Immunohistochemistry Protocol Guide – Introduction

Immunohistochemistry (IHC) is a technique widely used in histology and pathology laboratories. IHC enables the visual detection of proteins and other antigens in tissue, providing a method for the detection of abnormal cells or the characterization proteins within a biological sample.

Although considered less quantitative than other immunoassays such as ELISA or Western blot, IHC enables the localisation of protein expression in the context of intact tissue and therefore provides a means for assessing the progression and treatment options of diseases such as cancer.

IHC is dependent on the specificity of the antibody used. A highly specific antibody will ensure binding of the protein of interest in the tissue section. Visualisation of the antibody-antigen interaction can be achieved using either chromogenic or fluorescent detection. Chromogenic detection relies on the use of an antibody that is conjugated to an enzyme. This enzyme cleaves its substrate to produce a coloured product at the location of the protein. In contrast for fluorescent detection the antibody used is conjugated to a fluorophore, which can be visualised using a fluorescent microscope.

immunohistochemistry protocol guide pdf

IHC Antibody selection

Choosing the correct primary antibody, either monoclonal or polyclonal is the key to a successful and specific IHC assay with each having unique advantages and disadvantages. Monoclonal antibodies are generated from a single B-cell clone from one animal resulting in a homogenous population of immunoglobin directed against a single epitope. Polyclonal antibodies are derived from multiple B-cell clones resulting in a heterogenous mixture of antibodies directed against various epitopes of the same antigen.

Monoclonal antibodies are favoured as batches produced from the established hybridoma line allow for identical production and standardisation. Furthermore, the use of monoclonal antibodies has been shown to limit background staining and result in reduced cross-reactivity with other proteins. Using a polyclonal antibody can help increase the detection signal of the antigen and is the preferred choice when dealing with denatured protein. As polyclonal antibodies can recognise multiple epitopes they are also more tolerant of minor changes during fixation and processing when compared to monoclonal antibodies.

Species choice should be taken into consideration when choosing antibodies for IHC. In order to ensure low background, the primary and secondary antibodies should be raised against the same species.

IHC assay optimization and Variables

Below is a table of key components of an IHC assay and considerations which must be taking into account before beginning you IHC assay.

IHC assay component


AntigenSpecies, antigen expression levels
Antigen RetrievalPIER or HIER
Blocking ReagentNormal serum, protein, commercial buffer, other
Detection methodDirect/Indirect
FixativeFormaldehyde, alcohol, acetone
LabelFluorochrome or Chromogen
Primary antibodyMonoclonal or polyclonal
Secondary antibodySpecies and detection label
Visualisation and AnalysisFlorescence/Light microscope. Software analysis

1. IHC Sample preparation

Correct sample preparation is an essential component of a high quality IHC stain and involves several key steps outlined below.

1.1 Sample Fixation

The first step of an IHC assay is sample collection. Correct sample collection is critical in order avoid autolysis and necrosis of the excised tissue. Factors that will affect the quality of your sample for IHC analysis will include time until fixation and the temperature of the samples. It is therefore advised to place the sample in a fixative solution soon as possible.

Fixation ensures sample preservation, the immobilization of antigens and the maintenance of subcellular structures through cross-linking methylene bridges and Schiff bases between basic amino acid residues of proteins. An optimized fixation protocol is advised as an inappropriately fixed antigen may not be detected further on.

Different fixative agents maybe used depending on the antigen under investigation. The most widely used fixative for IHC is 10% neutral buffered formalin. Other fixatives include methanol, ethanol and acetone which may be used for fixation and permeabilization of the membrane. Below is a table outlining recommended fixation solutions for selected antigens in tissue.



Blood forming organs/connective tissueZenker’s or Helly Solution
Delicate TissueBouin’s Fixative
ImmunoglobulinsIce-cold Acetone or Methanol (100%)
Nuclear MorphologyZinc Formalin
Nucleic AcidsCarnoy’s Solution
Proteins, peptides and enzymes 10% Neutral Buffered Formalin
Small Molecule4% Formaldehyde
Click here for IHC Buffer Recipes

2. IHC Paraffin and Frozen Embedding

Embedding is an essential component of sample preparation to preserve morphology and provide tissue support during processing and sectioning. Like fixation various embedding compounds can be used depending of the specific requirements of the antibody. Frozen and paraffin embedding are the most widely used, each offer distinct advantages and disadvantages depending on the antibody used.

