{"product_id":"mass-spectrometrybased-chemical-proteomics-9781118969557","title":"Mass SpectrometryBased Chemical Proteomics","description":"\u003cb\u003eBook Synopsis\u003c\/b\u003e\u003cbr\u003e\u003cp\u003e\u003cb\u003ePROVIDES STRATEGIES AND CONCEPTS FOR UNDERSTANDING CHEMICAL PROTEOMICS, AND ANALYZING PROTEIN FUNCTIONS, MODIFICATIONS, AND INTERACTIONSEMPHASIZING MASS SPECTROMETRY THROUGHOUT\u003c\/b\u003e\u003c\/p\u003e \u003cp\u003eCovering 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.\u003c\/p\u003e \u003cp\u003eThe first section of\u003ci\u003eMass Spectrometry-Based Chemical Proteomics\u003c\/i\u003estarts 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 strategie\u003cbr\u003e\u003cbr\u003e\u003cb\u003eTable of Contents\u003c\/b\u003e\u003cbr\u003e\u003c\/p\u003e\u003cp\u003ePreface xv\u003c\/p\u003e \u003cp\u003e\u003cb\u003e1 Protein Analysis by Shotgun Proteomics 1\u003cbr\u003e \u003c\/b\u003e\u003ci\u003eYu Gao and John R. Yates III\u003c\/i\u003e\u003c\/p\u003e \u003cp\u003e1.1 Introduction 1\u003c\/p\u003e \u003cp\u003e1.1.1 Terminology 1\u003c\/p\u003e \u003cp\u003e1.1.2 Power of Shotgun Proteomics 1\u003c\/p\u003e \u003cp\u003e1.1.3 Advantage of Shotgun Proteomics 2\u003c\/p\u003e \u003cp\u003e1.2 Overview of Shotgun Proteomics 2\u003c\/p\u003e \u003cp\u003e1.3 Sample Preparation 4\u003c\/p\u003e \u003cp\u003e1.3.1 Protein Separation 4\u003c\/p\u003e \u003cp\u003e1.3.1.1 Overview 4\u003c\/p\u003e \u003cp\u003e1.3.1.2 2D‐Gel Approach 4\u003c\/p\u003e \u003cp\u003e1.3.1.3 Separation of Membrane Protein 5\u003c\/p\u003e \u003cp\u003e1.3.1.4 Subcellular Fractionation 5\u003c\/p\u003e \u003cp\u003e1.3.1.5 Protein Enrichment 6\u003c\/p\u003e \u003cp\u003e1.3.1.6 Phosphoprotein 6\u003c\/p\u003e \u003cp\u003e1.3.1.7 Glycoprotein 6\u003c\/p\u003e \u003cp\u003e1.3.1.8 AP–MS and Interactome 7\u003c\/p\u003e \u003cp\u003e1.3.2 Protein Modification 8\u003c\/p\u003e \u003cp\u003e1.3.2.1 Overview 8\u003c\/p\u003e \u003cp\u003e1.3.2.2 Reduction of Disulfide Bond and Alkylation 8\u003c\/p\u003e \u003cp\u003e1.3.2.3 Chemical Crosslinking 8\u003c\/p\u003e \u003cp\u003e1.3.2.4 Proximity Labeling 9\u003c\/p\u003e \u003cp\u003e1.3.3 Protein Digestion 9\u003c\/p\u003e \u003cp\u003e1.4 Peptide Separation and Data Acquisition 11\u003c\/p\u003e \u003cp\u003e1.4.1 Peptide Separation 11\u003c\/p\u003e \u003cp\u003e1.4.1.1 Reversed Phase (RP) 11\u003c\/p\u003e \u003cp\u003e1.4.1.2 HILIC 11\u003c\/p\u003e \u003cp\u003e1.4.1.3 MudPIT 11\u003c\/p\u003e \u003cp\u003e1.4.1.4 Capillary Electrophoresis 13\u003c\/p\u003e \u003cp\u003e1.4.2 Peptide Ionization 13\u003c\/p\u003e \u003cp\u003e1.4.3 Mass Analyzer 13\u003c\/p\u003e \u003cp\u003e1.4.4 Peptide Fragmentation Method 15\u003c\/p\u003e \u003cp\u003e1.4.4.1 CID\/HCD 15\u003c\/p\u003e \u003cp\u003e1.4.4.2 ETD\/ECD 16\u003c\/p\u003e \u003cp\u003e1.4.4.3 IRMPD\/UVPD 16\u003c\/p\u003e \u003cp\u003e1.4.5 Acquisition Mode 17\u003c\/p\u003e \u003cp\u003e1.5 Informatics 17\u003c\/p\u003e \u003cp\u003e1.5.1 Peptide Identification 18\u003c\/p\u003e \u003cp\u003e1.5.1.1 Database Search 18\u003c\/p\u003e \u003cp\u003e1.5.1.2 Spectral Library Search 