This document describes an experiment to optimize the purification of recombinant his-tagged ubiquitin protein using PhyTip micro-columns packed with Ni-NTA resin and automated liquid handling. The experiment varied capture cycles (2 vs 4), wash buffer imidazole concentration (0-20mM), and elution buffer imidazole concentration (150mM vs 250mM) across 96 samples in replicates. Following automated purification and analysis on a LabChip GXII, recovery amounts were reported in tables to identify optimal conditions for efficient purification of the target protein from E. coli lysate.