PXD047554-1
PXD047554 is an original dataset announced via ProteomeXchange.
Dataset Summary
Title | A Glycosidic-Bond-Based Mass-Spectrometry-Cleavable Cross-linker Enables In Vivo Cross-linking for Protein Complex Analysis |
Description | Chemical cross-linking mass spectrometry (CXMS) has emerged as a powerful technology to analyze protein complex structure and interaction. However, the spectral fragmentation behavior and spectral data retrieval of cross-linked peptides are more complex than single peptides. In this study, we designed and synthesized a trehalose-based MS-cleavable cross-linker, Trehalose Disuccinimidyl Ester (TDS), which possesses a CID/HCD-cleavable glycosidic bond and has good bioorthogonality and amphipathicity. Using TDS, the cross-linked peptides were simplified into conventional single peptides via the selective cleavage between glycosidic and peptide bonds under individual MS collision energy, which enhances the matching degree and retrieval throughput of spectral identification. The deep coverage of the TDS method facilitated the accurate resolution of the structural dynamics of purified proteins with different physicochemical properties and yeast 26S proteasome complex. Additionally, the bioorthogonality and amphipathicity of TDS enabled the cross-linking reaction to occur in vivo without the introduction of any organic solvent. Through coinciding with this feature and MS-cleavable capacity, TDS provided us a high throughput snapshot of the structural architecture of protein complex in live cells. These results provide a promising TDS toolkit to study CXMS and decipher the protein conformations and interactions with high accuracy and easy portability for cross-linker design. |
HostingRepository | iProX |
AnnounceDate | 2023-12-06 |
AnnouncementXML | Submission_2023-12-05_19:13:17.556.xml |
DigitalObjectIdentifier | |
ReviewLevel | Peer-reviewed dataset |
DatasetOrigin | Original dataset |
RepositorySupport | Unsupported dataset by repository |
PrimarySubmitter | Jing Chen |
SpeciesList | scientific name: Saccharomyces cerevisiae; NCBI TaxID: 4932; scientific name: Homo sapiens; NCBI TaxID: 9606; |
ModificationList | No PTMs are included in the dataset |
Instrument | Orbitrap Exploris 480 |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
---|---|---|---|
0 | 2023-12-05 19:12:46 | ID requested | |
⏵ 1 | 2023-12-05 19:13:18 | announced |
Publication List
Chen J, Zhao Q, Gao H, Zhao L, Chu H, Shan Y, Liang Z, Zhang Y, Zhang L, A Glycosidic-Bond-Based Mass-Spectrometry-Cleavable Cross-linker Enables In Vivo Cross-linking for Protein Complex Analysis. Angew Chem Int Ed Engl, 62(24):e202212860(2023) [pubmed] |
Keyword List
submitter keyword: cross-linker |
Contact List
Lihua Zhang | |
---|---|
contact affiliation | Dalian Institute of Chemical Physics, Chinese Academy of Sciences |
contact email | lihuazhang@dicp.ac.cn |
lab head | |
Jing Chen | |
contact affiliation | Dalian Institute of Chemical Physics, Chinese Academy of Sciences |
contact email | chenj1810@dicp.ac.cn |
dataset submitter |
Full Dataset Link List
iProX dataset URI |