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. 2022 Oct 10;13:5948. doi: 10.1038/s41467-022-33570-9

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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. 4 — a An MR-plot where dark green lines are drawn at suggested threshold and hits are highlighted in orange. b BANDLE rank plot showing the distribution of differentially localised proteins. c The top differentially localised proteins from BANDLE plotted with uncertainty estimates. d Bootstrap distributions of correlations with a phosphoproteomic time-course experiment. The BANDLE confidence intervals differ significantly from 0, while the MR method do not. 5000 bootstrap samples were used with data presented as medians with notches representing the interquartile range (IQR), and the whiskers extending to 1.5*IQR. e PCA plots with (smoothed) localisation probabilities project onto them. Each colour represents an organelle and ellipses represent lines of isoprobability. The inner ellipse corresponds to 0.99 and the proceed line 0.95 with further lines decreasing by 0.05 each time. The annotated proteins demonstrate examples of differential localisations. EGFR (P005330) clearly relocalises from the PM to endosome, while SHC-1 (P29353) and GRB2 (P62993) relocalise from unknown localisation to the lysosome. Source data are provided as a Source Data file in the Supplementary Material.