PXD000934

PXD000934 is an original dataset announced via ProteomeXchange.

Title	A COFRADIC protocol to study protein ubiquitination
Description	We here apply the COmbined FRActional DIagonal Chromatography (COFRADIC) technology to enrich for ubiquitinated peptides and identify sites of ubiquitination by mass spectrometry. Our technology bypasses the need to ectopically overexpress tagged variants of ubiquitin and the use of sequence-biased antibodies recognizing ubiquitin remnants. In brief, all protein primary amino groups are blocked by chemical acetylation after which ubiquitin chains are proteolytically and specifically removed by the catalytic core domain of the USP2 deubiquitinase (USP2cc). As USP2cc cleaves the isopeptidyl bond between the ubiquitin C-terminus and the ɛ-amino group of the ubiquitinated lysine, this enzyme re-introduces primary ɛ-amino groups in proteins. These amino groups are then chemically modified with a handle that allows specific isolation of ubiquitinated peptides during subsequent COFRADIC chromatographic runs. Our method allowed us to identify over 8,200 endogenous ubiquitination sites in more than 3,600 different proteins in a native human Jurkat cell lysate.
HostingRepository	PRIDE
AnnounceDate	2016-07-08
AnnouncementXML	Submission_2016-07-08_14:01:41.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Elisabeth Stes
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue; acetylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2014-04-28 00:55:13	ID requested
⏵ 1	2016-07-08 14:01:44	announced

Stes E, Laga M, Walton A, Samyn N, Timmerman E, De Smet I, Goormachtig S, Gevaert K, A COFRADIC protocol to study protein ubiquitination. J Proteome Res, 13(6):3107-13(2014) [pubmed]

curator keyword: Biomedical

submitter keyword: COFRADIC, Ubiquitin, Jurkat

Kris Gevaert
contact affiliation	VIB/UGent
contact email	kris.gevaert@vib-ugent.be
lab head
Elisabeth Stes
contact affiliation	VIB/UGent
contact email	elisabeth.stes@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/2016/07/PXD000934

PRIDE project URI

• PRIDE
  1. PXD000934
     1. Label: PRIDE project
     2. Name: A COFRADIC protocol to study protein ubiquitination