PXD072009

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

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PRIDE project URI

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