Biological Mass Spectrometry

00 420mie_0121828077.jpg......Page 1
01 fm.pdf......Page 2
02 preface.pdf......Page 3
03 toc.pdf......Page 5
04 contributors.pdf......Page 7
Mass Spectrometers for the Analysis of Biomolecules......Page 9
Some Definitions and Principles......Page 10
Resolving Power and Resolution......Page 12
Isotopes, Peak Shapes, and Mass Measurements......Page 13
Soft Ionization......Page 17
MALDI-TOF Mass Spectrometers......Page 24
Mass Spectrometers Optimized for ESI......Page 27
Biophysical Studies by ESI-MS......Page 31
The Need to Obtain Structural Information: Tandem Mass Spectrometry......Page 33
Quadrupoles and QITs......Page 38
The QqTOF......Page 41
FT-ICR......Page 42
High-Energy MALDI Tandem Mass Spectrometry......Page 43
Ion Detection......Page 46
Conclusions......Page 49
References......Page 50
Introduction......Page 55
Ion Production......Page 57
Orthogonal Injection......Page 58
Collisional Cooling......Page 59
Orthogonal Injection of MALDI Ions......Page 61
Flight Tube High Voltage......Page 65
Time Focusing, Resolution, and Mass Accuracy......Page 66
Duty Cycle and m/z Discrimination......Page 71
Ion Detection......Page 73
Throughput......Page 75
Quadrupole Operation......Page 77
Tandem MS Mode......Page 78
Parent Ion Scans in the Quadrupole......Page 79
References......Page 81
Further Reading......Page 84
Introduction......Page 85
Description of the Instrument......Page 86
Precursor Selection......Page 88
Sensitivity......Page 91
Fragmentation......Page 96
Applications to Protein Identification and Characterization......Page 106
Conclusion......Page 112
References......Page 113
Further Reading......Page 114
Introduction......Page 115
Overview......Page 116
Apparatus......Page 117
Higher Order Fields......Page 118
Resonance......Page 119
Bath Gas......Page 120
Trapping Ions......Page 121
Selective Accumulation......Page 122
Masss Elective Instability......Page 123
Resonance Ejection......Page 124
Image Current Detection......Page 125
Ion Manipulation......Page 126
Collisional Activation......Page 127
Resonance Excitation......Page 128
Boundary-Activated Dissociation......Page 130
Red-Shifted off-Resonance Large-Amplitude Excitation......Page 131
Nonresonance Excitation......Page 132
Surface-Induced Dissociation......Page 133
Gas-Phase Reactions......Page 134
Ion–Molecule Reactions......Page 135
Overview......Page 136
Principles......Page 137
Ion-Trapping Capacity and Space Charge......Page 138
Ion Sources......Page 139
Trapping Ions......Page 140
Image Current......Page 142
Resolution......Page 143
Quadrupolar Axialization......Page 144
Collisional Activation......Page 145
Gas-Phase Collisional Activation......Page 146
Blackbody Infrared Radiative Dissociation......Page 147
Electron-Capture Dissociation......Page 148
References......Page 149
Introduction......Page 155
Experimental Variables that Influence the CID Behavior of Biological Ions......Page 157
High-Energy CID (Fast Activation)......Page 164
Low-Energy CID (Slow Activation)......Page 168
Ion-Trapping CID (Very Slow Activation, Slow Heating)......Page 175
Quadrupole Ion Trap CID......Page 176
Fourier Transform–Ion Cyclotron Resonance CID......Page 181
Summary and Conclusions......Page 185
References......Page 186
Introduction......Page 193
Instrumentation......Page 196
Mechanism of Photodissociation......Page 200
Peptide Sequencing......Page 201
Conclusions......Page 212
References......Page 213
Further Reading......Page 216
Peptide Sequence Analysis......Page 217
Introduction......Page 218
Peptide Fragmentation Processes......Page 219
De Novo Sequence Determination......Page 225
Protein Identification Using MS/MS Data......Page 231
Altering the Dissociation Processes by Chemical Derivatization......Page 235
MS/MS Analysis of Covalently Modified Peptides......Page 239
References......Page 247
Proteomics......Page 253
Proteomics vs. Genomics......Page 260
Gel Electrophoresis, Staining, Imaging, and Protein Digestion......Page 261
Mass Measurement......Page 264
Sequence Database Searching......Page 266
Application: Drug-Induced Hypertrophy of Cardiomyocytes......Page 267
Gel-Based Methods......Page 270
Gel-Free Methods......Page 272
Impact on Biological Research......Page 276
Drug Target and Surrogate Marker Identification......Page 278
