Immunoprecipitation Troubleshooting IP Troubleshooting

By Ryan Hamnett, PhD

Immunoprecipitation (IP) is a technique that uses antibodies to enrich or purify a target protein from a complex biological sample. Below is our troubleshooting guide to help solve any issues that might be encountered with an IP experiment.

Potential issue: Possible solution:
Target protein is not expressed in cell or tissue sample Check literature or other resources to confirm that protein is expressed in cell type of interest

Use an alternative method to confirm expression, such as IHC or ELISA

Include positive control to ensure that IP is working correctly
Protein degraded during preparation Add protease and phosphatase inhibitors to lysis buffer immediately before use

Perform all steps on ice or at 4°C
Suboptimal lysis buffer was used Try an alternative lysis buffer. Use the least stringent lysis buffer that gives acceptable yield
Interfering substances present in lysate Lysates that contain dithiothreitol, β-mercaptoethanol or other reducing agents can impair antibody function
Insufficient antibody concentration for capture of target protein Optimize antibody concentration by titration
Antibody has not been immobilized to the beads Ensure that the bead immobilization method (e.g. Protein G) is compatible with antibody isotype - see our full guide on Immobilizing Antibodies to Beads for more detail.
Covalent bonding of antibody to beads or Protein A/G is interfering with capture of antigen Use standard IP approach of Protein A/G Ig immobilization

Covalently bond antibody to beads instead of to Protein A/G
Antibody is not suitable for IP or IP conditions Modify conditions (e.g. use a non-denaturing lysis buffer instead of denaturing)

Try an alternative antibody, e.g. a polyclonal antibody

Ensure antibody has been validated for IP

If using a polyclonal antibody, ensure that it has been affinity purified, as otherwise other immunoglobulins in the antisera will compete for Protein A/G binding
Off-target protein is successfully competing with target Pre-clear the lysate before IP to reduce non-specific binding

Try an alternative antibody with higher affinity or that recognizes a different epitope
Insufficient incubation to allow antigen capture Increase incubation times and incubate at 4ºC instead of room temperature
Washes were too stringent or harsh Optimize the stringency of washes by altering the salt or detergent concentration

Try an alternative antibody with higher affinity
Protein was not eluted from the beads Check elution buffer composition and pH

Try an alternative elution buffer

If mild elution buffer is suspected of being the issue, test whether protein is being sufficiently precipitated by eluting in a denaturing SDS buffer and running SDS-PAGE/western blot
Potential issue: Possible solution:
Non-specific binding of lysate components to antibody or beads Include a pre-clearing step with both the bead and an isotype control antibody

Block the beads with competitor protein such as 2% BSA.

Reduce the amount of sample lysate

Use antibodies that are directly bound to beads to exclude non-specific binding to Protein A/G
Antibody concentration too high Optimize antibody concentration by titration
Washes were not stringent enough Optimize the stringency of washes by altering the salt or detergent concentration

Increase the number of washes

Transfer bead pellet to a fresh tube for last washing step to avoid eluting off-target proteins bound to tube
Protein degraded during preparation Add protease and phosphatase inhibitors to lysis buffer immediately before use

Perform all steps on ice or at 4°C
Antibody used is not specific enough Use affinity purified antibody or monoclonal antibody
Carry-over of proteins from earlier steps Collect supernatant immediately after centrifugation following lysis or pre-clearing, and be careful not to disturb the pellet

Try to remove as much supernatant as possible during immunoprecipitation steps
Potential issue: Possible solution:
Secondary antibody recognizes IP antibody on SDS-PAGE or western blot, obscuring antigen band Use a secondary antibody that only recognizes native (WB) antibody and not denatured (IP) antibody

Use a light-chain-specific secondary antibody, which will result in a band at 25 kDa but not 50-55 kDa

Use a WB primary antibody that is a different species to the IP antibody to prevent recognition by the WB secondary antibody

If the same antibody must be used for both IP and WB, perform IP with a non-biotinylated form and the WB with a biotinylated form of the antibody, then detect using streptavidin-HRP
IP antibody elutes with the antigen Covalently link the IP antibody to Protein A/G or the beads to prevent antibody elution

Elute using a glycine buffer instead of SDS buffer
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