Standard operating procedure combined with comprehensive quality control system to enable large-scale urinary proteomics across multiple LC-MS platforms for precision medicine

ABSTRACT: 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.

ORGANISM(S): Homo Sapiens Escherichia Coli Saccharomyces Cerevisiae

SUBMITTER: Wei Sun  

PROVIDER: PXD050291 | iProX | Mon Oct 28 00:00:00 GMT 2024

REPOSITORIES: iProX