Quality control of urine proteome based on liquid chromatography-mass spectrometry

doi:10.16352/j.issn.1001-6325.2025.08.0992

Abstract

Abstract: With the development of automated sample pretreatment technologies and high-throughput mass spectrometry platforms, large-scale clinical cohort-based proteomic studies have progressively achieved systematic analysis at the scale of thousands of samples and tens of thousands of proteins. However, the heterogeneity of instruments across multiple centers may introduce batch effects, systematic bias in long-term experiments, and reliability issues in detecting low-abundance biomarkers, thereby imposing higher demands on the entire workflow quality control system.This review systematically summarizes multidimensional QC parameters including sample preparation, chromatographic separation, mass spectrometric acquisition and protein identification. In particular, this review focuses on mainstream QC tools for intra-experiment and inter-experiment, emphasizing their primary functions under different acquisition modes. Finally, it discusses the feasibility of dynamically integrated algorithm-based QC models and multi-omics QC strategies in future research.

Key words: proteomics, LC-MS/MS, quality control, quality control tools

CLC Number:

R318.04

LIU Xiang, WEI Jing. Quality control of urine proteome based on liquid chromatography-mass spectrometry[J]. Basic & Clinical Medicine, 2025, 45(8): 992-998.

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