High-throughput proteomics of nanogram-scale samples with Zeno SWATH MS

Area of Science:

• Proteomics
• Biomedical Research
• Analytical Chemistry

Background:

• High-throughput proteomic experiments are crucial for biomedical research, drug discovery, and systems biology.
• Current high-throughput methods often require large sample quantities and exhibit lower sensitivity.
• Existing limitations hinder the widespread application of high-throughput proteomics.

Purpose of the Study:

• Introduce and benchmark Zeno SWATH MS, a novel data-independent acquisition technique.
• Enhance sensitivity in high-throughput proteomic experiments.
• Enable sensitive proteomic analysis with reduced sample input.

Main Methods:

• Utilized Zeno SWATH MS, a technique incorporating linear ion trap pulsing (Zeno trap pulsing).
• Combined Zeno SWATH MS with fast micro-flow and analytical flow-rate chromatography.
• Benchmarked performance using varying sample loads and chromatography durations.

Main Results:

• Zeno SWATH MS significantly increased protein identification with low sample amounts.
• Identified over 5000 proteins consistently from 62.5 ng of human cell tryptic digest using 20 min micro-flow chromatography.
• Achieved identification of 4907 proteins from 2 µg and over 3000 proteins from 250 ng of human cell lysate using 5 min analytical flow chromatography.

Conclusions:

• Zeno SWATH MS effectively increases sensitivity in high-throughput proteomic experiments.
• The technique mitigates sample amount limitations in current proteomic workflows.
• Facilitates sensitive, high-throughput proteomic analyses crucial for various biomedical applications.