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. 2023 Jul 12;14:4154. doi: 10.1038/s41467-023-39869-5

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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. 3 — Source data are provided as a Source Data file. a Bar plots of the quantified peptides. The bar height is the average number of three replicates. The white dots indicate the numbers from individual replicates. The results from the original publication (obtained using EncyclopeDIA version 0.8.3) are shown. We also re-analyzed the data using the latest EncyclopeDIA (version 2.12.30). b Box plots of peptide CVs. There are 3 single-shot DIA runs from 3 replicates. Blue box plots represent overlapping peptides shared among all tools, while brown box plots depict unique peptides quantified exclusively by each specific tool. The box in each box plot captures the IQR, with the bottom and top edges representing the Q1 and Q3 respectively. The median is marked by a horizontal line within the box. The whiskers extend to the minima and maxima within 1.5 times the IQR below Q1 or above Q3.