Contributors to Volume 52 .................................... xiii
Volumes in the Series ......................................... xix
Foreword .................................................... xxiii
Preface ...................................................... xxix
Series Editor's Preface ...................................... xxxi
1 An Introduction to the Basic Principles and Concepts of
Mass Spectrometry ............................................ 1
Kym F. Faull, Alek N. Dooley, Frederic Halgand, Lorelei
D. Shoemaker, Andrew J. Norris, Christopher M. Ryan, Arthur
Laganowsky, Jodie V. Johnson and Jonathan E. Katz
1 Opening Remarks ........................................... 2
2 The Instrument ............................................ 4
3 Vacuum Systems ............................................ 4
4 Definitions ............................................... 5
5 Resolution ................................................ 6
6 Mass Accuracy ............................................. 8
7 Isotopes .................................................. 9
8 Reconciling Theoretical and Measured Masses .............. 11
9 Charge State Assignment .................................. 11
10 The Need for Chromatography .............................. 12
11 The Myth of Defining Elemental Compositions .............. 13
12 Desorption Ionization: Laser Desorption .................. 14
13 Spray Ionization: Electrospray Ionization ................ 16
14 Mass Analyzers ........................................... 19
15 Time-of-Flight Mass Spectrometers ........................ 20
16 Linear Quadrupole Mass Filters ........................... 22
17 Quadrupole Ion Traps ..................................... 23
18 Linear Ion Traps ......................................... 26
19 Ion Cyclotron Cells and Fourier Transform Mass
Spectrometry ............................................. 27
20 The Orbitrap ............................................. 29
21 Detectors ................................................ 30
22 Electron Multipliers ..................................... 31
23 Conversion Dynodes or High-Energy Dynodes ................ 32
24 Quantification ........................................... 32
25 Structural Elucidation by Mass Spectrometry .............. 34
26 Gas Phase Ion Stabilities and Energetics of the
Collisionally-Activated Dissociation Process ............. 35
27 Collision-Induced Dissociation ........................... 36
28 Electron Capture Dissociation ............................ 38
29 Electron Transfer Dissociation ........................... 40
30 Scan Modes in Tandem Mass Spectrometry ................... 40
31 Conclusions .............................................. 43
Acknowledgements ............................................ 44
References .................................................. 44
2 Characterization of Protein Higher Order Structure and
Dynamics with ESI MS ........................................ 47
Wendell P. Griffith, Anirban Mohimen, Rinat R. Abzalimov
and Igor A. Kaltashov
1 Introduction ............................................. 47
2 Charge-State Distributions of Protein Ions in ESI MS
and Large-Scale Conformational Dynamics of Single
Polypeptide Chains ....................................... 48
3 Conformational Dynamics in Multi-Component Systems:
Assembly of Hemoglobin Tetramers ......................... 51
4 Charge-State Distribution and the Estimation of the
Solvent-Exposed Surface Areas of Proteins ................ 55
5 Limitations of the Use of Charge-State Distributions
for Determining Protein Conformational Heterogeneity ..... 58
6 Future Outlook ........................................... 59
Acknowledgements ............................................ 60
References .................................................. 61
3 Noncovalent Protein Interactions ............................ 63
Summer L. Bernstein and Michael T. Bowers
1 Introduction ............................................. 63
2 Instrumentation and Technical Development ................ 64
3 Protein Misfolding and Aggregation ....................... 67
4 Ligand-Receptor Interactions ............................. 74
5 Heterogeneous Complexes: TRAP ............................ 76
6 Subunit Exchange of Transthyretin ........................ 78
7 Future Directions ........................................ 78
8 Conclusions .............................................. 79
Acknowledgments ............................................. 79
References .................................................. 79
4 Protein Analysis with Hydrogen-Deuterium Exchange Mass
Spectrometry ................................................ 83
Jennifer L. Mitchell and John R. Engen
1 Introduction ............................................. 83
2 Experimental Protocol .................................... 88
3 Illustrative Examples .................................... 96
4 Conclusions ............................................. 100
Acknowledgements ........................................... 101
References ................................................. 101
5 Biochemical Reaction Kinetics Studied by Time-Resolved
Electrospray Ionization Mass Spectrometry .................. 103
Lars Konermann, Jingxi Pan and Derek J. Wilson
1 Introduction ............................................ 103
