PXD030216 is an
original dataset announced via ProteomeXchange.
Dataset Summary
Title | Virotrap-based interactome analysis of a NTR protein |
Description | Ribosome profiling has revealed translation outside of canonical coding sequences (CDSs) including translation of short upstream ORFs, long non-coding RNAs, overlapping ORFs, ORFs in UTRs or ORFs in alternative reading frames. Studies combining mass spectrometry, ribosome profiling and CRISPR-based screens showed that hundreds of ORFs derived from non-coding transcripts produce (micro)proteins and might be functional, while other studies failed to find evidence for such types of non-canonical translation events. In this study we tried to detect (and characterize) proteins originating from these non-translated regions (NTRs). We attempted to discover translation products from non-coding regions at large scale by reducing the overall sample complexity (by enriching cytosolic N-terminal peptides) and combined it with an extend search space (combining UniProt proteins, UniProt isoforms and publicly available Ribo-seq data). Reasoning that this strategy would increase the likelihood of identifying proteins from NTRs. Further, we introduced rigorous data analysis and results curation workflows. This stringent filtering approach was found essential to retain confident translational evidence at the peptide level for NTRs. We show that, theoretically, our strategy facilitates the detection of translation events of transcripts from NTRs, but experimentally we find that less than 1% of all identified peptides might originate from such translation events. However, one NTR protein was further characterized by Virotrap based interaction analysis. This resulted in several potential interaction partners associated with membranes and vesicle transport. Showing that the non-translated regions that do result in proteins might be functional. |
HostingRepository | PRIDE |
AnnounceDate | 2023-11-14 |
AnnouncementXML | Submission_2023-11-14_08:56:43.272.xml |
DigitalObjectIdentifier | |
ReviewLevel | Peer-reviewed dataset |
DatasetOrigin | Original dataset |
RepositorySupport | Unsupported dataset by repository |
PrimarySubmitter | Annelies Bogaert |
SpeciesList | scientific name: Homo sapiens (Human); NCBI TaxID: 9606; |
ModificationList | No PTMs are included in the dataset |
Instrument | Q Exactive HF |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
0 | 2021-12-06 08:59:58 | ID requested | |
1 | 2022-07-12 02:23:02 | announced | |
⏵ 2 | 2023-11-14 08:56:43 | announced | 2023-11-14: Updated project metadata. |
Publication List
Dataset with its publication pending |
Keyword List
submitter keyword: Virotrap, protein-protein interaction, LC-MS/MS |
Contact List
Kris Gevaert |
contact affiliation | VIB center for Medical Biotechnology, VIB, Ghent, Belgium Department of Biomolecular Medicine, Ghent University, Ghent, Belgium |
contact email | kris.gevaert@vib-ugent.be |
lab head | |
Annelies Bogaert |
contact affiliation | VIB - Center for medical Biotechnology Ghent University - Department of Biomolecular Medicine |
contact email | Annelies.bogaert@vib-ugent.be |
dataset submitter | |
Full Dataset Link List
Dataset FTP location
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PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD030216
- Label: PRIDE project
- Name: Virotrap-based interactome analysis of a NTR protein