10 Tips for Reproducible Odyssey® Western Blots

When your results depend upon reproducible measurements of protein expression changes, minimize error and variation to maximize the accuracy of your data. Get the most out of your Odyssey Imaging System with these 10 tips for robust and replicable analysis of Western blots.

1. Use the Right Membrane

It is important that you consider a few factors before choosing the appropriate membrane for your experiment. Both PVDF and nitrocellulose membranes are available in two different pore sizes, 0.2 µm for proteins less than 20 kDa, and 0.45 µm for most Western blotting applications.

Consider other experimental conditions, as well, such as:

Condition PVDF Membranes Nitrocellulose
150-200 µg of protein/cm2 which
might result in increased background signal
80-100 µg of protein/cm2
Less fragile and a better choice for
experiments that require stripping and re-probing
of membrane
PVDF membranes must be pre-wetted with
methanol, but can be used with methanol-free
transfer buffer
Transfer buffer must contain methanol
Detection Low-fluorescence PVDF must be used
for near-infrared fluorescence detection to
avoid high background resulting from
autofluorescence of standard PVDF membranes.
It is recommended that you cut a small sample
of membrane and image it both wet and dry,
to check for autofluorescence and background.
All nitrocellulose membranes are
suitable for near-infrared detection

LI-COR has evaluated and compared different transfer membranes types, and overall, nitrocellulose membranes offer the lowest membrane autofluorescence.

Figure 1. Membrane autofluorescence from PVDF affects Western blot performance. Transferrin was detected by Western blotting, using various vendors and brands of PVDF membrane. Blots were imaged with the Odyssey Classic Infrared Imaging System in both the 700 and 800 nm channels.

2. Dry Membrane after Transfer

Once the transfer of proteins from the gel to membrane has been completed, it is recommended that you air-dry the membrane, before proceeding to the blocking step. By letting the membrane air-dry, you are essentially allowing the protein to get “fixed” in place. This helps ensure that proteins are not lost from the membrane during the subsequent processing steps like washes, blocking, and probing. It will also help retain low abundance proteins, giving you better sensitivity. Also, proteins at higher concentrations will not smear when the membrane is allowed to air-dry.

3. Optimize Blocking Conditions

The right blocking buffer can greatly enhance sensitivity of near-infrared Western blots by reducing background interference, promoting specific binding of primary antibody to target, and yielding high signal-to-noise ratios with minimal non-specific signals. However, there isn’t a universal blocking buffer suitable for all experimental conditions, so optimization is important.

Blocking reagents can influence antibody binding and specificity. For example, milk-based blockers can cause high background when using anti-goat antibodies, streptavidin-biotin based detection, or when probing phosphorylated target proteins.

Also consider the buffering system used in the experiment. Washing, blocking, and antibody dilutions must be performed using either Phosphate Buffered Saline (PBS) or Tris Buffered Saline (TBS) consistently throughout the protocol.

Additionally, exposure to detergent should be avoided until the blocking step is complete, as it may cause high membrane background.

Figure 2. Effect of various blocking agents on detection of pAkt and total Akt in Jurkat lysate after stimulation by calyculin A. Total and phosphorylated Akt were detected in calyculin A-stimulated (+) and non-stimulated (-) Jurkat lysate at 10 µg; 5 µg; and 2.5 µg/well. Blots were probed with pAkt Rabbit mAb (Santa Cruz P/N sc-135650) and Akt mAb (CST P/N 2967) and detected with IRDye® 800CW Goat anti-Rabbit IgG (LI-COR P/N 926-32211) and IRDye 680RD Goat anti-Mouse IgG (LI-COR P/N 926-68070); scanned on Odyssey® CLx (auto scan 700 & 800). pAkt (green) is only detected with Odyssey Blocking Buffer (TBS).

For more optimization tips, see the Odyssey Blocking Buffer optimization protocol.

4. Optimize the Dilution of Secondary Antibodies

Using secondary antibodies at the right concentration is critical to Western blotting success. Higher dilutions provide lower membrane background and fewer background bands. On the other hand, too much secondary antibody can result in strong bands and signal saturation. Therefore, it is recommended that you optimize the dilution range for your IRDye® 800CW and IRDye 680RD conjugated secondary antibodies within 1:10,000 to 1:40,000. Ideally, begin with a 1:20,000 dilution and then optimize according to primary antibody and preferred appearance of the blot.

