Proteomics in Systems Biology

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.