PXD008970 is an
original dataset announced via ProteomeXchange.
Dataset Summary
Title | Protein citrullination in human tissues |
Description | Citrullination is a post-translational modification of arginine catalyzed by five peptidylarginine deiminases (PADs) in humans. The loss of a positive charge may cause structural or functional alterations and while the modification has been linked to several diseases including rheumatoid arthritis and cancer, its physiological or pathophysiological roles remain largely unclear. In part this is owing to limitations in available methodology able to robustly enrich, detect and localize the modification. As a result, only few citrullination sites have been identified on human proteins with high confidence. In this study, we mined data from mass spectrometry-based deep proteomic profiling of 30 human tissues to identify citrullination sites on endogenous proteins. Database searching of ~70 million tandem mass spectra yielded ~13,000 candidate spectra which were further triaged by spectrum quality metrics and the detection of the specific neutral loss of isocyanic acid from citrullinated peptides to reduce false positives. Because citrullination is easily confused with deamidation, we synthetised ~2,200 citrullinated and 1,300 deamindated peptides to build a library of reference spectra. This led to the validation of 375 citrullination sites on 209 human proteins. Further analysis showed that >80% of the identified modifications sites were new and for 56% of the proteins, citrullination was detected for the first time. Sequence motif analysis revealed a strong preference for Asp and Gly, residues around the citrullination site. Interestingly, while the modification was detected in 26 human tissues with the highest levels found in brain and lung, citrullination levels did not correlate well with protein expression of the PAD enzymes. Even though the current work represents the largest survey of protein citrullination to date, the modification was mostly detected on high abundance proteins arguing that the development of specific enrichment methods would be required in order to study the full extent of cellular protein citrullination. |
HostingRepository | PRIDE |
AnnounceDate | 2023-11-14 |
AnnouncementXML | Submission_2023-11-14_08:49:24.065.xml |
DigitalObjectIdentifier | |
ReviewLevel | Peer-reviewed dataset |
DatasetOrigin | Original dataset |
RepositorySupport | Unsupported dataset by repository |
PrimarySubmitter | Chien-Yun Lee |
SpeciesList | scientific name: Homo sapiens (Human); NCBI TaxID: 9606; |
ModificationList | mono N-acetylated residue; monohydroxylated residue; iodoacetamide derivatized residue; deamidated residue; L-citrulline |
Instrument | Thermo Scientific instrument model; Q Exactive |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
0 | 2018-02-16 03:41:04 | ID requested | |
1 | 2018-04-04 03:28:52 | announced | |
2 | 2018-04-10 01:10:32 | announced | Updated publication reference for PubMed record(s): 29610271. |
⏵ 3 | 2023-11-14 08:49:25 | announced | 2023-11-14: Updated project metadata. |
Publication List
Lee CY, Wang D, Wilhelm M, Zolg DP, Schmidt T, Schnatbaum K, Reimer U, Pont, é, n F, Uhl, é, n M, Hahne H, Kuster B, Mining the Human Tissue Proteome for Protein Citrullination. Mol Cell Proteomics, 17(7):1378-1391(2018) [pubmed] |
Keyword List
ProteomeXchange project tag: ProteomeTools |
curator keyword: Biological |
submitter keyword: Citrullination, post-translational modification, peptidylarginine deiminase, human proteome, synthetic peptides |
Contact List
Bernhard Kuster |
contact affiliation | Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany Bavarian Center for Biomolecular Mass Spectrometry, Freising, Germany |
contact email | kuster@tum.de |
lab head | |
Chien-Yun Lee |
contact affiliation | Chair of Proteomics and Bioanalytics, Technical University of Munich, Germany |
contact email | chienyun.lee@tum.de |
dataset submitter | |
Full Dataset Link List
Dataset FTP location
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PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD008970
- Label: PRIDE project
- Name: Protein citrullination in human tissues