PXD050609 is an
original dataset announced via ProteomeXchange.
Dataset Summary
| Title | Urinary proteins from stone formers promote calcium oxalate crystallization, growth and aggregation via oxidative modifications |
| Description | Various urinary parameters have been used to determine kidney stone risk. However, almost all of the widely used lithogenic indices rely on urinary concentrations of small molecules/ions and pH. We hypothesized that urinary macromolecules (especially proteins) also play a critical role in determining the stone risk. Herein, we purified the complexed urinary proteins (proteome) from healthy individuals and calcium oxalate (CaOx) stone formers and performed various crystal assays and quantitative proteomics to compare them. While the normal urinary proteome inhibited CaOx stone-forming mechanisms (i.e., crystallization, growth and aggregation), the stone formers’ urinary proteome promoted all these CaOx crystal parameters. Descriptive proteomics by nanoLC-ESI-LTQ-Orbitrap-MS/MS analysis identified 203 and 381 proteins in the urine of healthy individuals and stone formers, respectively. Analyses of physicochemical properties revealed only molecular mass and isoelectric point that slightly increased in the stone formers’ urine, whereas instability index, grand average of hydrophathicity (GRAVY) and amino acid composition were comparable. Interestingly, proportion of oxidatively modified proteins (particularly those with methionine oxidation, methionine dioxidation and cysteine trioxidation) markedly increased (~2.5-fold) in the stone formers’ urine. Quantitative proteomics revealed 89 increased and 56 decreased proteins in the stone formers’ urine. The oxidized proteins had a greater proportion (>3-fold) in the increased proteins (77%) compared with the decreased ones (23%), whereas the non-oxidized proteins showed comparable proportions (54% and 46%, respectively). Functional enrichment analyses revealed a correlation between the increased proteins and oxidative stress biological processes and molecular functions. Finally, ELISA confirmed the significantly increased levels of oxidized proteins in the stone formers’ urine compared with that of healthy individuals. These data implicate that oxidatively modified proteome serves as the key pathogenic factor or risk for CaOx kidney stone formation. |
| HostingRepository | PRIDE |
| AnnounceDate | 2026-03-09 |
| AnnouncementXML | Submission_2026-03-08_17:13:22.825.xml |
| DigitalObjectIdentifier | https://dx.doi.org/10.6019/PXD050609 |
| ReviewLevel | Peer-reviewed dataset |
| DatasetOrigin | Original dataset |
| RepositorySupport | Supported dataset by repository |
| PrimarySubmitter | Visith Thongboonkerd |
| SpeciesList | scientific name: Homo sapiens (Human); NCBI TaxID: NEWT:9606; |
| ModificationList | dihydroxylated residue; monohydroxylated residue |
| Instrument | LTQ Orbitrap XL |
Dataset History
| Revision | Datetime | Status | ChangeLog Entry |
|---|
| 0 | 2024-03-13 23:17:39 | ID requested | |
| ⏵ 1 | 2026-03-08 17:13:24 | announced | |
Publication List
| 10.6019/PXD050609; |
| 10.1016/j.jare.2025.05.040; |
| Hadpech S, Peerapen P, Chaiyarit S, Sritippayawan S, Thongboonkerd V, Urinary proteins from stone formers promote calcium oxalate crystallization, growth and aggregation via oxidative modifications. J Adv Res, 81():125-141(2026) [pubmed] |
Keyword List
| submitter keyword: Nephrolithiasis |
| Oxidized protein |
| Risk factor |
| Stone modulator |
| Urinary protein |
| Urolithiasis |
Contact List
| Prof. Visith Thongboonkerd |
|---|
| contact affiliation | Medical Proteomics Unit, Research Department, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand |
| contact email | vthongbo@yahoo.com |
| lab head | |
| Visith Thongboonkerd |
|---|
| contact affiliation | Mahidol University |
| contact email | sirirajms@gmail.com |
| 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/2026/03/PXD050609 |
| PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD050609
- Label: PRIDE project
- Name: Urinary proteins from stone formers promote calcium oxalate crystallization, growth and aggregation via oxidative modifications
