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Mass Spectrometry-Based Chemical Proteomics


Mass Spectrometry-Based Chemical Proteomics


1. Aufl.

von: W. Andy Tao, Ying Zhang

134,99 €

Verlag: Wiley
Format: EPUB
Veröffentl.: 31.07.2019
ISBN/EAN: 9781118970201
Sprache: englisch
Anzahl Seiten: 448

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Beschreibungen

PROVIDES STRATEGIES AND CONCEPTS FOR UNDERSTANDING CHEMICAL PROTEOMICS, AND ANALYZING PROTEIN FUNCTIONS, MODIFICATIONS, AND INTERACTIONS—EMPHASIZING MASS SPECTROMETRY THROUGHOUT Covering mass spectrometry for chemical proteomics, this book helps readers understand analytical strategies behind protein functions, their modifications and interactions, and applications in drug discovery. It provides a basic overview and presents concepts in chemical proteomics through three angles: Strategies, Technical Advances, and Applications. Chapters cover those many technical advances and applications in drug discovery, from target identification to validation and potential treatments. The first section of Mass Spectrometry-Based Chemical Proteomics starts by reviewing basic methods and recent advances in mass spectrometry for proteomics, including shotgun proteomics, quantitative proteomics, and data analyses. The next section covers a variety of techniques and strategies coupling chemical probes to MS-based proteomics to provide functional insights into the proteome. In the last section, it focuses on using chemical strategies to study protein post-translational modifications and high-order structures. Summarizes chemical proteomics, up-to-date concepts, analysis, and target validation Covers fundamentals and strategies, including the profiling of enzyme activities and protein-drug interactions Explains technical advances in the field and describes on shotgun proteomics, quantitative proteomics, and corresponding methods of software and database usage for proteomics Includes a wide variety of applications in drug discovery, from kinase inhibitors and intracellular drug targets to the chemoproteomics analysis of natural products Addresses an important tool in small molecule drug discovery, appealing to both academia and the pharmaceutical industry Mass Spectrometry-Based Chemical Proteomics is an excellent source of information for readers in both academia and industry in a variety of fields, including pharmaceutical sciences, drug discovery, molecular biology, bioinformatics, and analytical sciences.
Preface xv 1 Protein Analysis by Shotgun Proteomics 1 Yu Gao and John R. Yates III 1.1 Introduction 1 1.1.1 Terminology 1 1.1.2 Power of Shotgun Proteomics 1 1.1.3 Advantage of Shotgun Proteomics 2 1.2 Overview of Shotgun Proteomics 2 1.3 Sample Preparation 4 1.3.1 Protein Separation 4 1.3.1.1 Overview 4 1.3.1.2 2D?Gel Approach 4 1.3.1.3 Separation of Membrane Protein 5 1.3.1.4 Subcellular Fractionation 5 1.3.1.5 Protein Enrichment 6 1.3.1.6 Phosphoprotein 6 1.3.1.7 Glycoprotein 6 1.3.1.8 AP–MS and Interactome 7 1.3.2 Protein Modification 8 1.3.2.1 Overview 8 1.3.2.2 Reduction of Disulfide Bond and Alkylation 8 1.3.2.3 Chemical Crosslinking 8 1.3.2.4 Proximity Labeling 9 1.3.3 Protein Digestion 9 1.4 Peptide Separation and Data Acquisition 11 1.4.1 Peptide Separation 11 1.4.1.1 Reversed Phase (RP) 11 1.4.1.2 HILIC 11 1.4.1.3 MudPIT 11 1.4.1.4 Capillary Electrophoresis 13 1.4.2 Peptide Ionization 13 1.4.3 Mass Analyzer 13 1.4.4 Peptide Fragmentation Method 15 1.4.4.1 CID/HCD 15 1.4.4.2 ETD/ECD 16 1.4.4.3 IRMPD/UVPD 16 1.4.5 Acquisition Mode 17 1.5 Informatics 17 1.5.1 Peptide Identification 18 1.5.1.1 Database Search 18 1.5.1.2 Spectral Library Search 21 1.5.1.3 De novo Sequencing 22 1.5.1.4 Peptide?Centric Analysis 23 1.5.2 Peptide/Protein Quantitation 23 1.5.2.1 Labeled