I am getting variable numbers. I have been sonicating with a probe sonicator after cutting tissue into small 2 mm pieces. After rotating ON in the acetic acid/pepsin buffer(0.5 M ,2.5 mg/ml) my supernatants are not completely clear. When I spin the supernatants themselves, I get a white pellet at the bottom. Is that the insoluble collagen that has been homogenized along with the soluble collagen?
Don't forget that the skin has a lot more in it than just collagen. There could be a number of insoluble components in skin. Almost regardless of the buffer and tissue used, any homogenization is likely to have components that spin down into a pellet.
However, if you homogenize and your resulting homogenate does not have a smooth consistency, that could also indicate that the homogenization is incomplete. I wouldn't be particularly surprised by that, as sonicators generally aren't recommended for tough and / or fibrous tissue, although your tissue may be in small enough pieces that it doesn't matter.
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