PXD056560

PXD056560 is an original dataset announced via ProteomeXchange.

Title	Deep Learning Enhances Precision of Citrullination Identification in Human and Arabidopsis Tissue Proteomes
Description	Citrullination is a key yet underexplored post-translational modification involved in various biological processes. Its identification via mass spectrometry faces challenges like limited enrichment tools and false positives due to mass overlap with deamidation (+0.9840 Da). To address this, we developed a data analysis pipeline integrating the deep learning model Prosit-Cit, trained on ~53,000 spectra from ~2,500 synthetic citrullinated peptides, which improves sensitivity and precision in identifying citrullination sites. This approach has identified up to 14 times more citrullinated sites in human tissue proteomes and revealed new insights, including the first large-scale citrullination mapping in Arabidopsis. This upload includes: 1) Raw files and search SEARCHs from the evaluation dataset, used to assess the precision of citrullination identifications. 2) Raw files, search SEARCHs, and rescoring outcomes from validation experiments conducted on Arabidopsis flowers. 4) Re-analyzed search and rescoring SEARCHs from human (PXD010154) and Arabidopsis (PXD013868) tissue proteomes.
HostingRepository	PRIDE
AnnounceDate	2025-02-11
AnnouncementXML	Submission_2025-02-11_07:26:18.979.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Wassim Gabriel
SpeciesList	scientific name: Arabidopsis thaliana (Mouse-ear cress); NCBI TaxID: 3702; scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue; L-citrulline; deamidated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Fusion Lumos; Q Exactive HF-X

Revision	Datetime	Status	ChangeLog Entry
0	2024-10-07 11:37:47	ID requested
⏵ 1	2025-02-11 07:26:19	announced

10.1016/J.MCPRO.2025.100924;

submitter keyword: proteomics, Prosit, mass spectrometry,citrullination, deep learning

Dr. Chien-Yun Lee
contact affiliation	Young Investigator Group: Mass Spectrometry in Systems Neurosciences, School of Life Sciences,Technical University of Munich
contact email	chienyun.lee@tum.de
lab head
Wassim Gabriel
contact affiliation	Technical University in Munich
contact email	wassim.gabriel@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/2025/02/PXD056560

PRIDE project URI

• PRIDE
  1. PXD056560
     1. Label: PRIDE project
     2. Name: Deep Learning Enhances Precision of Citrullination Identification in Human and Arabidopsis Tissue Proteomes