Integrated Network Discovery Using Multi-Proteomic Data

A fundamental goal of systems biology is to seek a better understanding of the cell's molecular mechanisms. Experimentalists most frequently rely upon reductionist methods to isolate and analyze discrete signaling compartments, including subcellular domains, organelles, and protein-protein interactions. Among the systems-biology community, there is a growing need to integrate multiple datasets to resolve complex cellular networks. In this chapter, we share our procedures for the discovery of integrated signaling networks, across multi-proteomic data. Demonstrating these procedures, we provide an integrated analysis of the cellular proteome and extracellular (secretome) of human glioma LN229.