Quantitation 23 1.5.2.2 Label?Free Quantitation 27 1.5.3 Protein Inference 29 References 31 2 Quantitative Proteomics for Analyses of Multiple Samples in Parallel with Chemical Perturbation 39 Amanda Rae Buchberger, Jillian Johnson, and Lingjun Li 2.1 Introduction 39 2.2 Relative and Absolute Label?Free Quantitation Strategies 40 2.3 Stable Isotope?Based Quantitative Proteomics 42 2.3.1 Relative Quantitation 42 2.3.2 Absolute Quantitation 47 2.4 Conclusion 48 2.5 Methodology 50 2.6 Notes 52 Acknowledgments 55 References 56 3 Chemoproteomic Analyses by Activity?Based Protein Profiling 67 Bryan J. Killinger, Kristoffer R. Brandvold, Susan J. Ramos?Hunter, and Aaron T. Wright 3.1 Introduction 67 3.2 How ABPP Works 68 3.3 ABPP Probe Design 71 3.3.1 Mechanism?Based Probes 72 3.3.2 Reactivity?Based Probes 74 3.3.3 Photoaffinity Probes 74 3.4 ABPP and Mass Spectrometry for Chemoproteomics 75 3.4.1 Determining ABP Target Identity 75 3.4.2 Considerations for Analyzing ABP Targets with MS 77 3.4.3 Determining the Site of ABP Labeling 78 3.4.4 Quantification of ABPP Probe Targets 80 3.4.4.1 Label?Free Methods 80 3.4.4.2 Isotopic Methods 81 3.5 ABPP Applications and Recent Advances 83 3.5.1 Using ABPs for Functional Protein Annotation 83 3.5.2 ABPPs Applied to Microbes and Their Communities 84 3.6 ABPP Applied to Drug Discovery 88 3.7 Comparative, Competitive, and Convolution ABPP 90 3.8 Conclusions and The Outlook of ABPP 91 Acknowledgements 91 References 91 4 Activity?Based Probes for Profiling Protein Activities 101 Kasi V. Ruddraraju and Zhong?Yin Zhang 4.1 Introduction 101 4.2 Design of Activity?Based Probes 102 4.2.1 The Reactive Group 102 4.2.2 The Linker 104 4.2.3 The Tag 104 4.3 Analytical Platforms for ABPP 105 4.3.1 Gel?Based Platforms 105 4.3.2 Mass Spectrometry Platforms for ABPP 106 4.3.3 Microarray Platform for ABPP 107 4.3.4 Capillary Electrophoresis Platform for ABPP 107 4.4 Classes of Enzymes Studied by ABPP 108 4.4.1 Serine Hydrolases 108 4.4.2 Cysteine Proteases 109 4.4.3 Metallohydrolases 110 4.4.4 Glycosidases 111 4.4.5 Protein Kinases 114 4.4.6 Protein Phosphatases 116 4.5 Conclusions 119 Acknowledgment 120 References 120 5 Chemical Probes for Proteins and Networks 127 Scott Lovell, Charlotte L. Sutherell, and Edward W. Tate 5.1 Introduction 127 5.1.1 Probe Design and Validation 128 5.1.2 Application to a Proteomics Workflow 129 5.1.3 Quantitative Chemical Proteomics 131 5.2 Application of Metabolic Chemical Probes to Lipidated Protein Networks 132 5.2.1 Chemical Probes for N?Myristoylation 133 5.2.2 Chemical Probes for Hedgehog Proteins 136 5.3 Chemical Probes for Target Identification 137 5.3.1 Identifying New Target Profiles of Sulforaphane in Breast Cancer Cells 138 5.3.2 Target Profiling of Zerumbone Using a Novel Clickable Probe 140 5.4 Protocol 143 5.4.1 Introduction 143 5.4.2 Materials 143 5.4.2.1 Chemical Tools 143 5.4.2.2 Cell Culture 143 5.4.2.3 Cell Lysis, Enrichment and Sample Preparation 144 5.4.2.4 Click Chemistry and Enrichment 144 5.4.2.5 Proteomics Sample Preparation 144 5.4.2.6 Proteomics Analysis 144 5.4.3 Method 144 5.4.3.1 HeLa Cell Culture and Preparation of Spike?in Standard 144 5.4.3.2 Preparation of Cell Lysates for Protein Enrichment 145 5.4.3.3 Pull?Down Experiments and Sample Preparation 145 5.4.3.4 LC–MS/MS Analysis 147 5.4.3.5 Data Analysis 147 5.4.3.6 Identification of N?Terminal Myristoylated Peptides 151 5.5 Notes 152 References 153 6 Probing Biological Activities with Peptide and Peptidomimetic Biosensors 159 Laura J. Marholz, Tzu-Yi Yang, and Laurie L. Parker 6.1 Introduction 159 6.2 Peptide Biosensors for Assignment and Characterization of Enzymatic Reactions and Substrate Specificity 160 6.3 Screening Inhibitors and Detecting Ligand Interactions 165 6.4 Diagnostic and Clinical Applications 