5. Validate Primary Antibodies

As primary antibodies bind directly to the molecule of interest to enable detection, it is critical to ensure that the antibodies are specific and bind with high affinity to the target (and isoform) of interest. A positive and negative control sample can identify non-specific interactions of the antibody. In addition, you may want to knockout the expression of your target to see if the antibody binds to any other proteins within the sample. Treating cells with growth factors that induce or inhibit expression of the target, or using a blocking peptide to inhibit binding of the antibody to the target protein are some of the other methods used to confirm antibody specificity.

When performing validation assays, do not use purified or overexpressed target protein. Also, examine different cell lines or tissues with known levels of expression of the target protein.

6. Determine the Combined Linear Range of Detection

For accurate quantitation of Western blots, it is essential that both the target protein and the internal loading control (whether total protein, housekeeping protein, or modified form of the target) are measured within the combined linear range of detection.

First, the linear range for target and internal loading control need to be determined separately. This can be performed using a dilution series of the sample and the appropriate internal loading control. The individual loading ranges obtained can then be combined to identify a loading amount within the combined linear range of detection. See the complete step-by-step protocol.

7. Use Proper Experimental Controls

Control samples are essential for generating reliable and reproducible data. Including both a positive and a negative control in your experimental design will serve as helpful checkpoints for accurate target detection. A positive control will help you confirm your antibody specificity to target within the experimental conditions. On the other hand, a negative control will help you identify any non-specific binding. Most journals recommend including a molecular size marker in Western blot data images submitted for publication. Markers aid in identifying and confirming the target within the expected molecular weight range.

“Positive and negative controls, as well as molecular size markers, should be included on each gel and blot…”
– Image Integrity, Authors and Referees, Nature; Author Guidelines, EMBO Molecular Medicine

8. Normalize Data to Internal Loading Controls

Normalization corrects for sample-to-sample and lane-to-lane variation by measuring data with reference to internal loading controls. If you do not normalize your samples, any observed changes in band intensity could be a result of error in sample preparation, loading, transfer, or actual experimental conditions.

Housekeeping proteins that have been validated for stable expression, total protein loading amounts, or modified forms of target proteins (e.g., phosphorylated and total) can all be used as internal loading controls. Housekeeping proteins or modified forms of target protein use a single or a few endogenous proteins as reference. On the other hand, total protein control takes into account the sum total of all proteins loaded within the lane. Learn more about Western blot normalization.

9. Perform Measurements in Replicates

Taking replicate measurements of experimental data are necessary for accurate, reliable results. Both technical and biological replicates help address different questions about data reproducibility.

Technical replicates are repeated measurements of the same sample that represent independent measures of the noise associated with protocols or equipment1. For example, by loading replicate lanes for each sample on a blot or repeating blots with same samples on different days, you can address the reproducibility of the technique.

Biological replicates are parallel measurements of biologically distinct samples that capture biological variation within the system1. For example, using samples derived from different cell types, tissue types, or organisms, you can evaluate if similar results can be observed, or whether your finding is an anomaly. This protocol – Quantitative Western Blot Analysis with Replicate Samples – will help you define and design your experimental replicate strategy.

10. Use Software That Does Not Modify Raw Data

Accurate data measurement and analysis is the foundation of your research findings. Image file modifications using unsupported image editing and analysis software programs can compromise the integrity of your data. Ensure that you are using a software program designed to analyze the results of your Western blot experiments that is compatible with your detection system, like Image Studio Software.

Image Studio only affects how raw data pixels are mapped to the screen, leaving your original experimental results secure. With data capture and analysis integrated in a single interface, you can keep variability from file transfers and digital adjustments from affecting your data.

Keep these ten tips for near-infrared fluorescent Western blots handy. Download this wallpaper for your computer or this flyer for quick references.

1. Blainey P, Krzywinski M, and Altman N. (2014) Points of Significance: Replication. Nature Methods 11(9): 879-880. doi:10.1038/nmeth.30

Possible Cause 10 for Weak Chemiluminescent Western Blot Signals: Diluting Substrates

westernsure-premium-926-95000Okay, I know, research budget money is tight and you want to make your reagents stretch as far as possible, but it really not a good idea to dilute your chemiluminescent Western blotting substrate.

