Accuracy & Reproducibility
Our 2D DIGE platform is highly accurate and reproducible, eliminating the need of running technical replicates, which translates into high quality data at a lower cost. The following examples assessed the effects of different CyDye, gel-to-gel variations and samples on the data output.
Example-1: Effects of different fluorescent dyes
The same liver lysate was labeled separately with Cy3 and Cy5, then resolved on the same 2D DIGE gel. All protein spots matched perfectly in the overlay image, indicating high accuracy and reproducibility regardless of fluorescent dyes.
Cy3: Liver Lysate

Cy5: Liver Lysate

Cy3 / Cy5 – Overlay

Example 2: Effects of in-gel and cross-gel 2D DIGE
The same cell lysate sample was labeled separately with Cy2, Cy3 and Cy5, then resolved on the same 2D DIGE gel (Gel-1). The same experiment was repeated and same set of data was collected (Gel-2). The data showed high reproducibility within the gel and across different gels.
DeCyder Software Analysis
Cy3 / Cy2 | Cy3 / Cy5 | Cy2 / Cy5 | |
Within Gel-1 2 S.D: after filter Total spot number Included spot number Excluded spot number | 1.22873 2235 915 1320 | 1.17503 2210 1070 1140 | 1.22577 2210 933 1277 |
Within Gel-2 2 S.D: after filter Total spot number Included spot number Excluded spot number | 1.21323 2256 1026 1230 | 1.18648 2250 1051 1199 | 1.22116 2246 1095 1151 |
Across Gels 2 S.D after filter | 1.29214 | 1.25791 | 1.31146 |
Example 3: Effects of freeze/thaw
The extracted cell lysate sample in 2D lysis buffer is stored at – 80oC. The same cell lysate sample was frozen/thaw a few times, then labeled with different CyDye and resolved on 2D DIGE. The data showed nearly identical protein profiling of these samples.




Example 4: Reproducibility of paired samples
The same pair of mouse liver proteins were run on 2 different 2D DIGE gels. The 2 overlay images showed that the unchanged (yellow) and changed (red and green) spots remained the same between the 2 gels, suggesting that 2D DIGE data is highly reproducible.
WT / S33A (pair 1)

WT / S33A (pair 2)
