Construction of protein interaction networks based on the label-free quantitative proteomics

Multiprotein complexes are essential building blocks for many cellular processes in an organism. Taking the process of transcription as an example, the interplay of several chromatin-remodeling complexes is responsible for the tight regulation of gene expression. Knowing how those proteins associate into protein complexes not only helps to improve our understanding of these cellular processes, but can also lead to the discovery of the function of novel interacting proteins. Given the large number of proteins with little to no functional annotation throughout many organisms, including human, the identification and characterization of protein complexes has grown into a major focus of network biology. Toward this goal, we have developed several computational approaches based upon label-free quantitative proteomics approaches for the analysis of protein complexes and protein interaction networks. Here, we describe the computational approaches used to build probabilistic protein interaction networks, which are detailed in this chapter using the example of complexes involved in chromatin remodeling and transcription.