Proteomics

Dataset Information

0

A Glycosidic-Bond-Based Mass-Spectrometry-Cleavable Cross-linker Enables In Vivo Cross-linking for Protein Complex Analysis


ABSTRACT: 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.

ORGANISM(S): Homo Sapiens Saccharomyces Cerevisiae

SUBMITTER: Lihua Zhang  

PROVIDER: PXD047554 | iProX | Wed Dec 06 00:00:00 GMT 2023

REPOSITORIES: iProX

altmetric image

Publications

A Glycosidic-Bond-Based Mass-Spectrometry-Cleavable Cross-linker Enables In Vivo Cross-linking for Protein Complex Analysis.

Chen Jing J   Zhao Qun Q   Gao Hang H   Zhao Lili L   Chu Huiying H   Shan Yichu Y   Liang Zhen Z   Zhang Yukui Y   Zhang Lihua L  

Angewandte Chemie (International ed. in English) 20230504 24


Chemical cross-linking mass spectrometry (CXMS) has emerged as a powerful technology to analyze protein complexes. However, the progress of in vivo CXMS studies has been limited by cross-linking biocompatibility and data analysis. Herein, a glycosidic bond-based MS-cleavable cross-linker of trehalose disuccinimidyl ester (TDS) was designed and synthesized, which was fragmented in MS under CID/HCD to simplify the cross-linked peptides into conventional single peptides via selective cleavage betwe  ...[more]

Similar Datasets

2019-10-14 | PXD015080 | Pride
2020-08-21 | MSV000085996 | MassIVE
2022-07-15 | PXD035355 | JPOST Repository
2022-07-14 | PXD035317 | JPOST Repository
2021-09-24 | PXD027611 | Pride
2021-07-30 | PXD012788 | Pride
2023-10-04 | PXD035589 | Pride
2021-12-20 | PXD030552 | iProX
2019-04-03 | PXD010796 | Pride
2019-04-01 | PXD010070 | Pride