Protein Standards & Ladders

Protein Size Estimation

In general, unstained standards provide a better estimation of size than pre-stained standards. However, pre-stained standards are ideal for confirming the electrophoresis run and estimating the efficiency of transfer onto a membrane. In both cases, the proteins have been modified and stabilized for use in electrophoresis. This often means that their apparent molecular weights are different from that of the proteins in their native state. With pre-stained standards, the difference between native and apparent molecular weights may be greater as proteins have been saturated with dye to ensure consistent migration. In addition, pre-stained standards may also appear less sharp than unstained standards.

Therefore, we recommend the BenchMark™ Protein Ladder, Mark12™ Unstained Standard, or HiMark™ HMW Unstained  Standard for accurate molecular weight estimation and our pre-stained standards for confirming migration and estimating blotting efficiency.

Calibration of Standards in Different Buffer Systems

The same molecular weight standard may have a different mobility and therefore a different apparent molecular weight when run in different SDS-PAGE buffer systems. Each buffer system has a slightly different pH which affects the charge of a protein and its binding capacity for SDS. This can be pronounced in chemically modified proteins such as pre-stained standards and affect their apparent molecular weights significantly. Therefore, it is important to use the correct calibration values for the buffer system you are using.