One-Tip enables comprehensive proteome coverage in minimal cells and single zygotes

Nat Commun. 2024 Mar 20;15(1):2474. doi: 10.1038/s41467-024-46777-9.

Abstract

Mass spectrometry (MS)-based proteomics workflows typically involve complex, multi-step processes, presenting challenges with sample losses, reproducibility, requiring substantial time and financial investments, and specialized skills. Here we introduce One-Tip, a proteomics methodology that seamlessly integrates efficient, one-pot sample preparation with precise, narrow-window data-independent acquisition (nDIA) analysis. One-Tip substantially simplifies sample processing, enabling the reproducible identification of >9000 proteins from ~1000 HeLa cells. The versatility of One-Tip is highlighted by nDIA identification of ~6000 proteins in single cells from early mouse embryos. Additionally, the study incorporates the Uno Single Cell Dispenser™, demonstrating the capability of One-Tip in single-cell proteomics with >3000 proteins identified per HeLa cell. We also extend One-Tip workflow to analysis of extracellular vesicles (EVs) extracted from blood plasma, demonstrating its high sensitivity by identifying >3000 proteins from 16 ng EV preparation. One-Tip expands capabilities of proteomics, offering greater depth and throughput across a range of sample types.

MeSH terms

  • Animals
  • HeLa Cells
  • Humans
  • Mass Spectrometry / methods
  • Mice
  • Proteome* / analysis
  • Reproducibility of Results
  • Zygote* / chemistry

Substances

  • Proteome