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Protein Assay Data Analysis

With most protein assays, sample protein concentrations are determined by comparing their assay responses to that of a dilution-series of standards whose concentrations are known. Protein samples and standards are processed in the same manner by mixing them with assay reagent and using a spectrophotometer to measure the absorbances. The responses of the standards are used to plot or calculate a standard curve. Absorbance values of unknown samples are then interpolated onto the plot or formula for the standard curve to determine their concentrations.

This comparative method for determining the concentration of an "unknown" is conceptually simple and straightforward. However, its implementation in an assay protocol is complicated by pipetting and dilution steps, evaluation of replicates, blank-corrections and other factors. These steps frequently cause confusion with regard to the calculations that are necessary to obtain a final determination.

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Protein Methods Library Home

 

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Overview of Protein Assays

Chemistry of Protein Assays

Protein Assay Selection Guide

Principles of Standard Curve Assays

BCA Protein Assay standard curves for BSA and BGG
Example standard curves for the Thermo Scientific Pierce BCA Protein Assay Kit. Eight concentrations of bovine serum albumin (BSA) and bovine gamma globulin (BGG) were assayed. The response values (absorbances) were plotted and a best-fit line drawn through the points. If unknown samples had been tested at the same time, their concentrations could be determined by reference to the one of these standard curves.

1. Identically assayed samples are directly comparable:

Sample assay responses are directly comparable to each other if they are processed in exactly the same manner. Variation in amount of protein is the only possible cause for differences in final absorbance (color intensity) if all three of the follow conditions are met:

  • Samples are dissolved in the same buffer
  • The same lot and stock of assay reagent is used for all samples
  • All samples are mixed and incubated at the same time and temperature
  • No pipetting errors are introduced

Of course, because of differences in the chemistry of protein assay methods, different proteins will generate different absorbance values even at the same concentration. This is called "protein-protein variation" or "protein uniformity" and is discussed more fully in other protein methods articles.

2. Units in equals units out:

The unit of measure used to express the standards is by definition the same unit of measure associated with the calculated value for the unknown sample (i.e., final results for unknown samples will be expressed in the same unit of measure as was used for the standards). For example, if the standards are expressed as micrograms per milliliter (µg/mL), then the value for the unknown sample, which is determined by comparison to the standard curve, is also expressed as micrograms per milliliter.

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BCA Protein Assay Kit

BCA-Reducing Agent Compatible

Micro BCA Kit

Pierce 660nm Protein Assay Kit

Coomassie Plus (Bradford) Kit

Coomassie (Bradford) Kit

Modified Lowry Assay Kit

BSA Protein Standards

BGG Protein Standards

 

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Protein-protein variation of protein assays (comparison table)

Common Misconceptions

1. Misconception: I need to know the amount of protein per well.

Contrary to what many people assume, it is neither necessary nor even helpful to know the actual amount (e.g., micrograms) of protein applied to each well or cuvette of the assay. Consider a simple example in which the Coomassie Plus Protein Assay Kit (Part No. 23236) is used to assay two protein samples: a test sample whose concentration is not known, and a standard whose concentration is 1mg/mL (= 1000 µg/mL). (Ordinarily, an entire set of standards is necessary to establish a response curve, but this is a simplified example.)

In the microplate protocol (see figure), one adds 10µL of sample (test or standard) and 300µL of assay reagent per well. Because 10µL of the standard sample is added to a well, there is 0.010mL x 1,000 µg/mL = 10µg of protein in the well. If the assay results in the test sample having the same final absorbance as the standard sample, then the conclusion is that the test sample contains the same amount of protein as the standard sample. Because there was 10µg of standard per well, one could report the determined concentration of test sample as 10µg/well. However, the amount of protein per well is almost certainly not the value of interest; instead, one usually wants to know the protein concentration of the original test sample. Because the original standard was 1000µg/mL, the test sample that produced the same absorbance in the assay also must be 1000µg/mL.

