PXD050960-1

PXD050960 is an original dataset announced via ProteomeXchange.

Title	2) Twisting Urea- to Imide-Based Mass Spectrometry-Cleavable Cross-Linkers to Embed Affinity Tags
Description	Disuccinimidyl dibutyric urea (DSBU) is a mass spectrometry (MS)-cleavable cross-linker that has been applied to multiple applications in structural biology, ranging from isolated protein complexes to comprehensive system-wide interactomics. DSBU facilitates a rapid and reliable identification of cross-links through the dissociation of its urea group in the gas-phase. In this study, we further advance the structural capabilities of DSBU by twisting the urea group into an imide, thus introducing a novel class of cross-linkers. This modification preserves the MS-cleavability of the amide bond, granted by the two acyl groups of the imide function. The central nitrogen atom enables the introduction of affinity purification tags. Here, we introduce disuccinimidyl dibutyric imide (DSBI) as prototype of this class of cross-linkers. It features a phosphonate handle for immobilized metal ion affinity chromatography (IMAC) enrichment. We detail DSBI synthesis and describe its behavior in solution and in the gas-phase while cross-linking isolated proteins and human cell lysates. DSBI and DSBU cross-links are compared at the same enrichment depths to bridge these two cross-linker classes. We validate DSBI cross-links by mapping them in high-resolution structures of large protein assemblies . The cross-links observed yield insights into the morphology of intrinsically disordered proteins (IDPs) and their complexes. The DSBI linker might spearhead a novel class of MS-cleavable and enrichable cross-linkers
HostingRepository	PRIDE
AnnounceDate	2024-09-04
AnnouncementXML	Submission_2024-09-03_17:13:57.824.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Christian Ihling
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	iodoacetamide derivatized residue
Instrument	timsTOF Pro

Revision	Datetime	Status	ChangeLog Entry
0	2024-03-25 09:21:36	ID requested
⏵ 1	2024-09-03 17:13:58	announced

10.1021/JACSAU.4C00282;

submitter keyword: protein-protein interactions

structural proteomics, DSBU,cross-linking mass spectrometry

XLMS, IDP, intrinsically disordered protein

Claudio Iacobucci
contact affiliation	Department of Physical and Chemical Sciences, University of L’Aquila, Via Vetoio, Coppito 1, 6701067100 L’Aquila, Italy
contact email	claudio.iacobucci@univaq.it
lab head
Christian Ihling
contact affiliation	MLU Halle, Inst. f. Pharmacy
contact email	christian.ihling@pharmazie.uni-halle.de
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD050960
     1. Label: PRIDE project
     2. Name: 2) Twisting Urea- to Imide-Based Mass Spectrometry-Cleavable Cross-Linkers to Embed Affinity Tags