Best practices for single-cell proteomics

In a Nature Methods Technology Feature in August 2019, Vivien Marx dreamt of single-cell proteomics. Today, thanks to some pioneers' groundbreaking efforts, we can confidently claim that a new and exciting single cell modality is available: mass spectrometry-based, that is un-targeted, single-cell proteomics.

Now that that dream has come true, a group of leading experts have joined forces to share their experiences and propose recommendations for performing, benchmarking and reporting single-cell proteomics experiments. In this paper, published in Nature Methods in March 2023, Gatto et al. focus their discussions on the several important aspects pertaining to experimental design, data evaluation and interpretation and reporting standards. These guidelines will enable establishing solid foundations for this emerging field.

Emerging applications of single-cell proteomics by MS. Single-cell proteomic measurements can define cell type and cell state clusters, support pseudotime inference, link protein levels to functional phenotypes, such as phagocytic activity, quantify protein covariation and apply it to study protein complexes, analyze protein conformations and quantify protein modifications, such as phosphorylation and proteolysis. Furthermore, integrating protein and RNA measurements from the same biological systems allows inferring transcriptional and post-translational regulation and investigating the covariation of transcription factors and downstream target transcripts.
Dim, dimension; PC, principal component.

Pr Laurent Gatto and Christophe Vanderaa, both from the Computational Biology and Bioinformatics laboratory (CBIO) at the de Duve Institute contributed to this publication. To learn more about their work, visit their website.

Article describing this research

Initial recommendations for performing, benchmarking and reporting single-cell proteomics experiments
Gatto L, Aebersold R, Cox J, Demichev V, Derks J, Emmott E, Franks AM, Ivanov AR, Kelly RT, Khoury L, Leduc A, MacCoss MJ, Nemes P, Perlman DH, Petelski AA, Rose CM, Schoof EM, Van Eyk J, Vanderaa C, Yates JR 3rd, Slavov N
Nat Methods. 2023 Mar 2. doi: 10.1038/s41592-023-01785-3

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