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

Author

Listed:
  • Zilu Ye

    (Chinese Academy of Medical Sciences & Peking Union Medical College
    University of Copenhagen)

  • Pierre Sabatier

    (University of Copenhagen
    Uppsala University)

  • Javier Martin-Gonzalez

    (University of Copenhagen)

  • Akihiro Eguchi

    (University of Copenhagen)

  • Maico Lechner

    (University of Copenhagen)

  • Ole Østergaard

    (University of Copenhagen)

  • Jingsheng Xie

    (Chinese Academy of Medical Sciences & Peking Union Medical College)

  • Yuan Guo

    (Tecan Group Ltd.)

  • Lesley Schultz

    (Tecan Group Ltd.)

  • Rafaela Truffer

    (Tecan Group Ltd.)

  • Dorte B. Bekker-Jensen

    (Evosep Biosystems)

  • Nicolai Bache

    (Evosep Biosystems)

  • Jesper V. Olsen

    (University of Copenhagen)

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.

Suggested Citation

  • Zilu Ye & Pierre Sabatier & Javier Martin-Gonzalez & Akihiro Eguchi & Maico Lechner & Ole Østergaard & Jingsheng Xie & Yuan Guo & Lesley Schultz & Rafaela Truffer & Dorte B. Bekker-Jensen & Nicolai Ba, 2024. "One-Tip enables comprehensive proteome coverage in minimal cells and single zygotes," Nature Communications, Nature, vol. 15(1), pages 1-10, December.
    • Handle: RePEc:nat:natcom:v:15:y:2024:i:1:d:10.1038_s41467-024-46777-9
    DOI: 10.1038/s41467-024-46777-9
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    References listed on IDEAS

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    1. Valdemaras Petrosius & Pedro Aragon-Fernandez & Nil Üresin & Gergo Kovacs & Teeradon Phlairaharn & Benjamin Furtwängler & Jeff Op De Beeck & Sarah L. Skovbakke & Steffen Goletz & Simon Francis Thomsen, 2023. "Exploration of cell state heterogeneity using single-cell proteomics through sensitivity-tailored data-independent acquisition," Nature Communications, Nature, vol. 14(1), pages 1-16, December.
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    Cited by:

    1. Claudia Ctortecka & Natalie M. Clark & Brian W. Boyle & Anjali Seth & D. R. Mani & Namrata D. Udeshi & Steven A. Carr, 2024. "Automated single-cell proteomics providing sufficient proteome depth to study complex biology beyond cell type classifications," Nature Communications, Nature, vol. 15(1), pages 1-10, December.
    2. Zhen Dong & Wenhao Jiang & Chunlong Wu & Ting Chen & Jiayi Chen & Xuan Ding & Shu Zheng & Kiryl D. Piatkevich & Yi Zhu & Tiannan Guo, 2024. "Spatial proteomics of single cells and organelles on tissue slides using filter-aided expansion proteomics," Nature Communications, Nature, vol. 15(1), pages 1-15, December.

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