PXD052480-1

PXD052480 is an original dataset announced via ProteomeXchange.

Title	PhoXplex: Combining phospho-enrichable crosslinking with isobaric labelling for quantitative proteome-wide mapping of protein interfaces
Description	Integrating crosslinking mass spectrometry (XL-MS) into structural biology workflows provides valuable information about the spatial arrangement of amino acid stretches, which can guide elucidation of protein assembly architecture. Additionally, combination of XL-MS with peptide quantitation techniques is a powerful approach to delineate protein interface dynamics across diverse conditions. While XL-MS is increasingly effective with isolated proteins or small complexes, its application to whole-cell samples poses technical challenges related to analysis depth and throughput. The use of enrichable crosslinkers has greatly improved the detectability of protein interfaces in a proteome-wide scale, facilitating global protein-protein interaction mapping. Therefore, bringing together enrichable crosslinking and multiplexed peptide quantification is an appealing approach to enable comparative characterization of structural attributes of proteins and protein interactions. Here, we combined phospho-enrichable crosslinking with TMT labelling to develop a streamline workflow (PhoXplex) for the detection of differential structural features across a panel of cell lines in a global scale. We achieved deep coverage with quantification of over 9000 crosslinking events including potentially novel interactions. Overlaying AlphaFold predictions and disorder protein annotations enables exploration of the quantitative crosslinking dataset, to reveal possible associations between mutations and protein structures. Lastly, we discuss current shortcomings and perspectives for deep whole-cell profiling of protein interfaces at large-scale.
HostingRepository	PRIDE
AnnounceDate	2024-10-21
AnnouncementXML	Submission_2024-10-21_10:04:47.372.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Graeme Benstead-Hume
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2024-05-22 08:28:32	ID requested
⏵ 1	2024-10-21 10:04:47	announced

10.1021/ACS.JPROTEOME.4C00567;

submitter keyword: isobaric labelling,phospho-enrichable crosslinking

Jytoi Choudhary
contact affiliation	Functional Proteomics, ICR
contact email	jyoti.choudhary@icr.ac.uk
lab head
Graeme Benstead-Hume
contact affiliation	ICR
contact email	ghume@icr.ac.uk
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/2024/10/PXD052480

PRIDE project URI

• PRIDE
  1. PXD052480
     1. Label: PRIDE project
     2. Name: PhoXplex: Combining phospho-enrichable crosslinking with isobaric labelling for quantitative proteome-wide mapping of protein interfaces