Analyte-Class-Dependent Electrophoretic Organization Enables Single-Run Proteome–Metabolome Analysis by CE–ESI–MS

Dual proteome–metabolome measurements from limited samples typically require sample splitting or sequential analyses using electrospray ionization mass spectrometry (ESI–MS). Here we show that capillary electrophoresis (CE) can avoid that tradeoff by organizing predominantly singly charged small molecules and multiply charged peptides into partially resolved, analyte-class-dependent regions of migration time–m/z space. Leveraging this intrinsic electrophoretic organization together with charge- and m/z-resolved precursor selection, we developed a single-run CE–ESI–MS workflow that combines single-vial sample processing with class-resolved tandem MS acquisition. In a HeLa digest spiked with 17 amino acids, the integrated analysis detected all amino acids while preserving proteomic depth relative to a dedicated proteomics run, yielding 1,221 versus 1,227 cumulative protein groups. Applied to identified single Xenopus laevis blastomeres, the method provided matched readouts of 86 metabolite features together with 1,097 and 1,083 protein groups from D1.1 and V1.1 cells, respectively. The paired measurements resolved cell-type-dependent molecular differences and mapped protein and metabolite changes into shared pathway context. These results establish analyte-class-dependent electrophoretic organization coupled to class-resolved MS acquisition as an analytical basis for single-run proteome–metabolome analysis by CE–ESI–MS in material-limited samples.