In the same cell, the proteome defines cellular state and the transcriptome marks transitions

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Summary Bulk transcriptome and proteome correlate only modestly, but this has not been investigated in the same cell or across cell-state changes. Here we introduce a scalable technology that quantifies thousands of proteins and transcripts in the same cell, separating RNA from protein by tip-based C18 capture and pairing full-length RNA sequencing with latest-generation mass spectrometry. In HeLa cells, transcript and protein abundances agree on the broad ranking within a cell (r = 0.45), but do not co-vary across the population (r = 0.038). In pluripotency transitions, only a third of matched transcripts and proteins change synchronously, yet the transcription factors defining each state stay tightly co-regulated. Transcript variance is several-fold larger than protein variance, reflecting transcriptional bursting and mRNA sampling noise. The proteome is thus the stable, low-noise definition of cell state, while the transcriptome marks cellular transitions; consequently, the proteome defines cell-state from far fewer cells. Highlights Multimodal workflow yields deep proteome and transcriptome from the same cells Transcript and protein rank similarly within a cell but are uncoupled across cells Only a third of RNA-protein pairs change together, yet state-defining TFs stay coupled Protein varies several-fold less than mRNA, defining state from far fewer cells

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