PXD015701

PXD015701 is an original dataset announced via ProteomeXchange.

Title	Confident identification of citrullinated peptides from P gingivalis
Description	Porphyromonas gingivalis is a key pathogen in the development of chronic periodontitis and has recently been linked to the development of rheumatoid arthritis and Alzheimer’s disease. In this project the outer membrane vesicles (OMV) from Pg have been analyzed using a two-dimensional HFBA-based separation system combined with LC-MS. Three strains from P. gingivalis was analyzed in order to elucidate their citrullinome: wild-type (WT), a mutant with the active site cysteine mutated to alanine (C351A), as well as a knock-out mutant of peptidyl arginine deiminase (ΔPPAD). For optimal and positive identification and validation of citrullinated peptides and proteins, high resolution mass spectrometers and strict MS criteria were utilized. This may have compromised the total number of identified citrullination, but increased the confidence of the validation. A new 2D separation system proved to increase the strength of validation, and along with the use of an in-house build program, Citrullia, we establish a fast and easy semi-automatic (manual) validation of citrullinated peptides. For WT we identified 78 citrullinated proteins having a total of 161 citrullination sites. For C351A a single citrullination site was found and no citrullinations was found for ΔPPAD.
HostingRepository	PRIDE
AnnounceDate	2019-11-22
AnnouncementXML	Submission_2019-11-25_00:41:47.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Peter Højrup
SpeciesList	scientific name: Porphyromonas gingivalis W83; NCBI TaxID: 242619;
ModificationList	deaminated residue; iodoacetamide derivatized residue; deamidated residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2019-10-04 04:11:09	ID requested
1	2019-11-22 05:38:52	announced
⏵ 2	2019-11-25 00:41:48	announced	2019-11-25: Updated publication reference for PubMed record(s): 31754044.

Larsen DN, Mikkelsen CE, Kierkegaard M, Bereta GP, Nowakowska Z, Kaczmarek JZ, Potempa J, H, ø, jrup P, Outer Membrane Vesicles: Confident Identification of Citrullinated Peptides. Mol Cell Proteomics, 19(1):167-180(2020) [pubmed]

submitter keyword: Phorphyromonas gingivalis, HFBA, Proteins, Citrullination, Citrulline

Peter Højrup
contact affiliation	PR group, Biochemistry and Molecular Biology, University of Southern Denmark, Denmark
contact email	php@bmb.sdu.dk
lab head
Peter Højrup
contact affiliation	University of Southern Denmark
contact email	php@bmb.sdu.dk
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/2019/11/PXD015701

PRIDE project URI

• PRIDE
  1. PXD015701
     1. Label: PRIDE project
     2. Name: Confident identification of citrullinated peptides from P gingivalis