The first consideration in using a specific mode of detection is availability. What modes of detection are available for an assay? Some assays are not available in one mode or another due to the chemistry of the reaction or availability of reagents for the reaction.
Secondly, does the experimental sample have color (absorbance) or autofluorescence? Some natural materials are naturally colored or fluorescent. Check your samples to see if they have a strong absorbance or absorbance over a broad range of wavelengths. This may limit your ability to use a colorimetric assay. If you are interested in a fluorescence-based assay, examine your samples, media, etc. for autofluorescence (fluorescence that is inherent to the sample due to various natural components) using all filters sets or channels available. Autofluorescent components include fluorescent proteins (GFP, etc.), porphyrins, dyes in media, some vitamins, natural pigments, etc. If a sample has high autofluorescence in a broad range of wavelengths, a fluorescence-based assay may not be compatible.
Time-resolved FRET (TR-FRET) and luminescence-based assays are desirable because endogenous sample absorbance and autofluorescence can be avoided in the detected signal. TR-FRET involves exciting the sample with defined wavelengths, turning the excitation light off and then reading emission within 50 to 100 µsec after the light has been turned off.
Luminescence-based assays, either bioluminescent or chemiluminescent assays, do not require that a sample be exposed to any excitation light; light is generated by the biological or chemical modification of the substrate.
Ratiometric assays reduce the effects of well-to-well and day-to-day variations.
Find additional tips, troubleshooting help, and resources within our Protein Assays and Analysis Support Center.
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