PXD022443

PXD022443 is an original dataset announced via ProteomeXchange.

Title	Characterizing protein conformers by cross-linking mass spectrometry and pattern recognition
Description	Motivation: Chemical cross-linking coupled to mass spectrometry (XLMS) emerged as a powerful technique for studying protein structures and large-scale protein-protein interactions. Nonetheless, XLMS lacks software tailored toward dealing with multiple conformers; this scenario can lead to high-quality identifications that are mutually exclusive. This limitation hampers the applicability of XLMS in structural experiments of dynamic protein systems, where less abundant conformers of the target protein are expected in sample. Results: We present QUIN-XL, a software that uses unsupervised clustering to group cross-link identifications by their quantitative profile across multiple samples. QUIN-XL highlights regions of the protein or system presenting changes in its conformation when comparing different biological conditions. We demonstrate the usefulness of our software by revisiting the HSP90 protein, comparing three of its different conformers. QUIN-XL’s clusters correlate directly to known protein 3D structures of the conformers and therefore validates our software.
HostingRepository	PRIDE
AnnounceDate	2025-01-03
AnnouncementXML	Submission_2025-01-03_14:27:22.609.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Louise Ulrich Kurt
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	iodoacetamide derivatized residue
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2020-11-10 01:59:55	ID requested
⏵ 1	2025-01-03 14:27:22	announced

10.1093/BIOINFORMATICS/BTAB149;

submitter keyword: hsp90, cross-link, quantification

Paulo Costa Carvalho
contact affiliation	Laboratory for Structural and Computational Proteomics, Carlos Chagas Institute, Fiocruz, Paraná, Brazil
contact email	paulo@pcarvalho.com
lab head
Louise Ulrich Kurt
contact affiliation	Carlos Chagas Institute - Fiocruz
contact email	lookurt27@gmail.com
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/2025/01/PXD022443

PRIDE project URI

• PRIDE
  1. PXD022443
     1. Label: PRIDE project
     2. Name: Characterizing protein conformers by cross-linking mass spectrometry and pattern recognition