PXD041148

PXD041148 is an original dataset announced via ProteomeXchange.

Title	Progress Toward Proteome-Wide Photo-Crosslinking to Enable Residue-Level Visualization of Protein Structure and Networks in vivo
Description	Crosslinking mass spectrometry (XL-MS) is emerging as a method at the crossroads of structural and cellular biology, uniquely capable of identifying protein-protein interactions with residue-level resolution and on the proteome-wide scale. With the development of crosslinkers that can form linkages inside cells and easily cleave during fragmentation on the mass spectrometer (MS-cleavable crosslinks), it has become increasingly facile to identify contacts between any two proteins in complex samples, including in live cells or tissues. Photo-crosslinkers possess the advantages of high temporal resolution and high reactivity, thereby engaging all residue-types (rather than just lysine); nevertheless, photo-crosslinkers have not enjoyed widespread use, and have yet to be employed for proteome-wide studies, because their products are challenging to identify. Here, we demonstrate the synthesis and application of two heterobifunctional photo-crosslinkers that feature diazirines and N-hydroxy-succinimidyl carbamate groups, the latter of which unveil symmetrical MS-cleavable linkages upon acyl transfer to protein targets. Moreover, these crosslinkers demonstrate high water-solubility and cell-permeability. Using these compounds, we demonstrate the feasibility of proteome-wide photo-crosslinking in cellulo. These studies elucidate a small portion of E. coli’s interaction network, albeit with residue-level resolution. With further optimization, these methods will enable the detection of protein quinary interaction networks in their native environment at residue-level resolution, and we expect they will prove useful toward the effort to explore the molecular sociology of the cell.
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_09:01:38.219.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Anneliese Faustino
SpeciesList	scientific name: Escherichia coli; NCBI TaxID: 562;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive HF-X

Revision	Datetime	Status	ChangeLog Entry
0	2023-03-27 20:15:15	ID requested
1	2023-06-27 07:15:22	announced
⏵ 2	2023-11-14 09:01:46	announced	2023-11-14: Updated project metadata.

Faustino AM, Sharma P, Manriquez-Sandoval E, Yadav D, Fried SD, Progress toward Proteome-Wide Photo-Cross-Linking to Enable Residue-Level Visualization of Protein Structures and Networks In Vivo. Anal Chem, 95(28):10670-10685(2023) [pubmed]

submitter keyword: Diazirines, Cleavable cross-linkers, Proteomics, Quinary Interactions, NHS-carbamate.,Photo-crosslinking, Protein interaction networks

Stephen Fried
contact affiliation	Johns Hopkins University, Department of Chemistry, Johns Hopkins University, Baltimore, MD 21218, USA, Thomas C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218, USA
contact email	sdfried@jhu.edu
lab head
Anneliese Faustino
contact affiliation	Johns Hopkins
contact email	anneliesefaustino@yahoo.com
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/2023/06/PXD041148

PRIDE project URI

• PRIDE
  1. PXD041148
     1. Label: PRIDE project
     2. Name: Progress Toward Proteome-Wide Photo-Crosslinking to Enable Residue-Level Visualization of Protein Structure and Networks in vivo