2.1 Frozen Tissue

Frozen tissue sections can be processed in a shorter amount of time when compared to paraffin embedded sections. Frozen tissue samples are prepared by immersing the tissue in liquid nitrogen, isopentane or by snap freezing in dry ice. Frozen samples require a short fixation after freezing and sectioning which is normally done with alcohol. Alcohol, unlike formaldehyde, does not mask epitopes and therefore antigen retrieval does not need to be done on tissue fixed with alcohol.

Long term storage of frozen tissue sections is not recommended, as the formation of ice crystals within cells may negatively affect subcellular detail. The recommended maximum storage of frozen sections is 1 year and -80C.

It should be noted that frozen sections are often thicker than paraffin sections which can result in lower microscopic resolution and poor images of tissue morphology. As frozen tissue often retains enzymatic activities, the activity of the endogenous enzymes may affect the IHC detection method

2.2 IHC Paraffin Embedded Tissue

Paraffin embedding is the best option for long term preservation of a tissue sample. Paraffin sections are generally cut between 3-5 microns using a microtome.

Prior to being embedded in paraffin the sample must be fixed, this can be done by perfusion or immersion directly after dissection generally requiring 4-24 hours. Do not fix your sample for longer than 24hrs as over-fixation may mask the antigen. The duration of fixation may require optimisation and vary depending on tissue and antigen.

As paraffin is immiscible with water the tissue sample must be dehydrated before the addition of the paraffin wax. The sample can be dehydrated by immersion in increasing concentrations of alcohol. The gradual increase in alcohol concentration minimizes cell damage. Once dehydration in alcohol is complete the sample is placed in xylene to remove any remaining ethanol.

The paraffin is heated to 60C for embedding and allowed to harden overnight. Following this the tissue can be cut into thin sections using a microtome. These tissue sections can be stored at room temperature until rehydration and initiation of the IHC protocol

*Some antigens, e.g. those with post-translationally modified residues, will not survive even mild aldehyde fixation, and in such cases, the tissue should be snap-frozen and sectioned in a cryostat and stored at -80 °C until fixing in alcohol or cold acetone.

2.3 Advantages and Disadvantages of Paraffin vs Frozen Embedding

 Paraffin EmbeddedFrozen Tissue
AdvantagesPreserves tissue morphologyPreserves enzyme and antigen function
DisadvantagesOver-fixation can mask the epitopeFormation of ice crystals can affect tissue structure
Downstream AssaysPCR amplificationDNA, RNA, FISH and cell cycle analysis
FixationPre-embeddingPre/Post Sectioning
PrecautionsDuration and intensity of tissue heating can be harmful to antigensFreeze quickly. Don’t cut directly from frozen
StorageYears at room temperature1 year at -80°C

3. Antigen Retrieval

The process of sample fixation although necessary for tissue preservation can mask the epitope of interest preventing binding of the primary antibody. Antigen retrieval therefore refers to any technique in which the masking of an epitope is reversed and epitope antigen binding restored. Antigen retrieval acts to break the cross-linkage induced by fixation and expose the antigen.

On paraffin embedded tissues it is necessary to perform a deparaffinisation step with xylene and alcohol prior to antigen retrieval. Deparaffinisation generally consists of 2 washes in xylene followed by three minutes each in 100%, 95% and 70% ethanol. To complete the rehydration process, wash sections two times in ddH2O for 5 minutes each.

There are 2 common processes for antigen retrieval:

Heat Mediated (Heat induced epitope retrieval – HIER)

Enzymatic digestion (Proteolytic-induced epitope retrieval – PIER)

3.1  Heat-Induced Epitope Retrieval – HIER

HIER uses heat to unmask the epitope. The source of which can be a microwave, pressure cooker, steamer, water bath or autoclave.

