Fig. 4: Overview of automated sample preparation for SARS-CoV-2 SP3-based extraction on a Hamilton Robotics Microlab STARlet liquid handling system.

a Patient samples were collected with swabs placed in virus transport medium or sterile saline solution and stored at −80 °C before automated sample processing. The highlighted nucleocapsid peptides were monitored by turbulent flow chromatography coupled to tandem mass spectrometry. b Schematic overview showing the steps and Hamilton desk setup for automated SP3 sample processing: (1) viral particle and internal standard precipitation on magnetic bead using ethanol (EtOH) to a final concentration of 50% (v/v); (2) one-step viral lysis using a sodium dodecyl sulfate-based (SDS) buffer and dithiothreitol (DTT) for 5 min at 65 °C followed by dilution and bead precipitation; (3) magnetic separation and three consecutive wash steps with ethanol 80% (v/v); (4) protein elution from magnetic bead followed by digestion with trypsin in triethylamonium bicarbonate buffer (TEAB) for 2 h at 37 °C, post-digestion acidification with trifluoroacetic acid (TFA), and recovery of peptides in a new sample plate.