Why? It’s because the rate of reaction is determined by the ratio of enzyme to substrate. Diluting substrates will dramatically impact the overall generation of light. Then, you will have to repeat the experiment, and you end up using more substrate anyway!

Optimal Blot Unsatisfactory Blot
Images Optimal Western Blot - Substrate Not Diluted Unsatisfactory Chemiluminescent Western Blot - Substrate Diluted
Substrate SuperSignal® West Dura1 SuperSignal® West Dura1
Substrate NOT diluted. Substrate diluted 1:1 (in water)
Performance LOD – 1.25 µg LOD – 2.5 µg

1Comparable to WesternSure® PREMIUM Chemiluminescent Substrate

So don’t skimp – use the substrate full strength the first time to ensure that you are seeing all of your protein bands. Or you might just have to repeat the experiment (and that will just cost you more time and money. . .)!

Here are the other nine possible causes of weak chemiluminescent Western blot signals:

Troubleshooting Chemiluminescent Western Blots: Possible Cause 4 for Weak Signals – Blot Processing

Sometimes life in the lab gets crazy, right? You are finishing a Western blot and you realize that you are supposed to be at an important lecture across campus in 10 min!! Or, your spouse calls to say that one of the kids needs to be picked up as soon as possible. Yikes! The challenge is that blots should be processed and detected on the same day. And, the secondary antibody should be incubated the day of imaging and fresh substrate added just before imaging. Is it that important to your results? Yes, it is and just to prove it, we did a few experiments.

In Table 1, we studied performance differences when the same blot is imaged immediately after processing vs. stored overnight dry and then imaged. In Table 2, we looked at performance differences when the same blot is imaged immediately after processing vs. stored overnight wet and then imaged. Blots in both tables were all imaged on the C-DiGit® Blot Scanner. (And, all images are normalized to the Lookup Tables (LUT) of the respective optimal blot.)

For both experiments, you can see that saving the blot to image the next day is not a very good choice. This is because the secondary antibody and/or the chemiluminescent Western blot substrate is not stable enough for acceptable photon emission when digitally images after the day it is applied.

Table 1 Optimal Blot Unsatisfactory Blot Unsatisfactory Blot
Images Optimal Chemiluminescent Western Blot Unsatisfactory Chemiluminescent Western Blot Unsatisfactory Chemiluminescent Western Blot
Substrate SuperSignal® West Dura1 SuperSignal West Dura1 SuperSignal West Dura1
Processing Time Same Day Next Day Next Day
Detection Process HRP secondary incubated, washed, and substrate added immediately before imaging. HRP secondary incubated, washed, and substrate added day before imaging. HRP secondary incubated, washed, and substrate added day before imaging, then re-incubated with HRP secondary and substrate added immediately before imaging.
Storage Conditions Blot stored overnight dry, at room temperature Blot stored overnight dry, at room temperature
Performance LOD – 640 ng LOD – None detected LOD – 1.25 μg
Table 2 Optimal Blot Unsatisfactory Blot Unsatisfactory Blot
Images Optimal Chemiluminescent Western Blot Unsatisfactory Optimal Chemiluminescent Western Blot Unsatisfactory Optimal Chemiluminescent Western Blot
Substrate SuperSignal® West Dura1 SuperSignal West Dura1 SuperSignal West Dura1
Process Time Same day Next day Next day
Detection Process HRP secondary incubated, washed, and substrate added immediately before imaging. HRP secondary incubated, washed, and substrate added day before imaging. HRP secondary incubated, washed, and substrate added day before imaging, then re-incubated with HRP secondary and substrate added immediately before imaging.
Storage Conditions Blot stored overnight wet in PBS, at room temperature Blot stored overnight wet in PBS, at room temperature
Performance LOD – 640 ng LOD – None detected LOD – 1.25 μg

1SuperSignal West Dura results are comparable to those obtained with WesternSure® PREMIUM Chemiluminescent Substrate.

For more hints and tips, stay tuned to future blog posts. And if you would like to try some FREE Western Blot Analysis Software, download Image Studio™ Lite today!

