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. 2023 Apr 3;20(5):714–722. doi: 10.1038/s41592-023-01830-1

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© The Author(s) 2023

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

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Extended Data Fig. 2 — The median coefficient of variation (that is the standard deviation scaled by the mean) of all peptide-level relative abundances that map to the same leading razor protein is used to separate successfully prepared single cells from those that will not generate accurate data. By choosing a CV threshold that separates control samples (droplets which received all reagents but did not contain a single cell) from single cells, cells with noisier protein-level quantitation can be removed prior to further data processing. The single-cell and control tallies above each figure represent the number of single cells or control wells that passed the CV threshold of 0.4. (a) contains the CV distributions for the single-cell samples associated with Fig. 2a–e, analyzed by shotgun LC-MS/MS methods. (b) contains the CV distributions for the single-cell samples associated with Fig. 2a, analyzed by pSCoPE. (c) contains the CV distributions for the single-cell samples associated with Fig. 2b–e, analyzed by pSCoPE. (d) contains the CV distributions for the single-cell samples associated with Figs. 4–6.