PXD032976

PXD032976 is an original dataset announced via ProteomeXchange.

Title	ProteasomeID: quantitative mapping of proteasome interactomes and substrates for in vitro and in vivo studies
Description	Proximity labeling coupled to mass spectrometry enables in situ mapping of protein-protein interactions. Here, we have developed a strategy based on tagging of proteasomes with promiscuous biotin ligases and a newly generated mouse model to monitor the interactome of proteasomes in vivo. We demonstrate that biotin ligases can be incorporated in fully assembled proteasomes without negative impact on proteasome activity. Analysis of proteins labeled by tagged proteasomes retrieved more than half of the known proteasome-interacting proteins in a single mass spectrometry analysis, including assembly factors, activators and ubiquitin-cycle related proteins. We optimized the protocol for processing of proximity labeled samples to minimize contamination from streptavidin and implemented Data Independent Acquisition (DIA) mass spectrometry for label-free analysis. We demonstrate the utility of our workflow by identifying novel proteasome-interacting proteins, charting interactomes across mouse organs, and showing that proximity-labeling can be used to identify both endogenous and small molecule-induced proteasome substrates.
HostingRepository	PRIDE
AnnounceDate	2024-07-06
AnnouncementXML	Submission_2024-07-05_16:13:40.256.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Emilio Cirri
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	biotinylated residue; acetylated residue; monohydroxylated residue
Instrument	Orbitrap Exploris 480

Revision	Datetime	Status	ChangeLog Entry
0	2022-04-03 08:11:21	ID requested
⏵ 1	2024-07-05 16:13:40	announced

10.7554/ELIFE.93256.2;

submitter keyword: proteasome, mass spectrometry, proximity labeling, protein degradation, BioID

Alessandro Ori
contact affiliation	Ori Research Group, The Leibniz Institute on Aging – Fritz Lipmann Institute, Jena, Germany
contact email	alessandro.ori@leibniz-fli.de
lab head
Emilio Cirri
contact affiliation	Leibniz Institute on Ageing Fritz Lipmann Institute Jena
contact email	emilio.cirri@fli-leibniz.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/2024/07/PXD032976

PRIDE project URI

• PRIDE
  1. PXD032976
     1. Label: PRIDE project
     2. Name: ProteasomeID: quantitative mapping of proteasome interactomes and substrates for in vitro and in vivo studies