Table of Contents .............................................. XI
1 Introduction ................................................. 1
Learning Objectives .......................................... 1
1.1 Aims and Scope .......................................... 3
1.1.1 Filling the Black Box ............................ 5
1.2 What Is Mass Spectrometry? .............................. 5
1.2.1 Mass Spectrometry ................................ 6
1.2.2 Mass Spectrometer ................................ 7
1.2.3 Mass Scale ....................................... 8
1.2.4 Mass Spectrum .................................... 9
1.3 Ion Chromatograms ...................................... 11
1.4 Performance of Mass Spectrometers ...................... 13
1.4.1 Sensitivity ..................................... 13
1.4.2 Detection Limit ................................. 14
1.4.3 Signal-to-Noise Ratio ........................... 14
1.5 Terminology - General Aspects .......................... 15
1.5.1 Basic Terminology in Describing Mass Spectra .... 16
1.6 Units, Physical Quantities, and Physical Constants ..... 17
References .................................................. 17
2 Principles of Ionization and Ion Dissociation ............... 21
Learning Objectives ......................................... 21
2.1 Gas Phase Ionization by Energetic Electrons ............ 21
2.1.1 Formation of Ions ............................... 22
2.1.2 Processes Accompanying Electron Ionization ...... 23
2.1.3 Ions Generated by Penning Ionization ............ 24
2.1.4 Ionization Energy ............................... 25
2.1.5 Ionization Energy and Charge-Localization ....... 25
2.2 Vertical Transitions ................................... 27
2.3 Ionization Efficiency and Ionization Cross Section ..... 29
2.4 Internal Energy and the Further Fate of Ions ........... 30
2.4.1 Degrees of Freedom .............................. 31
2.4.2 Appearance Energy ............................... 32
2.4.3 Bond Dissociation Energies and Heats of
Formation ....................................... 33
2.4.4 Randomization of Energy ......................... 35
2.5 Quasi-Equilibrium Theory ............................... 37
2.5.1 QET's Basic Premises ............................ 37
2.5.2 Basic QET ....................................... 38
2.5.3 Rate Constants and Their Meaning ................ 39
2.5.4 k(E) Functions - Typical Examples ............... 40
2.5.5 Reacting Ions Described by k{E) Functions ....... 40
2.5.6 Direct Cleavages and Rearrangement
Fragmentations .................................. 40
2.6 Time Scale of Events ................................... 42
2.6.1 Stable, Metastable, and Unstable Ions ........... 43
2.6.2 Time Scale of Ion Storage Devices ............... 44
2.7 Internal Energy - Practical Implications ............... 45
2.8 Reverse Reactions and Kinetic Energy Release ........... 46
2.8.1 Activation Energy of the Reverse Reaction ....... 46
2.8.2 Kinetic Energy Release .......................... 48
2.8.3 Energy Partitioning ............................. 49
2.9 Isotope Effects ........................................ 49
2.9.1 Primary Kinetic Isotope Effects ................. 50
2.9.2 Measurement of Isotope Effects .................. 51
2.9.3 Secondary Kinetic Isotope Effects ............... 53
2.10 Determination of Ionization Energies ................... 54
2.10.1 Conventional Determination of Ionization
Energies ........................................ 54
2.10.2 Improved IE Accuracy from Data
Post-Processing ................................. 54
2.10.3 IE Accuracy - Experimental Improvements ......... 55
2.10.4 Photoionization Processes ....................... 55
2.11 Determining the Appearance Energies .................... 58
2.11.1 Kinetic Shift ................................... 58
2.11.2 Breakdown Graphs ................................ 59
2.12 Gas Phase Basicity and Proton Affinity ................. 61
References .................................................. 62
3 Isotopic Composition and Accurate Mass ...................... 67
Learning Objectives ......................................... 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 Poly isotopic Elements .......................... 69
3.1.4 Representation of Isotopic Abundances ........... 69
3.1.5 Calculation of Atomic, Molecular, and Ionic
Mass ............................................ 71
3.1.6 Natural Variations in Relative Atomic Mass ...... 73
3.2 Calculation of Isotopic Distributions .................. 74
3.2.1 Carbon: An X+l Element ........................... 74
3.2.2 Terms Related to Isotopic Composition ........... 77
3.2.3 Binomial Approach ............................... 77
3.2.4 Halogens ........................................ 78
3.2.5 Combinations of Carbon and Halogens ............. 80
3.2.6 Polynomial Approach ............................. 81
3.2.7 Oxygen, Silicon, and Sulfur ..................... 81
3.2.8 Polyisotopic Elements ........................... 84
3.2.9 Practical Aspects of Isotopic Patterns .......... 84
3.2.10 Bookkeeping with Isotopic Patterns in Mass
Spectra ......................................... 85
3.2.11 Information from Complex Isotopic Patterns ...... 86
3.3 Isotopic Enrichment and Isotopic Labeling .............. 87
3.3.1 Isotopic Enrichment ............................. 87
3.3.2 Isotopic Labeling ............................... 88
3.4 Resolution and Resolving Power ......................... 88
3.4.1 Definitions ..................................... 88
3.4.2 Resolution and its Experimental Determination ... 90
3.4.3 Resolving Power and its Effect on Relative Peak
Intensity ....................................... 91
3.5 Accurate Mass .......................................... 92
3.5.1 Exact Mass and Molecular Formulas ............... 92
3.5.2 Mass Defect ..................................... 93
3.5.3 Mass Accuracy ................................... 95
3.5.4 Accuracy and Precision .......................... 96
3.5.5 Mass Accuracy and the Determination of
Molecular Formulas .............................. 97
3.5.6 Extreme Mass Accuracy - Special
Considerations .................................. 98
3.6 Applied High-Resolution Mass Spectrometry .............. 99
3.6.1 External Mass Calibration ....................... 99
3.6.2 Internal Mass Calibration ...................... 101
3.6.3 Compiling Mass Reference Lists ................. 103
3.6.4 Specification of Mass Accuracy ................. 104
3.6.5 Deltamass ...................................... 104
3.6.6 Kendrick Mass Scale ............................ 105
3.6.7 Van Krevelen Diagrams .......................... 106
3.7 Resolution Interacting with Isotopic Patterns ......... 107
3.7.1 Multiple Isotopic Compositions at Very High
Resolution ..................................... 107
3.7.2 Isotopologs and Accurate Mass .................. 110
3.7.3 Large Molecules - Isotopic Patterns at
Sufficient Resolution .......................... 110
3.7.4 Large Molecules - Isotopic Patterns at Low
Resolution ..................................... 112
3.8 Charge State and Interaction with Isotopic Patterns ... 112
References ................................................. 114
4 Instrumentation ............................................ 117
Learning Objectives ........................................ 117
4.1 How to Create a Beam of Ions .......................... 119
4.2 Time-of-Flight Instruments ............................ 120
4.2.1 Time-of-Flight - Basic Principles .............. 120
4.2.2 TOF Instruments - Velocity of Ions and Time-
of-Flight ...................................... 121
4.2.3 Linear Time-of-Flight Analyzer ................. 123
4.2.4 Reflector Time-of-Flight Analyzer .............. 126
4.2.5 Higher Vacuum Improves Resolving Power ......... 128
4.2.6 Delay Before Extraction to Improve Resolving
Power .......................................... 128
4.2.7 Analog-to-Digital Conversion ................... 131
4.2.8 Orthogonal Acceleration TOF Analyzers .......... 132
4.2.9 Operation of the oaTOF Analyzer ................ 133
4.2.10 Duty Cycle ..................................... 134
4.2.11 Time-to-Digital Conversion ..................... 135
4.3 Magnetic Sector Instruments ........................... 135
4.3.1 Evolution of Magnetic Sector Instruments ....... 135
4.3.2 Principle of the Magnetic Sector ............... 136
4.3.3 Focusing Action of the Magnetic Field .......... 138
4.3.4 Double-Focusing Sector Instruments ............. 139
4.3.5 Geometries of Double-Focusing Sector
Instruments .................................... 141
4.3.6 Adjusting the Resolving Power of a Sector
Instrument ..................................... 143
4.3.7 Innovations in Sector Instruments .............. 144
4.4 Linear Quadrapole Instruments ......................... 146
4.4.1 Introduction ................................... 146
4.4.2 The Linear Quadrapole .......................... 147
4.4.3 Resolving Power of Linear Quadrapoles .......... 151
4.4.4 RF-Only Quadrapoles, Hexapoles, and
Octopoles ...................................... 152
4.5 Linear Quadrapole Ion Traps ........................... 155
4.5.1 Linear RF-Only Multipole Ion Traps ............. 155
4.5.2 Mass-Analyzing Linear Quadrapole Ion Trap
with Axial Ejection ............................ 158
4.5.3 Mass-Analyzing Linear Ion Trap with Radial
Ejection ....................................... 160
4.6 Three-Dimensional Quadrapole Ion Trap ................. 164
4.6.1 Introduction ................................... 164
4.6.2 The Quadrapole Ion Trap ........................ 164
