Standard operating procedure combined with comprehensive quality control system for multiple LC-MS platforms urinary proteomics
Abstract
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.
Article Details
Authors (44)
Xiang Liu
Haidan Sun
Xinhang Hou
Jiameng Sun
Min Tang
Key Laboratory of Birth Defects and Related Diseases of Women and Children, Department of Paediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy, Sichuan University
Yong-Biao Zhang
Yongqian Zhang
Wei Sun
Chao Liu
Youhe Gao
Shuxuan Tang
Ziyun Shen
Kehui Liu
Lulu Jia
Jing Wei
State Key Laboratory of Electronic Thin Films and Integrated Devices, School of Optoelectronic Science and Engineering
Jianqiang Wu
Xiaoyue Tang
Yanchang Li
Guibin Wang
Xinying Sui
Lihua Zhang
Center for Functional Nanomaterials
Huiming Yuan
Xinxin Liu
Dong Liu
Hefei National Research Center for Physical Sciences at the Microscale, School of Chemistry and Materials Science, National Synchrotron Radiation Laboratory
Qi Zhang
Xindan Qiu
Guanbo Wang
Mo Hu
Ye Tian
Minjie Tan
Peng Xue
Liman Guo
Qing Zhang
Yongsheng Chen
Department of Neurosurgery The Tenth Affiliated Hospital Southern Medical University Dongguan China
Jianguo Ji
Weiyi Hu
Wenyuan Zhu
Min Huang
Yingzi Qi
Xianming Liu
Institutes of Biomedical Sciences and Department of Chemistry, Fudan University
Xiaoxian Du
Ji Luo
Lingsheng Chen
Yinghua Zhao