PXD050291
PXD050291 is an original dataset announced via ProteomeXchange.
Dataset Summary
| Title | Standard operating procedure combined with comprehensive quality control system to enable large-scale urinary proteomics across multiple LC-MS platforms for precision medicine |
| Description | In this study, we carried out a comprehensive evaluation of multiple LC-MS platforms in urinary proteomics including 756 proteome measurements. A series of interrelated studies was designed to assess the intra- and inter-platform consistency and reproducibility. First, we optimized the method for urinary proteome, including sample loading amount, chromatography, and DIA method. Second, a uniformly prepared urine sample is distributed to 20 LC-MS platforms, where a total of 160 data are generated to analyze the consistency and reproducibility across different LC-MS platforms. Third, benchmarking samples, which consist of tryptic digests of human, yeast, and E. coli proteins mixed in defined proportions, are generated to mimic differential expressed biological samples and provide proof of the robustness and reproducibility of the different LC-MS platforms. Finally, the above SOP are applied to actual clinical CRC cohort urinary proteome datasets derived from 3 LC-MS platforms to further demonstrate the performance of urinary proteomics cohorts from multi-platform in biomarker discovery. |
| HostingRepository | iProX |
| AnnounceDate | 2024-10-28 |
| AnnouncementXML | Submission_2025-12-16_01:27:39.833.xml |
| DigitalObjectIdentifier | |
| ReviewLevel | Peer-reviewed dataset |
| DatasetOrigin | Original dataset |
| RepositorySupport | Unsupported dataset by repository |
| PrimarySubmitter | Xiang Liu |
| SpeciesList | scientific name: Homo sapiens; NCBI TaxID: 9606; scientific name: Escherichia coli; NCBI TaxID: 562; scientific name: Saccharomyces cerevisiae; NCBI TaxID: 4932; |
| ModificationList | No PTMs are included in the dataset |
| Instrument | Orbitrap Fusion Lumos; Q Exactive HF; timsTOF Pro; Q Exactive HF-X; Orbitrap Exploris 480 |
Dataset History
| Revision | Datetime | Status | ChangeLog Entry |
|---|---|---|---|
| 0 | 2024-03-03 19:32:30 | ID requested | |
| 1 | 2024-03-03 19:33:12 | announced | |
| 2 | 2025-10-29 20:21:32 | announced | 2025-10-30: Add info |
| ⏵ 3 | 2025-12-16 01:27:40 | announced | 2025-10-30: Add info 2025-12-16: Add info. |
Publication List
| Liu X, Sun H, Hou X, Sun J, Tang M, Zhang YB, Zhang Y, Sun W, Liu C, Gao Y, Tang S, Shen Z, Liu K, Jia L, Wei J, Wu J, Tang X, Li Y, Wang G, Sui X, Zhang L, Yuan H, Liu X, Liu D, Zhang Q, Qiu X, Wang G, Hu M, Tian Y, Tan M, Xue P, Guo L, Zhang Q, Chen Y, Ji J, Hu W, Zhu W, Huang M, Qi Y, Liu X, Du X, Luo J, Chen L, Zhao Y, Standard operating procedure combined with comprehensive quality control system for multiple LC-MS platforms urinary proteomics. Nat Commun, 16(1):1051(2025) [pubmed] |
Keyword List
| submitter keyword: Urinary proteomics, Multiple LC-MS platforms |
Contact List
| Wei Sun | |
|---|---|
| contact affiliation | Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, Beijing, China |
| contact email | sunwei@ibms.pumc.edu.cn |
| lab head | |
| Xiang Liu | |
| contact affiliation | Beihang University; Peking Union Medical College |
| contact email | lx940527@126.com |
| dataset submitter | |
Full Dataset Link List
| iProX dataset URI |
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