What can be done if the protein pellet does not solubilize completely using the AllPrep DNA/RNA/Protein Mini Kit?
FAQ ID -1580

In the protein precipitation procedure of the AllPrep DNA/RNA/Protein protocol, be sure to dissolve the protein pellet completely in Buffer ALO or 1x SDS-PAGE sample buffer.

For easier dissolving of proteins, dissolve the pellet in 5% (w/v) SDS or 8 M urea. Commonly, there is insoluble material left even after vigorous shaking or heating. This is typical for all kinds of protein precipitation under heavily denaturing conditions.

Briefly centrifuge the sample and use the supernatant for downstream analysis.