I plan on capturing exosomes which exhibit a certain protein on their surface using antibodies fixed to magnetic beads. Once the exosome binds to the antibody and the magnetic beads are retrieved, is there a way to separate the surface protein from the antibody without damaging the protein or the exosome?
Difficult to predict. Usually, one breaks antibody/antigen interactions by changing pH (9) or possibly high salt (e.g. MgCl2), like in affinity chromatography. If your protein of interest and the exosomes will survive this procedure unharmed, needs experimental investigation with a functional test.
The antibody is directed to your protein or to a tag?
If it is against the protein, you will need to change the pH or salt concentration, if your AB is against a tag (ex. FLAG) you may use a peptide or a protein to compete with that tag and elute your protein-containing exosome.
Do you have the possibility to express a tag with your surface protein? Using a Twin-Strep-tag could circumvent the antibody problem, because you can just isolate your exosomes via the tag (e.g. by using Strep-Tactin TACS Agarose columns: https://www.iba-lifesciences.com/strep-tactin-tacs-agarose-column/6-6310-001). You can then elute the exosomes with biotin and no antibody will be attached to the surface.
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