168 6.5 Profiling Enzymatic Activity 172 6.6 Protocol 178 Materials 179 Methods 180 6.7 Conclusion 182 References 182 7 Chemoselective Tagging to Promote Natural Product Discovery 187 Emily J. Tollefson and Erin E. Carlson 7.1 Introduction 187 7.2 Nonreversible Mass Spectrometry Tags 189 7.2.1 Azides and Alkynes 189 7.2.2 Thiols 192 7.2.3 Aminooxy 194 7.3 Reversible Enrichment Tags 195 7.3.1 Boronic Acids 195 7.3.2 Hydrazines 196 7.3.3 Silanes 196 7.3.4 Disulfides 197 7.4 Conclusions 198 7.5 Protocol for Enrichment of Carboxylic?Acid?Containing Natural Products 198 7.5.1 Dialkylsiloxane Resin Synthesis 198 7.5.2 Production of S. rochei Extract 200 7.5.3 Chemoselective Capture 200 7.5.4 Release of Carboxylic?Acid?Containing Compounds from Resin 201 References 201 8 Identification and Quantification of Newly Synthesized Proteins Using Mass?Spectrometry Based Chemical Proteomics 207 Suttipong Suttapitugsakul, Haopeng Xiao, and Ronghu Wu 8.1 Introduction 207 8.2 Protein Labeling to Study Newly Synthesized Proteins 209 8.2.1 Radioactive Labeling 209 8.2.2 Protein Labeling with Fluorescent Probes 209 8.2.3 SILAC Labeling 210 8.2.4 Protein Labeling with Noncanonical Amino Acids 210 8.3 Global Identification of Newly Synthesized Proteins by Noncanonical Amino Acids and MS 212 8.4 Comprehensive Quantification of Newly Synthesized Proteins by MS 213 8.5 Materials 217 8.5.1 Cell Culture and AHA Labeling 217 8.5.2 Cell Lysis 218 8.5.3 Enrichment of Newly Synthesized Proteins Using Click Chemistry 218 8.5.4 On?Bead Protein Reduction, Alkylation, and Digestion 218 8.5.5 Peptide Desalting 218 8.5.6 TMT Labeling 219 8.5.7 Peptide Fractionation 219 8.5.8 StageTips 219 8.5.9 LC–MS/MS Analysis 219 8.5.10 Database Searches and Data Filtering 220 8.6 Methods 220 8.6.1 Cell Culture with AHA Labeling 220 8.6.2 Cell Lysis and Protein Extraction 220 8.6.3 Enrichment of Newly Synthesized Proteins 220 8.6.4 On?Bead Reduction, Alkylation, and Digestion 221 8.6.5 Peptide Desalting 221 8.6.6 TMT Labeling 222 8.6.7 Peptide Fractionation 222 8.6.8 StageTip Purification 222 8.6.9 LC–MS/MS Analysis 223 8.6.10 Database Searches, Data Filtering, and Half?Life Calculation of Newly Synthesized Proteins 223 Acknowledgements 224 References 224 9 Tracing Endocytosis by Mass Spectrometry 231 Mayank Srivastava, Ying Zhang, Linna Wang, and W. Andy Tao 9.1 Introduction 231 9.2 Clathrin?Mediated Endocytosis 232 9.2.1 Proteins Involved in the Formation of Clathrin?Coated Vesicles 233 9.2.2 Molecular Mechanism for CCV Formation 234 9.2.3 Vesicle Uncoating and Fusion with Endosomal Compartments 237 9.3 Mass Spectrometry as a Tool to Study Endocytosis 237 9.3.1 Isolation of Clathrin?Coated Vesicles and Analysis Using Mass Spectrometry 238 9.3.2 Chemical Proteomic Approaches for Studying the Endocytosis 240 9.3.2.1 Identification of Receptor by Ligand?based–Receptor Capture (LRC) Technology 240 9.3.2.2 Studying the Entry and Trafficking of Nanoparticles Using Time?Resolved Chemical Proteomic Approach 241 9.4 Protocols for TITAN 243 9.4.1 Materials 243 9.4.2 Dendrimer Functionalization 245 9.4.2.1 Synthesis of Masked Aldehyde Handle 245 9.4.2.2 Functionalization of Dendrimer 245 9.4.3 Internalization of Dendrimer by HeLa and MS Sample Preparation 247 9.4.4 Mass Spectrometry and Data Analysis 249 9.5 Conclusion and Future Directions 250 References 251 10 Functional Identification of Target by Expression Proteomics (FITExP) 257 Massimiliano Gaetani and Roman A. Zubarev 10.1 Introduction 257 10.2 FITExP Protocol 261 10.2.1 Cell Line(s) and Drugs/Compounds Selection 261 10.2.2 Drug Treatments of Cell Cultures 261 10.2.3 Cell Lysis and Protein Extraction 262 10.2.4 Estimation of Protein Concentration and Protein Sample Processing 263 10.2.5 Protein Digestion 263 10.2.6 Peptide TMT (Tandem