The main applications for prestained protein markers are the monitoring of protein migration during SDS-PAGE, verification of Western transfer efficiency on membranes, and estimation of protein sizes on SDS-polyacrylamide gels and Western blots.

Prestained protein markers are not recommended for precise determination of the molecular weight size since their behaviour during electrophoresis strongly depends on electrophoresis conditions. For exact determinations of protein sizes unlabelled marker proteins, i.e. non-prestained markers, are recommended.