PXD067266-1

PXD067266 is an original dataset announced via ProteomeXchange.

Title	APE1 (apurinic/apyrimidinic endonuclease 1): newly identified post-translational modifications (PTMs)
Description	APE1 (apurinic/apyrimidinic endonuclease 1) is a multifunctional protein essential for both DNA base excision repair and redox signaling. However, its post-translational modifications (PTMs), which are key to modulating its cellular functions, remain largely uncharacterized due to their dynamic and labile nature. In this study, we developed a novel biotin-regulated avidin-based magnetic nanoparticle platform (bMIPAPE1) that selectively captures active APE1 from living cells under native conditions. This approach preserves labile PTMs and enables downstream mass spectrometry-based proteomic analysis. Using this tool, we identified 27 previously unreported PTMs at 18 distinct residues, including modifications with critical functional implications, such as phosphorylation at Y269 and dual acetylation/palmitoylation at K228. Furthermore, we uncovered PTMs associated with subcellular localization, including modifications at K203, C208, and K63 that correlated with APE1 nuclear export. Beyond enrichment and profiling, bMIPAPE1 also inhibits the enzymatic functions of APE1 in cells, offering potential therapeutic relevance. This project showcases an innovative method for real-time PTM profiling of endogenous proteins in complex cellular environments, with implications for cancer biology and targeted drug discovery.
HostingRepository	PRIDE
AnnounceDate	2026-03-17
AnnouncementXML	Submission_2026-03-17_00:19:57.585.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD067266
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Meiping Zhao
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: NEWT:9606;
ModificationList	acetylated residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2025-08-12 07:14:00	ID requested
⏵ 1	2026-03-17 00:19:58	announced

10.6019/PXD067266;

submitter keyword: PTMs,APE1, Live-cell, LC-MS/MS

Meiping Zhao
contact affiliation	Peking University
contact email	mpzhao@pku.edu.cn
lab head
Meiping Zhao
contact affiliation	Peking University
contact email	mpzhao@pku.edu.cn
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD067266
     1. Label: PRIDE project
     2. Name: APE1 (apurinic/apyrimidinic endonuclease 1): newly identified post-translational modifications (PTMs)