.3 Overall Efficiency of an Electron Ionization Ion Source... 203 5.2.4 Optimization of Ion Beam Geometry... 205 5.3 Sample Introduction... 206 5.3.1 Direct Insertion Probe... 206 5.3.2 Direct Exposure Probe... 210 5.3.3 Reference Inlet System... 211 5.3.4 Gas Chromatograph... 213 5.3.5 Liquid Chromatograph... 213 5.4 Ion Chromatograms... 214 5.4.1 Total Ion Current... 214 5.4.2 Reconstructed Ion Chromatogram... 215 5.5 Mass Analyzers for EI... 217 5.6 Analytes for EI... 217 5.7 Mass Spectral Databases for EI... 218 Reference List... 218 6 Fragmentation of Organic Ions and Interpretation of EI Mass Spectra... 223 6.1 Cleavage of a Sigma-Bond... 223 6.1.1 Writing Conventions for Molecular Ions... 223 6.1.2 σ-bond Cleavage in Small Non-Functionalized Molecules... 225 6.1.3 'Even-Electron Rule'... 226 6.1.4 σ-bond Cleavage in Small Functionalized Molecules... 228 6.2 Alpha-Cleavage... 229 6.2.1 α-cleavage of Acetone Molecular Ion... 229 6.2.2 Stevenson's Rule... 230

XIII 6.2.3 α-cleavage of Non-Symmetrical Aliphatic Ketones...232 6.2.4 Acylium Ions and Carbenium Ions...234 6.2.5 α-cleavage of Amines, Ethers, and Alcohols...235 6.2.6 α-cleavage of Halogenated Hydrocarbons...243 6.2.7 Double α-cleavage...244 6.3 Distonic Ions...247 6.3.1 Definition of Distonic Ions...247 6.3.2 Formation and Properties of Distonic Ions...247 6.3.3 Distonic Ions as Intermediates...248 6.4 Benzylic Bond Cleavage...249 6.4.1 Cleavage of the Benzylic Bond in Phenylalkanes...249 6.4.2 The Further Fate of [C 6 H 5 ] + and [C 7 H 7 ] +...251 6.4.3 Isomerization of [C 7 H 8 ] + and [C 8 H 8 ] + Ions...252 6.4.4 Rings Plus Double Bonds...254 6.5 Allylic Bond Cleavage...255 6.5.1 Cleavage of the Allylic Bond in Aliphatic Alkenes...255 6.5.2 Methods for the Localization of the Double Bond...257 6.6. Cleavage of Non-Activated Bonds...258 6.6.1 Saturated Hydrocarbons...258 6.6.2 Carbenium Ions...260 6.6.3 Very Large Hydrocarbons...262 6.6.4 Recognition of the Molecular Ion Peak...263 6.7 McLafferty Rearrangement...264 6.7.1 McLafferty Rearrangement of Aldehydes and Ketones...264 6.7.2 Fragmentation of Carboxylic Acids and Their Derivatives...267 6.7.3 McLafferty Rearrangement of Aromatic Hydrocarbons...271 6.7.4 McLafferty Rearrangement with Double Hydrogen Transfer...272 6.8 Retro-Diels-Alder Reaction...276 6.8.1 Properties of the Retro-Diels-Alder Reaction...276 6.8.2 Influence of Positional Isomerism on the RDA Reaction...278 6.8.3 Is the RDA Reaction Stepwise or Concerted?...279 6.8.4 RDA Reaction in Natural Products...279 6.8.5 Widespread Occurrence of the RDA Reaction...280 6.9 Elimination of Carbon Monoxide...281 6.9.1 CO Loss from Phenols...281 6.9.2 CO and C 2 H 2 Loss from Quinones...283 6.9.3 Fragmentation of Arylalkylethers...285 6.9.4 CO Loss from Transition Metal Carbonyl Complexes...287 6.9.5 CO Loss from Carbonyl Compounds...288 6.9.6 Differentiation Between Loss of CO, N 2, and C 2 H 4...288 6.10 Thermal Degradation Versus Ion Fragmentation...289 6.10.1 Decarbonylation and Decarboxylation...289 6.10.2 Retro-Diels-Alder Reaction...289 6.10.3 Loss of H 2 O from Alkanols...290 6.10.4 EI Mass Spectra of Organic Salts...291 6.11 Alkene Loss from Onium Ions...292

