PXD056560 is an
original dataset announced via ProteomeXchange.
Dataset Summary
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 |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
0 | 2024-10-07 11:37:47 | ID requested | |
⏵ 1 | 2025-02-11 07:26:19 | announced | |
Publication List
Keyword List
submitter keyword: proteomics, Prosit, mass spectrometry,citrullination, deep learning |
Contact List
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 | |
Full Dataset Link List
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 |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD056560
- Label: PRIDE project
- Name: Deep Learning Enhances Precision of Citrullination Identification in Human and Arabidopsis Tissue Proteomes