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Hi.

I have experienced similar problems with the Amicon filters previously.  I
found that using a swing bucket rather than a fixed angle centrifuge and
keeping the speed at 4000 g, the recommended speed, resulted in better
yields.  If you have a large volume to concentrate (>12 mL), using an
Amicon stirred pressure cell first may work better.  This prevents
repeated spinning of the filter, which is not recommended by the company. 
In my experience, using the same filter a few times is ok, but I guess
that repeated centrifugation could eventually crack the filter.

Matt