PXD039392

PXD039392 is an original dataset announced via ProteomeXchange.

Title	N-terminal COFRADIC on cytosolic proteins of HEK293T cells - UniProt search
Description	N-terminal proteoforms stem from the same gene but differ at their N-terminus, and most of these are found to be truncated, though some are N-terminally extended caused by ribosomes starting translation from codons in the annotated 5’UTR, and/or carry modified N-termini different from those of the canonical protein. Biological functions of N-terminal proteoforms are emerging, however, it remains unknown to what extend N-terminal proteoforms further expand the functional complexity. To address this in a more global manner, we mapped the interactomes of several pairs of N-terminal proteoforms and their canonical counterparts. For this, we first generated an in-depth catalogue of N-terminal proteoforms in the cytosol of HEK293T cells. As the N-terminal region is the part that differs between the proteoforms, we performed N-terminal enrichment via COFRADIC on the cytosol of HEK293T cells. We combined three digestion enzymes to increase the depth of analysis. Data was searched twise: once with a regular UniProt database and a second time with a custom database (combining the sequences of UniProt proteins, UniProt isoforms and publicly available Ribo-seq data). Data was filtered and this resulted in a catalogue of 3,306 N-termini from which 20 pairs of canonical protein and N-terminal proteoform(s) were selected for interactome analysis. Our analysis of these pairs revealed that the overlap of the interactomes for both proteoforms is in general high, showing their functional relation. However, for all pairs tested we do report differences as well. We show that N-terminal proteoforms can be engaged in new/different interactions and as well can lose several interactions compared to the canonical protein.
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_09:00:52.919.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD039392
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	2023-01-13 05:48:29	ID requested
1	2023-06-08 03:06:05	announced
⏵ 2	2023-11-14 09:00:53	announced	2023-11-14: Updated project metadata.

10.6019/PXD039392;

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/2023/06/PXD039392

PRIDE project URI

• PRIDE
  1. PXD039392
     1. Label: PRIDE project
     2. Name: N-terminal COFRADIC on cytosolic proteins of HEK293T cells - UniProt search