PXD072009-1

PXD072009 is an original dataset announced via ProteomeXchange.

Title	Characterizing the dynamic oligomerization of Hsp90β using photo-cross-linking
Description	Cross-linking mass spectrometry (XL-MS) is a powerful tool for probing protein structures. While conventional chemical cross-linkers react with specific residues with defined chemistry, photo-cross-linkers, despite their superior reactivity, have been hindered by incomplete mechanistic understanding and lack of analytical framework. Here, we show that diazirine-based photo-cross-links are inherently MS-cleavable, generating composite backbone and side-chain fragments that complicates spectral interpretation. Yet, leveraging the side-chain fragmentation fingerprints, we developed a machine learning model that, when integrated with existing search algorithms, significantly improves ion coverage and reduces false discovery rate. Furthermore, we engineered a homo-bifunctional diazirine cross-linker, enabling true on-demand photo-cross-linking. Applying this workflow, we captured transient tetrameric assemblies of human Hsp90β and revealed structural transitions in association equilibrium upon heat stress, features inaccessible with conventional chemical cross-linking. Together, our work establishes a new paradigm in XL-MS, combining temporal resolution of photo-activation with analytical confidence for residue-level structural insights.
HostingRepository	PRIDE
AnnounceDate	2026-04-09
AnnouncementXML	Submission_2026-04-09_07:23:26.247.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	yida jiang
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: NEWT:9606;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2025-12-15 04:38:39	ID requested
⏵ 1	2026-04-09 07:23:26	announced

Dataset with its publication pending

submitter keyword: Hsp90, cleavable cross-linkers,diazirine, photo-cross-linking

Chun Tang
contact affiliation	Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China.
contact email	tang_chun@pku.edu.cn
lab head
yida jiang
contact affiliation	Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
contact email	jiangyida@pku.edu.cn
dataset submitter

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://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD072009

PRIDE project URI

• PRIDE
  1. PXD072009
     1. Label: PRIDE project
     2. Name: Characterizing the dynamic oligomerization of Hsp90β using photo-cross-linking