3.2  Preteolytic-induced epitope retrieval – PIER

This method uses enzymes such as Proteinase K, Trypsin and Pepsin to restore the binding of an antibody to its epitope. When using the enzymatic digestion reagents it is important to not over or under digest – the digestion time should be optimized. Caution should be exerted when using PIER as it has been shown in some cases to have a low success rate for restoring immunoreactivity and can destroy both tissue morphology and the antigen of interest.

*The technique used for tissue retrieval ultimately depends on the tissue, fixation method and primary antibody. Antigen retrieval is not required for frozen tissues as antigen masking is the result of cross-linking formed during formalin fixation.

3.3  HIER vs PIER

AdvantagesMaintains epitopeCommonly used for difficult to retrieve epitopes
Buffer CompositionDependent on pHNeutral buffer solutions are used of enzymes such as pepsin, proteinase K or trypsin
Incubation Time10-20 minutes5-30 minutes
pHpH 6 most widely used, optimum pH may varypH 7.4
PrecautionsHeating can lead to uneven antigen retrievalEnzymatic activity can damage the sample
Recommended AntigensNo specific antigenImmunoglobulins, cytokeratins

4. Permeabilization

Permeabilization may be required for certain samples whereby the antibody needs to gain access to the inside of cells to detect the protein.  Permeabilization is also required in order to detect transmembrane proteins if the epitope is located in the cytoplasmic region.

Permeabilization is achieved with solvents or detergents. Solvents such as acetone and methanol can be used after fixation with a crosslinking agent e. g Paraformaldehyde. Solvents are recommended for cytoskeletal, viral and enzyme antigens. Detergents  are generally much milder on the sample and will not dissolve the plasma membrane. Detergents such as Triton or Tween 20 are used for the permeabilization of antigens in the cytoplasm, plasma membrane or for soluble nuclear antigens.

5. Blocking

Blocking of you IHC sample is essential to achieve a good IHC signal to noise ratio. Inadequate blocking can result in a high level of background noise whilst over-blocking can mask your signal.

Blocking takes place after your sample has fixed, embedded, antigen retrieved and permeabilized if necessary. It is the last step you perform before incubating with your primary antibody. The duration of blocking depends on the sample ranging from 30 minutes to overnight. Blocking can be performed at 4C or at room temperature. Blocking is performed using a protein that does not specifically bind your epitope of interest or to the antibodies in your IHC assay.

The most commonly used blocking methods are outlined below:

5.1 Blocking Sera

The use of normal sera is considered one for the most effective blocking agents and is carried out using normal (unchallenged) sera from the same species that the secondary antibody was raised in. The antibodies in the normal sera will bind any non-specific epitopes in your sample and in turn prevent unconjugated antibodies from doing the same. Normal sera is an ideal blocking agent when using polyclonal antibodies.

5.2 Protein Buffers

Protein buffers can be used instead of sera to block your sample. Protein buffers compete with your antibody to bind non-specific epitopes therefore, the use of high concentrations of protein competitors can out-compete your antibody and ultimately lower background noise. Commonly used protein blocking buffers are: 0.1 to 0.5% bovine serum albumin (BSA), gelatin or non-fat dry milk.

5.3 Commercial Mixes

Commercial blocking buffers are also available.

5.4 Biotin Blocking

If an Avidin-biotin detection system is used it is recommended to block for endogenous biotin before addition of the secondary antibody.

5.5 Peroxidase blocking

If using a HRP conjugated antibody non-specific staining may occur due to the activity of endogenous peroxidases already in the tissue. The presence of peroxidases in your sample can be identified by incubating the sample with DAB substrate which will turn brown on peroxidase identification. To block peroxidases H202 is commonly used.

