Accessible single cell proteomics by mass spectrometry

Abstract

Biological function and disease often involve the regulation of proteins in tissues containingdifferent cell types. Understanding and controlling the function of these complex systems of cells demands study at single cell resolution. However, our ability to quantify proteins in individual cells has remained limited to a few dozen proteins, while thousands to tens of thousands act in a coordinated fashion in each single cell. The existing approaches to quantify proteins in single cells and opportunities to expand these techniques proteome-wide are described. For the first time, techniques were developed to realize proteomics measurements on single mammalian cells in the high-throughput and automated fashion necessary for studying complex biological systems. These approaches allowed the characterization of a previously unobserved phenomenon in macrophage polarization, wherein spontaneous polarization can occur in vitro in the absence of polarizing cytokines. Critical design considerations for single cell experiments, backed by empirical data, were shared to ease adoption by the broader community. The work presented in this thesis lays the groundwork to enable the field of single cell proteomics to become widely practiced.--Author's abstract