Protein mass spectrometry (Amsterdam; Oxford, 2009). - ОГЛАВЛЕНИЕ / CONTENTS
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ОбложкаProtein mass spectrometry / ed. by J.P.Whitelegge. - Amsterdam; Oxford: Elsevier, 2009. - xxxii, 518 p., [12] p. of plates: ill. (some col.). - (Wilson & Wilson's comprehensive analytical chemistry; vol.52). - Incl. bibl. ref. - Sub. ind.: p.515-518. - ISBN 978-0-444-53055-4; ISSN 0166-526X
 

Оглавление / Contents
 
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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