21\u003c\/p\u003e \u003cp\u003e1.5.1.3\u003ci\u003e De novo \u003c\/i\u003eSequencing 22\u003c\/p\u003e \u003cp\u003e1.5.1.4 Peptide‐Centric Analysis 23\u003c\/p\u003e \u003cp\u003e1.5.2 Peptide\/Protein Quantitation 23\u003c\/p\u003e \u003cp\u003e1.5.2.1 Labeled Quantitation 23\u003c\/p\u003e \u003cp\u003e1.5.2.2 Label‐Free Quantitation 27\u003c\/p\u003e \u003cp\u003e1.5.3 Protein Inference 29\u003c\/p\u003e \u003cp\u003eReferences 31\u003c\/p\u003e \u003cp\u003e\u003cb\u003e2 Quantitative Proteomics for Analyses of Multiple Samples in Parallel with Chemical Perturbation 39\u003cbr\u003e \u003c\/b\u003e\u003ci\u003eAmanda Rae Buchberger, Jillian Johnson, and Lingjun Li\u003c\/i\u003e\u003c\/p\u003e \u003cp\u003e2.1 Introduction 39\u003c\/p\u003e \u003cp\u003e2.2 Relative and Absolute Label‐Free Quantitation Strategies 40\u003c\/p\u003e \u003cp\u003e2.3 Stable Isotope‐Based Quantitative Proteomics 42\u003c\/p\u003e \u003cp\u003e2.3.1 Relative Quantitation 42\u003c\/p\u003e \u003cp\u003e2.3.2 Absolute Quantitation 47\u003c\/p\u003e \u003cp\u003e2.4 Conclusion 48\u003c\/p\u003e \u003cp\u003e2.5 Methodology 50\u003c\/p\u003e \u003cp\u003e2.6 Notes 52\u003c\/p\u003e \u003cp\u003eAcknowledgments 55\u003c\/p\u003e \u003cp\u003eReferences 56\u003c\/p\u003e \u003cp\u003e\u003cb\u003e3 Chemoproteomic Analyses by Activity‐Based Protein Profiling 67\u003cbr\u003e \u003c\/b\u003e\u003ci\u003eBryan J. Killinger, Kristoffer R. Brandvold, Susan J. Ramos‐Hunter, and Aaron T. Wright\u003c\/i\u003e\u003c\/p\u003e \u003cp\u003e3.1 Introduction 67\u003c\/p\u003e \u003cp\u003e3.2 How ABPP Works 68\u003c\/p\u003e \u003cp\u003e3.3 ABPP Probe Design 71\u003c\/p\u003e \u003cp\u003e3.3.1 Mechanism‐Based Probes 72\u003c\/p\u003e \u003cp\u003e3.3.2 Reactivity‐Based Probes 74\u003c\/p\u003e \u003cp\u003e3.3.3 Photoaffinity Probes 74\u003c\/p\u003e \u003cp\u003e3.4 ABPP and Mass Spectrometry for Chemoproteomics 75\u003c\/p\u003e \u003cp\u003e3.4.1 Determining ABP Target Identity 75\u003c\/p\u003e \u003cp\u003e3.4.2 Considerations for Analyzing ABP Targets with MS 77\u003c\/p\u003e \u003cp\u003e3.4.3 Determining the Site of ABP Labeling 78\u003c\/p\u003e \u003cp\u003e3.4.4 Quantification of ABPP Probe Targets 80\u003c\/p\u003e \u003cp\u003e3.4.4.1 Label‐Free Methods 80\u003c\/p\u003e \u003cp\u003e3.4.4.2 Isotopic Methods 81\u003c\/p\u003e \u003cp\u003e3.5 ABPP Applications and Recent Advances 83\u003c\/p\u003e \u003cp\u003e3.5.1 Using ABPs for Functional Protein Annotation 83\u003c\/p\u003e \u003cp\u003e3.5.2 ABPPs Applied to Microbes and Their Communities 84\u003c\/p\u003e \u003cp\u003e3.6 ABPP Applied to Drug Discovery 88\u003c\/p\u003e \u003cp\u003e3.7 Comparative, Competitive, and Convolution ABPP 90\u003c\/p\u003e \u003cp\u003e3.8 Conclusions and The Outlook of ABPP 91\u003c\/p\u003e \u003cp\u003eAcknowledgements 91\u003c\/p\u003e \u003cp\u003eReferences 91\u003c\/p\u003e \u003cp\u003e\u003cb\u003e4 Activity‐Based Probes for Profiling Protein Activities 101\u003cbr\u003e \u003c\/b\u003e\u003ci\u003eKasi V. Ruddraraju and Zhong‐Yin Zhang\u003c\/i\u003e\u003c\/p\u003e \u003cp\u003e4.1 Introduction 101\u003c\/p\u003e \u003cp\u003e4.2 