Part I: Introduction

1. Mass Spectrometry-Based Chemoproteomic Approaches

Marcus Bantscheff

2. Chemical Proteomics in Drug Discovery

Gerard Drewes

Part II: Small Molecules and Probe Design

3. Compound Immobilization and Drug-Affinity Chromatography

Uwe Rix, Manuela Gridling, and Giulio Superti-Furga

4. Affinity-based Chemoproteomics with Small Molecule-peptide Conjugates

Chaitanya Saxena

5. A Chemical Proteomic Probe for Detecting Dehydrogenases: Catechol Rhodanine

Xia Ge and Daniel S. Sem

6. Probing Proteomes with Benzophenone Photoprobes

Akira Kawamura and Doina M. Mihai

7. Biotinylated Probes for the Analysis of Protein Modification by Electrophiles

Simona G. Codreanu, Hye-Young H. Kim, Ned A. Porter, and Daniel C. Liebler

8. Profiling of Methyltransferases and Other S-adenosyl-L-homocysteine-binding Proteins by Capture Compound Mass Spectrometry (CCMS)

Thomas Lenz, Peter Poot, Elmar Weinhold, and Mathias Dreger

Part III: Target Discovery and Target Validation

9. Identifying Cellular Targets of Small-Molecule Probes and Drugs with Biochemical Enrichment and SILAC

Shao-En Ong, Xiaoyu Li, Monica Schenone, Stuart L. Schreiber, and Steven A. Carr

10. Determination of Kinase Inhibitor Potencies in Cell Extracts by Competition Binding Assays and Isobaric Mass Tags

Carsten Hopf, Dirk Eberhard, Markus Boesche, Sonja Bastuck, Birgit Dümpelfeld, and Marcus Bantscheff

11. Affinity-Based Profiling of Dehydrogenase Subproteomes

Xia Ge and Daniel S. Sem

Duangnapa Kovanich, Thin Thin Aye, Albert J.R. Heck, and Arjen Scholten

13. Fluorescence-Based Proteasome Activity Profiling

Annemieke de Jong, Karianne G. Schuurman, Boris Rodenko, Huib Ovaa, and Celia R. Berkers

14. Chemical Cross-Linking and High Resolution Mass Spectrometry to Study Protein-Drug Interactions

Mathias Q. Müller and Andrea Sinz

15. Monitoring Ligand Modulation of Protein-Protein Interactions by Chemical Cross-Linking and High-Mass MALDI Mass Spectrometry

Natalia Gasilova, Alexis Nazabal

16. Time-Controlled Transcardiac Perfusion Crosslinking for In Vivo Interactome Studies

Amy Hye Won Jeon, Gerold Schmitt-Ulms

Part IV: Ligand Discovery

17. Ligand Discovery Using Small-molecule Microarrays

Dominick E. Casalena, Dina Wassaf, and Angela N. Koehler

18. Working with Small-Molecules-Preparing and Storing Stock Solutions and Determination of Kinetic Solubility

Andrea Wolf, Satoko Shimamura and Friedrich B.M. Reinhard

19. A Database for Chemical Proteomics-ChEBI

Paula de Matos, Nico Adams, Janna Hastings, Pablo Moreno, and Christoph Steinbeck

20. Working with Small Molecules: Rules-of-Thumb of "Drug Likeness"

Ming-Qiang Zhang