Regardless of thermodynamic stability, less complex proteome than plasma, convenient and noninvasive sampling of urine, reproducibility and comparability of the data among laboratories are challenges for the urine proteome analysis. Pretreatment of urine with 10 mM EDTA in conjunction with desalting methods to remove interfering molecules significantly improved the presentation of urine proteome on 2-D gels. Statistical analysis of the average ratio of the spot numbers on 2-D gels between EDTA-treated and non-treated samples were 1.35 ± 0.167, 1.26 ± 0.091, and 1.24 ± 0.095 for dialysis, ultrafiltration, and desalting column, respectively, with the p-value of 5.85 × 10–6 for the overall comparison. This result came from the fact that EDTA-treated samples showed better resolutions with less streaks and clearer spots on 2-D gels than the control samples. The results suggest that a simple and non-fractionating EDTA-treatment can be employed to the procedures for the high resolution 2-D gel analysis and other urinary proteomic analysis.
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