Automated plate-to-peptide protocol for mass spectrometry sample preparation

Although advances in mass spectrometry now support proteomic screens of thousands of samples and sample preparation has been automated to match, most current protocols still start from pre-prepared cell lysates. Here, we present a protocol for automated mass spectrometry sample preparation starting at the cell culture plate level. We describe steps for cell seeding in 96-well plates, in-plate cell lysis, and single-pot solid-phase-enhanced sample preparation. This streamlined approach significantly reduces manual handling while yielding highly reproducible measurements from low cell numbers.