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Enhanced sensitivity and scalability with a Chip-Tip workflow enables deep single-cell proteomics
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Enhanced sensitivity and scalability with a Chip-Tip workflow enables deep single-cell proteomics
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Journal Article
Enhanced sensitivity and scalability with a Chip-Tip workflow enables deep single-cell proteomics
2025
Overview
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.
Chip-Tip is a label-free quantification-based single-cell proteomics workflow for deep single-cell proteomics, which identifies over 5,000 proteins and 40,000 peptides in single HeLa cells.
Publisher
Nature Publishing Group US,Nature Publishing Group
Subject
/ Biomedical and Life Sciences
/ Biomedical Engineering/Biotechnology
/ Ectoderm
/ Endoderm
/ Humans
/ Induced Pluripotent Stem Cells - cytology
/ Induced Pluripotent Stem Cells - metabolism
/ Labels
/ Mesoderm
/ Peptides
/ Protein Processing, Post-Translational
/ Proteins
/ Proteome
/ Proteomics - instrumentation
/ Single-Cell Analysis - instrumentation
/ Single-Cell Analysis - methods
/ Workflow
