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PXD030285

PXD030285 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleCheck of selected NTR peptide spectra by comparison with synthetic peptides
DescriptionRibosome 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, while other studies failed to find evidence for such types of non-canonical translation products. Here, we attempted to discover translation products from non-coding regions by strongly reducing the complexity of the sample prior to mass spectrometric analysis. We used an extended database as the search space and applied stringent filtering of the identified peptides to find evidence for novel translation events. Theoretically, we show that our strategy facilitates the detection of translation events of transcripts from non-coding regions, but experimentally only find 19 peptides (less than 1% of all identified peptides) that might originate from such translation events. However, curation and stringent validation further reduces this to 10 reliable identifications. The fragmentation of these 10 peptides was further validated by comparison with the fragmentation of synthetic peptides.
HostingRepositoryPanoramaPublic
AnnounceDate2022-08-02
AnnouncementXMLSubmission_2022-08-02_13:41:45.765.xml
DigitalObjectIdentifier
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportsupported by repository but incomplete data and/or metadata
PrimarySubmitterAnnelies Bogaert
SpeciesList scientific name: Homo sapiens; NCBI TaxID: 9606;
ModificationListAcetyl; Carbamidomethyl; Oxidation
InstrumentOrbitrap Fusion Lumos
Dataset History
RevisionDatetimeStatusChangeLog Entry
02021-12-09 10:18:37ID requested
12022-08-02 13:41:46announced
Publication List
Bogaert A, Fijalkowska D, Staes A, Van de Steene T, Demol H, Gevaert K, Limited Evidence for Protein Products of Noncoding Transcripts in the HEK293T Cellular Cytosol. Mol Cell Proteomics, 21(8):100264(2022) [pubmed]
Keyword List
submitter keyword: N-terminal enrichment, cytosol, HEK293T, ATIS, cells, NTR, COFRADIC
Contact List
Kris Gevaert
contact affiliationVIB center for Medical Biotechnology, VIB, Ghent, Belgium and Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
contact emailkris.gevaert@vib-ugent.be
lab head
Annelies Bogaert
contact affiliationVIB center for Medical Biotechnology, VIB, Ghent, Belgium and Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
contact emailannelies.bogaert@vib-ugent.be
dataset submitter
Full Dataset Link List
Panorama Public dataset URI