Elucidating mechanisms of life requires analysis of whole systems and understanding the complex interplay of the individual components. Proteins control and mediate the majority of biological activities and interactions among proteins play a decisive role in the dynamic modulation of cellular behavior. Protein-protein interactions are essential constituents of all cells and interactome analysis is an important component in the quest for a systems level understanding of life. We explore interactome networks for yeast, human and plant at ever increasing completeness and quality using both experimental and computational mapping and analysis tools. Based on benchmarking and standardized reference sets we have developed experimental approaches and mathematical models for the quantitative evaluation of the completeness and quality of interactome maps. These models enable a critical assessment of current maps and guide development of a roadmap towards completion. Recently mapping of the first binary interactome network for the reference plant Arabidopsis thaliana was completed. Using tools of graph theory we identify biologically relevant network communities from which a picture of the overall interactome network organization starts to emerge. Combination of interaction and comparative genomics data yielded insights into network evolution, and biological inspection resulted in many hypotheses for unknown proteins and revealed unexpected connectivity between previously studied components of phytohormone signaling pathways. Using the network we explored how bacterial and fungal pathogens perturb their host’s network. Pathogen effectors from evolutionary distant pathogens were found to converge on network hubs, which appear “guarded” by resistance proteins, and which we show to be functionally important for the host’s immune responses. Genetically, we were able to validate >90% of the Arabidopsis proteins targeted by both pathogens. Together, we show how high-quality protein interactome network maps provide us with tools for elucidating fundamental laws underlying biological systems.