Advances in Chemical Proteomics

Advances in Chemical Proteomics

1st Edition - October 22, 2021

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  • Editor: Xudong Yao
  • Paperback ISBN: 9780128214336
  • eBook ISBN: 9780128214350

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Advances in Chemical Proteomics provides essential concepts and recent applications on probes, tool compounds and concepts for chemical proteomics and then moves on to applications, including solid-phase reagents, fragment screening, designer compounds and protein lipidation. As the second volume in the Developments in Organic Chemistry series, each chapter is written by experts in the field. Users will find this to be a valuable reference for organic chemists and chemical biologists who are interested in developing tool compounds and reagents to measure and interrogate proteome, develop drug leads, and measure off-target effects and drug toxicity. Analytical chemists who are interested in better understanding organic chemistry behind commonly used reagents for quantitative proteomics and tools compounds in the emerging field of chemical proteomics will also benefit from this comprehensive resource on the topics presented.

Key Features

  • Provides an ideal, introductory book to chemical proteomics for organic chemists, pharmaceutical chemists and chemical biologists
  • Includes advanced, recent applications and reviews in chemical proteomics
  • Presents valuable work by a global team of experts from the field of proteomics


Organic chemists and chemical biologists who are interested in developing tool compounds and reagents to measure the proteome, develop drug leads, measure drug toxicity. Pharmaceutical scientists

Table of Contents

  • Cover image
  • Title page
  • Table of Contents
  • Copyright
  • Contributors
  • Biography
  • Part 1. Concepts and principles
  • Chapter 1. Introduction to proteomics for chemical biology
  • 1.1. Multi-omics as a promising path to precision healthcare
  • 1.2. The bottom-up proteomics workflow
  • 1.3. Tools and strategies in chemical proteomics
  • 1.4. Challenges and opportunities in chemical proteomics
  • 1.5. Conclusion
  • Chapter 2. Warheads for designing covalent inhibitors and chemical probes
  • 2.1. Definitions
  • 2.2. Foundational knowledge
  • 2.3. Recent developments
  • 2.4. Points of view/opinions
  • 2.5. Summary and outlook
  • Chapter 3. Chemical derivatization of peptides for quantitative proteomics
  • 3.1. Introduction
  • 3.2. Quantitative proteomics concepts
  • 3.3. Labeling techniques for MS1-based quantification
  • 3.4. Labeling techniques for MS2- and MS3-based quantification
  • 3.5. Achieving higher-order multiplexing by combining labeling strategies
  • 3.6. Summary and outlook
  • Chapter 4. Open search algorithms discover patterns of chemical modifications via LC-MS/MS
  • 4.1. Introduction
  • 4.2. Featured analyses
  • 4.3. Dissection of workflow
  • 4.4. Interpreting and validating results
  • 4.5. Conclusions
  • Part 2. Exemplary applications
  • Chapter 5. Utility of chemical probes for mass spectrometry based chemical proteomics
  • 5.1. Introduction
  • 5.2. Reactivity-based probes
  • 5.3. Photoaffinity probes
  • 5.4. Conclusion
  • Chapter 6. Chemical proteomics of reactive molecules
  • 6.1. Definitions
  • 6.2. Chapter overview
  • 6.3. Probes of the 2R type for chemical proteomics measurements
  • 6.4. The subtractive measurement of the reaction of small molecules using broadly reactive probes
  • 6.5. Generation of selective 3R probes for measuring the reactivity of small molecules
  • 6.6. Select perspectives
  • 6.7. Chapter summary
  • Chapter 7. Mass spectrometry for human kinome analysis
  • 7.1. Human kinome
  • 7.2. Enrichment methods for kinase proteins and peptides
  • 7.3. MS-based quantitative proteomics for human kinome analysis
  • 7.4. Human kinome analysis in discovery and targeted MS modes
  • 7.5. Summary
  • Chapter 8. Recent progress of subcellular-compartment-focused chemical proteomics
  • 8.1. Introduction
  • 8.2. Proximity proteomics
  • 8.3. Genetically engineered proximity labeling
  • 8.4. Photoactivatable proximity labeling
  • 8.5. Organelle-specific activity-based protein profiling (ABPP)
  • 8.6. Organelle-localizable reactive molecules
  • 8.7. Conditional proteomics
  • 8.8. Conclusion
  • Index

Product details

  • No. of pages: 268
  • Language: English
  • Copyright: © Elsevier 2021
  • Published: October 22, 2021
  • Imprint: Elsevier
  • Paperback ISBN: 9780128214336
  • eBook ISBN: 9780128214350

About the Editor

Xudong Yao

Xudong Yao obtained his B.S. in synthetic polymer materials in July 1984 and M.S. in polymer chemistry in July 1987, both from Nanjing University in China. After working with the Department of Fiber Materials at China Textile University (now Donghua University) in Shanghai, he moved to the University of Maryland Baltimore County in the United States for doctoral studies in mechanistic enzymology with Prof. Ralph M. Pollack from August 1995 to October 1999. He then waded into the beginning streams of proteomics and did postdoctoral research in mass spectrometry and proteomics with Prof. Catherine Fenselau in the Department of Chemistry and Biochemistry at the University of Maryland until March 2002. During that time, he co-invented a highly cited quantitative proteomics technology of enzymatic 18O-labeling. Recruited by GeneProt, he flew to Geneva to join an ahead-of-its-time venture on proteomics industrialization. In October 2002, he joined Millennium Pharmaceuticals in Boston, continuing his industrial exploration in the uncharted land of Antibody-drug conjugates using mass spectrometry. He resumed his academic pursuit in August 2004, joining the Department of Chemistry at the University of Connecticut where he currently is an associate professor. His research activities are centered on the development and application of novel mass spectrometry and omics technologies.

Affiliations and Expertise

Department of Chemistry, University of Connecticut, Storrs, CT, United States

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