PXD047554

PXD047554 is an original dataset announced via ProteomeXchange.

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

Revision	Datetime	Status	ChangeLog Entry
0	2023-12-05 19:12:46	ID requested
⏵ 1	2023-12-05 19:13:18	announced

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]

submitter keyword: cross-linker

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

iProX dataset URI