4.6.3 Visualization of Ion Motion in the Ion Trap .... 167
4.6.4 Mass-Selective Stability Mode .................. 168
4.6.5 Mass-Selective Instability Mode ................ 168
4.6.6 Resonant Ejection .............................. 169
4.6.7 Axial Modulation and Automatic Gain Control .... 170
4.6.8 Nonlinear Resonances ........................... 171
4.6.9 Digital Waveform Quadrapole Ion Trap ........... 172
4.6.10 External Ion Sources for the Quadrapole Ion
Trap ........................................... 173
4.7 Fourier Transform Ion Cyclotron Resonance ............. 174
4.7.1 Ion Cyclotron Resonance ........................ 174
4.7.2 Ion Cyclotron Motion ........................... 174
4.7.3 Cyclotron Motion - Excitation and Detection .... 175
4.7.4 Cyclotron Frequency Bandwidth and Energy-Time
Uncertainty .................................... 177
4.7.5 Fourier Transform - Basic Properties ........... 179
4.7.6 Nyquist Criterion .............................. 181
4.7.7 Excitation Modes in FT-ICR-MS .................. 182
4.7.8 Axial Trapping and Design of ICR Cells ......... 183
4.7.9 Magnetron Motion and Reduced Cyclotron
Frequency ...................................... 184
4.7.10 Detection and Accuracy in FT-ICR-MS ............ 186
4.7.11 FT-ICR Instruments ............................. 187
4.8 Orbitrap Analyzer ..................................... 189
4.8.1 Orbitrap - Principle of Operation .............. 189
4.8.2 Ion Detection and Resolving Power of the
Orbitrap ....................................... 191
4.8.3 Ion Injection into the Orbitrap ................ 192
4.8.4 Hybridization with a Linear Quadrapole Ion
Trap ........................................... 193
4.9 Hybrid Instruments .................................... 194
4.9.1 Evolution of Hybrid Mass Spectrometers ......... 196
4.9.2 Ion Mobility-Mass Spectrometry Systems ......... 198
4.10 Detectors ............................................. 202
4.10.1 Discrete Dynode Electron Multipliers ........... 203
4.10.2 Channel Electron Multipliers ................... 204
4.10.3 MicroChannel Plates ............................ 205
4.10.4 Post-Acceleration and Conversion Dynode ........ 206
4.10.5 Focal Plane Detectors .......................... 207
4.11 Vacuum Technology ..................................... 208
4.11.1 Basic Mass Spectrometer Vacuum System .......... 209
4.11.2 High Vacuum Pumps .............................. 209
4.12 Purchasing an Instrument .............................. 210
References ............................................ 210
5 Practical Aspects of Electron Ionization ................... 223
Learning Objectives ................................... 223
5.1 Electron Ionization Ion Sources ....................... 223
5.1.1 Layout of an Electron Ionization Ion Source .... 223
5.1.2 Generation of Primary Electrons ................ 225
5.1.3 Overall Efficiency and Sensitivity of an El
Ion Source ..................................... 226
5.1.4 Optimization of Ion Beam Geometry .............. 227
5.2 Sample Introduction ................................... 228
5.2.1 Reservoir or Reference Inlet System ............ 228
5.2.2 Direct Insertion Probe ......................... 231
5.2.3 Sample Vials for Use with Direct Insertion
Probes ......................................... 232
5.2.4 Fractionation When Using Direct Insertion
Probes ......................................... 233
5.2.5 Direct Exposure Probe .......................... 235
5.3 Pyrolysis Mass Spectrometry ........................... 237
5.4 Gas Chromatograph ..................................... 237
5.5 Liquid Chromatograph .................................. 238
5.6 Low-Energy Electron Ionization Mass Spectra ........... 239
5.7 Analytes for EI ....................................... 241
5.8 Mass Analyzers for EI ................................. 241
5.9 Mass Spectral Databases for EI ........................ 242
5.9.1 NIST/EPA/NIH Mass Spectral Database ............ 243
5.9.2 Wiley Registry of Mass Spectral Data ........... 244
5.9.3 Mass Spectral Databases - General Aspects ...... 244
References ................................................. 245
6 Fragmentation of Organic Ions and Interpretation of EI
Mass Spectra ............................................... 249
Learning Objectives ........................................ 249
6.1 Cleavage of a Sigma-Bond .............................. 250
6.1.1 Writing Conventions for Molecular Ions ......... 250
6.1.2 α-Bond Cleavage in Small Nonfunctionalized
Molecules ...................................... 251
6.1.3 Even-Electron Rule ............................. 252
6.1.4 α-Bond Cleavage in Small Functionalized
Molecules ...................................... 254
6.2 Alpha-Cleavage ........................................ 255
