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● we utilized fluorescence coupled capillary electrophoresis(CE-FL)to probe the self-assembly between Cy5 labeled tetrahistidine tagged peptide(Cy5-A6G2H4)and CdSe/ZnS quantum dots(QDs)inside the capillary.● QDs and Cy5-A6G2H4 were injected into a capillary one after another and self-assembled inside the capillary.● Such in-capillary self-assembly was driven by a metal-affinity force which yielded a new fluorescence signal due to F(o)rster resonance energy transfer(FRET).● Under optimal conditions,a linear relationship between the integrated peak areas(S665/S605)and H6G6 was obtained.● The present assay is universal and promises potential applications in the online detection of biomolecules.