A guide to antibody validation

The most commonly used method to validate antibody specificity

Antibodies are intrinsically variable reagents and so it’s important you take the time to ensure that the antibody performs as expected in your experimental setup. A good supplier will have already tested the antibody but it’s impossible to account for the huge number of different protocols and reagents that it may get used with once in the hands of the researcher. Your own validation steps are therefore so essential because they’re specific to your setup.

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Validation

Benefits

Limitations

KO models

 

Protein-encoding gene eliminated with genetic tools (eg CRISPR)

KO cell lines function as a true negative control

Guaranteed no expression of the target gene

A potentially large number of KO cell lines may be generated in a short period of time

Knockout cell lines may be used in all assays - western blot, IHC, ICC, flow cytometry

 

Knockout cell lines against specific genes are not always viable

Is a very powerful negative control, not a confirmation of binding

Mass spectrometry/ IP-MS

 

Protein complexes characterized by first immunoprecipitating them from a cell lysate and then analyzing with mass spectrometry

Amenable to a high throughput format

Potential to estimate abundance of target protein bound to the antibody of interest using normalization techniques

Can recognize all isoforms

Can identify PTMs

Can identify interacting partners and complexes

Can identify off-targets

Confirms specificity based upon digested protein fragments

Amenable to a high throughput format

Potential to estimate abundance of target protein bound to the antibody of interest using normalization techniques

IP-MS assays difficult to optimize

Too many washes of your IP could remove weak or moderate binders

Not all antibodies are suitable for IP

IP-MS assays difficult to optimize

Specialized technique that requires use of a mass spectrometer

For some targets, protein binding to the antibody of interest via IP is ineffective

Can be difficult to distinguish partner proteins pulled down in a complex from off-target binding

Interpreting the data can be tricky as the highest enrichment score does not always mean that this is the target the antibody preferentially binds to, eg

Large number of interactors found with higher fold enrichment: If your protein of interest is in high abundance in your sample but its interacting partners are not, then the fold enrichment for the interacting partners could be higher than for your protein of interest if it is pulling multiple units of your interacting partner

Antibody detecting multiple family members: if one is present at a lower level in the starting lysate, then the fold enrichment is likely to be higher

 

Western blot

 

Protein detected and quantified in a sample via initial separation by size and then blotting onto a membrane to be detected by an antibody

Useful for determining antibody specificity against target protein based upon molecular weight

Ideal for detecting either native or denatured proteins

Qualitative assay

Time-consuming assay

Difficult to determine the optimal experimental conditions (ie methodology and buffer)

Only a small number of antibodies may be validated per run

IHC and ICC

 

Protein in tissues (IHC) or cells (ICC) detected via specific antibodies and reporter molecules

Validates whether an antibody recognizes the correct protein based on cellular localization

Specificity confirmed based on cells that either do or do not express the target protein

Qualitative assay

Unable to determine if an antibody recognizes other proteins non-specifically with identical cellular localization

Often difficult to determine cell or tissue types that either do or do not target the protein

Protein/ peptide array

 

Antibody binding events detects by first spotting arrays are spotted with the peptides/protein and then adding the antibody (similar to ELISA)

Allows screening of a larger number of over-expressed proteins

Very high-throughput screening process

Requires very small sample volumes

Protein array only: unable to screen for post-translationally modified proteins

Only present linear epitopes for interrogation – do not usually present conformational epitopes

Do not usually present conformational epitopes

siRNA knockdown

 

Protein-encoding gene expression is lowered with genetic tools (eg interfering RNA)

Confirms specificity through target protein being downregulated

Knockdown cells lines may be used in all assays – western blot, IHC, ICC, flow cytometry

Knockdown is transient

Difficult experiment to optimize – often requiring several siRNA sequences

The KD could be ineffective so good controls are needed eg use of multiple RNAs targeting the same gene

Non-specific reduction in expression might be observed where the siRNA binds and silences “off-targets” due to binding to similar transcripts

Expression profiles (online)

 

Expected protein expression is checked via online databases

Quick and easy to run without the need for any equipment

Large number of online databases available, for example

www.genecards.org

 portals.broadinstitute.org/ccle

www.ncbi.nlm.nih.gov/gene

www.proteinatlas.org

 

Expression data may not be complete in some cases

Can be difficult to find negative cell lines or tissues

Cell treatment

 

Protein expression level manipulated within cells

Relatively straightforward to increase or reduce expression levels of certain proteins (eg via starvation or chemically)

These could serve as positive or negative controls

 

Phosphatase treatment: tells you it is phospho-specific but not to which site

You need to have additional controls in place to ensure the cell treatment worked


Additional points to consider when validating an antibody


There are other common methods available that do not test antibody specificity so we don’t recommend you use them alone. These include

  • Blocking with immunizing peptide: even non-specific abs will be blocked by immunizing peptide
  • Omission of primary: can be used to evaluable the tissue or secondary detection reagents but not the primary antibody


1. Choice and preparation of cell lines or tissue samples – true positive and negative controls are essential

It is obviously important to choose samples which express the target protein of interest as well as cell lines which do not express the protein to be used as a true negative control. Such information may be sourced from peer-reviewed papers and by using online protein databases. Furthermore, antibodies may or may not recognize the protein in its native or denatured state.  It is therefore important to prepare the test samples accordingly. For example, an antibody that recognizes the protein only in its native form should not be used on samples using denaturing conditions, for instance in western blotting.

See our sample preparation guides for WB or ELISA.

2. Protocols

It is important to ensure an optimized protocol is used to give the antibody the best chance of passing the validation process. For instance, incubation times can vary dramatically from a minimum of one hour to overnight at 4°C, so the optimal incubation period for each antibody will have to be determined. If the period is too short, sensitivity issues may be encountered. In contrast, if the period is too long, background staining may be problematic. Other factors - such as working dilutions, blocking conditions and the use of native vs denatured conditions - will also need to be individually optimized.

See our antibody protocols and troubleshooting tip guide.

3. The choice of buffers

The majority of antibody assays will use two buffer types: either PBS or TBS. The optimal buffer will need to be determined. Additionally, subtleties such as pH should also be taken into consideration.

See our buffer recommendations for optimal WB results and antibody storage.

Also link to the following pages:

•    KO validation overview page
•    http://www.abcam.com/content/validating-our-products
•    http://www.abcam.com/index.html?pageconfig=popular_protocols
•    http://www.abcam.com/tag/antibody%20guide
•    Scientists helping scientists- http://www.abcam.com/index.html?pageconfig=support
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