Bio-Rad EXQuest Spot Cutter - Manual (Page 214)

Analysis Tools
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Note: Importing sample pairs will overwrite any pair selections you have already
created containing samples that match imported pairs.
6.7 Normalization
When comparing gels in a MatchSet, there is often some variation in spot size and
intensity between gels that is not due to differential protein expression. This variation
can be caused by a number of factors, including:
• Inconsistent cell numbers (cell densities) in the sample prep,
• Inconsistent sample prep efficiency due to variations in reagents, protocols, etc.,
• Handling errors resulting in some sample loss during prep,
• Pipetting errors during sample prep,
• Sample loss during gel loading,
• Inconsistent staining times between gels,
• Inconsistent labeling efficiency with radioisotopes,
• Inconsistent excitation/emission efficiencies between different fluorescent tags,
• Inconsistent detection energy sources between gels during image acquisition, and
• Inconsistent exposure times between gels during image acquisition.
To accurately compare spot quantities between gels, you must compensate for these
nonexpression-related variations in spot intensity. This is called normalization.
With a MatchSet open, select Normalize from the Analyze menu.