Bio-Rad Experion Protein Analysis Kits - Manual (Page 17)

12. Clean the electrodes using the DEPC-treated water provided in the kit (see Appendix B,
routine cleaning). DEPC-treated water is not required for this cleaning application;
however, always use ultrapure (at minimum 0.2 µm-filtered) water.
13. Analyze the run and the data.
1.3 Data Analysis
Evaluate the performance of Test 1 and the analysis of the data by the Experion software.
1. Evaluate the virtual gel to ensure that all lanes (samples) are visible. Check that the
upper and lower markers are present in each sample (indicated by pink triangles) and
that they are aligned across all lanes (Figure 1.7).
2. Modify the gel view by changing the fluorescence intensity scale. By default, Experion
software displays the virtual gel and electropherograms as “scaled to local”, which
means the gel lane or trace of each sample is scaled to the highest peak intensity
detected in that sample. This is the best method for viewing an electropherogram. To
adjust the fluorescence intensity scale so that the virtual gel resembles an SDS-PAGE
separation, select Graph > Scale to Global. The virtual gel appears as it does in
Figure 1.7, right panel. All lanes are scaled to the highest peak found across the entire
chip, which enables better definition of the concentration differences among the samples
in the virtual gel.
Fig. 1.7. Virtual gel generated by Test 1. Left, virtual “scaled to local”. Right, virtual gel “scaled to global”.
L, Pro260 ladder; lanes 1, 4, 7, and 10, 250 ng/µl BGG; lanes 2, 5, and 8, 500 ng/µl BGG; lanes 3, 6,
and 9, 1,000 ng/µl BGG. Using the “scale to global” option allows clearer distinction of the concentration
differences among samples.
3. Evaluate the separation of the Pro260 ladder (Figure 1.8). This is a critical step in data
analysis because much of the automated data analysis performed by Experion software
is based on the successful separation of the Pro260 ladder. To display the ladder
electropherogram, click the ladder well in the project tree or click on the lane labeled L
in the virtual gel. The electropherogram should resemble the one shown below and
should have the following features:
• Two marker peaks and one set of system peaks
• 8 Pro260 ladder peaks located between the system peaks and upper marker
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