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Standard operating procedure combined with comprehensive quality control system for multiple LC-MS platforms urinary

Xiang Liu1, Haidan Sun2, Xinhang Hou1

  • 1School of Biological Science and Medical Engineering & School of Engineering Medicine, Beihang University, Beijing, China.

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|January 26, 2025
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This study introduces MSCohort, a quality control system and standard operating procedure (SOP) for urinary proteomics. It ensures robust and reproducible biomarker detection across multiple liquid chromatography-mass spectrometry (LC-MS) platforms for precision medicine.

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Area of Science:

  • Proteomics
  • Biomarker Discovery
  • Mass Spectrometry

Background:

  • Urinary proteomics offers non-invasive biomarker detection.
  • Comparability of data across different liquid chromatography-mass spectrometry (LC-MS) platforms is currently limited.

Purpose of the Study:

  • To evaluate urinary proteome data comparability across diverse LC-MS platforms.
  • To develop a quality control (QC) system and standard operating procedure (SOP) for high-throughput urinary proteome analysis.

Main Methods:

  • Developed the MSCohort QC system with 81 metrics for evaluating individual experiments and entire cohorts.
  • Established a unified SOP for high-throughput urinary proteome analysis.
  • Utilized data-independent acquisition (DIA) workflow on 20 LC-MS platforms.

Main Results:

  • The MSCohort QC system and unified SOP demonstrated high robustness, sensitivity, and reproducibility for urine QC samples across multiple LC-MS platforms.
  • Application of the SOP to benchmarking and colorectal cancer (CRC) samples showed high quantitative reproducibility and consistent disease patterns across three LC-MS platforms.

Conclusions:

  • A comprehensive QC system and unified SOP enable reliable, large-scale urinary proteomics across diverse LC-MS platforms.
  • This standardization facilitates multi-platform clinical studies and advances precision medicine research.