- If the ELECTROPHORESIS PARAMETERS & ELECTROPHORESIS
CELL panels are displayed advance to Setting Simulation
- Click on the Set Parameters button.
Experimental simulation parameters are set in this panel.
- Click on the Simulation button. This
panel is a representation of two wells in a slab gel
Simulation or Top
- Select an animation speed. This option was provided to
allow simulation speed adjustment based on your
- Unknown #1 is default.You can use unknown #1 or [Optional]
select 1 of the 10 unknowns from the drop down box.
- 7.5% Acrylamide is default. [Optional] Select 1
of the 4 concentrations. Increasing the % acrylamide will
result in smaller pore sizes in the gel. The smaller pore
sizes retard the migration of all the proteins in the
gel; larger protein are more affected than smaller
- Select 2 or more standards by clicking the check box next
to the name. You can see the full name of the protein and
its molecular weight by having the Check out Protein Information for
additional information on each standard.
- 100 Volts is default. [Optional] Select 1 of the 4
voltages. Increasing the voltage will increase protein
- Click on the Protein Info button. The
PROTEIN DATA panel displays select information on the
currently selected protein.
- Selected a protein on the PARAMETERS panel. The data
panel will be updated with information about the selected
- Insure that the PARAMETERS & ELECTROPHORESIS CELL
panels are displayed. Click on the Set Parameters
& Simulation buttons if
- Two or more standards should be selected.
- Click on the Add Standard button. A
simulation of the standard addition will run.
- Click on the Add Sample button. A
simulation of the sample addition will run.
- Click on the Start Run button. The
protein bands will elute down the cell and separate based
on molecular weight.
- Click on Stop Run before the first band,
the dye band reaches the bottom of the cell.
- Click on any of the bands in the cell and the relative
migration (RM) will be displayed at the top of the cell
- Click on the band from the unknown or sample side of the
cell. The RM of the unknown will be displayed.
- Click on the Plot Results button. A plot
of the log molecular weight (Log MW) vs relative
migration (RM) will be displayed.
- The line fitted through the standards RM results will be
displayed with its slope, y intercept and goodness of fit
- Slide the mouse pointer along the RM axis until the
displayed RM position is approximately the same as the
- Left click and a line will be plotted from the RM axis to
the fitted line and over to the Log MW axis.
- The experimental Log MW will be displayed near the axis
and the Experimental MW will be calculated and displayed
above the graph.
- If the Experimental MW is close to the unknowns actual
molecular weight the unknowns identity will be displayed.
- If you get a message indicating the RM was close but the
unknown's identity was not, check for a poor line fit.
Another possible cause is a % Acrylamide value that was
too high to allow the unknown to elute properly.
- r Squared is an indication of the "goodness of
fit" or how strong the coorelation was between
molecular weight and relative migration.
- A r Squared value of unity or 1 is ideal. Lower values
indicate less correlation.
- A possible cause for low coorelation values is a %
Acrylamide that is too high for the standands chosen.