PXD035764 is an
original dataset announced via ProteomeXchange.
Dataset Summary
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 |
Dataset History
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. |
Publication List
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] |
Keyword List
submitter keyword: Ghost proteome, Alternative Open Reading Frames, Cross-linking |
Contact List
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 | |
Full Dataset Link List
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 |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD035764
- Label: PRIDE project
- Name: Employing non-targeted interactomics approach and subcellular fractionation to increase our understanding of the ghost proteome