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. 2024 Mar 15;43(8):1653–1685. doi: 10.1038/s44318-024-00063-y

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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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ER-derived vesicles were isolated by MemPrep and subsequently analyzed by untargeted proteomics. An additional sodium carbonate wash step was performed on P100 to remove soluble proteins from the membrane preparation. (A) Limma analysis identified proteins that are accumulating in ER preparations after prolonged DTT-induced stress (top right quadrant of volcano plot). Proteins that are discussed in the text are indicated. The enrichment of proteins in preparations of the stressed ER membrane was considered significantly when they were at least twofold enriched compared to their abundance in pre-stress conditions with a P value < 0.01 (n = 3 biological replicates). (B) Limma analysis showing proteins that are accumulating in the ER upon prolonged TM-induced ER stress (top right quadrant of volcano plot). All proteins discussed in the text are labeled. The enrichment of proteins in the preparations of the stressed ER was considered significant when they were enriched at least twofold compared to their abundance in pre-stress conditions with a P value < 0.01 (n = 3 biological replicates). (C) Enriched gene ontology terms (GO terms) in the list of enriched proteins. GO terms are grouped by categories, FDR < 1% (n = 3 biological replicates). Data information: Data in (A, B) are presented as the mean from three biological replicates. We used the moderated t-test limma to test for differential enrichment. P values were corrected for multiple testing with the method from Benjamini and Hochberg. Data in (C) presented as mean from three biological replicates. P values were derived from a Fisher-test and corrected for multiple testing with the method of Benjamini and Hochberg. Source data are available online for this figure.