Sample pipetting and dilution for protein assays.
Diagram of protein assay steps. If standard (top row) and unknown (bottom row) samples are dispensed and mixed with the same amount of assay reagent, then they are directly comparable. If the absorbances of the final solutions (green) are identical, then the concentration of the unknown sample is determined to be 1mg/mL. The amount of protein in the assay well (middle) and the concentration in assay reagent (right) are irrelevant.

2. Misconception: I need to know the protein concentration in the assay reagent.

Furthermore, it is neither necessary nor helpful to know the protein concentration as it exists when diluted in assay reagent. In the above example, because the 10 µg standard was diluted to 310µL after adding 300µL of assay reagent, the final concentration in the well is 10µg/310µL = 0.0323µg/µL = 32.3µg/mL. Therefore, one could report the determined concentration of test sample as 32.3µg/mL. However, the protein concentration when diluted by assay reagent is almost certainly not the value of interest; instead, one wants to know the protein concentration of the original test sample. Because the original standard was 1000µg/mL, the test sample that produced the same assay absorbance also must be 1000µg/mL.

 

Applying Dilution Factors

One situation in which the dilution factor is important to consider is when the original sample has been pre-diluted relative to the standard sample. Continuing with the same example, suppose that the original protein sample is actually known to be approximately 5mg/mL. This is too concentrated to be assayed by the Coomassie Plus Protein Assay Kit, whose assay range in the standard microplate protocol is 100-1500µg/mL. However, one could dilute it 5-fold in buffer (i.e., 1 part sample plus 4 parts buffer) and then use that diluted sample as the test sample in the protein assay. If the test sample produces the same absorbance as the 1000µg/mL standard sample, then one can conclude that the test (5-fold diluted) sample is 1000µg/mL, and therefore the original (undiluted) sample is 5 x 1000µg/mL = 5000µg/mL = 5mg/mL.

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Tech Tip #57: How to use a protein assay standard curve

Curve-fitting and Interpolation

Unlike the example described above, most assays use an entire set of protein standards whose concentrations span the effective assay range (e.g., 100-1500µg/mL). Rarely, if ever, will the test sample produce an assay response that corresponds exactly to one of the specific standard samples. Therefore, a method is needed to calculate or interpolate between the standard sample points.

Example protein assay standard curve.
How to use a standard curve? Absorbance values for different known concentrations of a protein standard are plotted (diamonds). If a test sample produces an absorbance of 0.6, how does one use the standard curve to calculate the protein concentration?

Most plate readers and spectrophotometers have associated software that automatically plots a best-fit (linear or curvilinear) regression line through the standard points, interpolates the test samples on that regression line, and reports the calculated value. It is important to choose an appropropriate curve-fitting algorithm because the mathematical formula describing the fitted curve will be used to calculate the concentration of the test sample.

The following figures illustrate how different curve-fitting algorithms affect the accuracy of protein assay calculations. Few, if any, protein assays are perfectly linear over the entire useful assay range. As long as the appropriate curve-fit is used, an assay does not need to be linear to be accurate. If curve-fitting must be done manually, a point-to-point fit will usually be more accurate than a linear fit to the entire range of standard points (see figure). A "point-to-point" fit is a linear fit between each successive pair of points.

Linear fit standard curve for protein assays
Comparison of point-to-point and linear-fit standard curves. Interpolation and calculation for a test sample having absorbance 0.6 results in significantly different protein concentration values. In this case, the point-to-point method clearly provides a more accurate reference line for calculating the test sample.

 

Best fit standard curve for protein assays
Comparison of point-to-point and best-fit standard curves. Interpolation and calculation for an unknown sample having absorbance 0.6 results in slightly different protein concentration values. In this case, the best-fit curve provides a more accurate calculation than the point-to-point curve.

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Tech Tip #57: How to use a protein assay standard curve

(This Tech Tip describes curve-fitting in greater detail. It includes instructions for using Microsoft Excel Software to calculate a best-fit, 3- or 4-parameter trendline for calculating protein concentrations.)

