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Producing Reliable Quantitative Western Blot Data

Published: Monday, June 17, 2013
Last Updated: Monday, June 17, 2013
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The reporting of fold changes in protein expression from western blots is often viewed with skepticism due to questions about the validity of the technique as a quantitative method.

In the May issue of Molecular Biotechnology, researchers at Bio-Rad Laboratories, Inc. reported a method for producing quantitative and reproducible western blot data that could establish the technique’s reputation for reliable quantitation.

Western blotting has been practiced for several decades and is performed routinely in labs to assess the presence of specific target proteins in complex samples. Although the scientific community has historically reported fold changes in protein expression by measuring the differential density of the target protein bands among the samples on western blots, the technique is generally considered to yield only semi- or nonquantitative data because of the methods, reagents, and instruments used to generate these data. This shortcoming led the authors to undertake the present study.

“In my visits to labs, researchers having been asking me how to more rigorously approach western blotting quantitation,” said Dr. Sean Taylor, lead author and a Bio-Rad field applications specialist. “We wrote this article to demonstrate how the application of a simple workflow coupled with the use of updated reagent and instrument technologies can ensure the production of quantifiable results from chemiluminescent western blots.”

Accurate normalization for loading differences is a solvable challenge 
To ensure accuracy in western blotting, loading controls are used to normalize for errors that can result from imprecise protein estimation, pipetting inaccuracy, or uneven protein transfer. The most common loading controls are housekeeping proteins. However, these proteins are generally highly expressed in samples and are frequently overloaded in a gel lane with the much lower abundance target protein, thus reducing their usefulness for normalization.

In these instances, total protein normalization using stain-free technology may be a suitable alternative. The study found that using stain-free imaging to quantify the total amount of proteins in each lane yielded results that closely matched the confirmed amounts, supporting the validity of this normalization method. This result was in direct contrast to quantification using the relative density of GAPDH, a common housekeeping protein, which did not correspond well to the actual amounts due to signal saturation at high sample loads.

Modern imaging technology has a greater dynamic range than film
The study also dispelled the widely held view that film should be the method of choice for detecting chemiluminescent western blots. Using a twofold dilution series of a protein lysate, the researchers reported that the CCD-based imaging system provided a linear dynamic range nearly an order of magnitude greater than film (0.04–2.5 ng vs. 0.04–0.31 ng) for the probed target protein. This permitted accurate quantification of the relative target band density between the gel lanes with the imaging system versus film for the identical blots.

“This paper demonstrates how to validate antibodies using an imaging system to ensure that individual samples are diluted and loaded within the quantitative linear dynamic range of each antibody to produce excellent densitometric data,” Taylor said. “It also shows how stain-free technology is a great alternative to traditional housekeeping proteins for normalization.”

Click below to read the Molecular Biotechnology paper describing how to reliably quantify proteins in your next western blot experiment.

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