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Proteomics for Drug Discovery

Methods and Protocols

  • Book
  • © 2017

Overview

Editors:
  1. Iulia M. Lazar

    1. Department of Biological Sciences, Virginia Tech, Blacksburg, USA

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    You can also search for this editor in PubMed   Google Scholar

  2. Maria Kontoyianni

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

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    You can also search for this editor in PubMed   Google Scholar

  3. Alexandru C. Lazar

    1. ImmunoGen, Waltham, USA

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    You can also search for this editor in PubMed   Google Scholar

  • Includes cutting-edge techniques for the study of drug discovery via proteomics
  • Provides step-by-step detail essential for reproducible results
  • Contains key implementation advice from the experts

Part of the book series: Methods in Molecular Biology (MIMB, volume 1647)

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Table of contents (20 protocols)

  1. Front Matter

    Pages i-xi
    Download chapter PDF

  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
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Keywords

About this book

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.

Editors and Affiliations

  • 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

Bibliographic Information

  • Book Title: Proteomics for Drug Discovery

  • Book Subtitle: Methods and Protocols

  • Editors: Iulia M. Lazar, Maria Kontoyianni, Alexandru C. Lazar

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-4939-7201-2

  • Publisher: Humana New York, NY

  • eBook Packages: Springer Protocols

  • Copyright Information: Springer Science+Business Media LLC 2017

  • Hardcover ISBN: 978-1-4939-7200-5Published: 15 August 2017

  • Softcover ISBN: 978-1-4939-8414-5Published: 03 August 2018

  • eBook ISBN: 978-1-4939-7201-2Published: 14 August 2017

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 1

  • Number of Pages: XI, 302

  • Number of Illustrations: 16 b/w illustrations, 46 illustrations in colour

  • Topics: Pharmacology/Toxicology

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