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Automated High-Throughput Proteomics Sample Preparation Platform Using DNA Extraction Plate for Industrial
Zuoqing Zhang1,2, Manman Han1, Yujie Wang1
1Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Systems Biology Centre, Technical Support Core Facilities, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China.
Analytical Chemistry
|February 23, 2026
Summary
We developed an automated proteomics sample preparation workflow (AutoDEP) for industrial microorganisms, significantly improving efficiency and reproducibility. This high-throughput method accelerates cell factory design and systems biology.
Area of Science:
- Microbiology
- Proteomics
- Biotechnology
Background:
- Proteomic analysis is crucial for understanding microbial systems and designing cellular factories.
- Current methods are manual, time-consuming, costly, and prone to errors.
Purpose of the Study:
- To develop an automated, high-throughput proteomics sample preparation workflow (AutoDEP) for industrial microorganisms.
- To improve efficiency, reduce errors, and accelerate proteomic data generation.
Main Methods:
- Integration of a sodium dodecyl sulfate (SDS)-based lysis buffer with a 96-well DNA extraction plate.
- Utilized the Biomek i7 liquid handling system for full automation from cell lysis to peptide generation.
Main Results:
- AutoDEP achieved excellent sample preparation efficiency with over 81% zero missed cleavage rate.
- High reproducibility was demonstrated with intraplate CV median below 7% and interplate CVs below 20% for over 91% of proteins.
- Interday reproducibility showed a Pearson correlation coefficient (R²) exceeding 0.98.
- The workflow robustly handles protein loading amounts from 5 to 200 μg.
Conclusions:
- AutoDEP significantly accelerates the construction of cell models using industrial chassis cells.
- The workflow's robust performance indicates potential for large-scale studies, including clinical sample analysis.
