PXD052357-1
PXD052357 is an original dataset announced via ProteomeXchange.
Dataset Summary
| Title | Benchmarking and automating the biotinylation proteomics workflow |
| Description | While protein biotinylation has been widely used in biochemistry and biotechnology with various enrichment methods, different biotin enrichment strategies have not been systematically compared. Traditional biotinylation proteomics workflows suffer from complex sample preparation steps, non-specific bindings, limited throughput, and experimental variability. To address these critical challenges, we designed a two-proteome model, where yeast proteins were biotinylated in vitro and spiked in unlabeled human proteins, allowing us to distinguish true enrichment (yeast) from non-specific bindings (human) for comprehensively benchmarking of biotinylation proteomics methods. We also significantly optimized the entire workflow and reduced the sample preparation time from the traditional 3 days to just 9 hours, enabling a fully automated 96-well format sample processing for excellent reproducibility and throughput with minimized non-specific bindings. We then applied this optimized and automated workflow to proximity labeling proteomics and investigated the intricate interplay between mitochondria and lysosomes in living cells under both healthy state and mitochondrial damage. We demonstrated that mitochondrial damage led to an increased mitochondria-lysosome membrane contact and induced broad alternations in mitophagy-related proteins. We identified and quantified biotinylated proteins and precise amino acid residues at mitochondria-lysosome contact sites and within the mitophagy pathway, revealing an elevated level of interaction between mitochondria and lysosomes and proteome-wide remodeling in response to mitochondrial damage. |
| HostingRepository | MassIVE |
| AnnounceDate | 2024-06-24 |
| AnnouncementXML | Submission_2024-06-24_06:38:21.859.xml |
| DigitalObjectIdentifier | |
| ReviewLevel | Non peer-reviewed dataset |
| DatasetOrigin | Original dataset |
| RepositorySupport | Supported dataset by repository |
| PrimarySubmitter | Ling Hao |
| SpeciesList | scientific name: Homo sapiens; common name: human; NCBI TaxID: 9606; |
| ModificationList | unknown modification; unknown modification; unknown modification; unknown modification |
| Instrument | Q Exactive HF-X |
Dataset History
| Revision | Datetime | Status | ChangeLog Entry |
|---|---|---|---|
| 0 | 2024-05-17 17:45:27 | ID requested | |
| ⏵ 1 | 2024-06-24 06:38:22 | announced |
Publication List
| no publication |
Keyword List
| submitter keyword: biotinylation, proximity labeling, HeLa cell |
Contact List
| Ling Hao | |
|---|---|
| contact affiliation | The George Washington University |
| contact email | linghao@email.gwu.edu |
| lab head | |
| Ling Hao | |
| contact affiliation | George Washington University |
| contact email | haolab.19@gmail.com |
| dataset submitter | |
Full Dataset Link List
| MassIVE dataset URI |
| Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://massive.ucsd.edu/v07/MSV000094795/ |
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