The whole idea behind going to the trouble of synthesising isotope labelled standards is that they mimic the behaviour of the analyte at all stages of the analysis, but can still be distinguished from the analyte. In particular they extract from the sample in the same way as the analyte, and so a calibration against an isotope labelled standard added to the samples does not need a correction for recovery.
The one exception to this happy state of affairs is when the analyte is in a form which does not extract in the same way as labelled standard spiked into the sample. This might happen in your case if the analyte was incorporated by the live rat brain in a way that does not happen to the standard whn you add it to mashed brain. Nonetheless, the best that you can do is to spike your labelled standard into the samples, and calibrate using analyte and standard spiked into brain.
Peter