PXD065949

PXD065949 is an original dataset announced via ProteomeXchange.

Title	Expanding the crosslinking mass spectrometry toolbox with vinyl sulfone crosslinkers
Description	Crosslinking mass spectrometry (MS) is a powerful approach for probing protein structures. However, most widely used crosslinkers rely on N-hydroxysuccinimide (NHS) esters, restricting reactivity primarily to lysine residues and protein N-termini, and rendering them incompatible with many amine-containing buffers (e.g., Tris) and key biochemical cofactors (e.g., ATP). To address these limitations, we introduce two novel vinyl-sulfone-based crosslinkers. Alkyne-BVSC is an enrichable, homobifunctional crosslinker featuring an acid-cleavable alkyne handle for downstream peptide enrichment. VSD is a heterobifunctional crosslinker combining a vinyl sulfone with a diazirine moiety for UV-activated photo-crosslinking. Both reagents are synthetically accessible from inexpensive precursors and retain reactivity in amine-rich biochemical environments. We show that vinyl sulfones react with cysteine, histidine, and lysine residues, thereby expanding crosslinkable residues beyond those accessible to NHS-esters. Moreover, we develop a stub-based post-search filtering strategy that leverages the MS-cleavable nature of vinyl sulfone linkages to improve crosslink identification sensitivity. Together, these advances establish vinyl-sulfone-based crosslinkers as versatile and complementary tools for structural proteomics.
HostingRepository	PRIDE
AnnounceDate	2025-11-29
AnnouncementXML	Submission_2025-11-29_05:59:04.548.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD065949
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Anthony Ciancone
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: NEWT:9606;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Eclipse

Revision	Datetime	Status	ChangeLog Entry
0	2025-07-09 07:56:13	ID requested
⏵ 1	2025-11-29 05:59:05	announced

10.1016/J.MCPRO.2025.101315;

10.6019/PXD065949;

submitter keyword: vinyl sulfones, mass spectrometry,crosslinking

Francis J. O'Reilly
contact affiliation	NCI/NIH CSB
contact email	oreillyfj@nih.gov
lab head
Anthony Ciancone
contact affiliation	NCI Post-Doctoral Researcher
contact email	cianconeam@nih.gov
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD065949
     1. Label: PRIDE project
     2. Name: Expanding the crosslinking mass spectrometry toolbox with vinyl sulfone crosslinkers