PXD005878

PXD005878 is an original dataset announced via ProteomeXchange.

Title	Internally Tagged Ubiquitin: a Tool to Identify Linear Polyubiquitin-modified Proteins by Mass Spectrometry
Description	Even though ubiquitination controls a plethora of cellular processes, modifications by linear polyubiquitin have so far only been linked with acquired and innate immunity, lymphocyte development and genotoxic stress response. Until now, a single E3 ligase complex (LUBAC), one specific deubiquitinase (Otulin) and a very few substrates have been identified. The existing methods for the study of lysine-based polyubiquitination are not suitable for the detection of linear polyubiquitin-modified proteins. Here, we present a novel approach to discovering linear polyubiquitin-modified substrates by combining lysine-less internally tagged ubiquitin (INT-Ub.7KR) with SILAC-based mass spectrometry. We applied our approach in TNFα-stimulated T-Rex HEK293T cells and afterwards validated newly identified linear polyubiquitin targets. Moreover, we demonstrated that linear polyubiquitination of the novel LUBAC substrate TRAF6 is essential for the NFkappaB signalling. Overall, we have established a powerful method for the detection of linear polyubiquitin substrates.
HostingRepository	PRIDE
AnnounceDate	2017-10-24
AnnouncementXML	Submission_2017-10-24_04:06:07.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Nicolas Nalpas
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	ubiquitinylated lysine
Instrument	Q Exactive; LTQ Orbitrap Elite

Revision	Datetime	Status	ChangeLog Entry
0	2017-02-08 02:23:11	ID requested
1	2017-03-21 04:38:16	announced
2	2017-03-27 01:32:02	announced	Updated publication reference for PubMed record(s): 28319114.
3	2017-03-28 00:30:20	announced	Updated project metadata.
⏵ 4	2017-10-24 04:06:08	announced	Updated project metadata.

Kliza K, Taumer C, Pinzuti I, Franz-Wachtel M, Kunzelmann S, Stieglitz B, Macek B, Husnjak K, Internally tagged ubiquitin: a tool to identify linear polyubiquitin-modified proteins by mass spectrometry. Nat Methods, 14(5):504-512(2017) [pubmed]

curator keyword: Technical

submitter keyword: Ubiquitin, proteomics, pull-down, human

Koraljka Husnjak
contact affiliation	Institute of Biochemistry II Goethe University School of Medicine Germany
contact email	husnjak@biochem2.de
lab head
Nicolas Nalpas
contact affiliation	Tuebingen University
contact email	nalpas.nicolas@gmail.com
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/2017/03/PXD005878

PRIDE project URI

• PRIDE
  1. PXD005878
     1. Label: PRIDE project
     2. Name: Internally Tagged Ubiquitin: a Tool to Identify Linear Polyubiquitin-modified Proteins by Mass Spectrometry