Imaging the future: the emerging era of single-cell spatial proteomics

The proteome of a human cell is partitioned within organelles, such as the nucleus, and other subcellular compartments, such as the cytoplasm, forming a myriad of membrane-bound and membrane-free ultrastructures. This compartmentalization allows discrete biochemical processes to occur efficiently in isolation, with relevant proteins localized to appropriate niches to fulfill their biological function(s). Proper delivery and dynamic exchange of proteins between compartments underlie the regulation of many cellular processes, such as cell signaling, division, and programmed cell death. To this end, cells deploy dedicated trafficking mechanisms to ensure correct protein localization, as mis-localization can result in pathology. In addition to trafficking, variation in the expression, modification, and physical associations of proteins within and between cells can result in biological heterogeneity, motivating the need for single-cell measurements. In this review, we introduce diverse platform technologies developed for subcellular proteomics and high-throughput systems biology, with the aim of providing mechanistic insights into fundamental cell biological processes underlying healthy and diseased states, and valuable public data resources. In contrast to the rapidly advancing field of single-cell genomics, the single-cell spatial proteomics toolbox remains in its infancy, but is poised to make considerable advances in the coming years.