XIV Table of Contents 6.11.1 McLafferty Rearrangement of Onium Ions... 293 6.11.2 Onium Reaction... 296 6.12 Ion-Neutral Complexes... 300 6.13 Ortho Elimination (Ortho Effect)... 304 6.13.1 Ortho Elimination from Molecular Ions... 305 6.13.2 Ortho Elimination from Even-Electron Ions... 306 6.13.3 Ortho Elimination in the Fragmentation of Nitroarenes... 308 6.14 Heterocyclic Compounds... 311 6.14.1 Saturated Heterocyclic Compounds... 311 6.14.2 Aromatic Heterocyclic Compounds... 315 6.15 Guidelines for the Interpretation of Mass Spectra... 319 6.15.1 Summary of Rules... 319 6.15.2 Systematic Approach to Mass Spectra... 320 Reference List... 320 7 Chemical Ionization... 331 7.1 Basics of Chemical Ionization... 331 7.1.1 Formation of Ions in Chemical Ionization... 331 7.1.2 Chemical Ionization Ion Sources... 332 7.1.3 Sensitivity of Chemical Ionization... 333 7.2 Chemical Ionization by Protonation... 333 7.2.1 Source of Protons... 333 7.2.2 Methane Reagent Gas Plasma... 334 7.2.3 Energetics of Protonation... 336 7.2.4 Methane Reagent Gas PICI Spectra... 337 7.2.5 Other Reagent Gases in PICI... 338 7.3 Charge Exchange Chemical Ionization... 341 7.3.1 Energetics of CE... 341 7.3.2 Reagent Gases for CE-CI... 342 7.3.4 Compound Class-Selective CE-CI... 343 7.3.5 Regio- and Stereoselectivity in CE-CI... 344 7.4 Electron Capture... 345 7.4.1 Ion Formation by Electron Capture... 345 7.4.3 Energetics of EC... 345 7.4.4 Creating Thermal Electrons... 347 7.4.5 Appearance of EC Spectra... 348 7.4.6 Applications of EC... 348 7.5 Sample Introduction in CI... 348 7.5.1 Desorption Chemical Ionization... 349 7.6 Analytes for CI... 350 7.7 Mass Analyzers for CI... 351 Reference List... 351 8 Field Ionization and Field Desorption... 355 8.1 Field Ionization Process... 355 8.2 FI and FD Ion Source... 357

XV 8.3 Field Emitters...358 8.3.1 Blank Metal Wires as Emitters...358 8.3.2 Activated Emitters...358 8.3.3 Emitter Temperature...359 8.3.4 Handling of Activated Emitters...360 8.3.5 Liquid Injection Field Desorption Ionization...362 8.4 FI Spectra...363 8.4.1 Origin of [M+H] + Ions in FI-MS...363 8.4.2 Field-Induced Dissociation...364 8.4.3 Multiply-Charged Ions in FI-MS...364 8.5 FD Spectra...365 8.5.1 Ion Formation in FD-MS...365 8.5.2 Cluster Ion Formation in FD-MS...369 8.5.3 FD-MS of Ionic Analytes...371 8.5.4 Best Anode Temperature and Thermal Decomposition...372 8.5.5 FD-MS of Polymers...373 8.5.6 Sensitivity of FI-MS and FD-MS...373 8.5.7 Types of Ions in FD-MS...374 8.6 Analytes for FI and FD...375 8.7 Mass Analyzers for FI and FD...376 Reference List...376 9 Fast Atom Bombardment...381 9.1 Ion Sources for FAB and LSIMS...382 9.1.1 FAB Ion Sources...382 9.1.2 LSIMS Ion Sources...383 9.1.3 FAB Probes...383 9.2 Ion Formation in FAB and LSIMS...384 9.2.1 Ion Formation from Inorganic Samples...384 9.2.2 Ion Formation from Organic Samples...385 9.3 FAB Matrices...387 9.3.1 The Role of the Liquid Matrix...387 9.3.2 Characteristics of FAB Matrix Spectra...388 9.3.3 Unwanted Reactions in FAB-MS...389 9.4 Applications of FAB-MS...389 9.4.1 FAB-MS of Analytes of Low to Medium Polarity...389 9.4.2 FAB-MS of Ionic Analytes...391 9.4.3 High-Mass Analytes in FAB-MS...392 9.4.4 Accurate Mass Measurements in FAB...393 9.4.5 Continuous-Flow FAB...395 9.4.6 Low-Temperature FAB...396 9.4.7 FAB-MS and Peptide Sequencing...398 9.5 Massive Cluster Impact...400 9.6 252 Californium Plasma Desorption...400 9.7 General Characteristics of FAB and LSIMS...402 9.7.1 Sensitivity of FAB-MS...402

