Fast proteomics with dia-PASEF and analytical flow-rate chromatography

Area of Science:

• Proteomics
• Biomedical Research
• Systems Biology

Background:

• High-throughput proteomic experiments are crucial for advancing systems biology and biomedical research.
• Current methods face limitations in throughput and sample requirements.
• There is a need for cost-effective and accessible proteomic platforms.

Purpose of the Study:

• To develop a high-throughput proteomic workflow for analyzing limited sample amounts.
• To achieve high-quality proteomic data with improved speed and efficiency.
• To enable new approaches in systems biology and clinical research.

Main Methods:

• Combination of analytical flow rate chromatography with ion mobility separation of peptide ions.
• Utilizing data-independent acquisition (DIA) and the DIA-NN software suite for data analysis.
• Employing a workflow capable of processing up to 400 samples per day.

Main Results:

• Quantification of 5211 proteins from 2 μg of mammalian cell-line standard with high accuracy and precision.
• Successful analysis of COVID-19 patient plasma samples using short (3-min) chromatographic gradients.
• Demonstrated comprehensive profiling of the COVID-19 plasma proteome.

Conclusions:

• The developed high-throughput proteomic method significantly enhances experimental efficiency and accessibility.
• The workflow provides a comprehensive view of proteomes from limited samples, facilitating biomarker discovery.
• This approach supports patient stratification and advances understanding of disease mechanisms, such as in COVID-19.