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
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+l 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
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
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. a-Bond Cleavage in Small Non-Functionalized
Molecules ......................................... 225
6.1.3'Even-Electron Rule ................................. 226
6.1.4 a-Bond Cleavage in Small Functionalized
Molecules .......................................... 228
6.2. Alpha-Cleavage ........................................... 229
6.2.1. a-Cleavage of Acetone Molecular Ion ............... 229
6.2.2. Stevenson's Rule .................................. 230
6.2.3. a-Cleavage of Non-Symmetrical Aliphatic Ketones ... 232
6.2.4. Acylium Ions and Carbenium Ions ................... 234
6.2.5. a-Cleavage of Amines, Ethers, and Alcohols ........ 235
6.2.6. a-Cleavage of Halogenated Hydrocarbons ............ 243
6.2.7. Double a-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. Benzylie Bond Cleavage ................................... 249
6.4.1. Cleavage of the Benzylic Bond in Phenylalkanes .... 249
6.4.2. The Further Fate of [C6H5]+ and [C7H7]+ ............ 251
6.4.3. Isomerization of [C6H8]+ and [C8H8]+Tons ........... 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 C2H2 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, N2,
and C2H4 .......................................... 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 H20 from Alkanols ......................... 290
6.10.4.EI Mass Spectra of Organic Salts .................. 291
6.11.Alkene Loss from Onium Ions .............................. 292
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
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+Hf 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
9.2Л 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. 252Californium Plasma Desorption ......................... 400
9.7. General Characteristics of FAB and LSIMS ................. 402
9.7.1 Sensitivity of FAB-MS .............................. 402
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
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 Decon volution .................................... 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
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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