6.2.1 α-Cleavage of Acetone Molecular Ion ............ 255
6.2.2 Stevenson's Rule ............................... 257
6.2.3 α-Cleavage of Nonsymmetrical Aliphatic
Ketones ........................................ 259
6.2.4 Acylium Ions and Carbenium Ions ................ 260
6.2.5 α-Cleavage When Heteroatoms Belong to the
Aliphatic Chain ................................ 262
6.2.6 α-Cleavage of Aliphatic Amines ................. 262
6.2.7 Nitrogen Rule .................................. 265
6.2.8 α-Cleavage of Aliphatic Ethers and Alcohols .... 266
6.2.9 Charge Retention at the Heteroatom ............. 268
6.2.10 α-Cleavage of Thioethers ....................... 269
6.2.11 α-Cleavage of Halogenated Hydrocarbons ......... 269
6.2.12 Double α-Cleavage .............................. 271
6.2.13 Double α-Cleavage for the Identification of
Regioisomers ................................... 272
6.3 Distonic Ions ......................................... 273
6.3.1 Definition of Distonic Ions .................... 273
6.3.2 Formation and Properties of Distonic Ions ...... 274
6.3.3 Distonic Ions as Intermediates ................. 275
6.4 Benzylic Bond Cleavage ................................ 275
6.4.1 Cleavage of the Benzylic Bond in
Phenylalkanes .................................. 275
6.4.2 The Further Fate of [C6H5]+ and [C7H7]+ ........ 277
6.4.3 Isomerization of [C7H8]+* and [C8H8]+* Ions .... 279
6.4.4 Rings Plus Double Bonds ........................ 280
6.5 Allylic Bond Cleavage ................................. 281
6.5.1 Cleavage of the Allylic Bond in Aliphatic
Alkenes ........................................ 281
6.5.2 Methods for the Localization of the Double
Bond ........................................... 283
6.6 Cleavage of Non-Activated Bonds ....................... 284
6.6.1 Saturated Hydrocarbons ......................... 284
6.6.2 Carbenium Ions ................................. 286
6.6.3 Very Large Hydrocarbons ........................ 287
6.6.4 Recognition of the Molecular Ion Peak .......... 288
6.7 McLafferty Rearrangement .............................. 290
6.7.1 McL of Aldehydes and Ketones ................... 290
6.7.2 Fragmentation of Carboxylic Acids and Their
Derivatives .................................... 293
6.7.3 McL of Aromatic Hydrocarbons ................... 296
6.7.4 McL with Double Hydrogen Transfer .............. 297
6.8 Retro-Diels-Alder Reaction ............................ 300
6.8.1 Properties of the Retro-Diels-Alder Reaction .... 300
6.8.2 Influence of Positional Isomerism on the RDA
Reaction ....................................... 302
6.8.3 RDA Reaction in Natural Products ............... 303
6.8.4 Widespread Occurrence of the RDA Reaction ...... 303
6.9 Elimination of Carbon Monoxide ........................ 304
6.9.1 CO Loss from Phenols ........................... 304
6.9.2 CO and C2H2 Loss from Quinones ................. 307
6.9.3 Fragmentation of Arylalkylethers ............... 308
6.9.4 CO Loss from Transition Metal Carbonyl
Complexes ...................................... 310
6.9.5 CO Loss from Carbonyl Compounds ................ 311
6.9.6 Differentiation Between Loss of CO, N2, and
C2H4 ........................................... 311
6.10 Thermal Degradation vs. Ion Fragmentation ............. 312
6.10.1 Decarbonylation and Decarboxylation ............ 312
6.10.2 Retro-Diels-Alder Reaction ..................... 312
6.10.3 Loss of H2O from Alkanols ...................... 312
6.10.4 EI Mass Spectra of Organic Salts ............... 314
6.11 Alkene Loss from Onium Ions ........................... 315
6.11.1 McL of Onium Ions .............................. 316
6.11.2 Onium Reaction ................................. 319
6.12 Ion-Neutral Complexes ................................. 322
6.12.1 Evidence for the Existence of Ion-Neutral
Complexes ...................................... 322
6.12.2 Attractive Forces in Ion-Neutral Complexes ..... 323
6.12.3 Criteria for Ion-Neutral Complexes ............. 324
6.12.4 Ion-Neutral Complexes of Radical Ions .......... 325
6.13 Ortho Elimination (Ortho Effect) ...................... 326
6.13.1 Ortho Elimination from Molecular Ions .......... 327
6.13.2 Ortho Elimination from Even-Electron Ions ...... 328
6.13.3 Ortho Elimination in the Fragmentation of
Nitroarenes .................................... 331
6.14 Heterocyclic Compounds ................................ 332
6.14.1 Saturated Heterocyclic Compounds ............... 333
6.14.2 Aromatic Heterocyclic Compounds ................ 336
6.15 Guide to the Interpretation of Mass Spectra ........... 340
6.15.1 Summary of Rules ............................... 340
6.15.2 Systematic Approach to Mass Spectra ............ 341
References ............................................ 342
