Proteomics is considered a subdiscipline of systems biology. So what is systems biology? Weston and Hood define it as “the analysis of the relationships between elements in a system in response to genetic or environmental perturbations, with the goal of understanding the system or the emergent properties of the system” [6]. “System” is a broad term borrowed from other fields (e.g., engineering), but in a biological context the word usually refers to organelles, cells, organs, or organisms. Such a definition is therefore based largely on the physical location of the proteins studied, their network of interactions, and their collective role in defining a biological entity (such as a mitochondrion or a liver cell) or function (such as the immune response).