Artifacts in IHC: the usual suspects - part II

How to avoid artifacts in your IHC staining. Read on! Troubleshooting is nothing more than the logical elimination of variables.

I don’t know why I am doing this. I can’t handle it!” You thought you knew how to recognize and solve your IHC artifacts but after reading the troubleshooting guide the answers seem so far away. Long lists of tips. Examples too difficult to understand. Not-so-friendly images.

Feeling overwhelmed? You are not alone. Although sometimes troubleshooting seems unbearable, there is no need to worry! Troubleshooting is nothing more than the logical elimination of variables.

In our previous blog (Artifacts in IHC: the Usual Suspects - Part I) we have identified the major suspects (sample, antibodies, and protocol) responsible for the most common IHC artifacts such as lack of staining, nonspecific binding, and high background.

If you are now looking for tips on how to avoid artifacts in your IHC staining read on.

Overwhelmed by troubleshooting?

During the past few decades, improvements in the reagents and protocols used for immunohistochemistry have led to increased sensitivity of detection systems, contributing to the elimination of staining artifacts. However, it is still a daunting task to determine what is or is not nonspecific background staining and what is specific antigen staining or to identify the sources of background and the best approach to minimize noise and enhance the signal.

All that you need is a combination of the right elements, a dose of experience, a few tricks, and a grain of common sense. Take one thing at a time. Make a list of things you need to get done and start with it.


Cracking an artifact for perfection

Having a troubleshooting methodology is important. Due to the complexity of modern technologies, a wise researcher will have and follow a troubleshooting methodology. A formal methodology gives the technician a starting place and a logical sequence of steps to follow. If you do not have a methodology in place, you are much more likely to waste time and effort and create frustration—not only for yourself but also for your end-user.

Now we are going to look at some detailed strategies and tips for how you can make sure your IHC succeeds. Let’s jump in!


Tips to Address Lack of Staining

When the suspect is the sample.

  • Check protein expression in your tissue.

  • Insufficient penetration of detection reagents can be resolved by preparing thinner tissue sections.

  • Make sure the tissue is covered in liquid at all times.

  • Treat the tissue with antigen retrieval reagents to unmask antigen.

When the suspect is the antibody.

  • Make sure the antibody works in your specific context (application + tissue)

  • Store antibody aliquots properly. Avoid repeated freeze-thaw cycles.

  • Use a secondary antibody that is reactive to the host species: if the primary antibody was raised in rabbit, use an anti-rabbit secondary antibody.

When the suspect is the protocol.

  • Adjust the fixation time or use a different fixative.

  • Check the datasheet to make sure the antibody has been validated in your specific application.

  • Increase time of chromogenic detection

  • Increase or decrease incubation time of the counterstain (since too much of the counterstain often obscures the specific staining).


Tips to reduce high background

When the suspect is the sample  

  • Handle tissue specimens carefully during fixation to maintain their morphology: poor morphology makes the interpretation of the IHC staining inadequate no matter how good the antibody works.

When the suspect is the protocol

  • If you use streptavidin as a detection system, the endogenous biotin must be blocked with avidin-biotin blocking reagent before incubation with primary antibody. This is particularly true for mitochondria-rich tissues like muscle and liver.

  • Preincubation with 5–10% normal serum from the species that the secondary Ab is derived from will prevent non-specific binding of secondary Abs to endogenous FcRs.

  • Use 4% formaldehyde (10% buffered formalin for FFPE), acetone or alcohol as fixative whenever possible: endogenous FcRs do not bind the Fc portion of IgG Ab after fixation in formaldehyde, acetone, or alcohol.


Tips to reduce nonspecific binding

When the suspect is the sample

  • Always avoid drying out of the samples.

When the suspect is the antibody

  • Always titrate your primary antibody. If the antibody works properly, the nonspecific staining should decrease as the dilution increases.

  • Use the secondary antibody obtained from another animal species rather than in the species of the target antigen. Make sure that it has been preabsorbed for the particular species you are interested in. Moreover, the immunoglobulin (Ig) isotype (IgG, IgM, etc) should match the type of the primary antibody. 

When the suspect is the protocol

  • Before adding the primary antibody, block with either 5% BSA for up to an hour with either BSA, serum from the same species as the secondary antibody species, or casein blocking solution.

  • Washing steps between the staining, usually 3 washes with PBS or TBS for 5-10 mins each.

  • Use optimal antigen retrieval protocol for best specificity.

  • Move from RT to 4°C: cold temperatures slow down the reactions, increasing interactions specificity and incubate overnight.

  • For fixed tissue, you can remove free aldehyde groups with 0.1% sodium borohydride in PBS for 30 mins prior to staining.

  • Reduce DAB incubation time. If you add hydrogen peroxide in your DAB solution, the color will develop slower and you can control the reaction more easily.

  • To prevent background caused by FcR incubate with preimmune serum or normal serum.

  • To reduce the endogenous enzyme activity, protocols that include Horseradish Peroxidase (HRP) or Alkaline Phosphatase (AP) may require reagents added to the chromogen/substrate to prevent non-specific signals, such as hydrogen peroxide and levamisole, respectively. Remember that hydrogen peroxide is unstable so make sure you make it fresh every time. As for AP remember that the AP isoforms in some tissues, like the placenta and GI-tract, are resistant to levamisole and may require a heating step instead.

Reading Tip

Do you know how to control your IHC controls? Read more here in our previous blog post. 


Problem solved? prepare for future issues

Once everything is solved and fully functional, documenting the process becomes important. This is where you clearly document findings, actions, and outcomes. When the problem occurs again, there will be information available to walk someone through the means of troubleshooting and resolving the issue.

This documentation also captures a history of equipment and users so that perpetual issues become known and recorded. Remember that both positive and negative outcomes should be documented. This can save time during future troubleshooting and prevent others from making the same missteps you may have taken

Congratulations! As a crime-stopper, you are now ready to confidently report to your PI. Feel better already?


  • Ward J.M. and Rehg J.E. Veterinary Pathology, (2013) 51 (1) 88-101, Rodent Immunohistochemistry: Pitfalls and Troubleshooting

  • Buchwalow I. et al. Sci Rep. (2011) 1: 28. Non-specific binding of antibodies in immunohistochemistry: fallacies and facts

  • De Matos L.L., et al. Biomarker Insights (2010):5 9–20,  Immunohistochemistry as an Important Tool in Biomarkers Detection and clinical practice

  • Ramos-Vara J.A. and Miller M. A. Veterinary Pathology (2014) 51(1) 42-87, When tissue antigens and antibodies get along: revisiting the technical aspects of immunohistochemistry: the red, brown, and blue technique.