Compartmentalization is essential for all complex forms of life. In eukaryotic cells, membrane-bound organelles, as well as a multitude of protein- and nucleic acid-rich subcellular structures, maintain boundaries and serve as enrichment zones to promote and regulate protein function, including signalling events. Consistent with the critical importance of these boundaries, alterations in the machinery that mediates protein transport between these compartments have been implicated in a number of diverse diseases. Understanding the composition of each cellular “compartment” (be it a classical organelle or a large protein complex) remains a challenging task. For soluble protein complexes, approaches such as affinity purification other biochemical fractionation coupled to mass spectrometry provide important insight, but this is not the case for detergent-insoluble components. Classically, both microscopy and organellar purifications have been employed for identifying the composition of these structures, but these approaches have limitations, notably in resolution for standard high-throughput fluorescence microscopy and in the difficulty in purifying some of the structures (e.g. p-bodies) for approaches based on biochemical isolations. Prompted by the implementation in vivo biotinylation approaches such as BioID, we report here the systematic mapping of the composition of various subcellular structures, using as baits proteins (or protein fragments) which are well-characterized markers for a specified location. We defined how relationships between “prey” proteins detected through this approach can help to understand the protein organization inside a cell, which is further facilitated by newly developed computational tools. We will discuss our low-resolution map of a human cell containing major organelles and non-membrane bound structures, but also describe how this map can be harnessed to uncover new signalling components implicated in cancer and vascular diseases.