PXD001609 is an
original dataset announced via ProteomeXchange.
Dataset Summary
Title | Validation of a novel shotgun proteomic workflow for the discovery of protein-protein interactions: focus on ZNF521 |
Description | The study of protein-protein interactions is increasingly relying on mass spectrometry (MS). The classical approach of separating immunoprecipitated proteins by SDS-PAGE followed by in-gel digestion is long and labour-intensive. Besides, it is difficult to integrate it with most quantitative MS-based workflows, except for stable isotopic labelling of amino acids in cell culture (SILAC). This work describes a fast, flexible and quantitative workflow for the discovery of novel proteinprotein interactions. A cleavable cross-linker, dithiobis[succinimidyl propionate] (DSP), is utilized to stabilize protein complexes before immunoprecipitation. Protein complex detachment from the antibody is achieved by limited proteolysis. Finally, protein quantitation is performed via 18O labelling. The workflow has been optimized concerning: (i) DSP concentration and (ii) incubation times for limited proteolysis, using the stem cell-associated transcription co-factor ZNF521 as a model target. The interaction of ZNF521 with the core components of the nuclear remodelling and histone deacetylase (NuRD) complex, already reported in the literature, was confirmed. Additionally, interactions with newly discovered molecular partners of potentially relevant functional role, such as ZNF423, Spt16, Spt5, were discovered and validated by Western blotting. |
HostingRepository | PRIDE |
AnnounceDate | 2015-04-07 |
AnnouncementXML | Submission_2015-04-07_10:42:36.xml |
DigitalObjectIdentifier | https://dx.doi.org/10.6019/PXD001609 |
ReviewLevel | Peer-reviewed dataset |
DatasetOrigin | Original dataset |
RepositorySupport | Supported dataset by repository |
PrimarySubmitter | SHIBU KRISHNAN |
SpeciesList | scientific name: Homo sapiens (Human); NCBI TaxID: 9606; |
ModificationList | No PTMs are included in the dataset |
Instrument | Q Exactive |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
0 | 2014-12-15 03:00:46 | ID requested | |
⏵ 1 | 2015-04-07 10:42:37 | announced | |
Publication List
Bernaudo F, Monteleone F, Mesuraca M, Krishnan S, Chiarella E, Scicchitano S, Cuda G, Morrone G, Bond HM, Gaspari M, Validation of a novel shotgun proteomic workflow for the discovery of protein-protein interactions: focus on ZNF521. J Proteome Res, 14(4):1888-99(2015) [pubmed] |
Keyword List
curator keyword: Biological, Technical |
submitter keyword: AP-MS |
interactomics |
18O labelling |
ZNF521 |
ZNF423 |
Spt16 |
Spt5 |
NuRD core complex |
proteomics |
mass spectrometry |
shotgun proteomics |
Contact List
Professor Giovanni Cuda |
contact affiliation | University Magna Graecia of Catanzaro |
contact email | cuda@unicz.it |
lab head | |
SHIBU KRISHNAN |
contact affiliation | University Magna Graecia of Catanzaro |
contact email | shibu@unicz.it |
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/2015/04/PXD001609 |
PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD001609
- Label: PRIDE project
- Name: Validation of a novel shotgun proteomic workflow for the discovery of protein-protein interactions: focus on ZNF521