biostudies-literatureShen BNIA NIH HHSChan-Zuckerberg Initiative FoundationNational Institute of General Medical SciencesNational Institute on AgingNIGMS NIH HHSArnold and Mabel Beckman Foundatione202510692https://www.ebi.ac.uk/biostudies/studies/S-EPMC12582007biostudies-literatureUnknown64(45)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 speAngewandte Chemie (International ed. in English)Real-Time Eco-AI, Electrophoresis-Correlative Data-Dependent Acquisition with AI-Based Data Processing Broadens Access to Single-Cell Mass Spectrometry Proteomics.PMC12582007Beckman Young Investigator Award1R01AG088147R35GM124755Shen BZhou FNemes PfalseReal-Time Eco-AI, Electrophoresis-Correlative Data-Dependent Acquisition with AI-Based Data Processing Broadens Access to Single-Cell Mass Spectrometry Proteomics.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 spe2025-01-01T00:00:00Z2025 Nov2026-06-05T10:45:27.262Z2026-05-16T03:08:31.659ZS-EPMC125820074084774810.1002/anie.202510692