The first step that significantly improved single cell proteome analysis is the recently developed cell disruption technique called mPOP (minimal ProteOmics Preparation), which uses a physical rather than a chemical cell lysis protocol . To improve the procedure further we employed an automated sample preparation protocol based on a 96 well plate format using a Mantis™ (Formulatrix, MA) robot in which the sample preparation procedure was performed in low volume of buffer with much higher reproducibility than could have been achieved by the previous operator-based preparation technique.