Proteomics in Systems Biology Methods and Protocols Methods in Molecular Biology 2456 Jennifer Geddes-Mcalister (Ed.)

1. Review of the Real and Sometimes Hidden Costs in Proteomics Experimental Workflows

2. High-Throughput Mass Spectrometry-Based Proteomics with dia-PASEF

3. Isolation of Detergent Insoluble Proteins from Mouse Brain Tissue for Quantitative Analysis Using Data Independent Acquisition (DIA)

4. Rodent Lung Tissue Sample Preparation and Processing for Shotgun Proteomics

5. Protein Purification and Digestion Methods for Bacterial Proteomic Analyses

6. Mapping Cell Surface Proteolysis with Plasma Membrane-Targeted Subtiligase

7. N-Terminomics/TAILS of Tissue and Liquid Biopsies

8. HUNTER: Sensitive Automated Characterization of Proteolytic Systems by N Termini Enrichment from Microscale Specimen

9. Phosphoproteomics and Organelle Proteomics in Pancreatic Islets

10. Phosphoproteomic Sample Preparation for Global Phosphorylation Profiling of a Fungal Pathogen

11. Glycopeptide-Centric Approaches for the Characterization of Microbial Glycoproteomes

12. Integrated Network Discovery Using Multi-Proteomic Data

13. Targeted Cross-Linking Mass Spectrometry on Single-Step Affinity Purified Molecular Complexes in the Yeast Saccharomyces cerevisiae

14. A Crosslinking – Mass Spectrometry Protocol for the Structural Analysis of Microtubule-Associated Proteins

15. Comprehensive Interactome Mapping of Nuclear Receptors Using Proximity Biotinylation

16. Mining Proteomics Datasets to Uncover Functional Pseudogenes