& The practical aspects in the optimization of targeted isolations using two-dimensional HPLC in a heart cutting mode with emphasis on analytical scale analysis were investigated. Assessment of the experimental parameters that affect the purity of an isolated component from a complex mixture were evaluated by employing two different strategies; (1) recovering the target component from the central area of the band in both dimensions; and (2) recovering the target component from off-center of the band in the first dimension and from the central area of the band in the second dimension. For this particular sample, the results reveal that the highest purity product was a result of off-centering the heart-cut away from the central peak maxima in order to minimize contamination from the limiting impurity. However, the highest purity product was obtained at the lowest recovery.