Human beings have been mapping the earth, the oceans and the heavens for centuries, but it is only in recent decades that we have extended our explorations to the cell, at least in any molecular detail.

Not merely bags of cytoplasm, cells are highly organized. They are compartmentalized into organelles and domains with particular molecular compositions and physical properties, and they are also dynamic, with constant molecular flux into and out of such organizational units. There is little doubt that cellular processes depend on organization: cellular secretion takes place via a series of membrane-bounded compartments, and many signaling processes are organized via molecular scaffolds. Even gene expression is intricately linked with the spatial organization of the genome. Although cellular organization and protein localization have been appreciated since the dawn of cell biology, the ability to make systematic molecular maps of protein distribution across a cell is still evolving.

Maps of the cell will help us navigate biological processes. Credit: PhotoDisc/Getty Images

Early work using cell fractionation followed by biochemical analysis of protein locations has been rejuvenated by the use of mass spectrometry for a more comprehensive picture of protein distribution across the cell (Cell 125, 187–199, 2006). Workhorse methods such as antibody-based immunocytochemistry are being deployed in systematic efforts to generate subcellular maps. And genetically encoded tools such as ascorbate peroxidases and biotin ligases have been harnessed for proximity-based biotinylation, followed by capture and mass spectrometry, to determine what proteins are present at probed locations of a cell (Science 339, 1328–1331, 2013; J. Cell Biol. 196, 801–810, 2012). These tools are being constantly improved (Nat. Methods 12, 51–54, 2015) and are beginning to be applied in subcellular mapping experiments (Proc. Natl. Acad. Sci. USA 112, 12093–12098, 2015). It will be interesting to watch how the problem of specificity in proximity-based methods is contended with and to study the maps that emerge from all these efforts.

Although subcellular maps of protein locations will give us an unprecedented picture of the territory, proteins are only one of several types of molecule that make up the cellular landscape. Even with such maps, lipids and sugars will remain a relative terra incognita. But in explorations of the cell, protein maps are certainly the place to start.