PXD066889

PXD066889 is an original dataset announced via ProteomeXchange.

Title	pLink Characterizing the dynamic oligomerization of HSP90β using photo-cross-linking
Description	Cross-linking mass spectrometry (XL-MS) is a transformative tool for probing protein structures. While conventional chemical crosslinkers exhibit well-defined chemistry for specific residues, photo-crosslinkers, despite their superior reactivity, have been hindered by incomplete mechanistic understanding and a lack of analytical frameworks. Here, we demonstrate that diazirine-based photo-crosslinks are inherently MS-cleavable—a novel property but also complicates spectral interpretation for overlapping peptide backbone and crosslinker side-chain fragments. Leveraging diagnostic side-chain fragmentation fingerprints, we developed a machine learning model that significantly improves ion coverage and reduces false discovery rates when combined with existing search algorithms. Further, we designed a homo-bifunctional diazirine crosslinker that allows for true on-demand photo-crosslinking. Empowered, we captured transient tetrameric assemblies of human HSP90β and revealed structural transitions in association equilibrium upon heat stress—features inaccessible with conventional chemical crosslinking. Together, our work establishes a new paradigm of XL-MS, combining the temporal sensitivity and precision of photo-activation with analytical confidence.
HostingRepository	PRIDE
AnnounceDate	2026-04-09
AnnouncementXML	Submission_2026-04-09_07:14:58.613.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	carbamoylated residue; acetylated residue; monohydroxylated residue
Instrument	LTQ Orbitrap Elite

Revision	Datetime	Status	ChangeLog Entry
0	2025-08-03 00:56:07	ID requested
⏵ 1	2026-04-09 07:14:59	announced

Dataset with its publication pending

submitter keyword: cleavable cross-linkers,diazirine, photo-cross-linking, machine learning (decision tree), HSP90β

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/PXD066889

PRIDE project URI

• PRIDE
  1. PXD066889
     1. Label: PRIDE project
     2. Name: pLink Characterizing the dynamic oligomerization of HSP90β using photo-cross-linking