PXD035764

PXD035764 is an original dataset announced via ProteomeXchange.

Title	Employing non-targeted interactomics approach and subcellular fractionation to increase our understanding of the ghost proteome
Description	Eukaryotic mRNA has long been considered monocistronic, but nowadays, alternative proteins (AltProts) challenge this tenet. The alternative or ghost proteome has largely been neglected and the involvement of AltProts in biological processes. Here, we used subcellular fractionation to increase the information about AltProts and facilitate the detection of protein-protein interactions by the identification of crosslinked peptides. In total, 112 unique AltProts were identified, and we were able to identify 220 crosslinks without peptide enrichment. Among these, 16 crosslinks between AltProts and Referenced Proteins (RefProts) were identified. We further focused on specific examples such as the interaction between IP_2292176 (AltFAM227B) and HLA-B, in which this protein could be a potential new immunopeptide, and the interactions between HIST1H4F and several AltProts which can play a role in mRNA transcription. Thanks to the study of the interactome and the localization of AltProts, we can reveal more of the importance of the ghost proteome.
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_08:43:08.343.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	acetylated residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2022-08-02 10:48:27	ID requested
1	2023-03-11 06:04:24	announced
⏵ 2	2023-11-14 08:43:12	announced	2023-11-14: Updated project metadata.

Garcia-Del Rio DF, Cardon T, Eyckerman S, Fournier I, Bonnefond A, Gevaert K, Salzet M, Employing non-targeted interactomics approach and subcellular fractionation to increase our understanding of the ghost proteome. iScience, 26(2):105943(2023) [pubmed]

submitter keyword: Ghost proteome, Alternative Open Reading Frames, Cross-linking

PR. MICHEL SALZET
contact affiliation	Laboratoire PRISM - Unité Inserm 1192 Université de Lille - Campus Cité Scientifique Faculté des Sciences et Technologies Département de Biologie
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/2023/03/PXD035764

PRIDE project URI

• PRIDE
  1. PXD035764
     1. Label: PRIDE project
     2. Name: Employing non-targeted interactomics approach and subcellular fractionation to increase our understanding of the ghost proteome