Proteomics

Dataset Information

0

Employing non-targeted interactomics approach and subcellular fractionation to increase our understanding of the ghost proteome

ABSTRACT: 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.

INSTRUMENT(S):

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Ovary, Cell Culture

SUBMITTER: Diego Fernando Garcia del Rio  

LAB HEAD: PR. MICHEL SALZET

PROVIDER: PXD035764 | Pride | 2023-03-11

REPOSITORIES: Pride

Json Xml

Dataset's files

Source:
Action DRS
Chromatine_210827_Ctrl.msf Msf
Chromatine_210827_Ctrl.raw Raw
Chromatine_210827_XL.raw Raw
Chromatine_XL_211103_OpenProt_1pept.msf Msf
Cytoplasm_210827_Ctrl.msf Msf
Items per page:
1 - 5 of 100
altmetric image

Publications

Employing non-targeted interactomics approach and subcellular fractionation to increase our understanding of the ghost proteome.

Garcia-Del Rio Diego Fernando DF   Cardon Tristan T   Eyckerman Sven S   Fournier Isabelle I   Bonnefond Amelie A   Gevaert Kris K   Salzet Michel M  

iScience 20230106 2

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  ...[more]

Similar Datasets

Proteomics Monolinks Matter: Rational Modification of a Cross-Linker for Improved Flexible Protein Structure Modeling
2025-05-06 | PXD051742 | Pride
Proteomics Structure of herpes simplex virus pUL7:pUL51, a conserved complex required for efficient herpesvirus assembly
2020-05-11 | PXD015941 | Pride
Proteomics Histone proteomic associated with epigenetic studies revealed a Ghost proteome in PC1/3 KD macrophages involved in anti - tumoral resistance under IL - 10 stimulation
2021-02-12 | PXD020610 | Pride
Proteomics Analysis of conformational changes induced by binding of allosteric nanobodies to a bacterial LRRK2 homologue by CX-MS
2024-04-23 | PXD046634 | Pride
Proteomics Mapping of nanobody binding sites on human LRRK2 by CX-MS
2022-02-27 | PXD030063 | Pride
Proteomics Structure of Anabaena flos-aquae gas vesicles revealed by cryo-ET
2023-03-30 | PXD038631 | Pride
Proteomics Defining mechanisms of multifunctionality in the rabies virus P protein: key roles of conformational diversity and RNA interaction in forming host interfaces
2025-10-10 | PXD064535 | Pride
Proteomics Deciphering the ghost proteome in ovarian cancer cells by deep proteogenomic characterization.
2025-05-06 | PXD045689 | Pride
Proteomics Histone interaction landscapes visualized by crosslinking mass spectrometry in intact cell nuclei
2018-07-23 | PXD007513 | Pride
Proteomics Selennoprotein S interacts with the replication and transcription complex of the SARS-CoV-2 by binding nsp7
2023-03-11 | PXD038629 | Pride