Currently, the most common way of identifying proteins is the proteolytic digestion of the proteins followed by mass spectrometric analysis. The existing strong demand for automation of this process has emerged not only from a wish of higher throughput. Rather, automation provides higher reproducibility and prevents keratin contamination of the samples being processed. The “liquid-in-liquid-out” approach was the first one to be used for automation of this process, but has shown limited user friendliness as time consuming adjustment and fine-tuning of the instrument is mandatory for optimum performance. In addition, the process of purifying larger number of samples using ZipTips or ZipTip-like disposable tips is recommendable for low throughput only.

In this tutorial a new liquid handling system is presented where hardware as well as software have been specially designed and optimised for proteolytic digestion of proteins. The system introduces new plates for easy removal of liquid by means of vacuum. Novel, high performance SPE plates are used for peptide purification and direct transfer to MALDI-TOF sample plates. A graphical user interface has been established to guide the user through the application without compromising the flexibility needed in setting up this complex application. Careful optimisation of each step in the protocols has improved sensitivity and made protein identification in the low femtomole range possible.