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.
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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.
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.
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.
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.
Leduc, A. et al. Exploring functional protein covariation across single cells using nPOP. Preprint at bioRxiv https://doi.org/10.1101/2021.04.24.441211 (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.
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This is a summary of: Derks, J. et al. Increasing the throughput of sensitive proteomics by plexDIA. Nat. Biotechnol. https://doi.org/10.1038/s41587-022-01389-w (2021).
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Framework for multiplicative scaling of single-cell proteomics. Nat Biotechnol 41, 23–24 (2023). https://doi.org/10.1038/s41587-022-01411-1
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