Single-cell Proteomics: Progress and Prospects

Abstract

MS-based proteome profiling has become increasingly comprehensive and quantitative, yet a persistent shortcoming has been the relatively large samples required to achieve an in-depth measurement. Such bulk samples, typically comprising thousands of cells or more, provide a population average and obscure important cellular heterogeneity. Single-cell proteomics capabilities have the potential to transform biomedical research and enable understanding of biological systems with a new level of granularity. Recent advances in sample processing, separations and MS instrumentation now make it possible to quantify >1000 proteins from individual mammalian cells, a level of coverage that required an input of thousands of cells just a few years ago. This review discusses important factors and parameters that should be optimized across the workflow for single-cell and other low-input measurements. It also highlights recent developments that have advanced the field and opportunities for further development.

Keywords: Cell biology; Cell sorting; FAIMS; Label-free quantification; Mass Spectrometry; Tandem Mass Spectrometry; Tissues*; nanoLC; nanoPOTS; single-cell; ultrasensitive.

Graphical abstract

Fig. 1.

Strategies for sample preparation of low input samples based on (A) iPAD, (B) OAD, (C) nanoPOTS and (d) SCoPE-MS. Adapted with permission from References , , , and , respectively.

Fig. 2.

Separation methods for single cells and other trace samples. A, Narrow-bore packed LC columns. B, Porous layer open tubular columns. C, Capillary electrophoresis with electrokinetically driven sheath flow interface. D, Nanowell-mediated 2D LC. Adapted with permission from References , , and , respectively.