PXD068036-1

PXD068036 is an original dataset announced via ProteomeXchange.

Title	APEX2 and TurboID Define Unique Subcellular Proteomes
Description	Proximity labeling has emerged as a prominent, reliable tool for obtaining local proteomes from a wide range of cell-types. Two major classes of labeling reagents, peroxidase based (APEX family), or biotin-ligase based (BioID family) have been developed in parallel. These two approaches are often used interchangeably, or chosen based on availability of reagents, however each may produce a biased proteome which should be considered during experimental design. We compared proximity labeling with TurboID or APEX2 in HEK293 cells across cytosol, nucleus, and membrane compartments. Both enzymes enriched compartment-specific proteomes, validated by GO terms, but showed distinct protein profiles. TurboID identified more membrane proteins, favoring identification of proteins associated with RNA processing and protein localization, while APEX2 enriched for proteins involved in metabolic pathways. Trypsin digestion highlighted biases from TurboID’s lysine biotinylation, which we show can be mitigated by an endoproteinase GluC digestion during sample prep, yet these differences persist to some degree. We find that TurboID suits broader proteomic studies whereas APEX2 targets specific signaling pathways. We therefore show that strategic enzyme and protease selection is critical for optimizing proximity labeling-based proteomic studies, advancing cellular proteome mapping.
HostingRepository	PRIDE
AnnounceDate	2025-12-15
AnnouncementXML	Submission_2025-12-14_17:47:29.988.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Alexandria Battison
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: NEWT:9606;
ModificationList	biotinylated residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Eclipse

Revision	Datetime	Status	ChangeLog Entry
0	2025-09-03 12:44:13	ID requested
⏵ 1	2025-12-14 17:47:31	announced

Battison AS, Balsbaugh JL, Borniger JC, APEX2 and TurboID define unique subcellular proteomes. Sci Rep, 15(1):43547(2025) [pubmed]

10.1038/s41598-025-27545-1;

submitter keyword: proteomics, APEX, cellular compartments, TurboID,Proximity labeling

Jeremy Borniger
contact affiliation	Cold Spring Harbor Laboratory
contact email	bornige@cshl.edu
lab head
Alexandria Battison
contact affiliation	Cold Spring Harbor Laboratory
contact email	battison@cshl.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/2025/12/PXD068036

PRIDE project URI

• PRIDE
  1. PXD068036
     1. Label: PRIDE project
     2. Name: APEX2 and TurboID Define Unique Subcellular Proteomes