Proteomics

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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): Q Exactive

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

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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
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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]

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