I have ready protein isolates stored at -80 °C from cell culture (H9c2) and I wonder if i can use them if I do western blotting for the mitochondrial complexes/ Or do I have to do mitochondrial isolation all from the start?
mitochondrial isolation would be require only to demonstrate that your protein ./ complex is in that particular compartment. If you only wish to detect your protein, then whole cell lysate should be just fine.
As mentioned by others I would also suggest, you can use the whole cell lysate to detect the mitochondrial complex.
in case you need to show the translocation or the specific presence of the proteins in the mitochondrial compartment, then you would need to go for separation of mitochondrial fraction from the cytosolic fraction.