Design of Activity‐Based Probes 102\u003c\/p\u003e \u003cp\u003e4.2.1 The Reactive Group 102\u003c\/p\u003e \u003cp\u003e4.2.2 The Linker 104\u003c\/p\u003e \u003cp\u003e4.2.3 The Tag 104\u003c\/p\u003e \u003cp\u003e4.3 Analytical Platforms for ABPP 105\u003c\/p\u003e \u003cp\u003e4.3.1 Gel‐Based Platforms 105\u003c\/p\u003e \u003cp\u003e4.3.2 Mass Spectrometry Platforms for ABPP 106\u003c\/p\u003e \u003cp\u003e4.3.3 Microarray Platform for ABPP 107\u003c\/p\u003e \u003cp\u003e4.3.4 Capillary Electrophoresis Platform for ABPP 107\u003c\/p\u003e \u003cp\u003e4.4 Classes of Enzymes Studied by ABPP 108\u003c\/p\u003e \u003cp\u003e4.4.1 Serine Hydrolases 108\u003c\/p\u003e \u003cp\u003e4.4.2 Cysteine Proteases 109\u003c\/p\u003e \u003cp\u003e4.4.3 Metallohydrolases 110\u003c\/p\u003e \u003cp\u003e4.4.4 Glycosidases 111\u003c\/p\u003e \u003cp\u003e4.4.5 Protein Kinases 114\u003c\/p\u003e \u003cp\u003e4.4.6 Protein Phosphatases 116\u003c\/p\u003e \u003cp\u003e4.5 Conclusions 119\u003c\/p\u003e \u003cp\u003eAcknowledgment 120\u003c\/p\u003e \u003cp\u003eReferences 120\u003c\/p\u003e \u003cp\u003e\u003cb\u003e5 Chemical Probes for Proteins and Networks 127\u003cbr\u003e \u003c\/b\u003e\u003ci\u003eScott Lovell, Charlotte L. Sutherell, and Edward W. Tate\u003c\/i\u003e\u003c\/p\u003e \u003cp\u003e5.1 Introduction 127\u003c\/p\u003e \u003cp\u003e5.1.1 Probe Design and Validation 128\u003c\/p\u003e \u003cp\u003e5.1.2 Application to a Proteomics Workflow 129\u003c\/p\u003e \u003cp\u003e5.1.3 Quantitative Chemical Proteomics 131\u003c\/p\u003e \u003cp\u003e5.2 Application of Metabolic Chemical Probes to Lipidated Protein Networks 132\u003c\/p\u003e \u003cp\u003e5.2.1 Chemical Probes for \u003ci\u003eN\u003c\/i\u003e‐Myristoylation 133\u003c\/p\u003e \u003cp\u003e5.2.2 Chemical Probes for Hedgehog Proteins 136\u003c\/p\u003e \u003cp\u003e5.3 Chemical Probes for Target Identification 137\u003c\/p\u003e \u003cp\u003e5.3.1 Identifying New Target Profiles of Sulforaphane in Breast Cancer Cells 138\u003c\/p\u003e \u003cp\u003e5.3.2 Target Profiling of Zerumbone Using a Novel Clickable Probe 140\u003c\/p\u003e \u003cp\u003e5.4 Protocol 143\u003c\/p\u003e \u003cp\u003e5.4.1 Introduction 143\u003c\/p\u003e \u003cp\u003e5.4.2 Materials 143\u003c\/p\u003e \u003cp\u003e5.4.2.1 Chemical Tools 143\u003c\/p\u003e \u003cp\u003e5.4.2.2 Cell Culture 143\u003c\/p\u003e \u003cp\u003e5.4.2.3 Cell Lysis, Enrichment and Sample Preparation 144\u003c\/p\u003e \u003cp\u003e5.4.2.4 Click Chemistry and Enrichment 144\u003c\/p\u003e \u003cp\u003e5.4.2.5 Proteomics Sample Preparation 144\u003c\/p\u003e \u003cp\u003e5.4.2.6 Proteomics Analysis 144\u003c\/p\u003e \u003cp\u003e5.4.3 Method 144\u003c\/p\u003e \u003cp\u003e5.4.3.1 HeLa Cell Culture and Preparation of Spike‐in Standard 144\u003c\/p\u003e \u003cp\u003e5.4.3.2 Preparation of Cell Lysates for Protein Enrichment 145\u003c\/p\u003e \u003cp\u003e5.4.3.3 Pull‐Down Experiments and Sample Preparation 145\u003c\/p\u003e \u003cp\u003e5.4.3.4 LC–MS\/MS Analysis 147\u003c\/p\u003e \u003cp\u003e5.4.3.5 Data Analysis 147\u003c\/p\u003e \u003cp\u003e5.4.3.6 Identification of N‐Terminal