Discovery of Native Protein Complexes by Liquid Chromatography Followed by Quantitative Mass Spectrometry

Discovering protein complexes in vivo is of vital importance to understand the evolution and function of biological systems. Proteomics analysis has evolved as a state-of-the-art technique in elucidating the above information. A combination of liquid chromatography (LC) and liquid chromatography coupled to shotgun mass spectrometry (LC-MS) provides the most exhaustive information in this regard. However, a significant amount of computational effort is required for the meaningful interpretation of the generated datasets. In this chapter we describe in detail the state-of-the-art pipeline to discover soluble protein complexes and provide practical advice focusing on typical situations a biologist faces while analyzing such proteomics datasets. Furthermore, we briefly describe two commonly used software packages to solve the described problem: Weka for training protein-protein interactions (PPIs) using machine learning (ML) and Cytoscape for clustering the interaction network.