2 Time-Resolved ESI-MS .................................... 105
3 Selected Applications ................................... 109
4 Conclusions and Outlook ................................. 120
Acknowledgements ........................................... 121
References ................................................. 121
6 Thermodynamic Analysis of Protein Folding and Ligand
Binding by SUPREX .......................................... 127
Michael C. Fitzgerald, Liangjie Tang and Erin D. Hopper
1 Introduction ............................................ 127
2 The SUPREX Protocol ..................................... 128
3 Evaluation of Thermodynamic Parameters .................. 131
4 Quantitative Analysis of Ligand Binding ................. 136
5 Unique Applications ..................................... 141
6 Conclusion .............................................. 146
References ................................................. 146
7 Microsecond Time-Scale Hydroxyl Radical Profiling of
Solvent-Accessible Protein Residues ........................ 151
David M. Hambly and Michael L. Gross
1 Introduction ............................................ 151
2 Reagents for Surface Mapping ............................ 153
3 Fast Photochemical Oxidation of Proteins (FPOP) ......... 163
Acknowledgement ............................................ 172
References ................................................. 172
8 Intact Protein Mass Measurements and Тор-Down Mass
Spectrometry: Application to Integral Membrane Proteins .... 179
Julian P. Whitelegge
1 Introduction ............................................ 179
2 Intact Protein Mass Measurements ........................ 180
3 Ionization .............................................. 188
References ................................................. 194
9 Probing the Structure and Function of Integral Membrane
Proteins by Mass Spectrometry .............................. 197
Adam B. Weinglass
1 Introduction ............................................ 197
2 Technical Aspects of Mass Spectrometry of Integral
Membrane Proteins ....................................... 198
3 MS of Integral Membrane Proteins Provides Insight into
Structure, Function and Mechanism ....................... 199
4 Conclusions ............................................. 209
Acknowledgements ........................................... 209
References ................................................. 209
10 Bottom-Up Mass Spectrometry Analysis of Integral
Membrane Protein Structure and Topology .................... 213
Anna E. Speers and Christine C. Wu
1 Introduction ............................................ 214
2 IMP Structure and Characterization ...................... 214
3 Mass Spectrometry Instrumentation ....................... 216
4 General Considerations for Sample Preparation ........... 218
5 Localizing Glycosylation Sites .......................... 220
6 Limited Proteolysis ..................................... 222
7 Residue-Specific Chemical Modification .................. 226
8 Photoaffinity Labeling of Binding-Site Residues ......... 230
9 Cross-Linking ........................................... 233
10 H/D Exchange ............................................ 234
11 Summary and Future Directions ........................... 236
Abbreviations .............................................. 238
Acknowledgement ............................................ 239
References ................................................. 239
11 Covalent Trapping of Protein Interactions in Complex
Systems .................................................... 245
Rasanjala Weerasekera, Tujin Shi and Gerold Schmitt-Ulms
1 Introduction ............................................ 245
2 Protein Crosslinking .................................... 247
3 Interactome Methods ..................................... 251
4 Interface and Topology Mapping .......................... 259
5 Future Directions ....................................... 266
Abbreviations .............................................. 268
Acknowledgements ........................................... 268
References ................................................. 268
12 Phosphoproteomics .......................................... 275
Martin R. Larsen and Phillip J. Robinson
1 Introduction to Phosphoproteomics ....................... 275
2 Strategies for Enrichment of Phosphorylated Peptides .... 277
3 Mass Spectrometric Analysis of Phosphorylated
Peptides ................................................ 282
4 Quantitative Phosphoproteomics .......................... 285
5 Factors Affecting Phosphoproteomics ..................... 290
6 Conclusion .............................................. 292
Acknowledgements ........................................... 293
References ................................................. 293
13 Analysis of Protein-Tyrosine Phosphorylation by Mass
Spectrometry ............................................... 297
Guoan Zhang, Chong-Feng Xu and Thomas A. Neubert
1 Introduction ............................................ 297
2 Enrichment .............................................. 299
3 Qualitative Analysis .................................... 301
4 Quantitative Analysis ................................... 305
5 Future Directions ....................................... 309
