Capillary electrophoresis based separations of the hypothesized Parkinson’s disease biomarkers dopamine, epinephrine, pyrocatechol, L-3,4-dihydroxyphenylalanine (L-DOPA), glutathione, and uric acid are performed in the presence of a 1 nM 11-mercaptoundecanoic acid functionalized gold (Au@MUA) nanoparticle pseudostationary phase plug. Au@MUA nanoparticles are monitored in the capillary and remain stable in the presence of electrically-driven flow. Migration times, peak areas, and relative velocity changes (vs. no pseudostationary) are monitored upon varying (1) the Au@MUA nanoparticle pseudostationary phase plug length at a fixed separation voltage and (2) the separation voltage for a fixed Au@MUA nanoparticle pseudostationary phase plug length. For instance, the migration times of positively charged dopamine and epinephrine increase slightly as the nanoparticle pseudostationary phase plug length increases with concomitant decreases in peak areas and relative velocities as a result of attractive forces between the positively charged analytes and the negatively charged nanoparticles. Migration times for neutral pyrocatechol and slightly negative L-DOPA did not exhibit significant changes with increasing nanoparticle pseudostationary plug length; however, reduction in peak areas for these two molecules were evident and attributed to non-specific interactions (i.e. hydrogen bonding and van der Waals interactions) between the biomarkers and nanoparticles. Moreover, negatively charged uric acid and glutathione displayed progressively decreasing migration times and peak areas and as a result, increased relative velocities with increasing nanoparticle pseudostationary phase plug length. These trends are attributed to partitioning and exchanging with 11-mercaptoundecanoic acid on nanoparticle surfaces for uric acid and glutathione, respectively. Similar trends are observed when the separation voltage decreased thereby suggesting that nanoparticle-biomarker interaction time dictates these trends. Understanding these analyte migration time, peak area, and velocity trends will expand our insight for incorporating nanoparticles in separations.