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. 2023 Jul 27;14:4539. doi: 10.1038/s41467-023-40129-9

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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 and b Swarmplots of the number of peptides (a) or proteins (b) reported at 1% FDR. c and d The proportion of PSMs (c) or total number of PSMs (d) from each of the five ranks reported. The darker, diagonally dashed bars represent results after spectral and RT rescoring, while the lighter, solid bars represent the results without using deep learning features. Source data are provided as a Source Data file.