7 Chemical Ionization ........................................ 351
Learning Objectives ........................................ 351
7.1 Basics of Chemical Ionization ......................... 351
7.1.1 Formation of Ions in Positive-Ion Chemical
Ionization ..................................... 351
7.1.2 Chemical Ionization Ion Sources ................ 352
7.1.3 Sensitivity of Chemical Ionization ............. 353
7.1.4 Chemical Ionization Techniques and Terms ....... 353
7.2 Protonation in Chemical Ionization .................... 354
7.2.1 Source of Protons .............................. 354
7.2.2 Methane Reagent Gas Plasma ..................... 355
7.2.3 CH5+ and Related Ions .......................... 356
7.2.4 Energetics of Protonation ...................... 356
7.2.5 Impurities of Higher PA than the Reagent Gas ... 357
7.2.6 Methane Reagent Gas PICI Spectra ............... 358
7.2.7 Other Reagent Gases in PICI .................... 359
7.3 Proton Transfer Reaction Mass Spectrometry ............ 361
7.3.1 Reactant Ion Formation in PTR-MS ............... 362
7.3.2 Analyte Ion Formation in PTR-MS ................ 362
7.4 Charge Exchange Chemical Ionization ................... 364
7.4.1 Energetics of CE ............................... 365
7.4.2 Reagent Gases for CE-CI ........................ 365
7.4.3 Compound Class-Selective CE-CI ................. 366
7.4.4 Regio- and Stereoselectivity in CE-CI .......... 368
7.5 Negative-Ion Chemical Ionization ...................... 368
7.6 Electron Capture ...................................... 370
7.6.1 Ion Formation by Electron Capture .............. 370
7.6.2 Energetics of EC ............................... 370
7.6.3 Creating Thermal Electrons ..................... 372
7.6.4 Appearance of EC Spectra ....................... 373
7.6.5 Applications of EC ............................. 373
7.7 Desorption Chemical Ionization ........................ 374
7.8 Analytes for CI ....................................... 375
References ................................................. 376
8 Field Ionization and Field Desorption ...................... 381
8.2 FI and FD Ion Sources ................................. 383
8.3 Field Emitters ........................................ 385
8.3.1 Blank Metal Wires as Emitters .................. 385
8.3.2 Activated Emitters ............................. 385
8.3.3 Emitter Temperature ............................ 386
8.3.4 Handling of Activated Emitters ................. 387
8.4 Field Ionization Mass Spectrometry .................... 388
8.4.1 Origin of [M+H]+ Ions in FI-MS ................. 389
8.4.2 Multiply-Charged Ions in FI-MS ................. 389
8.4.3 Field-Induced Dissociation ..................... 390
8.4.4 Accurate Mass FI Spectra ....................... 390
8.4.5 Coupling Gas Chromatography to FI-MS ........... 391
8.5 FD Spectra ............................................ 392
8.5.1 Ion Formation by Field Ionization in FD-MS ..... 393
8.5.2 Desorption of Preformed Ions in FD-MS .......... 394
8.5.3 Cluster Ion Formation in FD-MS ................. 396
8.5.4 FD-MS of Ionic Analytes ........................ 397
8.5.5 Best Anode Temperature and Thermal
Decomposition .................................. 399
8.5.6 FD-MS of Polymers .............................. 400
8.5.7 Types of Ions in FD-MS ......................... 401
8.6 Liquid Injection Field Desorption Ionization .......... 402
8.7 General Properties of FI-MS and FD-MS ................. 405
8.7.1 Sensitivity of FI-MS and FD-MS ................. 405
8.7.2 Analytes and Practical Considerations for FI,
FD, and LIFDI .................................. 407
8.7.3 Mass Analyzers for FI and FD ................... 407
References ............................................ 408
9 Tandem Mass Spectrometry ................................... 415
Learning Objectives ................................... 415
9.1 Concepts of Tandem Mass Spectrometry .................. 415
9.1.1 Tandem-in-Space and Tandem-in-Time ............. 416
9.1.2 Pictograms for MS/MS Experiments ............... 418
9.2 Metastable Ion Dissociation ........................... 420
9.3 Collision-Induced Dissociation ........................ 420
9.3.1 Effecting Collisions in a Mass Spectrometer .... 420
9.3.2 Energy Transfer During Collisions .............. 421
9.3.3 Single and Multiple Collisions in CID .......... 424
9.3.4 Time Scale of Ion Activating Processes ......... 426
9.4 Surface-Induced Dissociation .......................... 426
9.5 Tandem MS on TOF Instruments .......................... 427
9.5.1 Utilizing a ReTOF for Tandem MS ................ 427
9.5.2 Curved-Field Reflectron ........................ 429
9.5.3 Tandem MS on True Tandem TOF Instruments ....... 429
9.6 Tandem MS with Magnetic Sector Instruments ............ 431
9.6.1 Dissociations in the FFR Preceding the
