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PXD035826 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleIn-Depth In Vivo Crosslinking in Minutes by a Compact, Membrane- Permeable, and Alkynyl-Enrichable Crosslinker
DescriptionChemical crosslinking coupled with mass spectrometry (CXMS) has emerged as a powerful technique to obtain the dynamic conformations and interaction interfaces of protein complexes. Limited by the poor cell membrane permeability, chemical reactivity, and biocompatibility of crosslinkers, in vivo crosslinking to capture the dynamics of protein complexes with finer temporal resolution and higher coverage is attractive but challenging. In this work, a trifunctional crosslinker bis(succinimidyl) with propargyl tag (BSP), involving compact size, proper amphipathy, and enrichment capacity, was developed to enable better cell membrane permeability and efficient crosslinking in 5 min without obvious cellular interference. Followed by a two-step enrichment method based on click chemistry at the peptide level, 13,098 crosslinked peptides (5068 inter-crosslinked peptides and 8030 intra-crosslinked peptides) were identified under the data threshold of peptide-spectrum matches (PSMs) ≥2 on the basic of the FDR control of 1%, which was the most comprehensive dataset for homo species cells by a non-cleavable crosslinker. Besides, the interactome network comprising 1519 proteins connected by 2913 interaction edges in various intracellular compartments, as well as 80S ribosome structural dynamics, were characterized, showing the great potential of our in vivo crosslinking approach in minutes. All these results demonstrated that our developed BSP could provide a valuable toolkit for the in-depth in vivo analysis of protein–protein interactions (PPIs) and protein architectures with finer temporal resolution.
ReviewLevelNon peer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterrong Bei Zhang
SpeciesList scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationListS-carboxamidomethyl-L-cysteine; alpha-amino acetylated residue; L-methionine sulfoxide
InstrumentLTQ Orbitrap
Dataset History
RevisionDatetimeStatusChangeLog Entry
02022-08-04 23:59:59ID requested
12022-08-05 04:24:57announced
22022-09-18 03:14:04announced2022-09-18: Updated FTP location.
Publication List
Dataset with its publication pending
Keyword List
submitter keyword: in vivo cross-linking, protein-protein interaction
Contact List
Lihua Zhang
lab head
rong Bei Zhang
contact affiliationDalian Institute of Chemical Physics, Chinese Academy of Sciences
dataset submitter
Full Dataset Link List
jPOST dataset URI
Dataset FTP location
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