PXD050960 is an
original dataset announced via ProteomeXchange.
Dataset Summary
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 |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
0 | 2024-03-25 09:21:36 | ID requested | |
⏵ 1 | 2024-09-03 17:13:58 | announced | |
Publication List
Keyword List
submitter keyword: protein-protein interactions |
structural proteomics, DSBU,cross-linking mass spectrometry |
XLMS, IDP, intrinsically disordered protein |
Contact List
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 | |
Full Dataset Link List
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/2024/09/PXD050960 |
PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD050960
- Label: PRIDE project
- Name: 2) Twisting Urea- to Imide-Based Mass Spectrometry-Cleavable Cross-Linkers to Embed Affinity Tags