PXD014642

PXD014642 is an original dataset announced via ProteomeXchange.

Title	Probing the Function of Alternative Proteins in Cell Reprogramming by Large Scale Proteomics and Cross - Linking Mass Spectrometry
Description	Many proteins are lacking from reference databases because they are issued from alternative ORFs neither respecting the rules decreed for the genome annotation or for the protein translation from mRNA. It was evidenced that not only a single protein is therefore translated from an mRNA. However, the function of these Alternative Proteins (AltProts) remain largely unknown. Here, we were interested by looking to the function of AltProts in the context of cancer cell reprogramming. We have developed a large scale approach based on shot-gun proteomics and cross-linking mass spectrometry (XL-MS) to identify the regulation of the reference proteins (RefProts) versus the AltProts and find the their interaction partners. The study was conducted from NCH82 human glioma cells which were stimulated by the protein kinase A (PKA) activator Forskolin upon 16H, 24H and 48H to induce cell differentiation and epithelial-mesenchymal transition (EMT). The data have shown to enable tracing back the function of the AltProts by combining experimental data to in silico analysis using cytoscape with ClueGo for GO Term annotation and enrichment of pathways with String. Very interestingly many AltProts demonstrate to be involved in the regulation of tRNA through their interaction with aaRS proteins and of the cellular mobility.
HostingRepository	PRIDE
AnnounceDate	2021-02-15
AnnouncementXML	Submission_2021-02-15_05:14:36.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Tristan Cardon
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	crosslinked residues; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2019-07-17 03:11:49	ID requested
⏵ 1	2021-02-15 05:14:36	announced

Dataset with its publication pending

submitter keyword: Alternative proteins, proteomics, cross-linking mass spectrometry, cell reprogramming

Michel Salzet
contact affiliation	Laboratory PRISM INSERM U1192 University of Lille, France
contact email	michel.salzet@univ-lille.fr
lab head
Tristan Cardon
contact affiliation	Laboratoire PRISM INSERM U1192
contact email	tristan.cardon@univ-lille.fr
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/2021/02/PXD014642

PRIDE project URI

• PRIDE
  1. PXD014642
     1. Label: PRIDE project
     2. Name: Probing the Function of Alternative Proteins in Cell Reprogramming by Large Scale Proteomics and Cross - Linking Mass Spectrometry