Data on the characterization of anion and cation micropreparative (50X1.6 mm i.d.) HPLC columns is presented. It is shown how subnanomole quantities of protein can be efficiently recovered from such columns, rendering them compatible for use in multidimensional chromatographic strategies for the purification of trace biological samples. By selection of appropriate solvent systems (e.g., buffer‐free sodium chloride solutions), the small eluant peak volumes can be loaded directly onto the gas phase sequencer, and N‐terminal sequence data obtained. The potential of the technique is illustrated for the purification of a GTPase activating protein (GAP‐3).