The performance of the Agilent 2100 bioanalyzer, the first commercial lab-on-a-chip system, and the Protein 200 Plus LabChip kit is compared with conventional protein analysis techniques such as SDS-PAGE, Lowry, or Bradford. Lab-on-a-chip technology for protein analysis allows for the integration of electrophoretic separation, staining, destaining, and fluorescence detection into a single process, and for it to be combined with data analysis. The chip-based protein assay allows purity analysis, sizing, and relative quantitation based on internal standards or absolute quantitation based on user-defined standards. The chip-based protein analysis is comparable in sensitivity, sizing accuracy, and reproducibility to SDS-PAGE stained with standard Coomassie. Resolution and linear dynamic range are improved. Absolute quantitation accuracy and reproducibility is improved in comparison to SDS-PAGE and is comparable to batch-based quantitation methods such as Lowry and Bradford. The lab-on-a-chip system has several additional advantages over conventional SDS-PAGE including fast analysis times, reduced manual labor, automated data analysis, and good reproducibility. With such a system, the protein of interest can be tracked during the whole purification procedure, for example, from cell lysates through column fractions to purified proteins.