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. 2023 Sep 19;14:5809. doi: 10.1038/s41467-023-41558-2

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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 Tripartite graph construction: connect peptides to all proteins that contain them, and proteins to the host genes, to form a tripartite graph. b SEPEP identification: identify and group structurally equivalent peptides (SEPEP), i.e., peptides connecting to the same set of proteins in the graph. c FDR control: calculate SEPEP-level FDR and remove SEPEPs with an FDR higher than the pre-specified threshold, e.g., FDR > 0.01. d SEPEP classification and reporting: classify SEPEPs based on their patterns of connections and report SEPEP-level quantification. e A comparison between SEPEP analysis procedure and the classical parsimony protein inference-based procedure.