I am doing mitochondrial swelling assay using potassium acetate buffer. Rather than swelling, it shows shrinking phenotype raising doubts on purity of mitochondria. Is there a way to check it's purity?
You could use Mitotracker staining to check under the microscope whether the pellet is really composed of mitochondria. Mitotracker red is dependent on membrane potential and should only stain intact mitochondria.
We saw a lot of intact mitochondria, however size will be depending on the organism and the tissue. We were working with moss. Here you can see some images in the supplement: