PXD061563

PXD061563 is an original dataset announced via ProteomeXchange.

Title	Employing Expression-Matched Controls Enables High Confidence Proximity-Based Interactome Classification ( Dataset 3)
Description	Proximity labeling approaches have been widely utilized to define protein interactomes. Due to the inherent promiscuity of proximity labeling using TurboID-based approaches, identification and adoption of appropriate labeling controls is a pivotal step to mitigate background interference and enhance interactome assignment accuracy. Here, we evaluate the effectiveness of both expression controls and data normalization strategies in generating high confidence interactome maps. This dataset contains whole-cell extract proteomics results, including the proximity labeling sections of TurboID-RNF10 based on the Flp-IN system and TurboID-HUWE1 based on the PiggyBac system. It serves as the raw data for Figures 3 and 5 in the article, as well as Supplementary Figures 3 and 5.
HostingRepository	PRIDE
AnnounceDate	2025-07-14
AnnouncementXML	Submission_2025-07-13_18:23:06.263.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Fulin Jiang
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	iodoacetamide derivatized residue
Instrument	timsTOF Pro 2

Revision	Datetime	Status	ChangeLog Entry
0	2025-03-06 22:21:36	ID requested
⏵ 1	2025-07-13 18:23:07	announced

10.1016/j.mcpro.2025.101001;

Jiang F, Ge X, Bennett EJ, Employing Expression-Matched Controls Enables High-Confidence Proximity-Based Interactome Classification. Mol Cell Proteomics, 24(7):101001(2025) [pubmed]

submitter keyword: Proximity labeling proteomics, TurboID expression, Control, Background protein, Interacting protein identification

Eric Bennett
contact affiliation	School of Biological Sciences, Department of Cell and Developmental Biology, University of California, San Diego, CA, USA
contact email	e1bennett@ucsd.edu
lab head
Fulin Jiang
contact affiliation	University of California San Diego
contact email	jiangflynn23@gmail.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/2025/07/PXD061563

PRIDE project URI

• PRIDE
  1. PXD061563
     1. Label: PRIDE project
     2. Name: Employing Expression-Matched Controls Enables High Confidence Proximity-Based Interactome Classification ( Dataset 3)