PXD081829

PXD081829 is an original dataset announced via ProteomeXchange.

Title	PerCap isolates native peroxisomes to reveal peroxisomal proteins and regulators
Description	Peroxisomes are highly heterogeneous organelles that exhibit remarkable functional diversity across different species and even within different tissues of the same organism. Comprehensive proteomic studies that investigate complex biological roles and regulatory mechanisms depend on the isolation of peroxisomes. Here, we discover that the N-terminal region of cyclic AMP-dependent transcription factor ATF-6 alpha (ATF6α) interacts with the peroxisomal membrane protein ATP-binding cassette sub-family D member 1 & 3 (ABCD1, ABCD3) directly in vitro, and develop an affinity-based strategy PerCap using the specific interactions between ATF6α and ABCDs to rapidly purify native peroxisomes. Using this approach, we isolated peroxisomes from human cells, validated their intactness, and identified the potential peroxisomal proteins by proteomic analysis. We show mitochondrial protein A-kinase anchor protein 1 (AKAP1), Carnitine O-palmitoyltransferase 1 (CPT1A) and NADH-cytochrome b5 reductase 1 (CYB5R1) also localize to peroxisomes, and the loss of AKAP1 affects peroxisome morphology. We also isolated peroxisomes from mouse tissues to compare tissue-specific peroxisomal proteins. Furthermore, by monitoring peroxisomal proteome dynamics during Torin1-induced pexophagy, we identified ubiquitin-conjugating enzyme E2 variant 1 (UBE2V1) as a contributor to this process. In summary, we developed a peroxisome isolation method by discovering the direct interactions between ATF6α and peroxisomal proteins, and established PerCap as a strategy for isolating native peroxisomes from human cells and mouse tissues for proteomic and functional analyses.
HostingRepository	iProX
AnnounceDate	2026-07-28
AnnouncementXML	Submission_2026-07-28_20:42:01.755.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Ting Dang
SpeciesList	scientific name: Homo sapiens; NCBI TaxID: 9606; scientific name: Mus musculus; NCBI TaxID: 10090;
ModificationList	No PTMs are included in the dataset
Instrument	Orbitrap Astral; timsTOF Pro

Revision	Datetime	Status	ChangeLog Entry
0	2026-07-28 20:41:14	ID requested
⏵ 1	2026-07-28 20:42:02	announced

Dataset with its publication pending

submitter keyword: peroxisome proteome

Wenqing Shui
contact affiliation	ShanghaiTech University
contact email	shuiwq@shanghaitech.edu.cn
lab head
Ting Dang
contact affiliation	ShanghaiTech University
contact email	dangting1@shanghaitech.edu.cn
dataset submitter

iProX dataset URI