Magnetic Sector ................................ 431
9.6.2 Mass-Analyzed Ion Kinetic Energy Spectra ....... 432
9.6.3 Determination of Kinetic Energy Release ........ 432
9.6.4 B/E = Const. Linked Scan ....................... 434
9.6.5 Additional Linked Scan Functions ............... 434
9.6.6 Multi-Sector Instruments ....................... 436
9.7 Tandem MS with Linear Quadrupole Analyzers ............ 437
9.7.1 Triple Quadrupole Mass Spectrometers ........... 437
9.7.2 Scan Modes for Tandem MS with Triple
Quadrupole Instruments ......................... 438
9.7.3 Penta Quadrapole Instruments ................... 438
9.8 Tandem MS with the Quadrupole Ion Trap ................ 439
9.9 Tandem MS with Linear Quadrapole Ion Traps ............ 443
9.9.1 Tandem MS on QqLIT Instruments ................. 444
9.9.2 Tandem MS on LITs with Radial Ejection ......... 444
9.10 Tandem MS with Orbitrap Instruments ................... 445
9.10.1 Higher-Energy C-Trap Dissociation .............. 446
9.10.2 Extended LIT-Orbitrap Hybrid Instruments ....... 446
9.11 Tandem MS with FT-ICR Instruments - Part I ............ 448
9.11.1 Sustained Off-Resonance Irradiation-CID in
ICR Cells ...................................... 448
9.12 Infrared Multiphoton Dissociation ..................... 451
9.12.1 IRMPD in QITs and LITs ......................... 452
9.13 Electron Capture Dissociation ......................... 452
9.13.1 Principles of Electron Capture Dissociation .... 452
9.13.2 Peptide Ion Cleavages Upon ECD ................. 454
9.14 Tandem MS with FT-ICR Instruments - Part II ........... 455
9.14.1 IRMPD for Tandem FT-ICR-MS ..................... 455
9.14.2 Infrared Photodissociation Spectroscopy ........ 456
9.14.3 Blackbody Infrared Radiative Dissociation ...... 457
9.14.4 ECD for Tandem FT-ICR-MS ....................... 458
9.15 Electron Transfer Dissociation ........................ 459
9.16 Electron Detachment Dissociation ...................... 461
9.17 Summary of Ion Activation Techniques .................. 462
9.18 Special Applications of Tandem MS ..................... 463
9.18.1 Ion-Molecule Reactions in Catalytic Studies .... 464
9.18.2 Gas Phase Hydrogen-Deuterium Exchange .......... 464
9.18.3 Determination of Gas Phase Basicities and
Proton Affinities .............................. 466
9.18.4 Neutralization-Reionization Mass
Spectrometry ................................... 467
References ............................................ 468
10 Fast Atom Bombardment ...................................... 479
Learning Objectives ................................... 479
10.1 Ion Sources for FAB and LSIMS ......................... 480
10.1.1 FAB Ion Sources ................................ 480
10.1.2 LSIMS Ion Sources .............................. 482
10.1.3 FAB Probes ..................................... 482
10.2 Ion Formation in FAB and LSIMS ........................ 483
10.2.1 Ion Formation from Inorganic Samples ........... 483
10.2.2 Ion Formation from Organic Samples ............. 484
10.3 Liquid Matrices for FAB and LSIMS ..................... 486
10.3.1 The Role of the Liquid Matrix .................. 486
10.3.2 FAB Matrix Spectra - General Characteristics ... 487
10.3.3 Unwanted Reactions in FAB-MS ................... 487
10.4 Applications of FAB-MS ................................ 488
10.4.1 FAB-MS of Analytes of Low to Medium Polarity ... 488
10.4.2 FAB-MS of Ionic Analytes ....................... 490
10.4.3 High-Mass Analytes in FAB-MS ................... 491
10.4.4 Accurate Mass Measurements in FAB Mode ......... 492
10.4.5 Continuous-Flow FAB ............................ 494
10.4.6 Low-Temperature FAB ............................ 495
10.4.7 FAB-MS and Peptide Sequencing .................. 496
10.5 FAB and LSIMS - General Characteristics ............... 496
10.5.1 Sensitivity of FAB-MS .......................... 496
10.5.2 Types of Ions in FAB-MS ........................ 497
10.5.3 Analytes for FAB-MS ............................ 497
10.5.4 Mass Analyzers for FAB-MS ...................... 497
10.6 Massive Cluster Impact ................................ 498
10.7 252Californium Plasma Desorption ...................... 498
References ................................................. 499
11 Matrix-Assisted Laser Desorption/Ionization ................ 507
Learning Objectives ........................................ 507
11.1 Ion Sources for LDI and MALDI ......................... 508
11.2 Ion Formation ......................................... 509
11.2.1 Ion Yield and Laser Fluence .................... 510
11.2.2 Effect of Laser Irradiation on the Surface ..... 511
11.2.3 Temporal Evolution of a Laser Desorption
Plume .......................................... 512
11.2.4 Processes of Ion Formation in MALDI ............ 513
