PXD007101

PXD007101 is an original dataset announced via ProteomeXchange.

Title	Improvement of ubiquitination site detection by Orbitrap mass spectrometry.
Description	We describe a modified workflow to enrich for and detect diGly peptides originating from ubiquitinated proteins using immunopurification. Using a combination of several relatively simple modifications in the sample preparation and mass spectrometric detection protocols, we now routinely detect over 24,000 diGly modified peptides in a single sample. We show the efficacy of this strategy for cell lysates from both non-labeled and metabolically labeled (SILAC) mammalian cells. Furthermore, we demonstrate that this optimized strategy is also useful for the in-depth identification of the endogenous, unstimulated ubiquitinome of in vivo samples such as mouse brain tissue. As such, this study presents an addition to the toolbox of the ubiquitination site analysis for the identification of the deep ubiquitinome.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_04:39:37.201.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Jeroen Demmers
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	ubiquitinylated lysine
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2017-07-21 06:32:13	ID requested
1	2017-11-14 00:56:49	announced
⏵ 2	2024-10-22 04:39:39	announced	2024-10-22: Updated project metadata.

10.1016/j.jprot.2017.10.014;

van der Wal L, Bezstarosti K, Sap KA, Dekkers DHW, Rijkers E, Mientjes E, Elgersma Y, Demmers JAA, Improvement of ubiquitylation site detection by Orbitrap mass spectrometry. J Proteomics, 172():49-56(2018) [pubmed]

curator keyword: Technical

submitter keyword: Ubiquitinome, SILAC, Hela, ubiquitination, U2OS, ubiquitin, Orbitrap Lumos, diGly peptides, mouse brain tissue

Jeroen Demmers
contact affiliation	Proteomics Center, Erasmus University Medical Center, Rotterdam, The Netherlands
contact email	j.demmers@erasmusmc.nl
lab head
Jeroen Demmers
contact affiliation	Proteomics Center, Erasmus University Medical Center, Rotterdam, The Netherlands
contact email	j.demmers@erasmusmc.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/2017/11/PXD007101

PRIDE project URI

• PRIDE
  1. PXD007101
     1. Label: PRIDE project
     2. Name: Improvement of ubiquitination site detection by Orbitrap mass spectrometry.