A method (200) for performing separation assays of biochemical samples includes computing a quality metric (210) based on peak data produced during the separation run. The quality metric is the basis for selecting a subsequent step in the assay, including whether to re-run the separation when the quality metric indicates a low quality separation run. In a preferred embodiment, the quality metric is computed based on a peak resolution metric indicative of the peak resolution of the sample peaks in the data and a signal-to-noise ratio of the data. When a co-migrating standard is included in the separation run, the quality metric is further based on the degree of migration linearity of the reference peaks produced by the standard. The method was reduced to practice in separations to size and sort DNA fragments in high-throughput capillary array electrophoresis separations.