PXD063145 is an
original dataset announced via ProteomeXchange.
Dataset Summary
| Title | APPLE-MS: A modular affinity purification-mass spectrometry method assisted by PafA- mediated proximity labeling |
| Description | While affinity purification-mass spectrometry (AP-MS) has significantly advanced protein-protein interaction (PPI) studies, its limitations in detecting weak, transient, and membrane-associated interactions remain. To address these challenges, we introduced an innovative proteomic method termed Affinity Purification coupled Proximity LabEling-Mass Spectrometry (APPLE-MS), which combines the high specificity of twin-strep-tag enrichment with PafA-mediated proximity labeling. This method achieves unprecedented sensitivity while maintaining high specificity (4.07-fold over AP-MS). APPLE-MS also revealed the dynamic mitochondrial interactome of SARS-CoV-2 ORF9B during antiviral responses, while endogenous PIN1 profiling uncovered novel roles in DNA replication. Notably, APPLE-MS enabled in situ mapping of GLP-1 receptor complexes, demonstrating its unique capabilities for membrane PPI studies. This versatile method advances interactome research by providing comprehensive, physiologically relevant PPI networks, opening new opportunities for mechanistic discovery and therapeutic targeting. |
| HostingRepository | PRIDE |
| AnnounceDate | 2025-10-27 |
| AnnouncementXML | Submission_2025-10-26_17:29:51.277.xml |
| DigitalObjectIdentifier | |
| ReviewLevel | Peer-reviewed dataset |
| DatasetOrigin | Original dataset |
| RepositorySupport | Unsupported dataset by repository |
| PrimarySubmitter | Shi-Han Luo |
| SpeciesList | scientific name: Homo sapiens (Human); NCBI TaxID: NEWT:9606; scientific name: Rattus norvegicus (Rat); NCBI TaxID: NEWT:10116; |
| ModificationList | No PTMs are included in the dataset |
| Instrument | Orbitrap Exploris 480 |
Dataset History
| Revision | Datetime | Status | ChangeLog Entry |
|---|
| 0 | 2025-04-20 23:11:54 | ID requested | |
| ⏵ 1 | 2025-10-26 17:29:52 | announced | |
Publication List
| 10.1016/j.crmeth.2025.101166; |
| Luo S, Xie L, Yang L, Hu Z, Wang L, Wang Y, Li Q, Guo S, Tao S, Jiang H, Sensitive and specific affinity purification-mass spectrometry assisted by PafA-mediated proximity labeling. Cell Rep Methods, 5(9):101166(2025) [pubmed] |
Keyword List
| submitter keyword: AP-MS, proximity labeling,protein-protein interaction, interactome |
Contact List
| Shengce Tao |
|---|
| contact affiliation | Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education),Shanghai Jiao Tong University, Shanghai 200240, China |
| contact email | taosc@sjtu.edu.cn |
| lab head | |
| Shi-Han Luo |
|---|
| contact affiliation | Shanghai Jiao Tong University |
| contact email | nanlouyue@sjtu.edu.cn |
| dataset submitter | |
Full Dataset Link List
Dataset FTP location
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| PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD063145
- Label: PRIDE project
- Name: APPLE-MS: A modular affinity purification-mass spectrometry method assisted by PafA- mediated proximity labeling
