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. 2023 Mar 23;41(12):1776–1786. doi: 10.1038/s41587-023-01714-x

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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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Fig. 2 — a, Number of proteins detected for each of the six cell lines and cumulative as a function of peptides from the various protease digests. b, Median sequence coverage of various cell line proteomes achieved by digests with individual proteases and by combining all protease results. Supplementary Fig. 2c shows sequence coverage distributions separately for all combinations of cell lines, proteases and fragmentation methods. c, Venn diagram of all observed amino acids digested by trypsin versus all proteases combined excluding trypsin. d, Sequence coverage for each of the detected proteins for the tryptic peptide data (red) and combined protease digests, including trypsin (gray). e, Observed (dark gray) and theoretical (light gray) distributions of sequence coverage achieved for various combinations of proteases. The top three combinations of 2, 3, 4 or 5 proteases are displayed. f, Protein coverage comparison of transmembrane and nonmembrane proteins. For e and f, the lower whisker/quartile and upper quartile/whisker show the 5th, 25th, 75th and 95th percentiles, accordingly. g, Relative protein coverage of N terminus (left) and C terminus (right) transmembrane segments. Chymo., chymotrypsin.