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. 2023 Jan 28;14:455. doi: 10.1038/s41467-023-36081-3

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© The Author(s) 2023

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. 5 — a–c Proximity labeling of synaptophysin and ATG9A vesicles using miniTurboID (mTB). a Experimental design. b Biotinylated proteins were affinity-purified on streptavidin magnetic beads and detected by SDS-PAGE and blotting with IRDye680-streptavidin. See also Supplementary Fig. 8a–c. c, Volcano plot of the proteins identified by LC-MS/MS. Significant hits (p-value < 0.05 and absolute fold-change > 1.5) are indicated in green (ATG9A enriched) or blue (synaptophysin enriched). p-values were calculated by the two-sided paired Student’s t-test. The list of proteins can be found in Supplementary Data 1. d–f Immunoisolation of synaptophysin-HA and ATG9A-HA vesicles on anti-HA magnetic beads. d Experimental design. e A small vesicle enriched cell fraction was immunoisolated on anti-HA magnetic beads. Then proteins were solubilized and processed by SDS-PAGE and immunoblotting with anti-HA antibodies. See also Supplementary Fig. 8d–f. f A volcano plot showing the proteins enriched in ATG9A-HA or synaptophysin-HA vesicles. Significant hits (p-value < 0.05 and absolute fold-change > 1.5) are indicated in green (ATG9A enriched) or blue (synaptophysin enriched). p-values were calculated by the two-sided paired Student’s t-test. The list of proteins can be found in Supplementary Data 1. g Ontology Analysis of the proteome using the SynGO tool showing enrichment of SV proteins in synaptophysin-HA but not in ATG9A-HA immunoisolated samples. Colors represent enrichment Q-value (–log10 values). Quantitative LC-MS/MS data from biological triplicates. Source data are provided as a Source Data file.