Observations on the reproducibility and matching efficiency of two-dimensional electrophoresis gels: Consequences for comprehensive data analysis

Protein expression profiling by proteomics has the potential to be an ideal tool for the description of changes in complex biological systems or in th e characterization of a disease. This study analyzes in more quantitative t erms how methodological drawbacks of the current technology can hamper the comprehensive analysis of large sets of spot patterns by statistical means. Irreproducibilities in spot intensities due to silver staining and geometr ic distortions of the spot patterns inherent to the electrophoresis procedu re push even the semiautomatic alignment and matching to their limits. This leads to reduced matching efficiencies for identical spots if no additiona l exhaustive manual matching is performed for every single spot in all gels . As a consequence, only a limited number of spots can be matched in all ge ls of a large set. The statistical pattern analysis of such data sets will thus not allow the comprehensive description of relevant pattern changes.