Myristoylated Peptides 151\u003c\/p\u003e \u003cp\u003e5.5 Notes 152\u003c\/p\u003e \u003cp\u003eReferences 153\u003c\/p\u003e \u003cp\u003e\u003cb\u003e6 Probing Biological Activities with Peptide and Peptidomimetic Biosensors 159\u003cbr\u003e \u003c\/b\u003e\u003ci\u003eLaura J. Marholz, Tzu-Yi Yang, and Laurie L. Parker\u003c\/i\u003e\u003c\/p\u003e \u003cp\u003e6.1 Introduction 159\u003c\/p\u003e \u003cp\u003e6.2 Peptide Biosensors for Assignment and Characterization of Enzymatic Reactions and Substrate Specificity 160\u003c\/p\u003e \u003cp\u003e6.3 Screening Inhibitors and Detecting Ligand Interactions 165\u003c\/p\u003e \u003cp\u003e6.4 Diagnostic and Clinical Applications 168\u003c\/p\u003e \u003cp\u003e6.5 Profiling Enzymatic Activity 172\u003c\/p\u003e \u003cp\u003e6.6 Protocol 178\u003c\/p\u003e \u003cp\u003eMaterials 179\u003c\/p\u003e \u003cp\u003eMethods 180\u003c\/p\u003e \u003cp\u003e6.7 Conclusion 182\u003c\/p\u003e \u003cp\u003eReferences 182\u003c\/p\u003e \u003cp\u003e\u003cb\u003e7 Chemoselective Tagging to Promote Natural Product Discovery 187\u003cbr\u003e \u003c\/b\u003e\u003ci\u003eEmily J. Tollefson and Erin E. Carlson\u003c\/i\u003e\u003c\/p\u003e \u003cp\u003e7.1 Introduction 187\u003c\/p\u003e \u003cp\u003e7.2 Nonreversible Mass Spectrometry Tags 189\u003c\/p\u003e \u003cp\u003e7.2.1 Azides and Alkynes 189\u003c\/p\u003e \u003cp\u003e7.2.2 Thiols 192\u003c\/p\u003e \u003cp\u003e7.2.3 Aminooxy 194\u003c\/p\u003e \u003cp\u003e7.3 Reversible Enrichment Tags 195\u003c\/p\u003e \u003cp\u003e7.3.1 Boronic Acids 195\u003c\/p\u003e \u003cp\u003e7.3.2 Hydrazines 196\u003c\/p\u003e \u003cp\u003e7.3.3 Silanes 196\u003c\/p\u003e \u003cp\u003e7.3.4 Disulfides 197\u003c\/p\u003e \u003cp\u003e7.4 Conclusions 198\u003c\/p\u003e \u003cp\u003e7.5 Protocol for Enrichment of Carboxylic‐Acid‐Containing Natural Products 198\u003c\/p\u003e \u003cp\u003e7.5.1 Dialkylsiloxane Resin Synthesis 198\u003c\/p\u003e \u003cp\u003e7.5.2 Production of\u003ci\u003e S. rochei\u003c\/i\u003e Extract 200\u003c\/p\u003e \u003cp\u003e7.5.3 Chemoselective Capture 200\u003c\/p\u003e \u003cp\u003e7.5.4 Release of Carboxylic‐Acid‐Containing Compounds from Resin 201\u003c\/p\u003e \u003cp\u003eReferences 201\u003c\/p\u003e \u003cp\u003e\u003cb\u003e8 Identification and Quantification of Newly Synthesized Proteins Using Mass‐Spectrometry Based\u003c\/b\u003e \u003cb\u003eChemical Proteomics 207\u003cbr\u003e \u003c\/b\u003e\u003ci\u003eSuttipong Suttapitugsakul, Haopeng Xiao, and Ronghu Wu\u003c\/i\u003e\u003c\/p\u003e \u003cp\u003e8.1 Introduction 207\u003c\/p\u003e \u003cp\u003e8.2 Protein Labeling to Study Newly Synthesized Proteins 209\u003c\/p\u003e \u003cp\u003e8.2.1 Radioactive Labeling 209\u003c\/p\u003e \u003cp\u003e8.2.2 Protein Labeling with Fluorescent Probes 209\u003c\/p\u003e \u003cp\u003e8.2.3 SILAC Labeling 210\u003c\/p\u003e \u003cp\u003e8.2.4 Protein Labeling with Noncanonical Amino Acids 210\u003c\/p\u003e \u003cp\u003e8.3 Global Identification of Newly Synthesized Proteins by Noncanonical Amino Acids and MS 212\u003c\/p\u003e \u003cp\u003e8.4 Comprehensive Quantification of Newly