This detailed volume explores a wide range of experimental and bioinformatic proteomics methods applicable to the drug discovery process. Focused on drug target discovery, validation, characterization, and quantitation, the book delves into bottom-up data-dependent (DDA) shotgun and data-independent acquisition (DIA) proteomics, cell surface proteomics, proteogenomics, chemoproteomics, methodologies focused on posttranslational modifications, single cell proteomics, 3D cell culture proteomics, organoids, and laser capture microdissection (LCM) assisted tissue proteogenomics. Advanced quantitative techniques, which include label-free, mass tagging, and targeted immuno-MRM proteomics, along with top-down proteomics for validation and characterization of selected protein targets, are also described. Written for the highly successful Methods in Molecular Biology series, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step and readily reproducible laboratory protocols, and tips on troubleshooting and avoiding foreseeable pitfalls.
Authoritative and practical, Proteomics for Drug Discovery serves as an ideal guide for researchers striving to push the field of drug discovery via MS-based proteomics to new frontiers.
A Multiplexed Single Cell Proteomic Workflow Applicable to Drug Treatment Studies.- Systematic Identification of Kinase Substrates Relationship by Integrated Phosphoproteome and Interactome Analysis.- Quantitative Membrane Proteomics for Discovery of Actionable Drug Targets at the Surface of RAS Driven Human Cancer Cells.- Using Photoreactive Probes to Identify Viable Drug Targets in NonSmall Cell Lung Cancer.- A Microdissection Protocol for Proteogenomic Analysis of Histological Sections to Advance Drug Development.- Unbiased Quantitative Proteomics of Organoid Models of Pancreatic Cancer.- Drug Screening Using Normal Cell and Cancer Cell Mixture in an Automated 3D Cell Culture System.- Proteogenomic Workflow for Characterization of Microphthalmia Transcription Factor (MiT) Family Translocation Renal Cell Carcinoma.- A Tip Based Workflow for Sensitive IMAC Based Low Nanogram Level Phosphoproteomics.- Microfluidic Sample Preparation for Multiplexed Single Cell Proteomics Using a Nested Nanowell Chip.- 12 Plex Isobaric Multiplex Labeling Reagents for Carbonyl Containing Compound (SUGAR) Tag Enabled High Throughput Quantitative Glycomics.- Automated Immunoprecipitation Workflow for Comprehensive Acetylome Analysis.- A Fast Tracking Sample Preparation Protocol for Proteomics of Formalin Fixed Paraffin Embedded Tumor Tissues.- Identification of Proteomic Biomarkers of Acetaminophen Induced Hepatotoxicity Using Stable Isotope Labeling.- Reusing Peptide Spectral Reference Libraries to Discover Putative Plasma Biomarkers of Response to Cancer Chemotherapy.- Targeted Mass Spectrometry for Quantification of Receptor Tyrosine Kinase Signaling.- Detection and Quantitation of Endogenous Membrane-Bound RAS Proteins and KRAS Mutants in Cancer Cell Lines Using 1D SDS PAGE LC-MS2.- Determining KRAS4B Targeting Compound Specificity by Top Down Mass Spectrometry.
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