Automated protein purification the multiwell format by vacuum filtration

The invention relates to a process and a reagent kit for obtaining clear solutions containing cell contents from biological samples in a high throughput process, comprising the steps of preparing a plurality of protein-containing solutions which contain insoluble ingredients, in separate chambers of a multi-chamber filtration unit, eliminating insoluble ingredients by filtering the solutions through the multi-chamber filtration unit with the application of a pressure differential, while preventing cross contamination between adjacent chambers by chemical and/or mechanical means, and collecting the individual filtrates separately in collecting containers, as well as a process for recovering cell contents from the clear solutions obtained. The invention further relates to the use of an apparatus for recovering clear protein-containing solutions from biological samples.