PXD039085

PXD039085 is an original dataset announced via ProteomeXchange.

Title	AP-MS-based interactome analysis of three pairs of N-terminal proteoforms and their canonical protein
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. From which 20 pairs of canonical protein and N-terminal proteoform(s) were selected. Protein-protein interaction profiling was done with Virotrap. Virotrap was selected as this methods avoids lysis before the isolation of the complexes and allows the detection of weak and cytosolic proteins as well. 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. We used AP-MS to validate differences in the interaction networks reported for three of these 20 pairs of N-terminal proteoform and canonical counterpart.
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_09:01:07.583.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD039085
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	No PTMs are included in the dataset
Instrument	Q Exactive HF

Revision	Datetime	Status	ChangeLog Entry
0	2022-12-22 04:26:46	ID requested
1	2023-06-08 01:24:41	announced
⏵ 2	2023-11-14 09:01:08	announced	2023-11-14: Updated project metadata.

10.6019/PXD039085;

submitter keyword: protein-protein interaction, N-terminal proteoform,AP-MS, FLAG tagged, LC-MS/MS

Kris Gevaert
contact affiliation	VIB Center for Medical Biotechnology, VIB, Ghent, B9052, Belgium Department of Biomolecular Medicine, Ghent University, Ghent, B9052, 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

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/PXD039085

PRIDE project URI

• PRIDE
  1. PXD039085
     1. Label: PRIDE project
     2. Name: AP-MS-based interactome analysis of three pairs of N-terminal proteoforms and their canonical protein