PXD032132-1

PXD032132 is an original dataset announced via ProteomeXchange.

Title	Cross-link assisted spatial proteomics to map sub-organelle proteomes and membrane protein topology
Description	The specific functions of cellular organelles and sub-compartments depend on their protein content, which can be characterized by spatial proteomics approaches. However, many spatial proteomics methods are limited in their ability to resolve organellar sub-compartments, profile multiple sub-compartments in parallel, and/or characterize membrane-associated proteomes. Here, we develop a cross-linking assisted spatial proteomics (CLASP) strategy that addresses these shortcomings. Using human mitochondria as a model system, we show that CLASP can elucidate spatial proteomes of all mitochondrial sub-compartments and provide topological insight into the mitochondrial membrane proteome in a single experiment. Biochemical and imaging-based follow-up studies demonstrate that CLASP allows discovering mitochondria-associated proteins and revising previous protein sub-compartment localization and membrane topology data. This study extends the scope of cross-linking mass spectrometry beyond protein structure and interaction analysis towards spatial proteomics, establishes a method for concomitant profiling of sub-organelle and membrane proteomes, and provides a resource for mitochondrial spatial biology.
HostingRepository	PRIDE
AnnounceDate	2024-02-21
AnnouncementXML	Submission_2024-02-21_10:58:47.428.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Zhu Ying
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090; scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2022-03-09 00:36:13	ID requested
⏵ 1	2024-02-21 10:58:47	announced
2	2024-10-22 06:31:27	announced	2024-10-22: Updated project metadata.

Dataset with its publication pending

submitter keyword: synaptic vesicles,XL-MS, mitochondria, spatial proteomics

Fan Liu
contact affiliation	Department of Structural Biology, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP)
contact email	FLiu@fmp-berlin.de
lab head
Zhu Ying
contact affiliation	Leibniz-Forschungsinstitut für Molekulare Pharmakologie
contact email	zhu@fmp-berlin.de
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/2024/02/PXD032132

PRIDE project URI

• PRIDE
  1. PXD032132
     1. Label: PRIDE project
     2. Name: Cross-link assisted spatial proteomics to map sub-organelle proteomes and membrane protein topology