Mass spectrometry has become an indispensable analytical tool for studies related to the structure and function of peptides and proteins. The variety of analytical methods, the range of instrument capabilities, and the complexity of the data obtained make it difficult for most laboratories to acquire the necessary expertise to make optimal use of their instrumentation.We describe an expert system approach to automating specific types of analyses in a way that makes it easier to transfer the capability to do specific experiments to other laboratories. Central to the approach is the creation of a computer program (ie, a virtual instrument) that controls the operation of physical components, analyzes incoming data, automatically adjusts instrument parameters to achieve the goal of the analysis, and reports the results. By interacting with the mass spectrometer through the computer operating system, it is possible to add useful functions to the system without altering any of the manufacturer-controlled data system software. The usefulness of this approach is illustrated by the automation of experiments to confirm the sequences of synthetic peptides and perform LC/MS/MS peak parking experiments and real-time database searches.