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<p>Single-cell proteomics (SCP) promises to revolutionize biomedicine by providing an unparalleled view of the proteome in individual cells. Here, we present a high-sensitivity SCP workflow named Chip-Tip, identifying &gt;5,000 proteins in individual HeLa cells. It also facilitated direct detection of post-translational modifications in single cells, making the need for specific post-translational modification-enrichment unnecessary. Our study demonstrates the feasibility of processing up to 120 label-free SCP samples per day. An optimized tissue dissociation buffer enabled effective single-cell disaggregation of drug-treated cancer cell spheroids, refining overall SCP analysis. Analyzing nondirected human-induced pluripotent stem cell differentiation, we consistently quantified stem cell markers OCT4 and SOX2 in human-induced pluripotent stem cells and lineage markers such as GATA4 (endoderm), HAND1 (mesoderm) and MAP2 (ectoderm) in different embryoid body cells. Our workflow sets a benchmark in SCP for sensitivity and throughput, with broad applications in basic biology and biomedicine for identification of cell type-specific markers and therapeutic targets.</p>

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Enhanced sensitivity and scalability with a Chip-Tip workflow enables deep single-cell proteomics

  • 期刊论文

  • 出版模式：

    开放获取

  • 发表日期：

    2025年1月16日

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  • Zilu Ye,
  • Pierre Sabatier,
  • Leander van der Hoeven,
  • Maico Y. Lechner,
  • Teeradon Phlairaharn,
  • Ulises H. Guzman,
  • Zhen Liu,
  • Haoran Huang,
  • Min Huang,
  • Xiangjun Li,
  • David Hartlmayr,
  • Fabiana Izaguirre,
  • Anjali Seth,
  • Hiren J. Joshi,
  • Sergey Rodin,
  • Karl-Henrik Grinnemo,
  • Ole B. Hørning,
  • Dorte B. Bekker-Jensen,
  • Nicolai Bache,
  • Jesper V. Olsen

摘要

Single-cell proteomics (SCP) promises to revolutionize biomedicine by providing an unparalleled view of the proteome in individual cells. Here, we present a high-sensitivity SCP workflow named Chip-Tip, identifying >5,000 proteins in individual HeLa cells. It also facilitated direct detection of post-translational modifications in single cells, making the need for specific post-translational modification-enrichment unnecessary. Our study demonstrates the feasibility of processing up to 120 label-free SCP samples per day. An optimized tissue dissociation buffer enabled effective single-cell disaggregation of drug-treated cancer cell spheroids, refining overall SCP analysis. Analyzing nondirected human-induced pluripotent stem cell differentiation, we consistently quantified stem cell markers OCT4 and SOX2 in human-induced pluripotent stem cells and lineage markers such as GATA4 (endoderm), HAND1 (mesoderm) and MAP2 (ectoderm) in different embryoid body cells. Our workflow sets a benchmark in SCP for sensitivity and throughput, with broad applications in basic biology and biomedicine for identification of cell type-specific markers and therapeutic targets.