The field of proteomics is evolving from cataloging proteins in various biological systems to elucidating the cellular functions of the proteins in both normal and pathological processes. Quantitative proteomics, based on either isotope labeling or label‐free, facilitates globally profiling changes in protein expression levels, but the abundance of a protein does not directly correlate with its activity. Mass spectrometry (MS)‐based chemical proteomics has emerged as an important high‐throughput tool for the study of functional proteomes of interest. Technical advances in MS instrumentation have allowed for the accurate and sensitive detection of proteins among complex biological matrices such as cell lysates and body fluids, complemented by chemical strategies and detection methods that give desirable specificity and versatility to the process.

Beyond quantitative comparison of proteomes, chemical strategies have been developed to tailor specific applications, including identification and validation of novel drug targets, quantification of ligand–protein or protein–protein interaction affinity, understanding the pathways involving in the drug action, measuring the kinase activity or screening the enzyme inhibitor, profiling posttranslational modifications (PTMs) in large‐scale and so on. In recent years, we have observed multiple robust and high‐throughput chemical proteomics approaches, which have greatly expanded the scope of proteomics research. This book thus seeks to outline the basic principle of chemical proteomics, summarize the recent developments in this fast‐evolving field, and provide a timely overview of the current outlook of the technology for the students and researchers who are interested in understanding the basics and utilizing the tool in their respective areas.

This book is divided into three parts. The first part of book including Chapters 1 and 2 describes the basic principle of MS‐based proteomics and commonly used high‐throughput techniques, focusing on shotgun/bottom‐up proteomics (Chapter 1), and quantitative proteomics covering label‐free quantitation, metabolic labeling, chemical stable isotope labeling, and strategies to select the appropriate labeling approach for the intended proteomic analysis (Chapter 2).

The second part of book (Chapters 3–11) covers a variety of techniques and strategies coupling chemical probes to MS‐based proteomics to provide functional insights into the proteome. Among this part, Chapters 3–6 place more emphasis on the techniques of classical chemical proteomics while Chapters 7–11 elaborate on the novel applications and expansion of chemical proteomics in broad term. Chapters 3 and 4 introduce the classical chemical proteomics approach of activity‐based protein profiling (ABPP) that uses site‐directed small chemical probes to directly measure the functional state of proteins in vitro and in vivo, including the general strategies to design probes, analytical platforms used in ABPP, and classes of enzyme studied by ABPP. The technique was uniquely presented in these two chapters by a MS expert and by chemical biologists, respectively. Chapter 5 focuses on key technologies of using metabolic and tagged probes for global profiling of protein networks and targeted identification. Chapter 6 shows how to use peptides as the biosensors to measure or report highly diverse information from biological systems and especially highlights and summarizes recent major discoveries in this field and a detailed protocol is included for quantitative measurement of the Bcr–Abl tyrosine kinase activity using a substrate peptide biosensor in a chronic myeloid leukemia (CML) cell line as a working example. From Chapter 7, expansion and applications of chemical proteomics are presented. Chapter 7 addresses the challenge of discovering extremely low abundant or unstable natural products through chemical proteomics and discusses the development of chemoselective probes (nonreversible and reversible chemoselective probes) to tag secondary metabolites by means of their functional group identity. Chapter 8 reviews the existing methods for the study of newly synthesized proteins, with an emphasis on protein labeling with noncanonical amino acids to allow for the use of bio‐orthogonal chemistry to enrich newly synthesized proteins for MS‐based analyses. Chapter 9 introduces a new chemical proteomics strategy termed Tracing Internalization and Trafficking of NAnomaterials (TITAN) for studying the endocytosis process, through chemically tracing nanoparticle cellular uptake and transportation and revealing real‐time protein−nanoparticle interactions. While all above chapters deal with the utility of probes or chemical labels to couple with proteomics, Chapters 10–11 introduce approaches without designing of functional probes. Chapter 10 describes a new approach called Functional Identification of Target by Expression Proteomics (FITExP) for the effective identification of drug target candidates in view of the observation that for the protein target of a small‐molecule drug, the abundance change in late apoptosis is exceptional compared to the expectations based on the abundances of coregulated proteins. Chapter 11 demonstrates a strategy called Thermal Proteome Profiling (TPP) that measures the heat‐induced denaturation of proteins and identifies drug‐bound targets based on altered thermal stability without the requirement of modifying the ligand molecules for studying the protein–ligand binding.

The last part of book (Chapters 12–15) focuses on using chemical strategies to study different protein PTMs or protein high‐order structures. Chapter 12 describes chemical strategies to glycoprotein analyses, focusing on sample preparation and MS analyses. Chapter 13 reviews a variety of proteomic analyses using metabolic labeling in conjunction with enrichment for several lipid modifications, and it provides a detailed protocol for the identification of prenylated proteins from Plasmodium falciparum. Chapter 14 describes an integrative proteomic platform using boronate‐affinity chromatography for enriching the Asp‐ and Glu‐ADP‐ribosylated proteins and the quantitative characterization of protein ADP‐ribosylation on a global scale. Chapter 15 sums up the recent advances of MS‐based protein footprinting as an effective analytical technique for characterizing protein high‐order structures and especially focuses on the application of the fast photochemical oxidation of proteins to observe protein conformational changes.

We thank all the contributors, who are leading researchers in chemical proteomics and developers or experts of these methods, for sharing their expertise in this area and related protocols. We hope that the critical review and the methodologies described in each chapter will be valuable guidance for researchers who are either new to the field or already working on some aspect of chemical proteomics, and we also hope this book will contribute to the further development and wider applications of chemical proteomics approaches.

01 January 2019