Combination of automated sample preparation and micro-flow LC–MS for high-throughput plasma proteomics

Ye，Xueting1,2,3; Cui，Xiaozhen3; Zhang，Luobin1; Wu，Qiong3; Sui，Xintong3; He，An3; Zhang，Xinyou1; Xu，Ruilian1; Tian，Ruijun3

2023-12-01

10.1186/s12014-022-09390-w

Clinical Proteomics   Impact Factor & Quartile

1542-6416

1559-0275

Background: Non-invasive detection of blood-based markers is a critical clinical need. Plasma has become the main sample type for clinical proteomics research because it is easy to obtain and contains measurable protein biomarkers that can reveal disease-related physiological and pathological changes. Many efforts have been made to improve the depth of its identification, while there is an increasing need to improve the throughput and reproducibility of plasma proteomics analysis in order to adapt to the clinical large-scale sample analysis. Methods: We have developed and optimized a robust plasma analysis workflow that combines an automated sample preparation platform with a micro-flow LC–MS-based detection method. The stability and reproducibility of the workflow were systematically evaluated and the workflow was applied to a proof-of-concept plasma proteome study of 30 colon cancer patients from three age groups. Results: This workflow can analyze dozens of samples simultaneously with high reproducibility. Without protein depletion and prefractionation, more than 300 protein groups can be identified in a single analysis with micro-flow LC–MS system on a Orbitrap Exploris 240 mass spectrometer, including quantification of 35 FDA approved disease markers. The quantitative precision of the entire workflow was acceptable with median CV of 9%. The preliminary proteomic analysis of colon cancer plasma from different age groups could be well separated with identification of potential colon cancer-related biomarkers. Conclusions: This workflow is suitable for the analysis of large-scale clinical plasma samples with its simple and time-saving operation, and the results demonstrate the feasibility of discovering significantly changed plasma proteins and distinguishing different patient groups.

Automated samples preparation High throughput Micro-flow LC–MS Plasma proteome profiling

SCI

English

First ; Corresponding

WOS:000910835400001

2-s2.0-85146047119

Scopus

1.The Second Clinical Medical College of Jinan University,the First Affiliated Hospital of Southern University of Science and Technology,Shenzhen People’s Hospital,Shenzhen,518020,China
2.The First Affiliated Hospital,Jinan University,Guangzhou,510632,China
3.Department of Chemistry and Research Center for Chemical Biology and Omics Analysis,School of Science,Southern University of Science and Technology,Shenzhen,518055,China

Ye，Xueting,Cui，Xiaozhen,Zhang，Luobin,等. Combination of automated sample preparation and micro-flow LC–MS for high-throughput plasma proteomics[J]. Clinical Proteomics,2023,20(1).

Ye，Xueting.,Cui，Xiaozhen.,Zhang，Luobin.,Wu，Qiong.,Sui，Xintong.,...&Tian，Ruijun.(2023).Combination of automated sample preparation and micro-flow LC–MS for high-throughput plasma proteomics.Clinical Proteomics,20(1).

Ye，Xueting,et al."Combination of automated sample preparation and micro-flow LC–MS for high-throughput plasma proteomics".Clinical Proteomics 20.1(2023).