Cookie Cutter Proteolysis: Achieving Reproducible, Efficient Digestions for Proteomic Workflows Protein sample preparation workflows for mass spectrometric analysis that involve proteolysis are often labor-intensive, time consuming and user dependent. These workflows often involve digestion, solid phase extraction, drying, and re-suspension prior to reversed phase separation into the mass spectrometer. The introduction of variability at many of these steps hinders discovery initiatives as well as the ability to convert these discoveries into viable assays. Recently, an automated protein digestion platform was developed which accelerates the digestion process through use of immobilized enzyme reaction (IMER) columns. Furthermore, online digestion is integrated with desalting and reversed phase chromatography to create a seamless workflow to the mass spectrometer once the sample is injected. As demonstrated here, it offers complete, reproducible protein digestions in as little as 30 seconds, allowing hundreds of samples to be run per day, and can be adapted to many applications.