PXD000523

PXD000523 is an original dataset announced via ProteomeXchange.

Title	Phosphoproteome dynamics in onset and maintenance of Oncogene-Induced Senescence, phosphoproteome dataset
Description	Expression of the BRAFV600E oncoprotein is known to cause benign lesions, for example melanocytic nevi (moles). In spite of the oncogenic function of mutant BRAF, these lesions are arrested by a cell-autonomous mechanism called Oncogene-Induced Senescence (OIS). Infrequently, nevi can progress to malignant melanoma, through mechanisms that are incompletely understood. To gain more insight into this vital tumor suppression mechanism, we performed a mass spectrometry-based screening of the proteome and phosphoproteome in cycling and senescent cells as well as cells that have abrogated senescence. Proteome analysis of senescent cells revealed the upregulation of established senescence biomarkers, including specific cytokines, but also several proteins not previously associated with senescence, including extracellular matrix-interacting. Using both general and targeted phosphopeptide enrichment by Ti4+-IMAC and phosphotyrosine antibody enrichment, we identified over 15,000 phosphorylation sites. Among the regulated phosphorylation sites we encountered components of the interleukin, BRAF/MAPK and CDK-retinoblastoma (Rb) pathways and several other factors. The extensive proteome and phosphoproteome dataset of BRAFV600E-expressing senescent cells provides molecular clues as to how OIS is initiated, maintained or evaded, serving as a comprehensive proteomic basis for functional validation.
HostingRepository	PRIDE
AnnounceDate	2015-01-12
AnnouncementXML	Submission_2015-01-12_08:36:27.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Erik L. de Graaf
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue; phosphorylated residue; 2x(13)C: 6x(2)H labeled dimethylated L-arginine; dimethylated residue; 4x(2)H labeled dimethylated residue
Instrument	LTQ Orbitrap Velos

Revision	Datetime	Status	ChangeLog Entry
0	2013-10-16 04:11:10	ID requested
⏵ 1	2015-01-12 08:36:28	announced

de Graaf EL, Kaplon J, Zhou H, Heck AJ, Peeper DS, Altelaar AF, Phosphoproteome dynamics in onset and maintenance of oncogene-induced senescence. Mol Cell Proteomics, 13(8):2089-100(2014) [pubmed]

ProteomeXchange project tag: PRIME-XS Project

submitter keyword: Human Fibroblasts

Albert Heck
contact affiliation	Utrecht University
contact email	a.j.r.heck@uu.nl
lab head
Erik L. de Graaf
contact affiliation	Biomolecular Mass Spectrometry and Proteomics Laboratory, Utrecht University, Utrecht, The Netherlands
contact email	e.l.degraaf@uu.nl
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/2015/01/PXD000523

PRIDE project URI

• PRIDE
  1. PXD000523
     1. Label: PRIDE project
     2. Name: Phosphoproteome dynamics in onset and maintenance of Oncogene-Induced Senescence, phosphoproteome dataset