Michael L. Gross, PhD, is a Professor in the Departments of Chemistry, Medicine, and Immunology at Washington University in St. Louis. He is also Principal Investigator at the National Institutes of Health (NIH) Research Resource in Mass Spectrometry.
 
Guodong Chen, PhD, is Principal Scientist in Bioanalytical and Discovery Analytical Sciences at Bristol-Myers Squibb in Princeton, New Jersey. He heads a mass spectrometry group in support of drug discovery as well as development programs in small molecule pharmaceuticals and biologics.
 
Birendra N. Pramanik, PhD, was a Distinguished Fellow at Schering-Plough Research Institute (SPRI), where he directed the spectroscopy, mass spectrometry, and NMR programs.

With chapters provided by international leading experts, this book covers the recent advances in protein and peptide mass spectrometry.

PREFACE xv
 
CONTRIBUTORS xvii
 
PART I METHODOLOGY 1
 
1 Ionization Methods in Protein Mass Spectrometry 3
Ismael Cotte-Rodriguez, Yun Zhang, Zhixin Miao, and Hao Chen
 
1.1 History of the Development of Protein Mass Spectrometry 4
 
1.2 Laser-Based Ionization Methods for Proteins 5
 
1.3 Spray-Based Ionization Methods for Proteins 13
 
1.4 Ambient Ionization Methods 20
 
1.5 Conclusions 30
 
Acknowledgments 30
 
References 30
 
2 Ion Activation and Mass Analysis in Protein Mass Spectrometry 43
Cheng Lin and Peter O'Connor
 
2.1 Introduction 43
 
2.2 Ion Activation and Tandem MS Analysis 46
 
2.3 Mass Analyzers 59
 
References 81
 
3 Target Proteins: Bottom-up and Top-down Proteomics 89
Michael Boyne and Ron Bose
 
3.1 Mass Spectral Approaches to Targeted Protein Identification 89
 
3.2 Bottom-up Proteomics 90
 
3.3 Top-down Approaches 96
 
3.4 Next-Generation Approaches 98
 
References 99
 
4 Quantitative Proteomics by Mass Spectrometry 101
Jacob Galan, Anton Iliuk, and W. Andy Tao
 
4.1 Introduction 101
 
4.2 In-Cell Labeling 105
 
4.3 Quantitation via Isotopic Labeling of Proteins 107
 
4.4 Quantitation via Isotopic Labeling on Peptides 112
 
4.5 Label-Free Quantitation 116
 
4.6 Conclusions 119
 
Acknowledgment 120
 
References 120
 
5 Comparative Proteomics by Direct Tissue Analysis Using Imaging Mass Spectrometry 129
Michelle L. Reyzer and Richard M. Caprioli
 
5.1 Introduction 129
 
5.2 Conventional Comparative Proteomics 130
 
5.3 Comparative Proteomics Using Imaging MS 131
 
5.4 Conclusions 136
 
Acknowledgments 137
 
References 137
 
6 Peptide and Protein Analysis Using Ion Mobility-Mass Spectrometry 139
Jeffrey R. Enders, Michal Kliman, Sevugarajan Sundarapandian, and John A. McLean
 
6.1 Ion Mobility-Mass Spectrometry: Instrumentation and Separation Selectivity 139
 
6.2 Characterizing and Interpreting Peptide and Protein Structures 147
 
6.3 Applications of IM-MS to Peptide and Protein Characterizations 152
 
6.4 Future Directions 158
 
Acknowledgments 159
 
References 160
 
7 Chemical Footprinting for Determining Protein Properties and Interactions 175
Sandra A. Kerfoot and Michael L. Gross
 
7.1 Introduction to Hydrogen-Deuterium Exchange 175
 
7.2 Experimental Procedures 178
 
7.3 Mass Spectrometry-Based HDX in Practice 182
 
7.4 Protein Footprinting via Free-Radical Oxidation 193
 
7.5 Chemical Crosslinking 198
 
7.6 Selective and Irreversible Chemical Modification 201
 
7.7 Conclusion 205
 
References 206
 
8 Microwave Technology to Accelerate Protein Analysis 213
Urooj A. Mirza, Birendra N. Pramanik, and Ajay K. Bose
 
8.1 Introduction 213
 
8.2 Microwave Technology 215
 
8.3 Summary 224
 
Acknowledgments 224
 
References 224
 
9 Bioinformatics and Database Searching 231
Surendra Dasari and David L. Tabb
 
9.1 Overview 231
 
9.2 Introduction to Tandem Mass Spectrometry 231
 
9.3 Overview of Peptide Identification with Database Searching 234
 
9.4 MyriMatch-IDPicker Protein Identification Pipeline 235
 
9.5 Results of a Shotgun Proteomics Study 246
 
9.6 Improvements to MyriMatch Database Search Engine 248
 
9.7 Applications of MyriMatch-IDPicker Pipeline 250
 
9.8 Conclusions 251
 
Acknowledgments 251
 
References 251
&nbs

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The book that highlights mass spectrometry and its application in characterizing proteins and peptides in drug discovery
 
An instrumental analytical method for quantifying the mass and characterization of various samples from small molecules to large proteins, mass spectrometry (MS) has become one of the most widely used techniques for studying proteins and peptides over the last decade. Bringing together the work of experts in academia and industry, Protein and Peptide Mass Spectrometry in Drug Discovery highlights current analytical approaches, industry practices, and modern strategies for the characterization of both peptides and proteins in drug discovery.
 
Illustrating the critical role MS technology plays in characterizing target proteins and protein products, the methods used, ion mobility, and the use of microwave radiation to speed proteolysis, the book also covers important emerging applications for neuroproteomics and antigenic peptides. Placing an emphasis on the pharmaceutical industry, the book stresses practice and applications, presenting real-world examples covering the most recent advances in mass spectrometry, and providing an invaluable resource for pharmaceutical scientists in industry and academia, analytical and bioanalytical chemists, and researchers in protein science and proteomics.