PXD045689

PXD045689 is an original dataset announced via ProteomeXchange.

Title	Deciphering the ghost proteome in ovarian cancer cells by deep proteogenomic characterization.
Description	Proteogenomics is becoming a powerful tool in personalized medicine by linking genomics, transcriptomics, and mass spectrometry (MS)-based proteomics. Due to increasing evidence of alternative open reading frame-encoded proteins (AltProts), proteogenomics has high potential to unravel the characteristics, variants, and expression levels of the alternative proteome in cells. To characterize a broader view of the proteome of ovarian cancer cells compared to ovarian epithelial cells, cell-specific RNA-sequencing databases were generated.128 reference proteins (RefProts) and 30 AltProts were identified exclusively shared by SKOV-3 and PEO-4. Among them, an AltProt variant of IP_715944 was identified mutated (Leu44Pro) and translated from DHX8. Additionally, the abundance level of the proteome was assessed, finding specific expression variation of RefProts and AltProts in different subcellular compartments. The identification of 117 RefProt and two AltProt variants was highlighted, along with their possible implications in the different physio-pathological characteristics. To identify the possible involvement of AltProts in cellular processes, crosslinking-MS (XL-MS) was performed in each cell line to identify AltProt-RefProt protein-protein interactions. An interaction of POLD3 and the AltProt IP_183088 was identified, which after molecular docking was placed between POLD3-POLD2 binding sites highlighting the possibility of the involvement of IP_183088 in the cellular processes of DNA replication and repair.
HostingRepository	PRIDE
AnnounceDate	2025-05-06
AnnouncementXML	Submission_2025-05-06_12:12:24.000.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Diego Fernando Garcia del Rio
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2023-09-26 02:15:30	ID requested
⏵ 1	2025-05-06 12:12:24	announced

10.1038/s41419-024-07046-1;

Garcia-Del Rio DF, Derhourhi M, Bonnefond A, Leblanc S, Guilloy N, Roucou X, Eyckerman S, Gevaert K, Salzet M, Cardon T, Deciphering the ghost proteome in ovarian cancer cells by deep proteogenomic characterization. Cell Death Dis, 15(9):712(2024) [pubmed]

submitter keyword: Alternative proteins, proteogenomics, ovarian cancer, crosslinking

Michel Salzet
contact affiliation	PRISM U1192 Université de Lille
contact email	michel.salzet@univ-lille.fr
lab head
Diego Fernando Garcia del Rio
contact affiliation	Laboratoire PRISM - Unité Inserm 1192 -Université de Lille
contact email	diego.garciadelrio@univ-lille.fr
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/2025/05/PXD045689

PRIDE project URI

• PRIDE
  1. PXD045689
     1. Label: PRIDE project
     2. Name: Deciphering the ghost proteome in ovarian cancer cells by deep proteogenomic characterization.