PXD040762

PXD040762 is an original dataset announced via ProteomeXchange.

Title	A proximity proteomics pipeline with improved reproducibility and throughput
Description	Proximity labeling coupled with mass spectrometry (proximity proteomics) have emerged as a powerful technique to map proximal protein interactions in living cells. However, the large-scale and unbiased sample analysis in proximity proteomics necessitates a universal and high-throughput workflow to reduce hands-on time and increase quantitative reproducibility. To address this issue, we developed a systematic and automated approach, including generation and characterization of monoclonal cell lines, automated enrichment of biotinylated proteins in a 96-well format, optimization of quantitative mass spectrometry acquisition methods, and advanced computational framework to deconvolute spatial and temporal protein interaction networks. The quantitative reproducibility and accuracy of this streamlined workflow clearly outperforms the conventional manual enrichment. We first applied this approach to investigate subcellular proteomics, including cytosol, endosome, Golgi, lysosome, and plasma membrane. Moreover, using serotonin receptor (5HT2A) as a model, we mapped dynamic protein-protein interactions of GPCR induced by agonist. Collectively, this systematic approach could be widely used in proximity proteomics with high throughput, high reproducibility, and minimal manual intervention.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_06:51:33.078.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Xiaofang Zhong
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	biotinylated residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Exploris 480

Revision	Datetime	Status	ChangeLog Entry
0	2023-03-10 02:30:51	ID requested
1	2024-07-26 02:44:48	announced
⏵ 2	2024-10-22 06:51:33	announced	2024-10-22: Updated project metadata.

10.1038/S44320-024-00049-2;

submitter keyword: Proximity proteomics

Ruth Huttenhain
contact affiliation	University of California-San Francisco
contact email	Ruth.Huttenhain@ucsf.edu
lab head
Xiaofang Zhong
contact affiliation	University of California-San Francisco
contact email	xiaofang.zhong@ucsf.edu
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/PXD040762

PRIDE project URI

• PRIDE
  1. PXD040762
     1. Label: PRIDE project
     2. Name: A proximity proteomics pipeline with improved reproducibility and throughput