Table II

Qualitative and quantitative assessment of the reproducibility

Extraction was performed in separate triplicates from samples S9 and S6 (see Table I). Resulting gels were scanned and analyzed using PDQuest software as mentioned under “Experimental Procedures.” Analysis was restricted to a relatively central area of the gels to avoid board effects and poor resolution in the pI dimension. Spots were detected automatically and corrected manually. They were counted and matched between gels. The number of detected spots is indicated as mean ± S.D. Unmatched spots are expressed as their average percentage relative to total spot numbers ± S.D. For quantification, spots common to all triplicates within each group were quantified and normalized to the total density of validated spots from the corresponding gel. For each spot, the CV between all three gels was calculated. The proportion of spots with a CV lower than the indicated cutoff is shown in the corresponding column as a percentage.

Tissue sampleQualitativeQuantitative (spot percentage with CV lower than the cutoff)
Spot count in investigated areaGel-to-gel unmatched spots0.30.40.50.60.70.80.91
%
S9558 ± 3918 ± 24159728391969899
S6613 ± 2218 ± 55975849297989999