Related posts:

Weak Chemiluminescent Western Blot Signals: Possible Cause 3 – Wrong Membrane Placement

How to Place the Blot on the C-DiGit Blot ScannerSo, we’ve talked about how the substrate rate of reaction can cause weak Western blotting signals and how the amount of substrate used can affect signals on chemiluminescent Western blots. But, there are other possible causes of weak signals.

The third possible cause of weak signals is the blot membrane placement for imaging on the detection systems, since systems may vary as to how the blot should be placed on the scanning surface. Why is this important? Well, if the blot is placed incorrectly, you may or may not be able to visualize bands. If bands are visualized, they will be substantially reduced in signal.

As an example, LI-COR has two imaging systems for chemiluminescent Western blots: the Odyssey® Fc Dual-Mode Imaging System and the C-DiGit® Blot Scanner. Blot membrane placement depends on which one you use.

For the Odyssey Fc Dual-Mode Imaging System, the membrane needs to be placed FACE UP on the imaging tray.

However, for the C-DiGit Blot Scanner, the membrane needs to be placed on the scanning surface FACE DOWN. (For a quick video demonstrating this, watch “How to Place Your Blot on the C-DiGit Blot Scanner“.) Below is an experiment we did to look at the performance differences between imaging the blot correctly (protein side down) and imaging the blot protein side up on the C-DiGit Scanner. (Images are normalized to the Lookup Table (LUT) of the correctly imaged blot.)

Correctly Imaged Blot Incorrectly Imaged Blot
Images Correctly Imaged Chemiluminescent Blot on C-DiGit Scanner Incorrectly Imaged Chemiluminescent Blot on C-DiGit Scanner
Substrate SuperSignal® West Dura1 SuperSignal® West Dura1
Imaging Method Blot imaged protein side facing down Blot imaged protein side facing up
Performance LOD – 156 ng LOD – 625 ng

1SuperSignal West Dura results are comparable to those obtained with WesternSure® PREMIUM Chemiluminescent Substrate.

For more hints and tips, stay tuned to future blog posts. And if you would like to try some FREE Western Blot Analysis Software, download Image Studio™ Lite today!

Related posts:
Weak Signals on Chemiluminescent Western Blots: Possible Cause 1 – Substrate Rate of Reaction
Weak Signals on Chemiluminescent Westerns: Possible Cause 2 – Not Enough Substrate

10 Possible Causes of Weak Signals on Chemiluminescent Western Blot Images

Weak Signals on Chemiluminescent Western BlotsAre you seeing weaker than expected (hoped for. . .) signal on your chemiluminescent Western blot images with your digital imager? Not sure what could be causing this? Well, here is a list of 10 possible reasons why you might be seeing weak signals in chemiluminescent Western blot data:

  1. The chemiluminescent substrate does not have a fast enough rate of reaction.
  2. Not enough substrate was added to the blot.
  3. Membrane was placed on the detection system incorrectly.
  4. Blot was not detected or processed on the same day it was imaged.
  5. Blot was not kept uniformly wet during the entire image acquisition.
  6. Blot was exposed to film BEFORE imaging on a digital imager.
  7. Blot was imaged using incorrect sensitivity setting (learn about the easy-to-use Image Studio™ Software. Try FREE Image Studio Lite Western Blot Analysis Software to see just how easy it is!)
  8. Chemiluminescent substrate was too cold.
  9. Chemiluminescent substrate was not incubated for 5 minutes.
  10. Substrate was diluted.

Hum, that’s quite a list! For details on ways to eliminate or avoid these causes and get great results with your chemiluminescent Western blots, read Good Westerns Gone Bad: Maximizing Sensitivity on Chemiluminescent Western Blots.

Troubleshooting In-Gel Westerns – Where’s the Signal?

In-Gel Western with Two-Color DetectionOkay, so you’re doing an in-gel western because you have a hard-to-transfer target (say, a glycoprotein). And you are using near-infrared fluorescence detection because it gets rid of inconsistencies due to transfer (and with an Odyssey it’s really fast and efficient to image and analyze!)

You read the In-Gel Western troubleshooting blog from March 6, 2012, but right now, what you’re seeing, or, um, well, NOT seeing is a signal. Rats! Where IS it?

