Proteomics for Drug Discovery

1. Front Matter

   Pages i-xi

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2. A Photoaffinity Labeling-Based Chemoproteomics Strategy for Unbiased Target Deconvolution of Small Molecule Drug Candidates

   • Jason R. Thomas, Scott M. Brittain, Jennifer Lipps, Luis Llamas, Rishi K. Jain, Markus Schirle

   Pages 1-18

3. Multiplexed Liquid Chromatography-Multiple Reaction Monitoring Mass Spectrometry Quantification of Cancer Signaling Proteins

   • Yi Chen, Kate J. Fisher, Mark Lloyd, Elizabeth R. Wood, Domenico Coppola, Erin Siegel et al.

   Pages 19-45

4. Monitoring Dynamic Changes of the Cell Surface Glycoproteome by Quantitative Proteomics

   • Mathias Kalxdorf, Hans Christian Eberl, Marcus Bantscheff

   Pages 47-59

5. High-Resolution Parallel Reaction Monitoring with Electron Transfer Dissociation for Middle-Down Proteomics: An Application to Study the Quantitative Changes Induced by Histone Modifying Enzyme Inhibitors and Activators

   • Michael J. Sweredoski, Annie Moradian, Sonja Hess

   Pages 61-69

6. Preparation and Immunoaffinity Depletion of Fresh Frozen Tissue Homogenates for Mass Spectrometry-Based Proteomics in the Context of Drug Target/Biomarker Discovery

   • DaRue A. Prieto, King C. Chan, Donald J. Johann Jr, Xiaoying Ye, Gordon Whitely, Josip Blonder

   Pages 71-90

7. Target Identification Using Cell Permeable and Cleavable Chloroalkane Derivatized Small Molecules

   • Jacqui L. Mendez-Johnson, Danette L. Daniels, Marjeta Urh, Rachel Friedman Ohana

   Pages 91-108

8. Microfluidics-Mass Spectrometry of Protein-Carbohydrate Interactions: Applications to the Development of Therapeutics and Biomarker Discovery

   • Alina D. Zamfir

   Pages 109-128

9. Studying Protein–Protein Interactions by Biotin AP-Tagged Pulldown and LTQ-Orbitrap Mass Spectrometry

   • Zhongqiu Xie, Yuemeng Jia, Hui Li

   Pages 129-138

10. Post-Translational Modification Profiling-Functional Proteomics for the Analysis of Immune Regulation

    • Avital Eisenberg-Lerner, Ifat Regev, Yifat Merbl

    Pages 139-152

11. Reverse Phase Protein Arrays and Drug Discovery

    • Kenneth G. Macleod, Bryan Serrels, Neil O. Carragher

    Pages 153-169

12. Probing Protein Kinase-ATP Interactions Using a Fluorescent ATP Analog

    • Leslie E. W. LaConte, Sarika Srivastava, Konark Mukherjee

    Pages 171-183

13. Preparation of Disease-Related Protein Assemblies for Single Particle Electron Microscopy

    • A. Cameron Varano, Naoe Harafuji, William Dearnaley, Lisa Guay-Woodford, Deborah F. Kelly

    Pages 185-196

14. Identification of Lipid Binding Modulators Using the Protein-Lipid Overlay Assay

    • Tuo-Xian Tang, Wen Xiong, Carla V. Finkielstein, Daniel G. S. Capelluto

    Pages 197-206

15. Resazurin Live Cell Assay: Setup and Fine-Tuning for Reliable Cytotoxicity Results

    • José Á. Rodríguez-Corrales, Jatinder S. Josan

    Pages 207-219

16. Exploring Protein-Protein Interactions as Drug Targets for Anti-cancer Therapy with In Silico Workflows

    • Alexander Goncearenco, Minghui Li, Franco L. Simonetti, Benjamin A. Shoemaker, Anna R. Panchenko

    Pages 221-236

17. Method to Identify Silent Codon Mutations That May Alter Peptide Elongation Kinetics and Co-translational Protein Folding

    • Ronald Worthington, Elijah Ball, Brentsen Wolf, Gregory Takacs

    Pages 237-243

18. In Silico Design of Anticancer Peptides

    • Shailesh Kumar, Hui Li

    Pages 245-254

19. Docking and Virtual Screening in Drug Discovery

    • Maria Kontoyianni

    Pages 255-266

20. Bioinformatics Resources for Interpreting Proteomics Mass Spectrometry Data

    • Iulia M. Lazar

    Pages 267-295

This book reflects the drug development community’s interest in proteomics methods by providing researchers with the necessary knowledge for the implementation of a number of basic experimental and bioinformatics protocols in the drug discovery research laboratory. The focus of the collection is on select protocols and methodologies that address the analysis of post-translational modifications, targeted protein quantification, protein-protein, protein-lipid, or protein-ATP interactions, in silico lead identification, protein arrays, tissue and cell extract preparation, labeling, chemoproteomics, and drug efficacy assessment. Emphasis was placed not just on methods that describe large-scale protein analysis, but also on ones that are amenable to future implementation in a high-throughput format. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. 

Practical and authoritative, Proteomics for Drug Discovery: Methods and Protocols aims to provide a deep knowledge of the fundamentals of disease biology as well the means that were developed for probing the complex biological milieu.

• Proteomic platforms
• Virtual screening
• Mass spectrometry data
• Large-scale protein analysis
• Bioinformatics
• Drug target discovery
• Disease biology

• Department of Biological Sciences, Virginia Tech, Blacksburg, USA

  Iulia M. Lazar

• Department of Pharmaceutical Sciences, School of Pharmacy, Southern Illinois University Edwardsville, Edwardsville, USA

  Maria Kontoyianni

• ImmunoGen, Waltham, USA

  Alexandru C. Lazar

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