Synthesized Proteins by MS 213\u003c\/p\u003e \u003cp\u003e8.5 Materials 217\u003c\/p\u003e \u003cp\u003e8.5.1 Cell Culture and AHA Labeling 217\u003c\/p\u003e \u003cp\u003e8.5.2 Cell Lysis 218\u003c\/p\u003e \u003cp\u003e8.5.3 Enrichment of Newly Synthesized Proteins Using Click Chemistry 218\u003c\/p\u003e \u003cp\u003e8.5.4 On‐Bead Protein Reduction, Alkylation, and Digestion 218\u003c\/p\u003e \u003cp\u003e8.5.5 Peptide Desalting 218\u003c\/p\u003e \u003cp\u003e8.5.6 TMT Labeling 219\u003c\/p\u003e \u003cp\u003e8.5.7 Peptide Fractionation 219\u003c\/p\u003e \u003cp\u003e8.5.8 StageTips 219\u003c\/p\u003e \u003cp\u003e8.5.9 LC–MS\/MS Analysis 219\u003c\/p\u003e \u003cp\u003e8.5.10 Database Searches and Data Filtering 220\u003c\/p\u003e \u003cp\u003e8.6 Methods 220\u003c\/p\u003e \u003cp\u003e8.6.1 Cell Culture with AHA Labeling 220\u003c\/p\u003e \u003cp\u003e8.6.2 Cell Lysis and Protein Extraction 220\u003c\/p\u003e \u003cp\u003e8.6.3 Enrichment of Newly Synthesized Proteins 220\u003c\/p\u003e \u003cp\u003e8.6.4 On‐Bead Reduction, Alkylation, and Digestion 221\u003c\/p\u003e \u003cp\u003e8.6.5 Peptide Desalting 221\u003c\/p\u003e \u003cp\u003e8.6.6 TMT Labeling 222\u003c\/p\u003e \u003cp\u003e8.6.7 Peptide Fractionation 222\u003c\/p\u003e \u003cp\u003e8.6.8 StageTip Purification 222\u003c\/p\u003e \u003cp\u003e8.6.9 LC–MS\/MS Analysis 223\u003c\/p\u003e \u003cp\u003e8.6.10 Database Searches, Data Filtering, and Half‐Life Calculation of Newly Synthesized Proteins 223\u003c\/p\u003e \u003cp\u003eAcknowledgements 224\u003c\/p\u003e \u003cp\u003eReferences 224\u003c\/p\u003e \u003cp\u003e\u003cb\u003e9 Tracing Endocytosis by Mass Spectrometry 231\u003cbr\u003e \u003c\/b\u003e\u003ci\u003eMayank Srivastava, Ying Zhang, Linna Wang, and W. Andy Tao\u003c\/i\u003e\u003c\/p\u003e \u003cp\u003e9.1 Introduction 231\u003c\/p\u003e \u003cp\u003e9.2 Clathrin‐Mediated Endocytosis 232\u003c\/p\u003e \u003cp\u003e9.2.1 Proteins Involved in the Formation of Clathrin‐Coated Vesicles 233\u003c\/p\u003e \u003cp\u003e9.2.2 Molecular Mechanism for CCV Formation 234\u003c\/p\u003e \u003cp\u003e9.2.3 Vesicle Uncoating and Fusion with Endosomal Compartments 237\u003c\/p\u003e \u003cp\u003e9.3 Mass Spectrometry as a Tool to Study Endocytosis 237\u003c\/p\u003e \u003cp\u003e9.3.1 Isolation of Clathrin‐Coated Vesicles and Analysis Using Mass Spectrometry 238\u003c\/p\u003e \u003cp\u003e9.3.2 Chemical Proteomic Approaches for Studying the Endocytosis 240\u003c\/p\u003e \u003cp\u003e9.3.2.1 Identification of Receptor by Ligand‐based–Receptor Capture (LRC) Technology 240\u003c\/p\u003e \u003cp\u003e9.3.2.2 Studying the Entry and Trafficking of Nanoparticles Using Time‐Resolved Chemical Proteomic Approach 241\u003c\/p\u003e \u003cp\u003e9.4 Protocols for TITAN 243\u003c\/p\u003e \u003cp\u003e9.4.1 Materials 243\u003c\/p\u003e \u003cp\u003e9.4.2 Dendrimer Functionalization 245\u003c\/p\u003e \u003cp\u003e9.4.2.1 Synthesis of Masked Aldehyde Handle 245\u003c\/p\u003e \u003cp\u003e9.4.2.2 Functionalization of Dendrimer 245\u003c\/p\u003e \u003cp\u003e9.4.3 Internalization of Dendrimer by HeLa and MS Sample Preparation 247\u003c\/p\u003e \u003cp\u003e9.4.4 Mass Spectrometry and Data Analysis 249\u003c\/p\u003e \u003cp\u003e9.5 Conclusion and Future Directions 250\u003c\/p\u003e \u003cp\u003eReferences 251\u003c\/p\u003e \u003cp\u003e\u003cb\u003e10 Functional Identification of Target by Expression Proteomics (FITExP) 257\u003cbr\u003e \u003c\/b\u003e\u003ci\u003eMassimiliano Gaetani and Roman A. Zubarev\u003c\/i\u003e\u003c\/p\u003e \u003cp\u003e10.1 Introduction 257\u003c\/p\u003e \u003cp\u003e10.2 FITExP Protocol 261\u003c\/p\u003e \u003cp\u003e10.2.1 Cell Line(s) and Drugs\/Compounds Selection 261\u003c\/p\u003e \u003cp\u003e10.2.2 Drug Treatments of Cell Cultures 261\u003c\/p\u003e \u003cp\u003e10.2.3 Cell Lysis and Protein Extraction 262\u003c\/p\u003e \u003cp\u003e10.2.4 Estimation of Protein Concentration and Protein Sample Processing 263\u003c\/p\u003e \u003cp\u003e10.2.5 Protein Digestion 263\u003c\/p\u003e \u003cp\u003e10.2.6 Peptide TMT (Tandem Mass Tag) Labeling and Desalting 263\u003c\/p\u003e \u003cp\u003e10.2.7 High pH Fractionation TMT 264\u003c\/p\u003e \u003cp\u003e10.2.8 Mass Spectrometry Analysis 264\u003c\/p\u003e \u003cp\u003e10.2.9 Data Analysis 265\u003c\/p\u003e \u003cp\u003eReferences 265\u003c\/p\u003e \u003cp\u003e\u003cb\u003e11 Target Discovery Using Thermal Proteome Profiling 267\u003cbr\u003e \u003c\/b\u003e\u003ci\u003eSindhuja Sridharan, Ina Günthner, Isabelle Becher, Mikhail Savitski, and Marcus Bantscheff\u003c\/i\u003e\u003c\/p\u003e \u003cp\u003e11.1 Introduction 267\u003c\/p\u003e \u003cp\u003e11.2 Thermodynamics of Ligand Binding as a Measure of Target Engagement 270\u003c\/p\u003e \u003cp\u003e11.3 Thermal Proteome Profiling – Proteome‐wide Detection of Drug–Target Interactions 273\u003c\/p\u003e \u003cp\u003e11.3.1 Overview 273\u003c\/p\u003e \u003cp\u003e11.3.2 Distinguishing Direct Drug Targets from Downstream Effectors of Drug Action 273\u003c\/p\u003e \u003cp\u003e11.4 Experimental Formats 275\u003c\/p\u003e \u003cp\u003e11.4.1 Temperature‐Range Experiment (TPP‐TR) 275\u003c\/p\u003e \u003cp\u003e11.4.2 Compound Concentration‐Range Experiment (TPP‐CCR) 277\u003c\/p\u003e \u003cp\u003e11.4.3 Two‐Dimensional TPP (2D‐TPP) 278\u003c\/p\u003e \u003cp\u003e11.5 Experimental Protocol 278\u003c\/p\u003e \u003cp\u003e11.6 Reagents 280\u003c\/p\u003e \u003cp\u003e11.6.1 Step 1: Compound Treatment 280\u003c\/p\u003e \u003cp\u003e11.6.2 Step 2: Temperature Treatment 281\u003c\/p\u003e \u003cp\u003e11.6.3 Step 3: Protein Digestion and Labeling 282\u003c\/p\u003e \u003cp\u003e11.6.4 Step 4: Mass Spectrometric Analysis of Samples 283\u003c\/p\u003e \u003cp\u003e11.6.5 Step 5: Peptide and Protein Identification and Quantification 283\u003c\/p\u003e \u003cp\u003e11.6.6 Step 6: Data Handling and Analysis 284\u003c\/p\u003e \u003cp\u003e11.7 Present Challenges with TPP 284\u003c\/p\u003e \u003cp\u003e11.8 CETSA to TPP – Where are We Heading? 