PXD071247

PXD071247 is an original dataset announced via ProteomeXchange.

Title	Decoding isozyme-specific substrate recognition in protein arginine deiminases by in vitro proteome-wide citrullination mapping
Description	Protein arginine deiminases (PADs) convert arginine to citrulline, altering protein structure and function. Of the five human isozymes, PAD1–4 are catalytically active with distinct tissue-specificities, yet isozyme-specific substrate recognition remains poorly defined. Here, we provide a systematic, isozyme-wide comparison of human PAD1–4 by combining controlled in vitro incubation of human cell lysates with recombinant enzymes, deep-coverage LC–MS/MS and advanced computational validation. Importantly, by incubating lysates under uniform, saturating enzyme and calcium conditions we aimed to isolate intrinsic substrate recognition potential from confounding factors such as isozyme expression levels, localization or intracellular calcium concentrations. We further leveraged deep-learning-based rescoring to elevate site-level confidence. With this approach we mapped ~30,000 citrullination sites across ~5,500 of proteins, enabling direct comparison of substrate repertoire, sequence motif, and structural context among PAD isozymes, setting the stage for mechanistic dissection of how binding-pocket homology and peripheral residues dictate specificity. Distinct isozyme-specific preferences persisted in time-course experiments (10 min–16 h), indicating sequence context rather than temporal dynamics drives specificity. Mutation analysis of eleven PAD4 variants revealed Q346, G403S, R639, and H640 as key determinants distinguishing substrate recognition from that of PAD2. This work provides the most comprehensive PADs substrate atlas to date, defining isozyme-specific motifs and molecular determinants, and guiding development of selective inhibitors and probes to interrogate citrullination mechanisms in health and disease.
HostingRepository	PRIDE
AnnounceDate	2026-04-22
AnnouncementXML	Submission_2026-04-22_14:12:30.829.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Sophia Laposchan
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: NEWT:9606;
ModificationList	L-citrulline
Instrument	Orbitrap Exploris 480

Revision	Datetime	Status	ChangeLog Entry
0	2025-11-25 20:56:22	ID requested
⏵ 1	2026-04-22 14:12:31	announced

Dataset with its publication pending

submitter keyword: None

Chien-Yun Lee
contact affiliation	Young Investigator Group: Mass Spectrometry in Systems Neurosciences, School of Life Sciences, Technical University of Munich, Freising, Germany
contact email	chienyun.lee@tum.de
lab head
Sophia Laposchan
contact affiliation	Young Investigator Group: Mass Spectrometry in Systems Neurosciences, Technical University of Munich
contact email	sophia.laposchan@tum.de
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/2026/04/PXD071247

PRIDE project URI

• PRIDE
  1. PXD071247
     1. Label: PRIDE project
     2. Name: Decoding isozyme-specific substrate recognition in protein arginine deiminases by in vitro proteome-wide citrullination mapping