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PXD056560

PXD056560 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleDeep Learning Enhances Precision of Citrullination Identification in Human and Arabidopsis Tissue Proteomes
DescriptionCitrullination 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.
HostingRepositoryPRIDE
AnnounceDate2025-02-11
AnnouncementXMLSubmission_2025-02-11_07:26:18.979.xml
DigitalObjectIdentifier
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterWassim Gabriel
SpeciesList scientific name: Arabidopsis thaliana (Mouse-ear cress); NCBI TaxID: 3702; scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationListmonohydroxylated residue; L-citrulline; deamidated residue; iodoacetamide derivatized residue
InstrumentOrbitrap Fusion Lumos; Q Exactive HF-X
Dataset History
RevisionDatetimeStatusChangeLog Entry
02024-10-07 11:37:47ID requested
12025-02-11 07:26:19announced
Publication List
10.1016/J.MCPRO.2025.100924;
Keyword List
submitter keyword: proteomics, Prosit, mass spectrometry,citrullination, deep learning
Contact List
Dr. Chien-Yun Lee
contact affiliationYoung Investigator Group: Mass Spectrometry in Systems Neurosciences, School of Life Sciences,Technical University of Munich
contact emailchienyun.lee@tum.de
lab head
Wassim Gabriel
contact affiliationTechnical University in Munich
contact emailwassim.gabriel@tum.de
dataset submitter
Full Dataset Link List
Dataset FTP location
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PRIDE project URI
Repository Record List
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