PXD023131

PXD023131 is an original dataset announced via ProteomeXchange.

Title	Characterization of Citrullination Sites in Neutrophils and Mast Cells Activated by Ionomycin via Integration of Mass Spectrometry and Machine Learning
Description	Citrullination is an important post-translational modification implicated in many diseases including rheumatoid arthritis (RA), Alzheimer's disease and cancer. Neutrophil and mast cells have different protein-arginine deiminases expression profile and ionomycin induced activation make them the ideal cellular models to study proteins susceptible to citrullination. We performed high resolution mass spectrometry and stringent data filtration to identify citrullination sites in neutrophil and mast cells treated with and without ionomycin. We identified a total of 831 validated citrullination sites on 393 proteins. Several of these citrullinated proteins are important component of pathways involved in innate immune responses. Using this benchmark primary sequence dataset, we developed machine learning models to predict citrullination in neutrophil and mast cells proteins. Our neutrophil protein citrullination prediction model achieved greater than 76% accuracy and 0.39 Matthews correlation coefficient (MCC) on an independent validation set. In summary, this study provides the largest number of validated citrullination sites in neutrophil and mast cell proteins. The use of our novel motif analysis approach to predict citrullination sites will facilitate the discovery of novel protein substrates of protein-arginine deiminases (PADs), which may be key to understanding immunopathologies of various diseases.
HostingRepository	PRIDE
AnnounceDate	2022-01-12
AnnouncementXML	Submission_2022-01-12_08:00:36.244.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Raghothama Chaerkady
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	L-citrulline
Instrument	Orbitrap Fusion

Revision	Datetime	Status	ChangeLog Entry
0	2020-12-15 01:41:16	ID requested
⏵ 1	2022-01-12 08:00:37	announced

Chaerkady R, Zhou Y, Delmar JA, Weng SHS, Wang J, Awasthi S, Sims D, Bowen MA, Yu W, Cazares LH, Sims GP, Hess S, Characterization of Citrullination Sites in Neutrophils and Mast Cells Activated by Ionomycin via Integration of Mass Spectrometry and Machine Learning. J Proteome Res, 20(6):3150-3164(2021) [pubmed]

submitter keyword: Citrullination,neutrophils, mast cells, mass spectrometry

Sonja Hess
contact affiliation	Dynamic Omics, Antibody Discovery and Protein Engineering (ADPE), R&D AstraZenecaGaithersburg, Maryland, US, 20878.
contact email	sonja.hess@astrazeneca.com
lab head
Raghothama Chaerkady
contact affiliation	MedImmune
contact email	chaerkadyr@medimmune.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/2022/01/PXD023131

PRIDE project URI

• PRIDE
  1. PXD023131
     1. Label: PRIDE project
     2. Name: Characterization of Citrullination Sites in Neutrophils and Mast Cells Activated by Ionomycin via Integration of Mass Spectrometry and Machine Learning