I have a PE conjugated mouse k isotype antibody..I would like to use it as control and add to cell culture .I would like to know whether conjugate will interfere in cell culture...
If it was small molecule fluorophore it would be a little more comfortable(still uncomfortable though) but PE is a larger protein(240kD!!) fluorophore. This raises risks of both protein-protein interaction(PE is "sticky") and other steric effects. While antigen binding capacity shouldn't be affected matching your control to your experimental antibody would be more appropriate.
The closest publication I can think off the top of my head that mentions these type of risks is the following paper addressing non-specific PE binding of mouse plasma cells during ICC. Very specific but it highlights the risks.
Article R-phycoerythrin-conjugated antibodies are inappropriate for ...