The utility of novel latex nanoparticles as pseudostationary phases for electrokinetic chromatography with UV and mass spectrometric detection is demonstrated. The nanoparticles are synthesized using ab initio RAFT (reversible addition−fragmentation chain transfer) in emulsion polymerization, which yields small (63 nm) particles with a narrow size distribution, a hydrophobic core, and an ionic shell. The nanoparticles are shown to provide efficient and selective separations, with retention and separation selectivity dominated by hydrophobic interactions. The nanoparticles are highly retentive, such that they are effective at relatively low concentrations. Addition of the nanoparticles to the background electrolyte at these concentrations has a minor effect on the noise with UV detection, no measurable effect on the separation current, and minor effects on analyte ionization efficiency during electrospray ionization. The nanoparticles do not cause fouling or degradation of the electrospray−mass spectrometer interface even after several weeks of use. The combination of online sample preconcentration via sweeping and selective mass spectrometric detection yields low detection limits (10−16 ppb), particularly for more hydrophobic compounds.