ArticlebioRxiv : the preprint server for biology2025
Subcellular Mass Spectrometry Reveals Proteome Remodeling in an Asymmetrically Dividing (Frog) Embryonic Stem Cell.
Article in bioRxiv : the preprint server for biology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
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Abstract
Subcellular proteomics holds the potential to reveal the molecular architecture of cellular processes with unprecedented spatial resolution. Performing these analyses deeply, at the level of hundreds to thousands of proteins in subcellular resolution, is a high and still unmet technical need. Here, we advance microprobe capillary electrophoresis-mass spectrometry (CE-MS) to achieve deep proteomic coverage-quantifying over 1,000 proteins within opposing poles of an asymmetrically dividing embryonic stem cell (blastomere). We integrated CE-electrospray ionization (CE-ESI) with trapped ion mobility spectrometry time-of-flight (timsTOF) MS, implementing data-independent acquisition (DIA) via parallel accumulation-serial fragmentation (diaPASEF). This CE-diaPASEF workflow identified 1,035 proteins from ∼200 pg of proteome digest, equivalent to ∼80% of the HeLa cell's content, with high reproducibility (coefficient of variation <15% across technical triplicates). With microprobe sampling, this technology quantified 808 to 1,022 proteins in opposing poles of a dorsal-animal (D1) blastomere in the 8-cell
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