PXD038702-1

PXD038702 is an original dataset announced via ProteomeXchange.

Title	A quantitative and site-specific atlas of the PADI4-induced citrullinome reveals widespread existence of citrullination
Description	Citrullination refers to the conversion of arginine into the non-essential amino acid citrulline. Despite its importance in physiology and disease, global identification of citrullinated proteins and modification sites has remained challenging. Here, we combined quantitative mass spectrometry-based proteomics with differentiation of a leukemia cell line into neutrophil-like cells to reveal a comprehensive atlas of citrullination sites. Collectively, we identified 14.056 citrullination sites within 4.008 proteins and quantified their regulation in response to PADI4-specific inhibitor GSK484. Hereby we uncovered general principles about the mechanistic and biological aspects of citrullination function, while providing site-specific and quantitative regulation of thousands of PADI4 substrates, including signature histone marks and numerous non-histone events on transcriptional regulators and chromatin-related signaling effectors. Collectively, we describe systems attributes of the human citrullinome, reveal the existence of thousands citrullinated autoantigens in neutrophil cells, and provide a resource framework for investigating PADI4-specific functions and substrates for years to come.
HostingRepository	PRIDE
AnnounceDate	2024-01-17
AnnouncementXML	Submission_2024-01-17_00:49:38.038.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Alexandra Rebak
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	L-citrulline
Instrument	Orbitrap Exploris 480; Q Exactive HF-X

Revision	Datetime	Status	ChangeLog Entry
0	2022-12-08 16:44:52	ID requested
⏵ 1	2024-01-17 00:49:38	announced
2	2024-10-22 06:22:28	announced	2024-10-22: Updated project metadata.

10.1038/S41594-024-01214-9;

submitter keyword: Citrullination, deamination, GSK-484, HL60, PADI, PADI4

Michael Lund Nielsen
contact affiliation	Proteomics program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
contact email	michael.lund.nielsen@cpr.ku.dk
lab head
Alexandra Rebak
contact affiliation	NNF Center for Protein Research
contact email	alexandrastripp@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/2024/01/PXD038702

PRIDE project URI

• PRIDE
  1. PXD038702
     1. Label: PRIDE project
     2. Name: A quantitative and site-specific atlas of the PADI4-induced citrullinome reveals widespread existence of citrullination