Mass Tag) Labeling and Desalting 263 10.2.7 High pH Fractionation TMT 264 10.2.8 Mass Spectrometry Analysis 264 10.2.9 Data Analysis 265 References 265 11 Target Discovery Using Thermal Proteome Profiling 267 Sindhuja Sridharan, Ina Günthner, Isabelle Becher, Mikhail Savitski, and Marcus Bantscheff 11.1 Introduction 267 11.2 Thermodynamics of Ligand Binding as a Measure of Target Engagement 270 11.3 Thermal Proteome Profiling – Proteome?wide Detection of Drug–Target Interactions 273 11.3.1 Overview 273 11.3.2 Distinguishing Direct Drug Targets from Downstream Effectors of Drug Action 273 11.4 Experimental Formats 275 11.4.1 Temperature?Range Experiment (TPP?TR) 275 11.4.2 Compound Concentration?Range Experiment (TPP?CCR) 277 11.4.3 Two?Dimensional TPP (2D?TPP) 278 11.5 Experimental Protocol 278 11.6 Reagents 280 11.6.1 Step 1: Compound Treatment 280 11.6.2 Step 2: Temperature Treatment 281 11.6.3 Step 3: Protein Digestion and Labeling 282 11.6.4 Step 4: Mass Spectrometric Analysis of Samples 283 11.6.5 Step 5: Peptide and Protein Identification and Quantification 283 11.6.6 Step 6: Data Handling and Analysis 284 11.7 Present Challenges with TPP 284 11.8 CETSA to TPP – Where are We Heading? 285 References 287 12 Chemical Strategies to Glycoprotein Analysis 293 Joseph L. Mertz, Christian Toonstra, and Hui Zhang 12.1 Introduction 293 12.2 Sample Preparation Strategies for Glycoproteomics 297 12.2.1 Enzymatic/Chemical Modification for Glycopeptide Enrichment 297 12.2.2 Enrichment of Glycans or Glycopeptides by Physical–Chemical Approaches 300 12.3 MS Analysis 302 12.3.1 Glycoproteomic Analysis by Mass Spectrometry 302 12.3.2 Bioinformatics and Data Analysis 304 12.4 Conclusions 306 References 307 13 Proteomic Analysis of Protein–Lipid Modifications: Significance and Application 317 Kiall F. Suazo, Garrett Schey, Chad Schaber, Audrey R. Odom John, and Mark D. Distefano 13.1 Introduction 317 13.2 Chemical Proteomic Approach to Identify Lipidated Proteins 318 13.2.1 Fatty Acylation 322 13.2.1.1 N?Myristoylation 323 13.2.1.2 S?Palmitoylation 325 13.2.2 Prenylation 328 13.2.3 Modification with Cholesterol and GPI Anchors 330 13.3 Protocol for Proteomic Analysis of Prenylated Proteins 331 13.3.1 Materials 332 13.3.1.1 Reagents 332 13.3.1.2 Equipment 333 13.3.1.3 Reagents and Instrument Setup 333 13.3.2 Procedure 334 13.3.2.1 Labeling with Probe 334 13.3.2.2 Isolating Parasites via Saponin Lysis 335 13.3.2.3 In?gel Fluorescence Analysis 335 13.3.2.4 Biotinylation and Streptavidin Pull?down 336 13.3.2.5 Sample Preparation for LC–MS/MS Analysis 337 13.3.2.6 LC–MS/MS Analysis 337 13.3.2.7 Proteomic Data Analysis Using Spectral Counting 338 13.3.3 Results 338 References 341 14 Site?Specific Characterization of Asp? and Glu?ADP?Ribosylation by Quantitative Mass Spectrometry 349 Shuai Wang, Yajie Zhang, and Yonghao Yu 14.1 Introduction 349 14.2 Materials 353 14.2.1 Cell Culture 353 14.2.2 Generation of Stable Cell Lines Expressing shPARG 353 14.2.3 Sample Preparation for Mass Spectrometry 353 14.2.4 Mass Spectrometry Analysis 354 14.2.5 Equipment 354 14.3 Methods 354 14.3.1 Generation of shPARG?Expressing Cell Line 354 14.3.2 SILAC Cell Culture 355 14.3.3 Cell Lysis 355 14.3.4 Reduction, Alkylation, and Precipitation of Proteins 355 14.3.5 Protein Digestion and Enrichment of the PARylated Peptides 356 14.3.6 Cleanup of the Peptide 357 14.3.7 Mass Spectrometry Analysis and Data Processing 357 14.4 Notes 357 Acknowledgements 358 References 358 15 MS?Based Hydroxyl Radical Footprinting: Methodology and Application of Fast Photochemical Oxidation of Proteins (FPOP) 363 Ben Niu and Michael L. Gross 15.1 Introduction 363 15.1.1 General Approaches for Mapping Protein Conformations 363 15.1.2 MS?Based Approaches 364 15.2 Generation of Hydroxyl Radicals 