Proteomics in Systems Biology

1. Front Matter

   Pages i-xii

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

   • Aicha Asma Houfani, Leonard James Foster

   Pages 1-14

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

   • Patricia Skowronek, Florian Meier

   Pages 15-27

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

   • Cristen Molzahn, Lorenz Nierves, Philipp F. Lange, Thibault Mayor

   Pages 29-51

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

   • Hadeesha Piyadasa, Ying Lao, Oleg Krokhin, Neeloffer Mookherjee

   Pages 53-62

6. Protein Purification and Digestion Methods for Bacterial Proteomic Analyses

   • Nicole Hansmeier, Samrachana Sharma, Tzu-Chiao Chao

   Pages 63-70

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

   • Aspasia A. Amiridis, Amy M. Weeks

   Pages 71-83

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

   • Anthonia Anowai, Sameeksha Chopra, Barbara Mainoli, Daniel Young, Antoine Dufour

   Pages 85-94

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

   • Anuli C. Uzozie, Janice Tsui, Philipp F. Lange

   Pages 95-122

10. Phosphoproteomics and Organelle Proteomics in Pancreatic Islets

    • Özüm Sehnaz Caliskan, Giorgia Massacci, Natalie Krahmer, Francesca Sacco

    Pages 123-140

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

    • Brianna Ball, Jonathan R. Krieger, Jennifer Geddes-McAlister

    Pages 141-151

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

    • Nichollas E. Scott

    Pages 153-171

13. Integrated Network Discovery Using Multi-Proteomic Data

    • Rafe Helwer, Vincent C. Chen

    Pages 173-183

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

    • Christian Trahan, Marlene Oeffinger

    Pages 185-210

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

    • Atefeh Rafiei, David C. Schriemer

    Pages 211-222

16. Comprehensive Interactome Mapping of Nuclear Receptors Using Proximity Biotinylation

    • Lynda Agbo, Sophie Anne Blanchet, Pata-Eting Kougnassoukou Tchara, Amélie Fradet-Turcotte, Jean-Philippe Lambert

    Pages 223-240

17. Mining Proteomics Datasets to Uncover Functional Pseudogenes

    • Anna Meller, François-Michel Boisvert

    Pages 241-251

18. Proteomic Profiling of the Interplay Between a Bacterial Pathogen and Host Uncovers Novel Anti-Virulence Strategies

    • Arjun Sukumaran, Jennifer Geddes-McAlister

    Pages 253-262

19. Affinity Enrichment of Salmonella-Modified Membranes from Murine Macrophages for Proteomic Analyses

    • Tzu-Chiao Chao, Samina Thapa, Nicole Hansmeier

    Pages 263-273

20. Proteomic Profiling of Interplay Between Agrobacterium tumefaciens and Nicotiana benthamiana for Improved Molecular Pharming Outcomes

    • Nicholas Prudhomme, Jonathan R. Krieger, Michael D. McLean, Doug Cossar, Jennifer Geddes-McAlister

    Pages 275-286

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.

• Bioinformatics platforms
• Sample preparation
• The interactome
• Biological systems
• Machine learning
• Data integration

• Department of Molecular and Cellular Biology, University of Guelph, Guelph, Canada

  Jennifer Geddes-McAlister

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