PXD060322

PXD060322 is an original dataset announced via ProteomeXchange.

Title	Utilization of high-resolution mass spectrometry and data-independent analysis to track the monoclonal antibody spatial stability
Description	Chemical cross-linking coupled with mass spectrometry (CXMS) offers the distance constraints critical for building the structural model of protein and protein complexes and understanding dynamics of biological systems. Originally developed for protein structural models, CXMS has evolved into method for studying protein complex formation, ligand-induced conformational changes, and quantitative structural analysis using isotopically labeled cross-linkers. In this study we tested the potential of isotopically labelled MS-cleavable cross-linker to track the stability of the therapeutic monoclonal antibodies. A novel isotopically labelled MS-cleavable cross-linker was synthesized, and its reactivity was successfully tested on peptide and protein standards. Further, the novel cross-linker was utilized to test the stability of selected therapeutical monoclonal antibodies, Avastin and Herceptin, adopting the data-independent acquisition. This study reports the advantages of using combination of 13C isotopically labelled MS-cleavable cross-linkers and data-independent mass spectrometry analysis for the automated identification of cross-linked products and thus monitoring the structural rearrangement of protein structure.
HostingRepository	PRIDE
AnnounceDate	2025-07-08
AnnouncementXML	Submission_2025-07-08_13:11:28.971.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Zdenek Kukacka
SpeciesList	scientific name: Bos taurus (Bovine); NCBI TaxID: 9913; scientific name: Homo sapiens (Human); NCBI TaxID: 9606; scientific name: Equus caballus (Horse); NCBI TaxID: 9796;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Bruker Daltonics solarix series

Revision	Datetime	Status	ChangeLog Entry
0	2025-01-29 07:40:04	ID requested
⏵ 1	2025-07-08 13:11:29	announced

10.1080/14789450.2025.2492763;

submitter keyword: antibody, mass spectrometry, protein structure,chemical cross-linking, data-independent analysis, stable isotopes

Petr Novak
contact affiliation	Laboratorz of structural biologz and cell signaling
contact email	pnovak@biomed.cas.cz
lab head
Zdenek Kukacka
contact affiliation	Institute of Microbiology, The Czech Academy of Sciences
contact email	zdenek.kukacka@biomed.cas.cz
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/2025/07/PXD060322

PRIDE project URI

• PRIDE
  1. PXD060322
     1. Label: PRIDE project
     2. Name: Utilization of high-resolution mass spectrometry and data-independent analysis to track the monoclonal antibody spatial stability