All the interactions that occur between the various molecules produced by an organism, in all its cells and tissues and at all stages of its life. For practical purposes, researchers focus on binary protein-protein interactions (PPIs), because these are the molecules encoded by the organism’s genes and are fundamental to all other cellular processes. Determining which proteins form complexes, or bind together in some way, enables researchers to identify the components of the complex pathways and networks that govern different aspects of cellular functioning and potentially play a role in health and disease. This information can then be correlated with data from genome mapping projects to pinpoint the genes corresponding to proteins of interest. This might allow the development of, for example, a genetic test to identify individuals with susceptibility to a certain condition. With the human genome containing roughly 21000 protein-coding genes, identifying all the protein interactions is a mammoth task. Numerous projects are underway to amass the interactome data, both in humans and in other organisms, including yeast (Saccharomyces cerevisiae), the fruit fly Drosophila melanogaster, and the nematode Caenorhabditis elegans. The data are stored on databases and can be visualized as three-dimensional network maps. Fast high-throughput experimental techniques are essential to identify protein-protein interactions on a large scale. A range of techniques are used; some use X-ray tomography or specialized microscopy to visualize cellular components in situ, whereas others treat the cell with antibodies or chemical reagents to pinpoint protein complexes, which can then be separated out and analysed, e.g. by mass spectrometry. Often a labelled ‘bait’ protein is tracked to determine which ‘prey’ proteins bind to it, e.g. by using yeast two-hybrid screens, in which pairwise protein interactions are linked to expression of reporter genes in yeast cells. Coexpression of proteins, as revealed by microarrays, can suggest functional relationships; alternatively, query proteins are allowed to interact with pure samples of known proteins on microarray slides to discover their binding affinities.