Protein identification by automated nanospray mass spectrometry- "zoomscan walking"

Nanospray mass spectrometry is an important tool for high-sensitivity protein identification. A disadvantage of nanospray infusion is that the operator must search for peptide ions from a protein digest for subsequent collision-induced fragmentation. In order to make the nanospray method less operator-dependent, we have implemented an automated procedure using commonly available tools. Protein digests are subjected to unattended nanospray analysis using an automatic "zoomscan walking" procedure. The identification of eight proteins from an SDS gel using automated "zoomscan walking" is shown as an example of the utility of the method.