Network-Based Proteomics

Proteomics, as the study of all expressed proteins within a given system, is a fast-growing field in which its importance in contemporary biological research remains understated. The study of network-based proteomics provides a wealth of direct information not inferable from indirect transcriptional measurements. This means that direct protein observations could yield deeper biological insight and the increased development of novel medical interventions.

This timely book offers insights into the technological developments in proteomics and introduces the reader to the issues in proteomic data and their origins. For each issue, key instances of network-based techniques are described alongside their shortcomings and comparative performance-based analysis. Just as proteomic technologies are evolving, so too are the data challenges and possibilities that emerge.

The authors are at the forefront of this rapidly evolving field, and thus present findings from a chronological perspective, allowing the readers to see that, as techniques become more difficult with each iteration, so too does the complexity of each new challenge. This specialized insight will interest practitioners and specialists actively working in proteomics and networks and those interested in developing translational research approaches utilizing cutting-edge informatics alongside high-throughput technologies.

• A Primer on Networks
• Networks in Clinical Proteomics
• Proteomics Profile Analysis
• Advances in Biological Network Analysis Methods Empowers Proteomics
• An Introduction to the Datasets Used in this Book
• Overcoming the Coverage Issue Using Cluster Discovery: Proteomics Expansion Pipeline (PEP)
• Improving Coverage via Non-Cluster Based Methods
• A Novel Feature-based Method Capable of Overcoming Both Consistency and Coverage Issues — Proteomics Signature Profiling (PSP)
• Expanding the Utility of PSP Using Pathway-Derived Subnets (PDS), False Positive Analysis and Advanced Ontologies
• Recovery Performance of the First-Generation Network-Based Strategies
• A Quantitative Variant of Proteomics Signature Profiling Benchmarked Using Swath-MS (QPSP)
• Overcoming Heterogeneity, Reproducibility and Cross-Batch Issues Using QPSP
• The Power of Rank-Based Network Approaches in Proteomic Analysis
• Negotiating Robustness Against Low-Abundance Variability Using Extremely Small-Subnet Analysis (ESSNET)
• Remarks
• Lessons Learnt and Final Remarks
• References
• Appendix: Supplementary Figures and Tables