PXD000934 is an
original dataset announced via ProteomeXchange.
Dataset Summary
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 |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
0 | 2014-04-28 00:55:13 | ID requested | |
⏵ 1 | 2016-07-08 14:01:44 | announced | |
Publication List
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] |
Keyword List
curator keyword: Biomedical |
submitter keyword: COFRADIC, Ubiquitin, Jurkat |
Contact List
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 | |
Full Dataset Link List
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 |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD000934
- Label: PRIDE project
- Name: A COFRADIC protocol to study protein ubiquitination