PXD068378-1

PXD068378 is an original dataset announced via ProteomeXchange.

Title	Uncovering the Glutamate Carboxypeptidase II Microenvironment Using a Multi-labeling Proteomic Approach
Description	Glutamate carboxypeptidase II (GCPII) is a membrane-bound metallopeptidase predominantly expressed in neural and prostatic tissues, with significantly elevated levels in prostate carcinoma that increase with tumor grade. Despite its significance as a target for imaging and therapy in prostate cancer, its physiological function in this tissue remains poorly understood. To help fill this knowledge gap, we developed an integrated approach combining proximity labeling technologies for proteomic profiling (horseradish peroxidase, µMap, and riboflavin tetraacetate labeling) with our previously established iBody platform, which targets GCPII with a small-molecule specific inhibitor with proven efficacy as a chemical probe. Proximity labeling proteomic experiments on U251 MG–GCPII cells were followed by mass spectrometry and statistical analysis of protein abundances obtained by label-free quantification. Additionally, selected identified proteins were further validated through Western blot analyses and GCPII pulldown assays using cell lysates. This work identifies a network of GCPII-associated proteins that are potentially involved in cancer metabolism, migration, invasiveness, progression, and immune evasion. Our novel proximity proteomics labeling strategy provides a low-background framework, efficient biotinylation, and enhanced target binding via the avidity effect. Among the approaches tested, riboflavin tetraacetate-based iBody labeling exhibited the highest precision, underscoring its potential for membrane protein interactome mapping.
HostingRepository	PRIDE
AnnounceDate	2026-01-12
AnnouncementXML	Submission_2026-01-11_16:51:37.790.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Alena Krenkova
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: NEWT:9606;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2025-09-15 05:33:05	ID requested
⏵ 1	2026-01-11 16:51:38	announced

Pokorn, á J, Hadzima M, K, ř, enkov, á A, Smith JD, Š, ubr V, Kry, š, t, ů, fek R, Hub, á, lek M, Starkov, á J, Š, r, á, mkov, á K, Etrych T, Kostka L, Sedl, á, k F, Konvalinka J, Š, á, cha P, Uncovering the glutamate carboxypeptidase II microenvironment using a multi-labeling proteomic approach. Sci Rep, 15(1):45461(2025) [pubmed]

10.1038/s41598-025-28826-5;

submitter keyword: µMap,PSMA, riboflavin, iBody, HRP, protein proximity labeling

Pavel Šácha
contact affiliation	Institute of Organic Chemistry and Biochemistry Czech Academy of Sciences Flemingovo nám 542/2, 160 00, Prague, Czech Republic
contact email	pavel.sacha@uochb.cas.cz
lab head
Alena Krenkova
contact affiliation	IOCB CAS CR
contact email	alena.krenkova@uochb.cas.cz
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/2026/01/PXD068378

PRIDE project URI

• PRIDE
  1. PXD068378
     1. Label: PRIDE project
     2. Name: Uncovering the Glutamate Carboxypeptidase II Microenvironment Using a Multi-labeling Proteomic Approach