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. 2022 Sep 8;10:134. doi: 10.1186/s40478-022-01424-6

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© The Author(s) 2022

Open AccessThis 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/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.

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Fig. 2 — Workflow of methodology. a Flowchart highlighting methods used within the experiment. Tissue was micro-dissected per region, tissue homogenised and proteins were extracted and digested into peptides. Samples were proteome profile using mass spectrometry. Candidates were selected before confirmatory targeted Multiple Reaction Monitoring LCMS/MS analysis was completed. Functional assays were performed. b Venn diagram indicating how many proteins were detected uniquely in the supernatant and pellet fractions and how many overlapped. c Heat map of alpha-synuclein expression as fold change in Braak stage 3/4 compared to control indicated by colour. Red indicated upregulation and green downregulation compared to controls with deeper colour indicating a higher level of change. White indicates no change in expression compared to controls. d Overall change in the brain proteome for each region and condition expressed as a percentage of total proteome either upregulated (red) or downregulated (green) by more than 1.5 fold. S represents the supernatant fraction and P represents the pellet fraction. Graph created in GraphPad Prism v8