Standard operating procedure combined with comprehensive quality control system for multiple LC-MS platforms urinary proteomics
Abstract Urinary proteomics is emerging as a potent tool for detecting sensitive and non-invasive biomarkers. At present, the comparability of urinary proteomics data across diverse liquid chromatography−mass spectrometry (LC-MS) platforms remains an area that requires investigation. In this study,...
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| Format: | Article |
| Language: | English |
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Nature Portfolio
2025-01-01
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| Series: | Nature Communications |
| Online Access: | https://doi.org/10.1038/s41467-025-56337-4 |
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| author | Xiang Liu Haidan Sun Xinhang Hou Jiameng Sun Min Tang Yong-Biao Zhang Yongqian Zhang Wei Sun Chao Liu Urine Test Sample Working Group |
| author_facet | Xiang Liu Haidan Sun Xinhang Hou Jiameng Sun Min Tang Yong-Biao Zhang Yongqian Zhang Wei Sun Chao Liu Urine Test Sample Working Group |
| author_sort | Xiang Liu |
| collection | DOAJ |
| description | Abstract Urinary proteomics is emerging as a potent tool for detecting sensitive and non-invasive biomarkers. At present, the comparability of urinary proteomics data across diverse liquid chromatography−mass spectrometry (LC-MS) platforms remains an area that requires investigation. In this study, we conduct a comprehensive evaluation of urinary proteome across multiple LC-MS platforms. To systematically analyze and assess the quality of large-scale urinary proteomics data, we develop a comprehensive quality control (QC) system named MSCohort, which extracted 81 metrics for individual experiment and the whole cohort quality evaluation. Additionally, we present a standard operating procedure (SOP) for high-throughput urinary proteome analysis based on MSCohort QC system. Our study involves 20 LC-MS platforms and reveals that, when combined with a comprehensive QC system and a unified SOP, the data generated by data-independent acquisition (DIA) workflow in urine QC samples exhibit high robustness, sensitivity, and reproducibility across multiple LC-MS platforms. Furthermore, we apply this SOP to hybrid benchmarking samples and clinical colorectal cancer (CRC) urinary proteome including 527 experiments. Across three different LC-MS platforms, the analyses report high quantitative reproducibility and consistent disease patterns. This work lays the groundwork for large-scale clinical urinary proteomics studies spanning multiple platforms, paving the way for precision medicine research. |
| format | Article |
| id | doaj-art-e5ca0b1fcabd4b74992b612b41f7cf6d |
| institution | Kabale University |
| issn | 2041-1723 |
| language | English |
| publishDate | 2025-01-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Nature Communications |
| spelling | doaj-art-e5ca0b1fcabd4b74992b612b41f7cf6d2025-01-26T12:41:06ZengNature PortfolioNature Communications2041-17232025-01-0116111810.1038/s41467-025-56337-4Standard operating procedure combined with comprehensive quality control system for multiple LC-MS platforms urinary proteomicsXiang Liu0Haidan Sun1Xinhang Hou2Jiameng Sun3Min Tang4Yong-Biao Zhang5Yongqian Zhang6Wei Sun7Chao Liu8Urine Test Sample Working GroupSchool of Biological Science and Medical Engineering & School of Engineering Medicine, Beihang UniversityProteomics Center, Core Facility of Instrument, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical CollegeSchool of Biological Science and Medical Engineering & School of Engineering Medicine, Beihang UniversityProteomics Center, Core Facility of Instrument, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical CollegeSchool of Biological Science and Medical Engineering & School of Engineering Medicine, Beihang UniversitySchool of Biological Science and Medical Engineering & School of Engineering Medicine, Beihang UniversitySchool of Medical Technology, Beijing Institute of TechnologyProteomics Center, Core Facility of Instrument, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical CollegeSchool of Biological Science and Medical Engineering & School of Engineering Medicine, Beihang UniversityAbstract Urinary proteomics is emerging as a potent tool for detecting sensitive and non-invasive biomarkers. At present, the comparability of urinary proteomics data across diverse liquid chromatography−mass spectrometry (LC-MS) platforms remains an area that requires investigation. In this study, we conduct a comprehensive evaluation of urinary proteome across multiple LC-MS platforms. To systematically analyze and assess the quality of large-scale urinary proteomics data, we develop a comprehensive quality control (QC) system named MSCohort, which extracted 81 metrics for individual experiment and the whole cohort quality evaluation. Additionally, we present a standard operating procedure (SOP) for high-throughput urinary proteome analysis based on MSCohort QC system. Our study involves 20 LC-MS platforms and reveals that, when combined with a comprehensive QC system and a unified SOP, the data generated by data-independent acquisition (DIA) workflow in urine QC samples exhibit high robustness, sensitivity, and reproducibility across multiple LC-MS platforms. Furthermore, we apply this SOP to hybrid benchmarking samples and clinical colorectal cancer (CRC) urinary proteome including 527 experiments. Across three different LC-MS platforms, the analyses report high quantitative reproducibility and consistent disease patterns. This work lays the groundwork for large-scale clinical urinary proteomics studies spanning multiple platforms, paving the way for precision medicine research.https://doi.org/10.1038/s41467-025-56337-4 |
| spellingShingle | Xiang Liu Haidan Sun Xinhang Hou Jiameng Sun Min Tang Yong-Biao Zhang Yongqian Zhang Wei Sun Chao Liu Urine Test Sample Working Group Standard operating procedure combined with comprehensive quality control system for multiple LC-MS platforms urinary proteomics Nature Communications |
| title | Standard operating procedure combined with comprehensive quality control system for multiple LC-MS platforms urinary proteomics |
| title_full | Standard operating procedure combined with comprehensive quality control system for multiple LC-MS platforms urinary proteomics |
| title_fullStr | Standard operating procedure combined with comprehensive quality control system for multiple LC-MS platforms urinary proteomics |
| title_full_unstemmed | Standard operating procedure combined with comprehensive quality control system for multiple LC-MS platforms urinary proteomics |
| title_short | Standard operating procedure combined with comprehensive quality control system for multiple LC-MS platforms urinary proteomics |
| title_sort | standard operating procedure combined with comprehensive quality control system for multiple lc ms platforms urinary proteomics |
| url | https://doi.org/10.1038/s41467-025-56337-4 |
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