5.6 Alkaline Phosphate (AP) Blocking

Endogenous alkaline phosphate (AP) can produce a high background when using AP chromogen substrates. Endogenous AP is typically found in kidney, intestine, osteoblasts, lymphoid tissue and placenta. Tissue can be tested for endogenous AP through incubation with BCIP/NBT, if a blue colour is observed endogenous AP is present and blocking is necessary. Endogenous AP can be blocked by including levamisole in the chromogen substrate

* Not all blocking agents and buffers are compatible with all detection methods. For example, alkaline phosphatase conjugates are not compatible with any sodium azide preservative in your buffers and avidin-biotin complex system is not compatible with non-fat dry milk.

6. Immunostaining procedure

Following successful sample preparation the tissue can now be incubated with selected antibodies for the detection of a targeted antigen.There are multiple labelling techniques available such as direct, indirect and indirect with signal amplification.

Direct labelling uses a primary antibody directly conjugated to a signalling source, while indirect labelling has a signal generating secondary antibody that will attach to the primary antibody making contact with the antigen. Direct detection is quicker and simpler than indirect detection, as the label is attached via a covalent bond directly to the primary antibody. This means you only need one incubation step and one round of washes.

It is important to note that a primary antibody produced from a mouse would be detected using a secondary antibody that is anti-mouse and conjugated to a detecting probe. Finally, the indirect with signal amplification technique is accomplished using a biotinylated secondary antibody and an amplification reagent such as streptavidin.

6.1 Direct vs Indirect Immunostaining

Limited amount of directly conjugated antibodies availableOnly a small number of standard conjugated antibodies required
Low signal amplificationStrong signal amplification
No species cross reactivityCommonly used technique
No Non-specific bindingNon-specific binding may occur
Short protocolExtra Incubation and wash steps required
Straightforward Dual stainingDual staining is difficult to achieve

6.2 Primary Antibody

When choosing a primary antibody you must consider its specificity for your antigen of interest and its suitability for IHC. Antibodies that are designed for western blot or ELISA assays may not always work for your target antigen which has been crosslinked in fixed tissue. Therefore, it is paramount to identify examples of IHC on the commercial antibody data sheet.

Primary antibodies can be used for multiple targets in one incubation solution once they are of different host origins and as result detected with different secondary antibodies.

6.3 Secondary Antibodies

Choose your secondary antibody for its specificity to your primary antibody. For example, a primary antibody raised in rabbit requires a secondary antibody against rabbit, anti-rabbit. Multiple antigens can be assessed through the use of secondary antibodies linked to contrasting fluorophores that distinguish between your primary antibodies based on host origin. Secondary antibody incubation should be carried out in the dark to protect the fluorophore.

It is also important that the isotype of your secondary antibody matches your primary antibody. Affinity purified antibodies are widely used as they provide the lowest amount of non-specific binding. It should be noted though that IgG fractions can potentially contain very high affinity antibodies and may be of use when an antigen is poorly expressed or in low abundance.

7. Counterstaining and Mounting

Counterstaining can be used to identify all the cells in your sample that do not express your antigen of interest. Counterstaining can be performed using haematoxylin or DAPI (If you have not used this already).

To mount coverslips to slides, use mounting medium designated for fluorescence microscopy to help preserve the fluorescent signal in your sample. Apply the coverslip with enough mounting medium, taking care to eliminate bubbles that can distort or obscure your images.

8. IHC Controls

IHC like all other assays requires controls to confirm that the staining pattern is accurate and reliable. For IHC both an antigen control and reagent control is advised.

Antigen Control – There should be both a positive and negative antigen control. The positive control maybe a tissue known to express the protein you are detecting. The negative control a tissue known not to express the protein you are detecting. Using a negative control will help identify non-specific bonding and false positives.

Reagent Control – A reagent control is used to ensure that staining is produced from primary antibody staining the antigen and not from detection system or the specimen. This can be determined by using the detection system with diluent alone and no primary antibody.

For each experiment, it is also recommended to include a tissue section incubated with a non-specific isotype control antibody that matches the class and type of the primary antibody (if the primary antibody is a monoclonal antibody), but does not recognize the target epitope. Isotype controls help distinguish non-specific background fluorescence from specific fluorescent labelling of your target antigen. If the primary antibody is a polyclonal antibody, include a tissue section incubated with a non-specific, species-matched polyclonal antibody.