The HeLa Spatial Proteome

Subcellular localization critically influences protein function, and cells regulate protein localization to control biological processes. We have developed dynamic organellar maps, for the rapid and global determination of protein subcellular localization through quantitative mass spectrometry. All major organelles are resolved; cross-validation of a 1,000-member organellar marker set shows a median prediction accuracy of >94%. The absolute abundances of proteins are concomitantly obtained, allowing quantitative modelling of cellular compartments. We provide an online interactive database with subcellular localization information for 8,700 proteins from HeLa cells, approaching comprehensive coverage of the proteome. Two tiers of classification are provided; a global classifier which reveals how the protein is distributed over the nucleus, cytosol, and organelles; while the second level of classification gives the association of the protein with a particular organelle.