Other Factors Affecting Assay Accuracy and Precision

Replicates

Several factors affect protein assay accuracy and precision. The only way to evaluate the extent of random error is to include replicates of each standard and test sample. Because all test samples are evaluated by comparison to the standard curve, it is especially important to run the standards in triplicate. The standard deviation (SD) and coefficient of variation (CV) can then be calculated, providing a degree of confidence in the technician's pipetting precision. If replicates are used, curve-fitting is done on the average value (minus obvious outliers).


Blank Correction

Published graphs of standard curves (as in the figures on this page) usually show the line going through the origin (0,0). Although visually appealing, this is irrelevant to the calculations. Most protein assay working reagents have absorptivity at the detection wavelength (i.e., they have positive absorbance even when there is no protein present, see figures below).

It is common practice to subtract the absorbance of the zero assay standard(s) from the all other sample absorbance values. However, if replicate zero-assay standards will be used to calculate error statistics, then another independent value may be required for blank-correction. If the standards were prepared in a buffer to match that of the test samples, and this buffer contains components that may interfere with the assay chemistry, it is informative to blank the absorbances with a "water reference" (i.e., a zero-protein, water sample). Differences between the water reference and zero standard sample are then indicative of buffer effects.


Standard Curve Slope and Measurement Wavelength

The standard curve slope is directly related to assay accuracy and sensitivity. All else being equal, the steepest part of the curve is the most reliable. For most protein assays, the standard curve is steepest (i.e., has the greatest positive slope) in the bottom half of the assay range. In fact, the upper limit of an assay range is determined by the point at which the slope approaches zero; the line there is so flat that even a tiny difference in measured absorbance translates to a large difference in calculated concentration.

However, the very lowest part of the assay range, while having the steepest slope, is not always optimal because random errors and interfering substances have greater relative effects in samples containing very small amounts of protein. Therefore, the clearest results are usually obtained with test samples that are pre-diluted so that they correspond to the lower-middle portion of the assay range. Many technicians test samples at two or three dilutions to ensure that at least one of them "lands" in this part of the assay range.

The measurement wavelengths that are recommended for each protein assay method are optimal because they yield standard curves with maximal slope. This usually, but not always, corresponds to the absorbance maximum. (In certain circumstances, other considerations are also important in choosing the best possible measurement wavelength, such as avoiding interference from sample components that absorb at similar wavelengths).

In fact, for most protein assays, depending on the precision required, acceptable results can be obtained using any measurement wavelengths within a certain range. The following figures illustrate this point (see Tech Tip #25 for details).

BCA Assay absorbance spectra
BCA protein assay absorbance spectra. Scans of eight BSA standards (0 to 2000µg/mL) tested with the Thermo Scientific Pierce BCA Protein Assay Kit (Part No. 23225). The thick line is the 2000µg/mL sample. The optimum measurement wavelength for this assay is 562nm.

 

Coomassie assay absorbance spectra
Coomassie (Bradford) protein assay absorbance spectra. Scans of eight BSA standards (0 to 2000µg/mL) tested with the Thermo Scientific Pierce Coomassie Plus Protein Assay Reagent (Part No. 23236). The thick line is the 2000µg/mL sample. The optimum measurement wavelength for this assay is 595nm. An inverse standard curve can be generated by measuring at 465nm. Notice that the baseline absorbance of this reagent is ~0.4 at 595nm (measured in a 1-cm cuvette).

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Tech Tip #25: Determine acceptable wavelengths for measuring protein assays

(This document describes several protein assay absorbance spectra in greater detail.)

 

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BCA Protein Assay

Coomassie Plus (Bradford) Assay

Pierce 660nm Assay

Interfering Substances

The possible effects of interfering substances were not discussed in this article because the assumption was that all protein samples were treated exactly the same, including the buffers in which the proteins were dissolved. In this situation, any interference caused by components of the buffers is exactly the same for both test and standard samples. Nevertheless, interference by non-protein substances in the samples that block or contribute to the assay color reaction is an important issue for any protein assay system. Refer to related articles and documents for further discussion this topic.

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Chemistry of protein assays

Protein assay selection guide

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Tech Tip #68: Protein assay compatibility table

Written and/or reviewed by Douglas Hayworth, Ph.D.

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