285\u003c\/p\u003e \u003cp\u003eReferences 287\u003c\/p\u003e \u003cp\u003e\u003cb\u003e12 Chemical Strategies to Glycoprotein Analysis 293\u003cbr\u003e \u003c\/b\u003e\u003ci\u003eJoseph L. Mertz, Christian Toonstra, and Hui Zhang\u003c\/i\u003e\u003c\/p\u003e \u003cp\u003e12.1 Introduction 293\u003c\/p\u003e \u003cp\u003e12.2 Sample Preparation Strategies for Glycoproteomics 297\u003c\/p\u003e \u003cp\u003e12.2.1 Enzymatic\/Chemical Modification for Glycopeptide Enrichment 297\u003c\/p\u003e \u003cp\u003e12.2.2 Enrichment of Glycans or Glycopeptides by Physical–Chemical Approaches 300\u003c\/p\u003e \u003cp\u003e12.3 MS Analysis 302\u003c\/p\u003e \u003cp\u003e12.3.1 Glycoproteomic Analysis by Mass Spectrometry 302\u003c\/p\u003e \u003cp\u003e12.3.2 Bioinformatics and Data Analysis 304\u003c\/p\u003e \u003cp\u003e12.4 Conclusions 306\u003c\/p\u003e \u003cp\u003eReferences 307\u003c\/p\u003e \u003cp\u003e\u003cb\u003e13 Proteomic Analysis of Protein–Lipid Modifications: Significance and Application 317\u003cbr\u003e \u003c\/b\u003e\u003ci\u003eKiall F. Suazo, Garrett Schey, Chad Schaber, Audrey R. Odom John, and Mark D. Distefano\u003c\/i\u003e\u003c\/p\u003e \u003cp\u003e13.1 Introduction 317\u003c\/p\u003e \u003cp\u003e13.2 Chemical Proteomic Approach to Identify Lipidated Proteins 318\u003c\/p\u003e \u003cp\u003e13.2.1 Fatty Acylation 322\u003c\/p\u003e \u003cp\u003e13.2.1.1 N‐Myristoylation 323\u003c\/p\u003e \u003cp\u003e13.2.1.2 S‐Palmitoylation 325\u003c\/p\u003e \u003cp\u003e13.2.2 Prenylation 328\u003c\/p\u003e \u003cp\u003e13.2.3 Modification with Cholesterol and GPI Anchors 330\u003c\/p\u003e \u003cp\u003e13.3 Protocol for Proteomic Analysis of Prenylated Proteins 331\u003c\/p\u003e \u003cp\u003e13.3.1 Materials 332\u003c\/p\u003e \u003cp\u003e13.3.1.1 Reagents 332\u003c\/p\u003e \u003cp\u003e13.3.1.2 Equipment 333\u003c\/p\u003e \u003cp\u003e13.3.1.3 Reagents and Instrument Setup 333\u003c\/p\u003e \u003cp\u003e13.3.2 Procedure 334\u003c\/p\u003e \u003cp\u003e13.3.2.1 Labeling with Probe 334\u003c\/p\u003e \u003cp\u003e13.3.2.2 Isolating Parasites via Saponin Lysis 335\u003c\/p\u003e \u003cp\u003e13.3.2.3 In‐gel Fluorescence Analysis 335\u003c\/p\u003e \u003cp\u003e13.3.2.4 Biotinylation and Streptavidin Pull‐down 336\u003c\/p\u003e \u003cp\u003e13.3.2.5 Sample Preparation for LC–MS\/MS Analysis 337\u003c\/p\u003e \u003cp\u003e13.3.2.6 LC–MS\/MS Analysis 337\u003c\/p\u003e \u003cp\u003e13.3.2.7 Proteomic Data Analysis Using Spectral Counting 338\u003c\/p\u003e \u003cp\u003e13.3.3 Results 338\u003c\/p\u003e \u003cp\u003eReferences 341\u003c\/p\u003e \u003cp\u003e\u003cb\u003e14 Site‐Specific Characterization of Asp‐ and Glu‐ADP‐Ribosylation by Quantitative Mass Spectrometry 349\u003cbr\u003e \u003c\/b\u003e\u003ci\u003eShuai Wang, Yajie Zhang, and Yonghao Yu\u003c\/i\u003e\u003c\/p\u003e \u003cp\u003e14.1 Introduction 349\u003c\/p\u003e \u003cp\u003e14.2 Materials 353\u003c\/p\u003e \u003cp\u003e14.2.1 Cell Culture 353\u003c\/p\u003e \u003cp\u003e14.2.2 Generation of Stable Cell Lines Expressing shPARG 353\u003c\/p\u003e \u003cp\u003e14.2.3 Sample Preparation for Mass Spectrometry 353\u003c\/p\u003e \u003cp\u003e14.2.4 Mass Spectrometry Analysis 354\u003c\/p\u003e \u003cp\u003e14.2.5 Equipment 354\u003c\/p\u003e \u003cp\u003e14.3 Methods 354\u003c\/p\u003e \u003cp\u003e14.3.1 Generation of shPARG‐Expressing Cell Line 354\u003c\/p\u003e \u003cp\u003e14.3.2 SILAC Cell Culture 355\u003c\/p\u003e \u003cp\u003e14.3.3 Cell Lysis 355\u003c\/p\u003e \u003cp\u003e14.3.4 Reduction, Alkylation, and Precipitation of Proteins 355\u003c\/p\u003e \u003cp\u003e14.3.5 Protein Digestion and Enrichment of the PARylated Peptides 356\u003c\/p\u003e \u003cp\u003e14.3.6 Cleanup of the Peptide 357\u003c\/p\u003e \u003cp\u003e14.3.7 Mass Spectrometry Analysis and Data Processing 357\u003c\/p\u003e \u003cp\u003e14.4 Notes 357\u003c\/p\u003e \u003cp\u003eAcknowledgements 358\u003c\/p\u003e \u003cp\u003eReferences 358\u003c\/p\u003e \u003cp\u003e\u003cb\u003e15 MS‐Based Hydroxyl Radical Footprinting: Methodology and Application of Fast Photochemical Oxidation of Proteins (FPOP) 363\u003cbr\u003e \u003c\/b\u003e\u003ci\u003eBen Niu and Michael L. Gross\u003c\/i\u003e\u003c\/p\u003e \u003cp\u003e15.1 Introduction 363\u003c\/p\u003e \u003cp\u003e15.1.1 General Approaches for Mapping Protein Conformations 363\u003c\/p\u003e \u003cp\u003e15.1.2 MS‐Based Approaches 364\u003c\/p\u003e \u003cp\u003e15.2 Generation of Hydroxyl Radicals 365\u003c\/p\u003e \u003cp\u003e15.2.1 Fenton and Fenton‐like Chemistry 365\u003c\/p\u003e \u003cp\u003e15.2.2 Electron-Pulse Radiolysis 368\u003c\/p\u003e \u003cp\u003e15.2.3 High‐Voltage Electrical Discharge 370\u003c\/p\u003e \u003cp\u003e15.2.4 Synchrotron X‐ray Radiolysis of Water 371\u003c\/p\u003e \u003cp\u003e15.2.5 Plasma Formation of OH Radicals 372\u003c\/p\u003e \u003cp\u003e15.2.6 Photolysis of Hydrogen Peroxide 374\u003c\/p\u003e \u003cp\u003e15.3 Fast Photochemical Oxidation of Proteins (FPOP) 375\u003c\/p\u003e \u003cp\u003e15.3.1 FPOP Footprints Faster than Protein Folding\/Unfolding 377\u003c\/p\u003e \u003cp\u003e15.3.2 FPOP Dosimetry 378\u003c\/p\u003e \u003cp\u003e15.3.3 Primary Radical Lifetime and Adjustment of Radical Scavengers 379\u003c\/p\u003e \u003cp\u003e15.3.4 Radical Lifetimes Can Be Milliseconds 381\u003c\/p\u003e \u003cp\u003e15.3.5 Differential Scavenging and Use of a Reporter Peptide in FPOP 381\u003c\/p\u003e \u003cp\u003e15.3.6 New Reactive Reagents for the FPOP Platform 383\u003c\/p\u003e \u003cp\u003e15.4 Applications of FPOP 384\u003c\/p\u003e \u003cp\u003e15.4.1 FPOP for Protein–Protein Interactions and Epitope Mapping 384\u003c\/p\u003e \u003cp\u003e15.4.2 FPOP for Protein Aggregation\/Oligomerization 387\u003c\/p\u003e \u003cp\u003e15.4.3 FPOP for Protein Dynamics 390\u003c\/p\u003e \u003cp\u003e15.4.4 FPOP for Protein Folding 391\u003c\/p\u003e \u003cp\u003e15.4.5 FPOP for Characterizing Membrane Proteins 394\u003c\/p\u003e \u003cp\u003e15.5 Conclusions 395\u003c\/p\u003e \u003cp\u003eReferences 396\u003c\/p\u003e \u003cp\u003eIndex 417\u003c\/p\u003e","brand":"John Wiley \u0026 Sons Inc","offers":[{"title":"Default Title","offer_id":49406958502231,"sku":"9781118969557","price":131.35,"currency_code":"GBP","in_stock":true}],"thumbnail_url":"\/\/cdn.shopify.com\/s\/files\/1\/0817\/1739\/5799\/files\/9781118969557.jpg?v=1730497692","url":"https:\/\/bookcurl.com\/products\/mass-spectrometrybased-chemical-proteomics-9781118969557","provider":"Book Curl","version":"1.0","type":"link"}