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. 2023 Sep 22;14:5910. doi: 10.1038/s41467-023-41602-1

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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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Fig. 4 — a Density plots showing the log2 transformed light and heavy protein abundance ratios. Proteins quantified with directDIA shown in top and high-load (HL) library in the middle and gas-phase fractionated (GPF) in the bottom. Dashed lines denote expected ratios and numbers indicate the total number of identified proteins in each mix. MS1-based quantification is used throughout. b Similar to A, but showing the distribution of proteins identified with directDIA and gained with either HL or GPF libraries only (the directDIA found proteins are removed from these datasets). c Histogram showing protein distribution across the log2 transformed abundance range. Only the 1:1 (L:H) mix data is shown. d Hexbin plot showing the distribution of light and heavy (L:H) log2 transformed protein ratios for proteins found with directDIA and gained by the HL and GPF libraries. Source data are provided as a Source Data file.