Skip to main content

Thank you for visiting You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

Framework for multiplicative scaling of single-cell proteomics

Many biomedical questions demand scalable, deep, and accurate proteome analysis of small samples, including single cells. A scalable framework of multiplexed data-independent acquisition for mass spectrometry enables time saving by parallel analysis of both peptide ions and protein samples, thereby realizing multiplicative gains in throughput.

Your institute does not have access to this article

Access options

Buy article

Get time limited or full article access on ReadCube.


All prices are NET prices.

Fig. 1: Increasing the throughput and accuracy of sensitive proteomics.


  1. Slavov, N. Driving single cell proteomics forward with innovation. J. Proteome Res. 20, 4915–4918 (2021). A Perspective that explains the need and opportunities for developing plexDIA.

    CAS  Article  Google Scholar 

  2. Specht, H. et al. Single-cell proteomic and transcriptomic analysis of macrophage heterogeneity using SCoPE2. Genome Biol. 22, 50 (2021). This article reported automated and multiplexed MS proteomics analysis of about 3,000 proteins across 1,490 single human cells.

    CAS  Article  Google Scholar 

  3. Venable, J. D. et al. Automated approach for quantitative analysis of complex peptide mixtures from tandem mass spectra. Nat. Methods 1, 39–45 (2004). This article introduced the concept of DIA for MS proteomics.

    CAS  Article  Google Scholar 

  4. Slavov, N. Scaling up single-cell proteomics. Mol. Cell. Proteom. 21, 100179 (2022). A Perspective discussing strategies for increasing the throughput of single-cell proteomic analysis.

    CAS  Article  Google Scholar 

  5. Leduc, A. et al. Exploring functional protein covariation across single cells using nPOP. Preprint at bioRxiv (2022). A preprint introducing surface droplets for single-cell proteomics sample preparation, which prepare thousands of single cells in parallel and easily scale to different multiplexing formats.

Download references

Additional information

Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

This is a summary of: Derks, J. et al. Increasing the throughput of sensitive proteomics by plexDIA. Nat. Biotechnol. (2021).

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Framework for multiplicative scaling of single-cell proteomics. Nat Biotechnol (2022).

Download citation

  • Published:

  • DOI:


Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing