EZQ™ Protein Quantitation Kit - FAQs

I am using the EZQ Protein Quantitation Kit and the filter paper has curled up during drying. What should I do?

It is not unusual for the filter paper to bend and warp on drying. It is very important that the paper be flat when scanning or the signal will be uneven and give very inaccurate quantitation values. If this is a problem, wet the paper in water and scan it while it is wet.

Find additional tips, troubleshooting help, and resources within our Protein Assays and Analysis Support Center.

I am using the EZQ Protein Quantitation Kit and after staining, I notice some large spots or marks on the paper. Why is this?

Protein on the skin (e.g. keratin) will transfer to the filter paper and be stained with the EZQ Protein Quantitation Reagent. We recommend handling the filter paper with tweezers and cleaning the staining dish and tweezers before use to minimize marks.

Find additional tips, troubleshooting help, and resources within our Protein Assays and Analysis Support Center.

I spotted my protein samples onto the EZQ protein assay filter paper and I do not have time to complete the assay? Can I stop the procedure and finish later?

Yes, once the samples have dried onto the filter paper, the filter paper can be stored and stained at a later date. After the staining procedure is complete, the signal is very stable, so the paper can be dried again and scanned at a later date as well. The paper can be scanned dry or after dipping it in water. If storing the paper before staining, we recommend storing it in a plastic bag to prevent contamination that could affect the staining pattern.

Find additional tips, troubleshooting help, and resources within our Protein Assays and Analysis Support Center.

I ran out of filter paper for the EZQ Protein Quantitation Kit. Can I just cut any filter paper to fit inside the microplate?

No. The filter paper that is supplied with the EZQ Protein Quantitation Kit is a very specific filter paper and the identity is proprietary. Most lab filter papers will not provide similar results as the paper provided in the kit, so substitutions are not recommended.

Find additional tips, troubleshooting help, and resources within our Protein Assays and Analysis Support Center.

My buffer or components of my buffer are not listed in the compatibility table for my protein assay. What should I do?

You can test the tolerance of the assay for your specific buffer formulation. For in-house generated compatibility information, substances were considered compatible at the indicated concentration in the Standard Test Tube Protocol (found in the manual for each protein assay) if the error in protein concentration estimation caused by the presence of the substance was less than or equal to 10%. The substances were tested using WR prepared immediately before each experiment. Blank-corrected 562nm absorbance measurements (for a 1000µg/mL BSA standard + substance) were compared to the net 562nm measurements of the same standard prepared in 0.9% saline.

Find additional tips, troubleshooting help, and resources within our Protein Assays and Analysis Support Center.

All the components of my sample buffer are at or below the indicated compatible concentration for my protein assay, but I am still seeing too much/too little color development. What could be the problem?

It is possible to have a substance additive affect such that even though a single component is present at a concentration below its listed compatibility, a sample buffer containing a combination of substances could interfere with the assay. You should take steps to eliminate or minimize the effects of the interfering substance(s) by diluting or removing the substance.

Find additional tips, troubleshooting help, and resources within our Protein Assays and Analysis Support Center.

My protein assay is not developing color or is developing too much color. What can I do?

Refer to the information in the product-specific instruction booklet or our Tech Tip: Protein Quantitation Assay Compatibility Table (https://assets.thermofisher.com/TFS-Assets/LSG/Application-Notes/TR0068-Protein-assay-compatibility.pdf).

Find additional tips, troubleshooting help, and resources within our Protein Assays and Analysis Support Center.

My spectrophotometer doesn’t have a filter set for the absorbance maximum. Can I use an alternate wavelength to read the protein assay?

Often, an alternative wavelength can be used, although the slope of the standard curve and the overall assay sensitivity will most likely be reduced. Our Tech Tip (https://tools.thermofisher.com/content/sfs/brochures/TR0025-Protein-assay-spectra.pdf) offers additional information on determining acceptable wavelengths for measuring protein assays.

Find additional tips, troubleshooting help, and resources within our Protein Assays and Analysis Support Center.

My protein samples are already labeled with a fluorescent dye. Can I still quantitate them and if so, what kit can I use? Can I still quantitate them using the EZQ Protein Quantitation Kit?

For most fluorescent dyes, the EZQ Protein Quantitation Kit is the best choice and quantitation will not be affected by the presence of the dye. The one caution is if the protein is heavily labeled with a dye with an absorbance that overlaps the EZQ Protein Quantitation Reagent emission (approximately 600 nm), then the dye will quench the EZQ Protein Quantitation Reagent signal and not be compatible. A heavily labeled protein would have a pellet that is a very visible blue color; other color pellets or pellets with a pale blue color can be quantified with the EZQ Protein Quantitation kit. You can even label your proteins with a fluorescent dye that has similar excitation/emission properties as the EZQ Protein Quantitation Reagent; the EZQ Protein Quantitation Reagent produces a very strong signal that will dominate the combined signal of the two dyes.

You can image or scan the filter paper after the methanol wash (either wet or dried) before adding the EZQ Protein Quantitation Reagent using appropriate settings for your fluorescent dye, then scan again after performing the EZQ protein staining, at settings appropriate for the EZQ Protein Quantitation Reagent, to obtain a relative dye signal/protein amount quantitation.

Find additional tips, troubleshooting help, and resources within our Protein Assays and Analysis Support Center.

I am using the EZQ Protein Quantitation Kit and have samples in several different buffers. What buffer is best to dissolve the ovalbumin stock in to prepare the standard curve?

Even though most of the non-protein components of the buffer are washed away as part of the staining procedure, the buffer composition affects the spread of the spot on the filter paper, which does affect the resulting signal and quantitation. Thus, for accurate quantitation, you need to prepare a standard curve for each general buffer your samples are in. Although the standard curve and sample buffers should be similar, there is some tolerance for buffers to be at different concentrations. If you have samples in different buffers, make an ovalbumin stock solution at 10 mg/mL in deionized water and then prepare serial dilutions with each buffer your samples are in, so that samples in different buffers have a buffer-specific standard curve.

Find additional tips, troubleshooting help, and resources within our Protein Assays and Analysis Support Center.

I have reducing agents in my protein samples, which protein assay kit should I use?

The NanoOrange Protein Quantitation Kit and EZQ Protein Quantitation Kit are both compatible with reducing agents.

Find additional tips, troubleshooting help, and resources within our Protein Assays and Analysis Support Center.

I have cell lysates that were extracted with detergent, which kit should I use for protein quantitation?

The EZQ Protein Quantitation Kit is the most tolerant of non-protein components. It is compatible with samples in SDS-PAGE sample buffer, urea- or guanidine-containing buffers, and detergents. After the protein component is bound to the paper filter, any tracking dyes, detergents, and salts are removed by a methanol wash, so they are no longer present to affect protein quantitation.

Other protein assays that are compatible with detergents are colorimetric BCA assays, Detergent Compatible Bradford Assay Kit, and the 660 nm Protein Assay Kit.

Find additional tips, troubleshooting help, and resources within our Protein Assays and Analysis Support Center.

I normally use a Bradford or Lowry Assay for protein quantitation. How are fluorescence-based protein quantitation assays better?

Fluorescent protein assays can be from 10X more sensitive (EZQ Protein Quantitation Kit) to 100X more sensitive (NanoOrange Protein Quantitation Kit and CBQCA Protein Quantitation Kit) than colorimetric assays. They also have a more simplified workflow and can be performed in about an hour.

Find additional tips, troubleshooting help, and resources within our Protein Assays and Analysis Support Center.

What are the fluorescent protein assays you offer and how do they differ? Which one should I choose for my samples?

All the above assay kits come with either concentrated assay reagent and dilution buffer or a pre-diluted quantitation reagent and protein standards. The EZQ Protein Quantitation Kit also comes with a specially-designed 96-well microplate and filter paper that fits inside this microplate.

Find additional tips, troubleshooting help, and resources within our Protein Assays and Analysis Support Center.

What other factors affect the protein assay accuracy and precision?

Several factors affect protein assay accuracy and precision:
Replicates: 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 at least triplicate. The standard deviation (SD) and coefficient of variation (CV) can then be calculated, providing a degree of confidence in your pipetting precision. If replicates are used, curve-fitting is done with the average values (minus obvious outliers).
Blank correction: 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: 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.
Measurement wavelength: 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.

Find additional tips, troubleshooting help, and resources within our Protein Assays and Analysis Support Center.

When does a dilution factor need to be applied in a protein assay?

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. Suppose the original protein sample is actually known to be approximately 5 mg/mL. This is too concentrated to be assayed by the Pierce Bradford Plus Protein Assay Kit, for example, whose assay range in the standard microplate protocol is 100-1500 µg/mL. However, you 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 1000 µg/mL standard sample, then you can conclude that the test (5-fold diluted) sample is 1000 µg/mL, and therefore the original (undiluted) sample is 5 x 1000 µg/mL = 5000 µg/mL = 5 mg/mL.

Find additional tips, troubleshooting help, and resources within our Protein Assays and Analysis Support Center.

Do I need to know the protein concentration in the assay reagent for my protein assay?

No. It is neither necessary nor helpful to know the protein concentration as it exists when the samples are diluted in assay reagent. 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.

Find additional tips, troubleshooting help, and resources within our Protein Assays and Analysis Support Center.

Do I need to know the amount of protein per well for my protein assay?

No. 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. 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.

Find additional tips, troubleshooting help, and resources within our Protein Assays and Analysis Support Center.

How can I utilize Excel software to plot and apply the standard curve for my protein assay?

Enter the concentration values for the standards in Column A and their corresponding absorbance data in Column B. Highlight both columns and from the Insert menu select Chart and XY (Scatter). Click on the resulting graph and select Add Trendline from the Chart menu. While viewing the graph next to the open Format Trendline window, choose Polynomial and set the Order to 2, 3 or 4 until the best-fit appears. Check the box near the bottom called Display Equation on Chart; then close the Format Trendline window. Use the resulting equation to determine protein concentration (y) of an unknown sample by inserting the sample’s absorbance value (x). 

Find additional tips, troubleshooting help, and resources within our Protein Assays and Analysis Support Center.

How can I interpolate my protein assay data?

Most modern plate readers and spectrophotometers have associated software that automatically plots a linear or curvilinear regression line through the standard points, interpolates the test samples on that regression line, and reports the calculated value. However, there are different methods for making the calculations “by hand”. You can find a detailed explanation and example in our Tech Tip. 

Find additional tips, troubleshooting help, and resources within our Protein Assays and Analysis Support Center.

How can I accurately analyze my protein assay data?

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. 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. The most accurate results are possible only when unknown and standard samples are treated identically. This includes assaying them at the same time and in the same buffer conditions, if possible. Because different pipetting steps are involved, replicates are necessary if you wish to calculate statistics (e.g., standard deviation, coefficient of variation) to account for random error. It is imperative to run a new standard curve for each set of samples to be tested

Find additional tips, troubleshooting help, and resources within our Protein Assays and Analysis Support Center.

It was necessary to dilute my sample in order to run the protein assay (i.e,. due to an incompatible substance). How do I account for this when determining the concentration?

Simply multiply the calculated concentration of the diluted sample by the dilution factor. For example: A protein sample is known to be approximately 5 mg/mL. This is too concentrated to be assayed by the Pierce Bradford Plus Protein Assay Kit, whose assay range in the standard microplate protocol is 100-1500 µg/mL. However, you 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 1000 µg/mL standard sample, then you can conclude that the test (5-fold diluted) sample is 1000 µg/mL, and therefore the original (undiluted) sample is 5 × 1000 µg/mL = 5000 µg/mL = 5 mg/mL.

Find additional tips, troubleshooting help, and resources within our Protein Assays and Analysis Support Center.

In my protein assay, what unit of measurement will my sample concentration be in after calculating the concentration?

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 standard concentrations are expressed as micrograms per milliliter, then the concentrations for the unknown samples, which are determined by comparison to the standard curve, are also expressed as micrograms per milliliter.

Find additional tips, troubleshooting help, and resources within our Protein Assays and Analysis Support Center.

What should I dilute my protein standard in for my protein assay?

Protein standards should preferably be diluted using the same diluent as the sample(s). Sample assay responses are directly comparable to each other if they are processed in exactly the same manner. Variance in protein quantity is the only possible cause for differences in final absorbance (color intensity) if samples are dissolved in the same buffer and the same stock solution of assay reagent is used for all samples.

However, if only a “rough” estimate of protein concentration is needed, a blank-only correction can be used. In this case, a blank is prepared in the diluent of the sample to correct for its raw absorbance. The concentration of the sample is then determined from a standard curve obtained from a series of dilutions of the protein of known concentration prepared in water or saline solution.

Find additional tips, troubleshooting help, and resources within our Protein Assays and Analysis Support Center.

What protein should I use to generate my standard curve?

Protein concentrations are generally determined and reported with reference to standards of a common protein, such as bovine serum albumin (BSA). If precise quantitation of an unknown protein is required, it is advisable to select a protein standard that is similar in quality to the unknown; for example, a bovine gamma globulin (BGG) standard may be used when assaying immunoglobulin samples.

Find additional tips, troubleshooting help, and resources within our Protein Assays and Analysis Support Center.

Why is the choice of protein standard important in a protein assay?

Because proteins differ in their amino acid compositions, each one responds somewhat differently in each type of protein assay. Therefore, the best choice for a reference standard is a purified, known concentration of the most abundant protein in the samples. This is usually not possible to achieve, and it is seldom convenient or necessary. If a highly purified version of the protein of interest is not available or it is too expensive to use as the standard, the alternative is to choose a protein that will produce a very similar color response curve in the selected protein assay method and is readily available to any laboratory at any time. Generally, bovine serum albumin (BSA) works well as a protein standard because it is widely available in high purity and relatively inexpensive. Alternatively, bovine gamma globulin (BGG) is a good standard when determining the concentration of antibodies because BGG produces a color response curve that is very similar to that of immunoglobulin G (IgG).

Find additional tips, troubleshooting help, and resources within our Protein Assays and Analysis Support Center.

What are the basic principles of standard curve assays?

• 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 the samples are dissolved in the same buffer, the same lot and stock solution of assay reagent is used, all samples are mixed and incubated at the same time and temperature, and no pipetting errors were introduced. 
• Units in equals the 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).

Which protein assays are dye-binding based chemistries?

Pierce Bradford Protein Assay Kit and Pierce Bradford Plus Protein Assay Kit are variations on the use of Coomassie G-250 dye as a colorimetric reagent for the detection and quantitation of total protein first reported by Bradford in 1976. The Thermo Scientific 660 nm Protein Assay is a dye-based reagent that offers the same convenience as Coomassie-based assays while overcoming several of their disadvantages. In particular, the 660 nm Assay is compatible with most detergents and produces a more linear response curve (the detailed assay chemistry is proprietary). Our fluorometric protein assays are also based on dye binding chemistries.

Find additional tips, troubleshooting help, and resources within our Protein Assays and Analysis Support Center.

What is protein-to-protein variation?

Each protein in a sample responds uniquely in a given protein assay, and this protein-to-protein variation is observed as differences in the amount of color (absorbance) obtained when the same mass of various proteins is assayed concurrently by the same method. These differences in color response relate to differences in amino acid sequence, isoelectric point (pI), secondary structure, and the presence of certain side chains or prosthetic groups.

Depending on the sample type and purpose for performing an assay, protein-to-protein variation is an important consideration in selecting a protein assay method and in selecting an appropriate assay standard (e.g., BSA vs. BGG). Protein assay methods based on similar chemistry have similar protein-to-protein variation.

Find additional tips, troubleshooting help, and resources within our Protein Assays and Analysis Support Center.

How should a sample be prepared before a protein assay?

Before the sample is analyzed, it must be solubilized in a buffered aqueous solution. Depending on the source material and the procedures involved before performing the protein assay, the sample will likely contain a variety of non-protein components. Awareness of these components is critical for choosing an appropriate assay method and evaluating the cause of anomalous results. Every type of protein assay is adversely affected by substances of one sort or another. Components of a protein solution are considered interfering substances in a protein assay if they artificially suppress the response, enhance the response, or cause elevated background by an arbitrarily chosen degree (e.g., 10% compared to control). Additional components can include reducing agents, chelators, crowding agents, and protease inhibitors.

Find additional tips, troubleshooting help, and resources within our Protein Assays and Analysis Support Center.

What should I consider when choosing a protein assay?

There are several criteria that should be considered, including compatibility with the sample type and components, assay range and required sample volume, protein-to-protein uniformity, speed and convenience for the number of samples to be tested, and the availability of spectrophotometer or plate reader necessary to measure the color produced (absorbance) by the assay.

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Why does the protein assay method matter?

Unfortunately, no protein assay method exists that is either perfectly specific to proteins (i.e., not affected by any nonprotein components) or uniformly sensitive to all protein types (i.e., not affected by differences in protein composition). Therefore, successful use of protein assays involves selecting the method that is most compatible with the samples to be analyzed, choosing an appropriate assay standard, and understanding and controlling the particular assumptions and limitations that remain. The objective is to select a method that requires the least manipulation or pre-treatment of the samples to accommodate substances that interfere with the assay. Each method has its particular advantages and disadvantages. Because no one reagent can be considered the ideal or best protein assay method for all circumstances, most researchers have more than one type of protein assay available in their laboratories.

Find additional tips, troubleshooting help, and resources within our Protein Assays and Analysis Support Center.

What protein assay is best?

Unfortunately, no protein assay method exists that isn’t affected by any non-protein component or uniformly sensitive to all protein types. One must select an appropriate assay method based on compatibility with the sample type or one that requires the least manipulation of the sample to accommodate the assay. Most researchers will have more than one type of assay available in their laboratories.

Find additional tips, troubleshooting help, and resources within our Protein Assays and Analysis Support Center.

What protein assays do you offer for total protein quantitation?

We offer several types of protein assays including the: BCA Assay, BCA-RAC (Reducing Agent Compatible) Assay, Micro BCA Assay, 660 nm Protein Assay, Pierce Bradford Plus Protein Assay Kit, Pierce Bradford Protein Assay Kit, Modified Lowry Assay, colorimetric and fluorometric Peptide Assays, CBQCA kit, EZQ kit, Quant-iT kits, NanoOrange, and the Qubit kits.

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Why would I use the EZQ Protein Quantitation Kit in lieu of other methods of protein quantitation?

Your protein sample need not be purified further to remove common lysis buffer components such as urea, thiourea, detergents, and reducing agents that are not tolerated by other protein quantitation reagents. These small molecular weight components will wick through the assay paper, leaving only the protein on the surface of the membrane.

Find additional tips, troubleshooting help, and resources within our Cell Analysis Support Center.

Can we purchase the EZQ Assay paper (Component C) separately?

The proprietary Assay paper (Component C) cannot be purchased separately.

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