Advances in spatial and single-cell proteomics have increased the need for workflows capable of handling extremely low input while maintaining quantitative reliability. Foundational methodology studies in this area helped establish the importance of controlled, reproducible upstream sample preparation as experiments moved toward smaller and more heterogeneous samples.
The study below describes the development of SCoPE-MS, a widely cited approach for single-cell proteomics. In the methods, the authors report using Adaptive Focused Acoustics® (AFA®) technology for controlled mechanical sample disruption as part of the upstream workflow, highlighting the role of precise, reproducible processing when working at very low input.
SCoPE-MS: mass spectrometry of single mammalian cells quantifies proteome heterogeneity during cell differentiation.
Budnik, B., Levy, E., Harmange, G. et al.
Genome Biol 19, 161 (2018).
https://doi.org/10.1186/s13059-018-1547-5
Abstract
Some exciting biological questions require quantifying thousands of proteins in single cells. To achieve this goal, we develop Single Cell ProtEomics by Mass Spectrometry (SCoPE-MS) and validate its ability to identify distinct human cancer cell types based on their proteomes. We use SCoPE-MS to quantify over a thousand proteins in differentiating mouse embryonic stem cells. The single-cell proteomes enable us to deconstruct cell populations and infer protein abundance relationships. Comparison between single-cell proteomes and transcriptomes indicates coordinated mRNA and protein covariation, yet many genes exhibit functionally concerted and distinct regulatory patterns at the mRNA and the protein level.