11.2.5 "Lucky Survivor" Model of Ion Formation ........ 514
11.3 MALDI Matrices ........................................ 516
11.3.1 Role of the Solid Matrix ....................... 516
11.3.2 Matrices in UV-MALDI ........................... 516
11.3.3 Characteristics of MALDI Matrix Spectra ........ 519
11.4 Sample Preparation .................................... 519
11.4.1 MALDI Target ................................... 519
11.4.2 Standard Sample Preparation .................... 520
11.4.3 Cationization .................................. 522
11.4.4 Cation Removal ................................. 524
11.4.5 Solvent-Free Sample Preparation ................ 526
11.4.6 Additional Methods of Sample Supply ............ 527
11.5 Applications of LDI ................................... 527
11.6 Applications of MALDI ................................. 529
11.6.1 Protein Analysis by MALDI-MS ................... 529
11.6.2 Peptide Sequencing and Proteomics .............. 531
11.6.3 Carbohydrate Analysis by MALDI-MS .............. 536
11.6.4 Oligonucleotide Analysis by MALDI-MS ........... 538
11.6.5 MALDI-MS of Synthetic Polymers ................. 539
11.7 Special Surfaces to Mimic the Matrix .................. 541
11.7.1 Desorption/Ionization on Silicon ............... 541
11.7.2 Nano-Assisted Laser Desorption/Ionization ...... 542
11.7.3 Further Variations of the MALDI Theme .......... 543
11.8 MALDI Imaging ......................................... 544
11.9 Atmospheric Pressure MALDI ............................ 546
11.10 General Characteristics of MALDI ..................... 547
11.10.1 Sample Consumption and Detection Limit ........ 547
11.10.2 Analytes for MALDI ............................ 547
11.10.3 Types of Ions in LDI and MALDI-MS ............. 548
11.10.4 Mass Analyzers for MALDI-MS ................... 548
References ................................................. 549
12 Electrospray Ionization .................................... 561
Learning Objectives ........................................ 561
12.1 Development of ESI and Related Methods ................ 562
12.1.1 Atmospheric Pressure Ionization ................ 563
12.1.2 Thermospray .................................... 564
12.1.3 Electrohydrodynamic Ionization ................. 565
12.1.4 Electrospray Ionization ........................ 565
12.2 Ion Sources for ESI ................................... 566
12.2.1 Basic Design Considerations .................... 566
12.2.2 Adaptation to Different Flow Rates ............. 568
12.2.3 Improved Electrospray Configurations ........... 569
12.2.4 Advanced Electrospray Interface Designs ........ 571
12.2.5 Nozzle-Skimmer Dissociation .................... 573
12.3 Nanoelectrospray ...................................... 574
12.3.1 Practical Considerations forNanoESI ............ 575
12.3.2 Spray Modes of NanoESI ......................... 576
12.3.3 Nanoelectrospray from a Chip ................... 577
12.4 Ion Formation in ESI .................................. 578
12.4.1 Formation of the Electrospray Plume ............ 578
12.4.2 Disintegration of Charged Droplets ............. 581
12.4.3 Formation of Ions from Charged Droplets ........ 582
12.5 Multiply Charged Ions and Charge Deconvolution ........ 585
12.5.1 Dealing with Multiply Charged Ions ............. 585
12.5.2 Mathematical Charge Deconvolution .............. 587
12.5.3 Computerized Charge Deconvolution .............. 588
12.5.4 Hardware Charge Deconvolution .................. 590
12.5.5 Controlled Charge Reduction in ESI ............. 592
12.6 Applications of ESI-MS ................................ 593
12.6.1 ESI-MS of Small Molecules ...................... 593
12.6.2 ESI of Metal Complexes ......................... 594
12.6.3 ESI of Surfactants ............................. 596
12.6.4 Oligonucleotides, DNA, and RNA ................. 596
12.6.5 ESI-MS of Oligosaccharides ..................... 599
12.6.6 High-Mass Proteins and Protein Complexes ....... 600
12.7 Summary of ESI Characteristics ........................ 601
12.7.1 Sample Consumption ............................. 603
12.7.2 Types of Ions in ESI ........................... 603
12.7.3 Mass Analyzers for ESI ......................... 603
12.8 Atmospheric Pressure Chemical Ionization .............. 604
12.8.1 Ion Sources for APCI ........................... 604
12.8.2 Ion Formation in APCI .......................... 605
12.8.3 APCI Spectra ................................... 605
12.9 Atmospheric Pressure Photoionization .................. 608
12.9.1 Ion Formation in APPI .......................... 608
12.9.2 APPI Spectra ................................... 610
References ............................................ 612
13 Ambient Mass Spectrometry .................................. 621
