Main description:

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.

Contents:

1. 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, and Markus Schirle

2. 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, David Shibata, Yian A. Chen, and John M. Koomen

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

Mathias Kalxdorf, Hans Christian Eberl, and Marcus Bantscheff

4. High Resolution Parallel Re

action 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, and Sonja Hess

5. 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,2Donald J. Johann, Jr., Xiaoying Ye, Gordon Whitely, and Josip Blonder

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

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

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

Alina D. Zamfir

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

Zhongqiu Xie, Yuemeng Jia, and Hui Li

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

Avital Eisenberg-Lerner, Ifat Regev, and Yifat Merbl

10. Reverse Phase Protein Arrays and Drug Discovery

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

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lt;11. Probing Protein Kinase-ATP Interactions Using a Fluorescent ATP Analog

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

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

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

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

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

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

Jose A. Rodriguez-Corrales and Jatinder S. J

osan

15. Exploring Protein-Protein Interactions as Drug Targets for Anti-Cancer Therapy with In Silico Workflows

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

16. Method to Identify Silent Codon Mutations that May Alter Peptide Elongation Kinetics and Co-Translational Protein Folding

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

17. In Silico Design of Anticancer Peptides

Shailesh Kumar and Hui Li

18. Docking and Virtual Screening in Drug Discovery

Maria Kontoyianni

19. Bioinfo

rmatics Resources for Interpreting Proteomics Mass Spectrometry Data

Iulia M. Lazar