Raw, untreated beads contain impurities which significantly affect homogenization and downstream biological processes. With silica beads, impurities can attain a concentration enough to inhibit many enzymes and reduce the affect the amount of analytes. Quality control analysis of raw silica and zirconium beads has identified dust, hair, and insects as contaminants. 
Beads need to be cleaned prior to use, one such accepted process is to acid wash. By washing in diluted acid it helps to reduce and eliminate fine particles and contaminants. Acid washing also removes potentially deleterious heavy metals adsorbed to the surface of the bead.
The beads are washed with diluted acid, beads are oven dried and baked, at which time they are suitable for most applications.
Silica beads are suitable for general grinding applications while zirconium beads have greater density and thus higher impact power.
| Beads | Silica (Glass) | Zirconium |
| 100 µm | Bacteria gram (-) | Bacteria gram (+), sonication additive |
| 200 µm | N/A | Bacteria, small yeasts (e.g.,Pichia) |
| 400µm | Yeasts (Saccharomyces) | Yeasts (Saccharomyces) |
| 800 µm | Molds, pollen | Molds, pollen |
| 1 mm | N/A | Soft tissue, leaf tissue, insects, finer soils |
| 1.4 mm | N/A | Soft tissue, leaf tissue, insects, |
| 1.7 mm | N/A | Animal Tissue, Leaf Tissue |
| 3 mm | N/A | Resilient tissue |
| 4 mm | Plant Tissue | N/A |