PXD064228-1

PXD064228 is an original dataset announced via ProteomeXchange.

Title	FAIMS-GPF XL-MS: crosslinking-mass spectrometry based on gas-phase fractionation
Description	Protein-protein interactions (PPIs) underpin nearly all cellular processes; therefore, mapping PPI and protein-protein association networks is critical for understanding how biological systems function in health and disease. However, many functionally relevant PPIs are transient and mediated by weak affinity interactions, making them challenging to detect. Using chemical cross-linking together with mass spectrometry (XL-MS) has emerged as an important category of methods for mapping PPIs, including those that are more dynamic and transient, although XL-MS workflows face limitations which hinder their routine use, especially in proteomic platforms. Here, to address these limitations, we developed a XL-MS workflow based on gas-phase fractionation (GPF) using high-field asymmetric waveform ion mobility spectrometry (FAIMS). Our optimized FAIMS-GPF XL-MS protocols exhibited improved performance when handling both low-complexity samples, such as purified Cdk7-Activating Kinase (CAK) heterotrimer, and high-complexity cross-linked HeLa lysates. In HeLa lysate we identified 1,278 cross-links accounting for 213 PPIs without in-solution fractionation, starting from less than 20 µg of sample. The method also proved effective for analyzing low-abundance, high-complexity samples such as spliceosomes. Overall, FAIMS-GPF enhanced the detection of cross-linked peptides and improved PPI coverage, thus offering a scalable, high-sensitivity solution for XL-MS integration with structural biology and functional proteomics applications.
HostingRepository	PRIDE
AnnounceDate	2026-05-27
AnnouncementXML	Submission_2026-05-27_09:52:35.308.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Hugo Gizardin-Fredon
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: NEWT:9606;
ModificationList	acetylated residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Eclipse

Revision	Datetime	Status	ChangeLog Entry
0	2025-05-23 01:42:07	ID requested
⏵ 1	2026-05-27 09:52:35	announced

Dataset with its publication pending

submitter keyword: FAIMS,Cross-linking mass spectrometry, structural biology, interactomics

Sarah Cianférani
contact affiliation	BioOrganique Mass Spectrometry Lab (LSMBO), Institut Pluridisciplinaire hubert Curien (IPHC) UMR7178, CNRS, University of Strasbourg
contact email	sarah.cianferani@unistra.fr
lab head
Hugo Gizardin-Fredon
contact affiliation	IPHC LSMBO, CNRS/Université de Strasbourg
contact email	hugo.gizardin-fredon@etu.unistra.fr
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/2026/05/PXD064228

PRIDE project URI

• PRIDE
  1. PXD064228
     1. Label: PRIDE project
     2. Name: FAIMS-GPF XL-MS: crosslinking-mass spectrometry based on gas-phase fractionation