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Deep single-cell proteomics quantifies low-abundant embryonic transcription factors and lineage markers during induced pluripotent stem cell differentiation

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 identifying >5000 proteins in individual HeLa cells. It also facilitated direct detection of post-translational modifications (PTMs) in single-cells, negating the need for specific PTM-enrichment. Our study demonstrates the feasibility of processing up to 80 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 non-directed induced pluripotent stem cell (iPSC) differentiation, we consistently quantified stem cell markers OCT4 and SOX2 in hiPSCs and lineage markers like GATA4 (mesoderm), HAND1 (endoderm) and MAP2 (ectoderm) in different embryoid body cells. Our workflow sets a new 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.

INSTRUMENT(S): Orbitrap Astral

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Cell Culture

SUBMITTER: Pierre Sabatier

LAB HEAD: Jesper V. Olsen

PROVIDER: PXD054066 | Pride | 2024-08-17

REPOSITORIES: Pride

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			Action	DRS
	20230809_Report_BGS_Factory_Report_Normal_blank_40SPD.tsv	Tabular
	20240522_AST5_Evo3_PS_240kMS1_4Th3ms_120SPDz_HeLa_1c_01.raw	Raw
	20240522_AST5_Evo3_PS_240kMS1_4Th3ms_120SPDz_HeLa_1c_02.raw	Raw
	20240522_AST5_Evo3_PS_240kMS1_4Th3ms_120SPDz_HeLa_1c_03.raw	Raw
	20240522_AST5_Evo3_PS_240kMS1_4Th3ms_120SPDz_HeLa_1c_04.raw	Raw

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Deep single-cell proteomics quantifies low-abundant embryonic transcription factors and lineage markers during induced pluripotent stem cell differentiation

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