Lead Optimization for Traditional Pharmaceuticals: Toxicology and Efficacy......Page 279
Sample Preparation......Page 281
Sensitivity, Dynamic Range, and Automation......Page 283
Method for Reduction/Alkylation in Sample Buffer......Page 284
For Coomassie-Stained Gels......Page 285
References......Page 286
Bioinformatic Methods to Exploit Mass Spectrometric Data for Proteomic Applications......Page 298
Mass Spectrometric Analysis of Peptides and Proteins......Page 299
Existing Tools for Protein Identification: What Is Available?......Page 302
Anatomy of a Web-Based Package: ProteinProspector......Page 305
What do You do When Your Protein is Not in the Database?......Page 310
Quantitation of Proteins......Page 311
The Challenge of Automation and High Throughput......Page 314
Acknowledgments......Page 317
References......Page 318
Protein Conformations, Interactions, and H/D Exchange......Page 322
Introduction......Page 323
The ESI Method......Page 325
Charge-State Distributions......Page 327
Comparison of ESI-MS with Other Spectroscopic Methods......Page 328
Negative Ion ESI-MS Charge-State Distributions......Page 334
Protein Folding Kinetics by "Time-Resolved"-ESI-MS......Page 335
Hydrogen Exchange Chemistry......Page 336
The Influence of Solution Temperature, pH, and Composition on Amide Hydrogen Exchange......Page 337
Hydrogen Exchange Mechanism: Ex1 and Ex2......Page 339
Hydrogen Isotope Exchange Monitored by Mass Spectrometry......Page 342
Determination of H/D-Exchange Mechanisms: EX1 and EX2 Types......Page 345
Peak Width Analysis......Page 349
Regional Structural and Dynamic Information from Medium Spatial Resolution Data......Page 352
Continuous Vs. Pulse Labeling......Page 353
High-Resolution Mass Spectrometry (FT-ICR-MS) for H/D Exchange Studies......Page 354
The bn-Ions......Page 355
Correlation of H/D Ratios and NMR-Derived Exchange Rates......Page 357
Conformations and Site-Specific Hydrogen Bonds......Page 359
Conformations in the Gas Phase......Page 360
References......Page 362
Introduction......Page 371
Interface Parameters (Vc, P, T)......Page 373
Protein–Metal Interactions......Page 375
Protein–Ligand Interactions......Page 377
Principle......Page 378
Limitations in the Determination of Binding Constants by ESI-MS......Page 380
Definition of Cooperative Binding......Page 381
Application of Supramolecular MS to Cooperativity Studies......Page 382
Validity of the Approach......Page 383
Application to the Characterization of Orphan Proteins......Page 385
Screening of Ligands Using Mass Spectrometry......Page 386
Relationship between Gas-Phase and Solution-Phase Stability......Page 389
From Solution Phase to the Gas Phase: Possible Origins of Distortion......Page 391
Ionization Efficiency and Ion Transmission......Page 392
Influence of the Nature of the Interactions Involved in the Complex......Page 393
Acknowledgments......Page 394
References......Page 395
Further Reading......Page 399
Introduction......Page 400
Optimization of Peptic Digestion......Page 402
Strategies for the Assignment of Peptic Fragments......Page 403
Mass Spectrometry......Page 405
The Two Mutational Variants Populate Partially Folded States......Page 406
Localization of the Unfolding Domain in the D67H Variant......Page 407
Conclusions......Page 410
References......Page 412
Quantitating Isotopic Molecular Labels with Accelerator Mass Spectrometry......Page 414
Introduction......Page 415
Decay Counting Efficiency......Page 416
Accelerator Mass Spectrometry......Page 417
Units......Page 420
Range, Resolution, and Sample Size......Page 421
Dose Estimation......Page 424
Data Interpretation......Page 427
Radiation Exposure and Wastes......Page 429
Conclusion......Page 431
References......Page 432
Introduction......Page 435
Instrumentation......Page 436
Sample Preparation: Methodology and Practical Considerations......Page 439
Data Manipulation......Page 443
Applications......Page 444
AMS Determination of Radioisotope Concentrations: Pharmacokinetic Studies......Page 445
HPLC-AMS......Page 447
AMS Detection of Chemically Modified DNA and Protein......Page 449
The Future......Page 452
References......Page 453
x subject index.pdf......Page 456
xx author index.pdf......Page 464
xxx mie index.pdf......Page 490