XVI Table of Contents 9.7.2 Types of Ions in FAB-MS... 402 9.7.3 Analytes for FAB-MS... 403 9.7.4 Mass Analyzers for FAB-MS... 403 Reference List... 404 10 Matrix-Assisted Laser Desorption/Ionization... 411 10.1 Ion Sources for LDI and MALDI... 411 10.2 Ion Formation... 413 10.2.1 Ion Yield and Laser Fluence... 413 10.2.2 Effect of Laser Irradiation on the Surface... 414 10.2.3 Temporal Evolution of a Laser Desorption Plume... 415 10.2.4 Ion Formation in MALDI... 416 10.3 MALDI Matrices... 416 10.3.1 Role of the Solid Matrix... 416 10.3.2 Matrices in UV-MALDI... 417 10.3.3 Characteristics of MALDI Matrix Spectra... 418 10.4 Sample Preparation... 419 10.4.1 Standard Sample Preparation... 419 10.4.2 Cationization and Cation Removal... 420 10.4.3 Solvent-Free Sample Preparation... 421 10.4.4 Sample Introduction... 422 10.4.5 Additional Methods of Sample Supply... 423 10.4 Applications of LDI... 423 10.5 Applications of MALDI... 425 10.5.1 MALDI-MS of Synthetic Polymers... 425 10.5.2 Fingerprints by MALDI-MS... 427 10.5.3 Carbohydrates by MALDI-MS... 427 10.5.4 Structure Elucidation of Carbohydrates by MALDI... 428 10.5.5 Oligonucleotides in MALDI... 429 10.6 Desorption/Ionization on Silicon... 430 10.7 Atmospheric Pressure MALDI... 431 10.8 General Characteristics of MALDI... 432 10.8.1 Sample Consumption and Detection Limit... 432 10.8.2 Analytes for MALDI... 432 10.8.3 Types of Ions in LDI and MALDI-MS... 433 10.8.4 Mass Analyzers for MALDI-MS... 433 Reference List... 434 11 Electrospray Ionization... 441 11.1 Development of ESI and Related Methods... 441 11.1.1 Atmospheric Pressure Ionization... 441 11.1.2 Thermospray... 442 11.1.3 Electrohydrodynamic Ionization... 443 11.1.4 Electrospray Ionization... 444 11.2 Ion Sources for ESI... 444 11.2.1 Basic Design Considerations... 444

XVII 11.2.2 ESI with Modified Sprayers...445 11.2.3 Nano-Electrospray...447 11.2.4 ESI with Modified Spray Geometries...449 11.2.5 Skimmer CID...451 11.3 Ion Formation...451 11.3.1 Formation of an Electrospray...451 11.3.2 Disintegration of Charged Droplets...453 11.3.3 Formation of Ions from Charged Droplets...454 11.4 Charge Deconvolution...455 11.4.1 Problem of Multiple Charging...455 11.4.2 Mathematical Charge Deconvolution...458 11.4.3 Hardware Charge Deconvolution...460 11.4.4 Controlled Charge Reduction in ESI...461 11.5 Applications of ESI...462 11.5.1 ESI of Small Molecules...462 11.5.2 ESI of Metal Complexes...462 11.5.3 ESI of Surfactants...464 11.5.4 Oligonucleotides, DNA, and RNA...464 11.5.5 ESI of Oligosaccharides...465 11.6 Atmospheric Pressure Chemical Ionization...465 11.7 Atmospheric Pressure Photoionization...467 11.8 General Characteristics of ESI...467 11.8.1 Sample Consumption...467 11.8.2 Types of Ions in ESI...468 11.8.3 Mass Analyzers for ESI...468 Reference List...468 12 Hyphenated Methods...475 12.1 General Properties of Chromatography-Mass Spectrometry Coupling..475 12.1.1 Chromatograms and Spectra...477 12.1.2 Selected Ion Monitoring...478 12.1.3 Quantitation...479 12.2 Gas Chromatography-Mass Spectrometry...482 12.2.1 GC-MS Interfaces...482 12.2.2 Volatility and Derivatization...483 12.2.3 Column Bleed...483 12.2.4 Fast GC-MS...484 12.3 Liquid Chromatography-Mass Spectrometry...485 12.3.1 LC-MS Interfaces...485 12.3.2 Multiplexed Electrospray Inlet Systems...487 12.3 Tandem Mass Spectrometry...488 12.4. Ultrahigh-Resolution Mass Spectrometry...490 Reference List...491

XVIII Table of Contents Appendix... 495 1 Isotopic Composition of the Elements... 495 2 Carbon Isotopic Patterns... 501 3 Silicon and Sulfur Isotopic Patterns... 502 4 Chlorine and Bromine Isotopic Patterns... 503 5 Characteristic Ions... 503 6 Frequent Impurities... 505 Subject Index... 507

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