6 Conclusions ............................................. 310
Abbreviations .............................................. 310
Acknowledgement ............................................ 311
References ................................................. 311
14 Protein Histidine Phosphorylation .......................... 315
Xin-Lin Zu, Paul G. Besant and Paul V. Attwood
1 Introduction ............................................ 316
2 Chemistry of Phosphohistidine ........................... 317
3 Protein Histidine Phosphorylation ....................... 318
4 Detection of Histidine Phosphorylation .................. 331
5 Future Directions ....................................... 339
6 Conclusion .............................................. 346
Acknowledgements ........................................... 346
References ................................................. 346
15 O-GlcNAc Proteomics: Mass Spectrometric Analysis of O-GlcNAc
Modifications on Proteins .................................. 353
Robert J. Chalkley, Lance Wells and Keith Vosseller
1 Introduction ............................................ 354
2 Challenges to Mapping Sites of O-GlcNAc Modification .... 358
3 Early Efforts in O-GlcNAc Site-Mapping .................. 360
4 Enzymatic Tagging of O-GlcNAc to Facilitate Enrichment
and Identification of Modification Sites ................ 361
5 Chemoenzymatic Approaches in O-GlcNAc Proteomics ........ 362
6 Beta-Elimination/Michael Addition Strategies for
O-GlcNAcylation Site-Mapping ............................ 363
7 Direct Enrichment of Native O-GlcNAc Modified Proteins
with WGA Lectin Weak Affinity Chromatography (LWAC) ..... 365
8 Ion Trap MS2/MS3 for O-GlcNAc Modified Peptide
Identification .......................................... 366
9 Electron Capture Dissociation (ECD) for O-GlcNAc Site-
Mapping ................................................. 366
10 Interpretation of O-GlcNAcylated Peptide Mass
Spectrometry ............................................ 368
11 Conclusions ............................................. 369
References ................................................. 370
16 Analysis of Deamidation in Proteins ........................ 375
Jason J. Cournoyer and Peter B. O'Connor
1 What is Deamidation? .................................... 376
2 How Does Deamidation Occur? ............................. 377
3 Biological Significance of Deamidation .................. 380
4 Non-MS Based Methods for Studying Deamidation ........... 385
5 Mass Spectrometry Based Methods for Studying
Deamidation ............................................. 390
6 Quantitation of Deamidation and Its Products ............ 397
7 Isotopic Labeling Methods ............................... 399
8 Summary ................................................. 401
References ................................................. 402
17 Mass Spectrometry-Driven Approaches to Quantitative
Proteomics and Beyond ...................................... 411
Silke Oeljeklaus, Jon Barbour, Helmut E. Meyer and Bettina
Warscheid
1 Why to Use Mass Spectrometry in Quantitative Proteomics . 411
2 MS-Based Approaches to Quantitative Proteomics .......... 413
3 Applications in Functional Proteomics ................... 426
4 How to Obtain Meaningful Data in MS-Based Quantitative
Proteomics .............................................. 437
5 Perspectives ............................................ 439
References ................................................. 439
18 Multiplexed Quantitative Proteomics Using Mass
Spectrometry ............................................... 449
Philip L. Ross, Xunming Chen, Esteban Тоrо, Leticia Britos,
Lucy Shapiro and Darryl Pappin
1 Introduction ............................................ 449
2 Isobaric N-Terminal Peptide Tagging ..................... 452
3 Mass Spectrometry ....................................... 457
4 Quantitative Applications Using Isobaric Tagging ........ 461
References ................................................. 466
19 Large-Scale Subcellular Localization of Proteins by Protein
Correlation Profiling ...................................... 467
Leonard J. Foster
1 Introduction ............................................ 467
2 Peptide Correlation Profiling ........................... 468
3 Other Quantitative Methods .............................. 473
4 Software for PCP ........................................ 474
5 Hardware Requirements for PCP ........................... 475
6 The Future for PCP and Organelle Proteomics ............. 475
Acknowledgements ........................................... 476
References ................................................. 476
20 Metabolic Labeling Approaches for the Relative
Quantification of Proteins ................................. 479
Edward L. Huttlin, Adrian D. Hegeman and Michael R. Sussman
1 Introduction ............................................ 480
2 Selected Metabolic Labeling Strategies .................. 483
3 Practical Experimental Considerations ................... 487
4 Comparison of Full versus Partial Labeling .............. 498
5 Future Directions ....................................... 507
References ................................................. 509
Subject Index ................................................. 515
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