PXD046500-1

PXD046500 is an original dataset announced via ProteomeXchange.

Title	Chemical proteomics of RID substrates
Description	To globally profile the fatty-acylation substrate proteins of RID, we utilized the bioorthogonal chemical reporter Alk-16, an alkynyl-functionalized fatty acid analogue, to metabolically label fatty-acylated proteins in living cells. To identify the substrate proteins of RID, we sought to perform quantitative chemical proteomics experiments by combining the Alk-16 metabolic labeling and stable isotope labeling by amino acids in cell culture (SILAC) . In order to eliminate potential false positives due to isotope labeling and to increase identification reliability, we designed a dual SILAC workflow. In the “Forward” SILAC experiment, cells were cultured in standard SILAC heavy and light media before transfection to express RID-WT and RID-CA, respectively. In the “Reverse” SILAC experiment, the isotope labeling was switched and the heavy- and light-labeled cells were transfected with RID-CA and RID-WT, respectively. Cells were labeled with Alk-16 and the lysates were then mixed equally. The combined lysates were treated with NH2OH, followed by click reaction with azido-biotin, streptavidin enrichment, and trypsin digestion. The resulting peptide samples were analyzed by mass spectrometry for protein identification. The heavy-to-light (H/L) SILAC ratios of identified proteins were quantified to evaluate the extent of enrichment.
HostingRepository	PRIDE
AnnounceDate	2024-06-22
AnnouncementXML	Submission_2024-06-22_08:36:49.403.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Tao Peng
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive HF

Revision	Datetime	Status	ChangeLog Entry
0	2023-10-30 05:30:04	ID requested
⏵ 1	2024-06-22 08:36:50	announced
2	2024-10-22 06:46:28	announced	2024-10-22: Updated project metadata.

10.1016/j.mcpro.2024.100730;

Xu Y, Ding K, Peng T, -Fatty-Acylation of Septins by Rho Inactivation Domain (RID) of the Vibrio MARTX Toxin to Alter Septin Localization and Organization. Mol Cell Proteomics, 23(3):100730(2024) [pubmed]

submitter keyword: RID,Chemical proteomics

Tao Peng
contact affiliation	Peking University Shenzhen Graduate School
contact email	tpeng@pku.edu.cn
lab head
Tao Peng
contact affiliation	Peking University Shenzhen Graduate School
contact email	penglab@yeah.net
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/2024/06/PXD046500

PRIDE project URI

• PRIDE
  1. PXD046500
     1. Label: PRIDE project
     2. Name: Chemical proteomics of RID substrates