PXD040466

PXD040466 is an original dataset announced via ProteomeXchange.

Title	Identification of NEDD8 sites at endogenous levels of NEDD8 expression upon NEDP1 (SENP8, DEN1) knockout.
Description	We developed a strategy that allows the identification of NEDP1 dependent NEDDylation sites under endogenous expression of wild type NEDD8. We combined the use of anti-diGly antibodies that recognise both ubiquitin and NEDD8 modified peptides upon trypsin digestion with short treatment of cells with the ubiquitin E1 inhibitor MLN7243 (UAEi), that dramatically reduces ubiquitin but not NEDD8 modification. By eliminating the majority of ubiquitin-derived diGly peptides upon MLN7243 treatment, we would be able to quantify NEDP1 dependent diGly peptides. Extracts from parental and NEDP1 knockout HCT116 cells both treated with UAEi were used for the isolation of diGly modified peptides and mass spectrometry analysis.
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_08:47:27.404.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Dimitris Xirodimas
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	ubiquitinylated lysine
Instrument	LTQ Orbitrap Velos

Revision	Datetime	Status	ChangeLog Entry
0	2023-02-27 07:36:10	ID requested
1	2023-05-10 14:21:00	announced
⏵ 2	2023-11-14 08:47:28	announced	2023-11-14: Updated project metadata.

Kassouf T, Shrivastava R, Meszka I, Bailly A, Polanowska J, Trauchessec H, Mandrioli J, Carra S, Xirodimas DP, Targeting the NEDP1 enzyme to ameliorate ALS phenotypes through stress granule disassembly. Sci Adv, 9(13):eabq7585(2023) [pubmed]

submitter keyword: antibody, diGly, inhibitor, NEDD8,NEDDylation, UAEi, anti-diGly antibodies, ubiquitin

Dimitris Xirodimas
contact affiliation	CRBM-CNRS, Montpellier, France
contact email	dimitris.xirodimas@crbm.cnrs.fr
lab head
Dimitris Xirodimas
contact affiliation	CRBM-CNRS
contact email	dimitris.xirodimas@crbm.cnrs.fr
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/2023/05/PXD040466

PRIDE project URI

• PRIDE
  1. PXD040466
     1. Label: PRIDE project
     2. Name: Identification of NEDD8 sites at endogenous levels of NEDD8 expression upon NEDP1 (SENP8, DEN1) knockout.