Proteomics in Systems Biology: Methods and Protocols

ISBN-13: 9781071621233 / Angielski / Twarda / 2022

Geddes-McAlister, Jennifer

Opis

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.

Spis treści

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

            Aicha Asma Houfani and Leonard James Foster

 

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

            Patricia Skowronek and Florian Meier

 

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

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

 

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

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

 

5. Protein Purification and Digestion Methods for Bacterial Proteomic Analyses

            Nicole Hansmeier, Samrachana Sharma, and Tzu-Chiao Chao

 

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

            Aspasia A. Amiridis and Amy M. Weeks

 

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

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

 

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

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

 

9. Phosphoproteomics and Organelle Proteomics in Pancreatic Islets

            Özum Sehnaz Caliskan, Giorgia Massacci, Natalie Krahmer, and Francesca Sacco

 

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

            Brianna Ball, Jonathan Krieger, and Jennifer Geddes-McAlister

 

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

            Nichollas E. Scott

 

12. Integrated Network Discovery Using Multi-Proteomic Data

            Rafe Helwer and Vincent C. Chen

 

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

            Christian Trahan and Marlene Oeffinger

 

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

            Atefeh Rafiei and David C. Schriemer

 

15. Comprehensive Interactome Mapping of Nuclear Receptors Using Proximity Biotinylation

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

 

16. Mining Proteomics Datasets to Uncover Functional Pseudogenes

            Anna Meller and François-Michel Boisvert

 

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

            Arjun Sukumaran and Jennifer Geddes-McAlister

 

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

            Tzu-Chiao Chao, Samina Thapa, and Nicole Hansmeier

 

19. 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, and Jennifer Geddes-McAlister

 

20. Label-Free Quantitative Proteomic Profiling of Fusarium Head Blight in Wheat

            Boyan Liu, Danisha Johal, Mitra Serajazari, and Jennifer Geddes-McAlister

 

21. DIA Proteomics and Machine Learning for the Fast Identification of Bacterial Species in Biological Samples

            Florence Roux-Dalvai, Mickaël Leclercq, Clarisse Gotti, and Arnaud Droit

 

22. Novel Bioinformatics Strategies Driving Dynamic Metaproteomic Studies

            Caitlin M.A. Simopoulos, Daniel Figeys, and Mathieu Lavallée-Adam

 

23. MaxQuant Module for the Identification of Genomic Variants Propagated into Peptides

            Pavel Sinitcyn, Maximilian Gerwien, and Jürgen Cox

 

24. Untargeted Metabolomic Profiling of Fungal Species Populations

            Thomas E. Witte and David P. Overy