Protein Abundance Determination: An Optimized Western Blot Workflow

We report that the quantitative western blot (qWB) analysis requires a target protein-specific approach, and we provide a workflow that streamlines development of this process. First, the optimal primary antibody dilution is determined. Blots containing 15 μg total protein per lane are probed with the primary antibody at three concentrations and a secondary antibody concentration that is defined by the manufacturer. The lowest primary antibody concentration that detects a discrete band at the correct molecular weight is used in the remaining two steps. Secondly, the optimal protein load is determined. Blots containing 3.75 to 60 μg protein per lane are probed using the antibody concentrations defined in step 1. A target protein band intensity vs. protein load plot is used to determine the linear dynamic range (LDR) for the target protein. The midpoint of the LDR is defined as the optimal protein load. Finally, an appropriate loading control (LC) is identified. We found that the LDR for β-actin, a commonly used LC, exhibited a narrow range, 3.75 to 15 μg. In contrast, the total protein assessed by a Ponceau staining method exhibited a broader LDR, 3.75 to 60 μg. Thus, the total protein is used as a LC. We conclude that the sensitivity and accuracy of the qWB method is dependent on the use of an optimal: 1) primary antibody dilution; 2) total protein load; 3) and LC. Our workflow simplifies the identification of these values.