Proteomics in Systems Biology

This detailed book highlights the diverse techniques and applications of proteomics in an accessible, informative, and concise manner. The collection features sample preparation from distinct extraction, quantification, enrichment, modification, as well as interactome methodology for the in-depth exploration of biological systems, and the application of proteomics to clinical, infectious disease, and agricultural practices. Moreover, cutting-edge bioinformatics tools, encompassing machine learning and data integration strategies, are explored, as are techniques expanding beyond proteomics into the realm of metabolomics. 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, readily reproducible laboratory protocols, and tips on troubleshooting known pitfalls.
Comprehensive and practical, Proteomics in Systems Biology:Methods and Protocols emphasizes the importance of proteomics and demonstrates a plethora of approaches for investigating diverse biological entities from a systems perspective.

Includes cutting-edge techniques Provides step-by-step detail essential for reproducible results Contains key implementation advice from the experts

Inhalt
Review of the Real and Sometimes Hidden Costs in Proteomics Experimental Workflows.- High-Throughput Mass Spectrometry-Based Proteomics with dia-PASEF.- Isolation of Detergent Insoluble Proteins from Mouse Brain Tissue for Quantitative Analysis Using Data Independent Acquisition (DIA).- Rodent Lung Tissue Sample Preparation and Processing for Shotgun Proteomics.- Protein Purification and Digestion Methods for Bacterial Proteomic Analyses.- Mapping Cell Surface Proteolysis with Plasma Membrane-Targeted Subtiligase.- N-Terminomics/TAILS of Tissue and Liquid Biopsies.- HUNTER: Sensitive Automated Characterization of Proteolytic Systems by N Termini Enrichment from Microscale Specimen.- Phosphoproteomics and Organelle Proteomics in Pancreatic Islets.- Phosphoproteomic Sample Preparation for Global Phosphorylation Profiling of a Fungal Pathogen.- Glycopeptide-Centric Approaches for the Characterization of Microbial Glycoproteomes.- Integrated Network Discovery Using Multi-Proteomic Data.- Targeted Cross-Linking Mass Spectrometry on Single-Step Affinity Purified Molecular Complexes in the Yeast Saccharomyces cerevisiae.- A Crosslinking Mass Spectrometry Protocol for the Structural Analysis of Microtubule-Associated Proteins.- Comprehensive Interactome Mapping of Nuclear Receptors Using Proximity Biotinylation.- Mining Proteomics Datasets to Uncover Functional Pseudogenes.- Proteomic Profiling of the Interplay between a Bacterial Pathogen and Host Uncovers Novel Anti-Virulence Strategies.- Affinity-Enrichment of Salmonella-Modified Membranes from Murine Macrophages for Proteomic Analyses.- Proteomic Profiling of Interplay between Agrobacterium tumefaciens and Nicotiana benthamiana for Improved Molecular Pharming Outcomes.- Label-Free Quantitative Proteomic Profiling of Fusarium Head Blight in Wheat.- DIA Proteomics and Machine Learning for the Fast Identification of Bacterial Species in Biological Samples.- Novel Bioinformatics Strategies Driving Dynamic Metaproteomic Studies.- MaxQuant Module for the Identification of Genomic Variants Propagated into Peptides.- Untargeted Metabolomic Profiling of Fungal Species Populations.