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. 2024 May 3;20(6):651–675. doi: 10.1038/s44320-024-00037-6

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© The Author(s) 2024

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 licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence 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 licence, visit http://creativecommons.org/licenses/by/4.0/. Creative Commons Public Domain Dedication waiver http://creativecommons.org/publicdomain/zero/1.0/ applies to the data associated with this article, unless otherwise stated in a credit line to the data, but does not extend to the graphical or creative elements of illustrations, charts, or figures. This waiver removes legal barriers to the re-use and mining of research data. According to standard scholarly practice, it is recommended to provide appropriate citation and attribution whenever technically possible.

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(A) Barplot with the numbers of altered LiP peptides (blue) and corresponding structurally altered proteins (green) for aSyn monomer (left) and amyloid fibrils (right). (B) Venn diagram with the numbers of structurally altered proteins for aSyn monomer (blue) and for amyloid fibrils (green). The overlap of structurally altered proteins identified for both aSyn monomer and amyloid fibrils is indicated in gray. (C) The plots show the fraction of known aSyn interactors (based on the STRING database) in structurally altered proteins (right) versus all detected proteins (left) upon spike-in of aSyn monomer into an iPSC-derived cortical neuron extract. The p value assessing enrichment (Fisher’s exact test) is shown. (D) Enrichment plot as in (C) upon spike-in of aSyn fibrils. (E, F) Functional enrichment analyses of structurally altered proteins upon spike-in of aSyn monomer (E) or fibril (F), based on the indicated ontologies (molecular function in light green, cellular component in green, biological process in dark green); the plots show the size (i.e., a score calculated based on q value) of the top6 significant gene ontology terms upon removal of redundant terms (q value <0.01, Benjamini–Hochberg FDR, minimum hypergeometric test, SimRel functional similarity, size = 0.7). (G) Identified modules with enriched GOBP (q value <0.05, Fisher’s exact test, one-sided) that are linked to either common (yellow node) or rare variants (red node) of PD genes for aSyn monomer (blue) or fibrils (green). The thickness of lines represents the Jaccard index (red for Jaccard index >0.7, gray for Jaccard index <0.7). (H) Heatmap showing the top4 GOBP terms within each module as indicated in (B). The gradient color indicates the significance based on the results of a GOBP enrichment test (purple = low significance, yellow = high significance).