Real-Time Eco-AI, Electrophoresis-Correlative Data-Dependent Acquisition with AI-Based Data Processing Broadens Access to Single-Cell Mass Spectrometry Proteomics.

ABSTRACT: Single-cell mass spectrometry (MS) offers unprecedented sensitivity for profiling cellular proteomes, yet widespread adoption is hindered by the cost of advanced instrumentation. Here, we broaden access to single-cell proteomics by combining capillary electrophoresis (CE), data-dependent acquisition (DDA) with electrophoresis-correlative (Eco) ion sorting, and artificial intelligence (AI)-assisted spectral deconvolution via CHIMERYS (Eco-AI). This "Real-Time Eco-AI" workflow was implemented on a custom-built CE platform coupled to a legacy hybrid quadrupole-orbitrap mass spectrometer (Q Exactive Plus). Despite slower scan speed, lower resolution, and inferior ion transmission efficiency, real-time Eco-DDA sampling and CHIMERYS processing enabled identification of up to ∼15 peptides per spe

SUBMITTER: Shen B 

PROVIDER: S-EPMC12582007 | biostudies-literature | 2025 Nov

REPOSITORIES: biostudies-literature