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. 2022 May 18;13:2736. doi: 10.1038/s41467-022-30376-7

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© The Author(s) 2022

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. 5 — Network analysis of proteins and their Ub sites identified in all five UbiSite DIA replicates of MG132 or PR619-treated cells. Networks were generated using the STRING database of protein-protein interactions (confidence cutoff = 0.9) and subclustered into the most interconnected networks using MCODE (default settings). A functional enrichment was performed on each subcluster with the human genome as background. The most significant biological process or complex is displayed as a title for each subcluster, or colour coded in the node centre for larger subclusters. The dynamics of each Ub site in response to proteasome (MG132) or DUB inhibition (PR619) was colour coded according to the fold-change vs DMSO (log2), where a grey colour indicates that the Ub site was not identified in that treatment. The most N-terminal Ub site is visualised at 12 o’clock of the node, and progresses clockwise to the most C-terminal Ub site at 11 o’clock. The outer ring colour represents PR619 fold-change vs DMSO and the inner ring colour represents MG132 fold-change vs DMSO. The size of the node represents the number of Ub sites identified on that protein. Source data are provided as a Source Data file.