PXD007101 is an
original dataset announced via ProteomeXchange.
Dataset Summary
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 |
Dataset History
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. |
Publication List
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] |
Keyword List
curator keyword: Technical |
submitter keyword: Ubiquitinome, SILAC, Hela, ubiquitination, U2OS, ubiquitin, Orbitrap Lumos, diGly peptides, mouse brain tissue |
Contact List
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 | |
Full Dataset Link List
Dataset FTP location
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PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD007101
- Label: PRIDE project
- Name: Improvement of ubiquitination site detection by Orbitrap mass spectrometry.