Well, here are some possible causes with ways to solve or prevent this from happening:

Not enough antibody.
— Increase amount of primary and/or secondary antibody. Extend primary antibody incubation to overnight at 4°C to increase signal.
— Remember that In-Gel detection is not as sensitive as blot detection; adjust sample loading and antibody concentrations accordingly.
Antibody dilution buffer is not optimal for your primary antibody.
— Try a different dilution buffer; this can significantly affect performance of some primary antibodies.
— Suggested buffers include 3-5% BSA, Odyssey Blocking Buffer (PBS), or Odyssey Blocking Buffer (TBS), and PBS or TBS (all with 0.1% Tween® 20). Other blockers (milk, casein, commercial blockers) and Tween 20 concentrations can also be tested.
Gel type is not optimal.
— Amresco NEXT gels or NuPAGE® Bis-Tris pre-cast gels are recommended for In-Gel detection. Other commercial gel sources and homemade gels can be used, but may show reduced sensitivity and require further optimization.
Antibody did not penetrate gel sufficiently or evenly.
— Acrylamide percentage was too high. Try a lower percentage or a gradient gel.
— Increase volume for antibody incubations so that gel is completely immersed in antibody solution.
— Make sure gel is adequately fixed. Some monoclonal antibodies may be sensitive to residual acid in the gel; in this situation, eliminate acetic acid from the fix or extend the water wash step.
Gel was left in isopropanol/acetic acid too long.
— This may cause protein to be lost from the gel. Fix for 15 minutes only.

Whew! Well, hopefully by using one of these tips, you are NOW seeing a signal from your protein. Stay tuned for more troubleshooting tips for near-infrared fluorescent In-Gel Westerns in future blogs!
In-Gel detection of Cytochrome P450 3A4 (CYP3A4).

In-Gel detection of Cytochrome P450 3A4 (CYP3A4). Fixed gel was probed with anti-CYP3A4 primary antibody and IRDye® 800 secondary antibody. The limit of detection is approximately 3 ng. Reprinted with permission from Theisen, M. J. and Chiu, M. L. LI-COR Biosciences (2004)

Digital Western Blots – Chemiluminescent Substrate Selection is Critical

Chemiluminescent Western BlotSo, you’ve selected your primary antibodies with care (see Know Thy Primary Antibody), and you’re using a great HRP-conjugated secondary antibodies. NOW – what about the chemiluminescent substrate?

Yes, I know, there are tons of different substrates and vendors out there – all claiming to be the best, right? So, how do you choose the right one for your chemiluminescence Western blot?

One thing to keep in mind is that in this wide variety of chemiluminescent substrates for HRP detection, there are some that are better suited for digital Western imaging than others. In general, choose a substrate with a faster rate of reaction for use with the Odyssey Fc Dual-Mode Chemiluminescent and IR Fluorescent Imaging System or other digital chemiluminescent imaging systems.

Some substrates that are designed for optimal performance on film may not be suitable for detection on a CCD-based imaging system. Try different substrates to find the one that gives the most desirable image. As you can see from the images below, the substrate you pick DOES make a difference! So choose carefully!

In the three images below, two-fold serial dilutions of HRP-conjugated secondary antibody (1 ng-1.25 fg) were spotted onto nitrocellulose using a slot blot apparatus. Blots were detected with various chemiluminescent substrates.

Chemiluminescent Substrate Comparison

Here are 2 documents with more troubleshooting information:

Updated February 18, 2015.

Chemiluminescent Western Blots – FAQs about Primary and Secondary Antibodies

We’ve discussed some hints on how there can be considerable difference in primary antibodies – so “Know thy Primary Antibody.

In addition, we’ve received some questions that are frequently asked – hence called frequently asked questions or FAQs – about primary and secondary antibodies when doing chemiluminescent Western blots. So here they are. I am sure there are more. . .so send them our way by commenting on this post!

Why is the signal missing in the middle of the bands?
Too much secondary antibody on the membrane results in consumption of all the substrate in that area. Without substrate, there is no chemiluminescent signal and a white spot appears in the center of the band. Try different dilutions of the primary and secondary antibodies to find what gives the best results, or try changing the substrate.

