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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.
List of contents
A Photoaffinity Labeling-Based Chemoproteomics Strategy for Unbiased Target Deconvolution of Small Molecule Drug Candidates.- Multiplexed Liquid Chromatography-Multiple Reaction Monitoring Mass Spectrometry Quantification of Cancer Signaling Proteins.- Monitoring Dynamic Changes of the Cell Surface Glycoproteome by Quantitative Proteomics.- 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.- Preparation and Immunoaffinity Depletion of Fresh Frozen Tissue Homogenates for Mass Spectrometry-Based Proteomics in the Context ofDrug Target/Biomarker Discovery.- Target Identification Using Cell Permeable and Cleavable Chloroalkane Derivatized Small Molecules.- Microfluidics-Mass Spectrometry of Protein-Carbohydrate Interactions: Applications to Development of Therapeutics and Biomarker Discovery.- Studying Protein-Protein Interactions by Biotin AP-Tagged Pulldown and LTQ-Orbitrap Mass Spectrometry.- Post-Translational Modification Profiling-Functional Proteomics for the Analysis of Immune Regulation.- Reverse Phase Protein Arrays and Drug Discovery.- Probing Protein Kinase-ATP Interactions Using a Fluorescent ATP Analog.- Preparation of Disease-Related Protein Assemblies for Single Particle Electron Microscopy.- Identification of Lipid-Binding Modulators Using the Protein-Lipid Overlay Assay.- Resazurin Live Cell Assay: Setup and Fine-Tuning for Reliable Cytotoxicity.- Exploring Protein-Protein Interactions as Drug Targets for Anti-Cancer Therapy with In Silico Workflows.- Method to Identify Silent Codon Mutations that May Alter Peptide Elongation Kinetics and Co-Translational Protein Folding.- In Silico Design of Anticancer Peptides.- Docking and Virtual Screening in Drug Discovery.- Bioinformatics Resources for Interpreting Proteomics Mass Spectrometry Data.
Summary
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.
