OptiMS: An Accessible Program for Automating Mass Spectrometry Parameter Optimization and Configuration

Mass spectrometers have an enormous number of user-changeable parameters that drastically affect the observed mass spectrum. Using optimal parameters can significantly improve mass spectrometric data by increasing signal stability and signal to noise ratio, which decreases the limit of detection, thus revealing previously unobservable species. However, ascertaining optimal parameters is time consuming, tedious, and made further challenging by the fact that optimizing one parameter may deoptimize another. Consequently, suboptimal parameters are frequently used during characterization, reducing quality of results. OptiMS, an open-source cross-platform program, was developed to simplify and more accurately determine optimal mass spectrometer parameters for a given system. OptiMS efficacy was demonstrated through its application to multiple systems, quickly and successfully optimizing instrument parameters unassisted, to maximize a user-defined metric, for example, intensity of a particular species. Additionally, amongst other features, OptiMS allows running of a sequence of predefined parameters, reducing workload for users wishing to obtain mass spectra under multiple sets of conditions.