Accidental Bead Loss During Aspiration

Symptom

Inconsistent or absent target protein signal across replicate samples, with visible reduction in bead pellet volume, indicating beads were aspirated during wash or supernatant removal steps.

1. 1 Agarose beads resuspend easily and are accidentally aspirated into pipette during supernatant removal
2. 2 Incomplete pelleting of agarose beads due to insufficient centrifugation speed or time
3. 3 Loose bead pellet disturbed when pipette tip contacts tube wall or bottom during aspiration

1. 1 Use magnetic beads (e.g., PureProteome Protein A Magnetic Bead System) instead of agarose beads to minimize/eliminate bead loss
2. 2 With magnetic beads, place tube on magnetic rack and allow complete separation before aspirating supernatant
3. 3 If using agarose beads, ensure complete pelleting by centrifugation before carefully aspirating from the top without disturbing pellet
4. 4 Visually confirm bead pellet is intact after each wash step; if beads are lost, increase centrifugation time or switch to magnetic beads

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