PXD046382-1

PXD046382 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_08:02:17.524.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Kerem Akkaya
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2023-10-25 05:57:26	ID requested
⏵ 1	2024-02-21 08:02:17	announced
2	2024-10-22 06:31:26	announced	2024-10-22: Updated project metadata.

Dataset with its publication pending

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

Fan Liu
contact affiliation	Department of Structural Biology, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP)
contact email	FLiu@fmp-berlin.de
lab head
Kerem Akkaya
contact affiliation	Leibniz-Forschungsinstitut für Molekulare Pharmakologie
contact email	akkaya@fmp-berlin.de
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD046382
     1. Label: PRIDE project
     2. Name: Cross-link assisted spatial proteomics to map sub-organelle proteomes and membrane protein topology