PXD027358

PXD027358 is an original dataset announced via ProteomeXchange.

Title	A streamlined data analysis pipeline for the identification of sites of citrullination
Description	Citrullination is an enzyme-catalyzed post-translational modification (PTM) that is essential for a host of biological processes including gene regulation, programmed cell death, and organ development. While this PTM is required for normal cellular functions, aberrant citrullination is a hallmark of numerous autoimmune disorders as well as cancer. Although aberrant citrullination is linked to human pathology, the exact role of citrullination in disease remains poorly characterized, in part because of the challenges associated with identifying the specific arginine residues that are citrullinated. Tandem mass spectrometry is the most precise method to uncover sites of citrullination, however, due to the small mass shift (+0.984 Da) that results from citrullination, current database search algorithms commonly misannotate spectra leading to a high number of false-positive assignments. To address this challenge, we developed an automated workflow to rigorously and rapidly mine proteomic data to unambiguously identify the sites of citrullination from complex peptide mixtures. The crux of this streamlined workflow is the ionFinder software program, which classifies citrullination sites with high confidence based on the presence of diagnostic fragment ions. These diagnostic ions include the neutral loss of isocyanic acid, which is a dissociative event that is unique to citrulline residues. Using the ionFinder program, we have mapped the sites of autocitrullination on purified protein arginine deiminases (PADs 1-4) and mapped the global citrullinome in a PAD2 over-expressing cell line. The ionFinder algorithm is a highly versatile, user-friendly, and open-source program that is agnostic to the type of instrument and mode of fragmentation that is used.
HostingRepository	PRIDE
AnnounceDate	2021-11-25
AnnouncementXML	Submission_2021-11-25_07:36:41.005.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Aaron Maurais
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	deamidated residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2021-07-16 03:54:46	ID requested
⏵ 1	2021-11-25 07:36:41	announced

Dataset with its publication pending

submitter keyword: citrullination

Eranthie Weerapana
contact affiliation	Chemistry Department, Boston College
contact email	eranthie.weerapana@bc.edu
lab head
Aaron Maurais
contact affiliation	Boston College Chemistry Department
contact email	aaron.maurais@bc.edu
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/2021/11/PXD027358

PRIDE project URI

• PRIDE
  1. PXD027358
     1. Label: PRIDE project
     2. Name: A streamlined data analysis pipeline for the identification of sites of citrullination