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

Elife. 2022 Nov 30:11:e83947. doi: 10.7554/eLife.83947.

Abstract

The possibility to record proteomes in high throughput and at high quality has opened new avenues for biomedical research, drug discovery, systems biology, and clinical translation. However, high-throughput proteomic experiments often require high sample amounts and can be less sensitive compared to conventional proteomic experiments. Here, we introduce and benchmark Zeno SWATH MS, a data-independent acquisition technique that employs a linear ion trap pulsing (Zeno trap pulsing) to increase the sensitivity in high-throughput proteomic experiments. We demonstrate that when combined with fast micro- or analytical flow-rate chromatography, Zeno SWATH MS increases protein identification with low sample amounts. For instance, using 20 min micro-flow-rate chromatography, Zeno SWATH MS identified more than 5000 proteins consistently, and with a coefficient of variation of 6%, from a 62.5 ng load of human cell line tryptic digest. Using 5 min analytical flow-rate chromatography (800 µl/min), Zeno SWATH MS identified 4907 proteins from a triplicate injection of 2 µg of a human cell lysate, or more than 3000 proteins from a 250 ng tryptic digest. Zeno SWATH MS hence facilitates sensitive high-throughput proteomic experiments with low sample amounts, mitigating the current bottlenecks of high-throughput proteomics.

Keywords: biochemistry; chemical biology; data-independent acquisition; high-throughput screening; liquid chromatography; proteomics.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Biomedical Research*
  • Drug Discovery
  • Humans
  • Proteome
  • Proteomics*
  • Systems Biology

Substances

  • Proteome