Does it matter where I purchased the HRP-conjugated secondary antibodies?
The reactivity of secondary antibodies ranges widely between vendors. As well, the ratio of HRP enzyme to antibody varies, and may affect the detection of the target. If the secondary antibodies from one vendor are not working, trying antibodies from other vendors may be helpful.

Should the HRP-conjugated secondary antibodies be highly cross-adsorbed?
Although highly cross-adsorbed antibodies are essential for two-channel, multiplex detection, it is not always necessary with chemiluminescent blotting for a single target.

What questions do you have?

Optimizing Chemiluminescent Western blots Technical Note might be a good place to start to get some of those questions answered. And remember you save time and money by going digital with the Odyssey® Fc Chemiluminescent and Infrared Fluorescent Imaging System!

Happy Blotting!

Select the Primary Antibodies You Use with Care for Western Blot Success

“Know Thyself – and Thy Primary Antibody!”

Okay, so you’ve done your experiments, run your sample on a gel, and transferred the proteins to a membrane. Now, you need to see if you can detect the protein, what happened to it, how much is there, etc.

After you block (remember we talked about how important the right blocker is), you will probe with a primary antibody (that is, an antibody produced to detect a specific antigen) to see your molecule of interest. Now, primary antibodies can be produced in a wide variety of species such as mouse, rabbit, goat, chicken, rat, guinea pig, human, etc. There are lots of suppliers of antibodies out there, so it is important to realize primary antibodies for the same antigen can perform very differently. It may be necessary to test multiple primary antibodies for the best performance in your Western blot system.

In the images below, you can see how different primary antibodies to the same target may react. Serial dilutions of NIH/3T3 lysate were probed with Akt monoclonal primary antibodies from three different vendors. All blots were blocked with 5% skim milk and detected with HRP-conjugated Goat Anti-Mouse and SuperSignal® West Dura chemiluminescent substrate. Western blots were imaged on the Odyssey Fc Chemi channel for 2 minutes, shown with normalized image display settings. You can see that the primary antibodies varied quite a bit. The number and intensity of bands you can detect and the amount of non-specific binding that occurs are definitely different for each one.

So, take a cue from ancient Greece and get to know your Primary Antibody by doing some testing and optimization.

The result = GREAT Western Blots!

Optimizing Chemiluminescent Western Blots – The Best Offense is a Good Blocker

Okay, it’s football season, and I thought the analogy fit. 🙂 Seriously, the right Blocking Buffer is critical to getting that great chemiluminescent Western blot.

Incubating the membrane in blocking buffer after the transfer step will result in enhanced sensitivity of your blot. Blocking buffer contains proteins that stick to the membrane, promoting specific binding of the primary antibody and minimizing non-specific interactions. Various blocking buffers are available, and it’s important to try several blockers to find the optimal solution for each antigen and antibody pair. There is not a best blocker for all conditions – so you will need to do some testing.

One very, very, very important thing to keep in mind is that the blocker used with HRP-conjugated secondary antibodies in the secondary antibody incubation step of chemiluminescent Western blotting cannot contain sodium azide.

Why?, you ask.

Well, sodium azide binds irreversibly to the HRP enzyme, inhibiting the binding of the substrate and slowing the chemiluminescent reaction. This results in less light production that may affect the appearance of less intense bands or even the entire blot. See the figures below – the blot on the left was done with blocker that did not contain azide; the Western blot on the right used Western blocking buffer with azide.

Blocking buffer with and without azide

Nota bene: Odyssey® Blocking Buffer (PBS or TBS) (which does contain sodium azide) CAN be used to block the blot and to dilute the primary antibody but not to block or dilute in the secondary antibody incubation step when using HRP-conjugated secondary antibodies.

On Another Note: Milk is a common blocking buffer; however, milk-based blockers that contain endogenous biotin and glycoproteins may result in higher background on the membrane when detecting with streptavidin. Milk may also contain active phosphatases that can de-phosphorylate phosphoproteins on the membrane.

Maximizing Sensitivity on Chemiluminescent Western Blots Technical Note

Go Digital with the Odyssey Fc Chemiluminescent and Infrared Fluorescent Imaging System or the C-DiGit® Chemiluminescent Western Blot Scanner!