Protein and Peptide Mass Spectrometry in Drug Discovery

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.

• PREFACE xv CONTRIBUTORS xviiPART I METHODOLOGY 11 Ionization Methods in Protein Mass Spectrometry 3Ismael Cotte-Rodriguez, Yun Zhang, Zhixin Miao, and Hao Chen1.1 History of the Development of Protein Mass Spectrometry 41.2 Laser-Based Ionization Methods for Proteins 51.3 Spray-Based Ionization Methods for Proteins 131.4 Ambient Ionization Methods 201.5 Conclusions 30Acknowledgments 30References 302 Ion Activation and Mass Analysis in Protein Mass Spectrometry 43Cheng Lin and Peter O’Connor2.1 Introduction 432.2 Ion Activation and Tandem MS Analysis 462.3 Mass Analyzers 59References 813 Target Proteins: Bottom-up and Top-down Proteomics 89Michael Boyne and Ron Bose3.1 Mass Spectral Approaches to Targeted Protein Identification 893.2 Bottom-up Proteomics 903.3 Top-down Approaches 963.4 Next-Generation Approaches 98References 994 Quantitative Proteomics by Mass Spectrometry 101Jacob Galan, Anton Iliuk, and W. Andy Tao4.1 Introduction 1014.2 In-Cell Labeling 1054.3 Quantitation via Isotopic Labeling of Proteins 1074.4 Quantitation via Isotopic Labeling on Peptides 1124.5 Label-Free Quantitation 1164.6 Conclusions 119Acknowledgment 120References 1205 Comparative Proteomics by Direct Tissue Analysis Using Imaging Mass Spectrometry 129Michelle L. Reyzer and Richard M. Caprioli5.1 Introduction 1295.2 Conventional Comparative Proteomics 1305.3 Comparative Proteomics Using Imaging MS 1315.4 Conclusions 136Acknowledgments 137References 1376 Peptide and Protein Analysis Using Ion Mobility–Mass Spectrometry 139Jeffrey R. Enders, Michal Kliman, Sevugarajan Sundarapandian, and John A. McLean6.1 Ion Mobility–Mass Spectrometry: Instrumentation and Separation Selectivity 1396.2 Characterizing and Interpreting Peptide and Protein Structures 1476.3 Applications of IM-MS to Peptide and Protein Characterizations 1526.4 Future Directions 158Acknowledgments 159References 1607 Chemical Footprinting for Determining Protein Properties and Interactions 175Sandra A. Kerfoot and Michael L. Gross7.1 Introduction to Hydrogen–Deuterium Exchange 1757.2 Experimental Procedures 1787.3 Mass Spectrometry-Based HDX in Practice 1827.4 Protein Footprinting via Free-Radical Oxidation 1937.5 Chemical Crosslinking 1987.6 Selective and Irreversible Chemical Modification 2017.7 Conclusion 205References 2068 Microwave Technology to Accelerate Protein Analysis 213Urooj A. Mirza, Birendra N. Pramanik, and Ajay K. Bose8.1 Introduction 2138.2 Microwave Technology 2158.3 Summary 224Acknowledgments 224References 2249 Bioinformatics and Database Searching 231Surendra Dasari and David L. Tabb9.1 Overview 2319.2 Introduction to Tandem Mass Spectrometry 2319.3 Overview of Peptide Identification with Database Searching 2349.4 MyriMatch-IDPicker Protein Identification Pipeline 2359.5 Results of a Shotgun Proteomics Study 2469.6 Improvements to MyriMatch Database Search Engine 2489.7 Applications of MyriMatch-IDPicker Pipeline 2509.8 Conclusions 251Acknowledgments 251References 251PART II Applications 25310 Mass Spectrometry-Based Screening and Characterization of Protein–Ligand Complexes in Drug Discovery 255Christine L. Andrews, Michael R. Ziebell, Elliott Nickbarg, and Xianshu Yang10.1 Introduction 25510.2 Affinity Selection Mass Spectrometry (AS-MS) 25610.3 Solution-Based AS-MS as Screening Technologies 25810.4 Gas-Phase Interactions 26710.5 Enzyme Activity Assays Using MS for Screening or Confirming Drug Candidates 27110.6 Conclusions and Future Directions 276References 27711 Utilization of Mass Spectrometry for the Structural Characterization of Biopharmaceutical Protein Products 287Amareth Lim and Catherine A. Srebalus Barnes11.1 Introduction 28711.2 MS-Based Approach for the Characterization of Recombinant Therapeutic Proteins 28811.3 Cell Culture Development 29011.4 Purification Development 29411.5 Formulation Development 30011.6 Analytical Method Development 30411.7 Confirmation of Structure/Product Comparability Assessment 31111.8 Conclusions 313Acknowledgments 315References 31512 Post-translationally Modified Proteins: Glycosylation, Phosphorylation, and Disulfide Bond Formation 321Anthony Tsarbopoulos and Fotini N. Bazoti12.1 Introduction 32112.2 Glycosylation 32212.3 Phosphorylation 33812.4 Disulfide Bond Detection and Mapping 34712.5 Future Perspectives 350Acknowledgments 352Abbreviations 353References 35413 Mass Spectrometry of Antigenic Peptides 371Henry Rohrs13.1 Introduction 37113.2 Analysis of Antigenic Peptides 37413.3 Examples of the Application of Mass Spectrometry to Antigenic Peptide Study 38113.4 Future Work 385Acknowledgments 386Abbreviations 387References 38714 Neuropeptidomics 393Jonathan V. Sweedler, Fang Xie, and Adriana Bora14.1 Introduction 39314.2 Neuropeptidomics: Characterizing Peptides in the Brain 39414.3 Sample Preparation for Mass Spectrometry 39514.4 Separations 40514.5 Peptide Characterization via Mass Spectrometry 40714.6 Conclusions 41914.7 Future Perspectives 419Acknowledgments 420References 42015 Mass Spectrometry for the Study of Peptide Drug Metabolism 435Patrick J. Rudewicz15.1 Introduction 43515.2 Peptide Drug Metabolism 43615.3 LC-MS/MS for Metabolite Identification 43715.4 Quantitative Analysis 43915.5 Case Study: IL-1b Protease Inhibitors 44015.6 Future Directions 445References 445INDEX 449

"This book will be a valuable reference as it contains plenty of depth and substance to be of interest to experienced practitioners of mass spectrometry and related techniques, but is still accessible to pharmaceutical researchers who want to learn more about MS technologies and its applications."  (American Society for Mass Spectrometry, 1 July 2012)