Linking the proteins—Elucidation of proteome‐scale networks using mass spectrometry

Abstract Proteomes are intricate. Typically, thousands of proteins interact through physical association and post‐translational modifications (PTMs) to give rise to the emergent functions of cells. Understanding these functions requires one to study proteomes as “systems” rather than collections of individual protein molecules. The abstraction of the interacting proteome to “protein networks” has recently gained much attention, as networks are effective representations, that lose specific molecular details, but provide the ability to see the proteome as a whole. Mostly two aspects of the proteome have been represented by network models: proteome‐wide physical protein–protein‐binding interactions organized into Protein Interaction Networks (PINs), and proteome‐wide PTM relations organized into Protein Signaling Networks (PSNs). Mass spectrometry (MS) techniques have been shown to be essential to reveal both of these aspects on a proteome‐wide scale. Techniques such as affinity purification followed by MS have been used to elucidate protein–protein interactions, and MS‐based quantitative phosphoproteomics is critical to understand the structure and dynamics of signaling through the proteome. We here review the current state‐of‐the‐art MS‐based analytical pipelines for the purpose to characterize proteome‐scale networks. © 2010 Wiley Periodicals, Inc., Mass Spec Rev 30:268–297, 2011