365 15.2.1 Fenton and Fenton?like Chemistry 365 15.2.2 Electron-Pulse Radiolysis 368 15.2.3 High?Voltage Electrical Discharge 370 15.2.4 Synchrotron X?ray Radiolysis of Water 371 15.2.5 Plasma Formation of OH Radicals 372 15.2.6 Photolysis of Hydrogen Peroxide 374 15.3 Fast Photochemical Oxidation of Proteins (FPOP) 375 15.3.1 FPOP Footprints Faster than Protein Folding/Unfolding 377 15.3.2 FPOP Dosimetry 378 15.3.3 Primary Radical Lifetime and Adjustment of Radical Scavengers 379 15.3.4 Radical Lifetimes Can Be Milliseconds 381 15.3.5 Differential Scavenging and Use of a Reporter Peptide in FPOP 381 15.3.6 New Reactive Reagents for the FPOP Platform 383 15.4 Applications of FPOP 384 15.4.1 FPOP for Protein–Protein Interactions and Epitope Mapping 384 15.4.2 FPOP for Protein Aggregation/Oligomerization 387 15.4.3 FPOP for Protein Dynamics 390 15.4.4 FPOP for Protein Folding 391 15.4.5 FPOP for Characterizing Membrane Proteins 394 15.5 Conclusions 395 References 396 Index 417
W. ANDY TAO, PHD, is a Professor in the Department of Biochemistry at Purdue University. He is also the Founder and Chief Scientific Officer at Tymora Analytical Operations, LLC, which provides lab R&D products for life sciences. Dr. Tao is the recipient of awards, such as the American Society of Mass Spectrometry Research Award, and author of more than 140 articles and book chapters on proteomics and mass spectrometry. YING ZHANG, PHD, is a Professor at Fudan University. Her research focuses on the development of mass spectrometry-based new approaches for the analysis of low abundant proteins and posttranslational proteins.
PROVIDES STRATEGIES AND CONCEPTS FOR UNDERSTANDING CHEMICAL PROTEOMICS, AND ANALYZING PROTEIN FUNCTIONS, MODIFICATIONS, AND INTERACTIONS—EMPHASIZING MASS SPECTROMETRY THROUGHOUT Covering mass spectrometry for chemical proteomics, this book helps readers understand analytical strategies behind protein functions, their modifications and interactions, and applications in drug discovery. It provides a basic overview and presents concepts in chemical proteomics through three angles: Strategies, Technical Advances, and Applications. Chapters cover those many technical advances and applications in drug discovery, from target identification to validation and potential treatments. The first section of Mass Spectrometry-Based Chemical Proteomics starts by reviewing basic methods and recent advances in mass spectrometry for proteomics, including shotgun proteomics, quantitative proteomics, and data analyses. The next section covers a variety of techniques and strategies coupling chemical probes to MS-based proteomics to provide functional insights into the proteome. In the last section, it focuses on using chemical strategies to study protein post-translational modifications and high-order structures. Summarizes chemical proteomics, up-to-date concepts, analysis, and target validation Covers fundamentals and strategies, including the profiling of enzyme activities and protein-drug interactions Explains technical advances in the field and describes on shotgun proteomics, quantitative proteomics, and corresponding methods of software and database usage for proteomics Includes a wide variety of applications in drug discovery, from kinase inhibitors and intracellular drug targets to the chemoproteomics analysis of natural products Addresses an important tool in small molecule drug discovery, appealing to both academia and the pharmaceutical industry Mass Spectrometry-Based Chemical Proteomics is an excellent source of information for readers in both academia and industry in a variety of fields, including pharmaceutical sciences, drug discovery, molecular biology, bioinformatics, and analytical sciences.

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