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Several variables that can affect reproducibility of both the peak height and the migration time in capillary electrophoresis (CE) were investigated here. A great part of the imprecision in CE for migration time is related to the interaction of the analyte with the capillary wall. Within a run, acidic compounds with long migration times have a higher relative standard deviation. In general, conditions that decreased the migration time, such as a short capillary length, tended to enhance the reproducibility of the migration time. Sample size also affected the reproducibility of peak height. Too small or too large an injection volume diminished the reproducibility. Sample matrix, such as high levels of proteins or salts in the sample, decreased the reproducibility. Furthermore, improvement in reproducibility can be achieved by using internal standards (especially for migration time), thorough washing of the capillary, or removing the excess proteins by acetonitrile deproteinization. Acetonitrile has an added effect of producing sample stacking. Depending on the migration time and analyte concentration, the peak height and area yielded different reproduciblity results.

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