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. 2024 Feb 27;12:35. doi: 10.1186/s40478-024-01740-z

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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/. 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 — Identification of commonly abundant proteins among the diverse surface-endocytome in GBM. A Quantification of biotinylated surfaceome and endocytome in primary GBM cultures and U87MG cell line by FACS. B Fraction of endocytosed proteins expressed as the percentage of total surfaceome shown in (A). Data are presented as the mean ± S.D. from three independent experiments, each performed in triplicates. C, D, Analysis of LC–MS/MS profiling data confirms significant enrichment of SURFME protein identities by the TS-MAP approach in surface (C) and endocytome (D) samples when compared with control. E Heatmap of normalized TS-MAP data shows the heterogeneous abundance in surfaceome and endocytome identities between GBM cultures. F Kendall’s Tau correlation of SURFME identity ranks displays a weak association between transcriptomics and TS-MAP proteomics. G Ranking of SURFME proteins according to abundance (most abundant = first position) shows a strong association between surfaceome and endocytome in the respective GBM cell type. Top-right quadrants: proteins with high surface abundance and efficient endocytic capacity, highlighting some identities common across GBM cultures (see also, Additional file 4: Data File S3)