PXD030601

PXD030601 is an original dataset announced via ProteomeXchange.

Title	N-terminal COFRADIC on cytosolic proteins of HEK293T cells
Description	Ribosome profiling revealed translation outside of canonical coding sequences (CDSs) including translation of short upstream open-reading frames (ORFs), long non-coding RNAs, ORFs in UTRs or ORFs in alternative reading frames. Ribo-seq but also bioinformatics-based prediction and RNA-sequencing reported translation of thousands of ORFs derived from non-translated regions (NTRs). Although such ORFs gained increased attention over the years, their actual coding potential remains debated as protein products of only a fraction of them were identified by mass spectrometry. Here, we introduced a new workflow to discover translation products of NTRs at a large-scale. We combined reducing sample complexity (by enriching N-terminal peptides of cytosolic proteins as such peptides are ideal proxies for translation) with and extend search space (combining the sequences of UniProt proteins, UniProt isoforms and publicly available Ribo-seq data) reasoning that this combination increased chances of identifying proteins from NTRs. Further, we introduced rigorous data analysis and results curation workflows to cope with the increased complexity of the search space and to mine identified peptides. 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 less than 1% of all identified peptides might originate from such translation events.
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_08:55:06.153.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD030601
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Annelies Bogaert
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	acetylated residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2021-12-22 02:51:56	ID requested
1	2022-07-12 05:10:53	announced
⏵ 2	2023-11-14 08:55:06	announced	2023-11-14: Updated project metadata.

10.6019/PXD030601;

submitter keyword: cytosol,HEK293T cells, N-terminal peptides, 3 proteases, COFRADIC, ATIS, LC-MS/MS

Kris Gevaert
contact affiliation	VIB Center for Medical Biotechnology, VIB, Ghent Department of Biomolecular Medicine, Ghent University, Ghent
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

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/2022/07/PXD030601

PRIDE project URI

• PRIDE
  1. PXD030601
     1. Label: PRIDE project
     2. Name: N-terminal COFRADIC on cytosolic proteins of HEK293T cells