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

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.