Focus on single-cell proteomics

Single-cell proteomics is a challenging goal and an area of rapid methods development. This Focus issue highlights the many paths toward high-throughput, high-sensitivity measurements.

New instruments are emerging in single-cell and single-molecule proteomics. This will offer labs a choice of technologies.

This Review covers the state of the art in applying mass spectrometry- or next-generation sequencing-based techniques for single-cell proteomics analysis, offering suggestions for maximizing the advantages of both approaches.

A community of researchers working in the emerging field of single-cell proteomics propose best-practice experimental and computational recommendations and reporting guidelines for studies analyzing proteins from single cells by mass spectrometry.

Recent technological advances in mass spectrometry promise to add single-cell proteomics to the biologist’s toolbox. Here we discuss the current status and what is needed for this exciting technology to lead to biological insight — alone or as a complement to other omics technologies.

The development of mass spectrometry-based single-cell proteomics technologies opens unique opportunities to understand the functional crosstalk between cells that drive tumor development.

Increasing evidence suggests that the spatial distribution of biomolecules within cells is a critical component in deciphering single-cell molecular heterogeneity. State-of-the-art single-cell MS imaging is uniquely capable of localizing biomolecules within cells, providing a dimension of information beyond what is currently available through in-depth omics investigations.

We argue that the study of single-cell subcellular organelle omics is needed to understand and regulate cell function. This requires and is being enabled by new technology development.

The nanopore community is stepping toward a new frontier of single-molecule protein sequencing. Here, we offer our opinions on the unique potential for this emerging technology, with a focus on single-cell proteomics, and some challenges that must be overcome to realize it.

Mammalian cells have about 30,000 times as many protein molecules as mRNA molecules, which has major implications in the development of proteomics technologies. We discuss strategies that have been helpful for counting billions of protein molecules by liquid chromatography–tandem mass spectrometry and suggest that these strategies can benefit single-molecule methods, especially in mitigating the challenges posed by the wide dynamic range of the proteome.