articleNature MethodsJan 16, 2025HYBRID OA

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

ZYZilu YePSPierre SabatierLVLeander van der HoevenMLMaico LechnerTPTeeradon Phlairaharn

Chinese Academy of Medical Sciences & Peking Union Medical College · Novo Nordisk Foundation · +4 more institutions

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Abstract

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…

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Keywords
  • Induced pluripotent stem cell
  • Proteomics
  • Computational biology
  • SOX2
  • Biology
  • Cell biology
  • Biomedicine
  • Stem cell
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