Learning Objectives ................................... 621
13.1 Desorption Electrospray Ionization .................... 622
13.1.1 Experimental Setup for DESI .................... 622
13.1.2 Mechanisms of Ion Formation in DESI ............ 626
13.1.3 Analytical Features of DESI .................... 627
13.2 Desorption Atmospheric Pressure Chemical Ionization ... 631
13.3 Desorption Atmospheric Pressure Photoionization ....... 632
13.4 Other Methods Related to DESI ......................... 634
13.4.1 Desorption Sonic Spray Ionization .............. 635
13.4.2 Extractive Electrospray Ionization ............. 635
13.4.3 Electrospray-Assisted Laser Desorption/
Ionization (ELDI) .............................. 637
13.4.4 Laser Ablation Electrospray Ionization ......... 638
13.4.5 Atmospheric Pressure Solids Analysis Probe ..... 640
13.5 Direct Analysis in Real Time .......................... 640
13.5.1 Experimental Setup for DART .................... 640
13.5.2 Ion Formation in DART .......................... 642
13.5.3 Analytical Applications of DART ................ 642
13.6 Overview of Ambient Mass Spectrometry ................. 644
References ................................................. 645
14 Hyphenated Methods ......................................... 651
Learning Objectives ........................................ 651
14.1 Concept of Chromatography-Mass Spectrometry ........... 652
14.1.1 Ion Chromatograms .............................. 653
14.1.2 Repetitive Acquisition of Mass Spectra During
Elution ........................................ 654
14.1.3 Selected Ion Monitoring ........................ 656
14.1.4 Selected Reaction Monitoring ................... 658
14.2 Quantitation .......................................... 659
14.2.1 Quantitation by External Standardization ....... 659
14.2.2 Quantitation by Internal Standardization ....... 660
14.2.3 Quantitation by Isotope Dilution ............... 661
14.2.4 Retention Times of Isotopologs ................. 663
14.3 Gas Chromatography-Mass Spectrometry .................. 663
14.3.1 GC-MS Interfaces ............................... 663
14.3.2 Volatility and Derivatization .................. 664
14.3.3 Column Bleed ................................... 665
14.3.4 Fast GC-MS ..................................... 667
14.3.5 Multiplexing for Increased Throughput .......... 667
14.4 Liquid Chromatography-Mass Spectrometry ............... 668
14.4.1 Multiplexed LC-ESI-MS .......................... 671
14.5 Ion Mobility Spectrometry-Mass Spectrometry ........... 673
14.6 Tandem MS as a Complement to LC-MS .................... 675
14.7 Ultrahigh-Resolution Mass Spectrometry ................ 678
References ................................................. 680
15 Inorganic Mass Spectrometry ................................ 685
Learning Objectives ........................................ 685
15.1 Thermal Ionization Mass Spectrometry .................. 689
15.2 Spark Source Mass Spectrometry ........................ 691
15.3 Glow Discharge Mass Spectrometry ...................... 694
15.4 Inductively Coupled Plasma Mass Spectrometry .......... 697
15.4.1 Laser Ablation ICP-MS .......................... 700
15.5 Secondary Ion Mass Spectrometry ....................... 701
15.5.1 Atomic SIMS .................................... 701
15.5.2 Instrumentation for Atomic SIMS ................ 703
15.5.3 Molecular SIMS ................................. 704
15.5.4 Polyatomic Primary Ion Beams ................... 705
15.6 Accelerator Mass Spectrometry ......................... 707
15.7 Conclusion ............................................ 710
References ................................................. 711
Appendix ...................................................... 717
A.l Units, Physical Quantities, and Physical Constants .... 717
A.2 Isotopic Composition of the Elements .................. 718
A.3 Carbon Isotopic Patterns .............................. 725
A.4 Chlorine and Bromine Isotopic Patterns ................ 726
A.5 Silicon and Sulfur Isotopic Patterns .................. 727
A.6 Isotopologs and Accurate Mass ......................... 727
A.7 Characteristic Ions ................................... 728
A.8 Common Impurities ..................................... 729
A.9 Amino Acids ........................................... 730
A.10 Method Selection Guide ................................ 731
A.l1 How to Recognize Cationization ........................ 732
A.12 Systematic Approach to Mass Spectra ................... 733
A.13 Rules for the Interpretation of Mass Spectra .......... 733
A.14 Nobel Prizes for Mass Spectrometry .................... 734
Subject Index ................................................. 735
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