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Transient-mediated simulations of FTMS isotopic distributions and mass spectra to guide experiment design and data analysis.

Fourier transform mass spectrometry (FTMS) applications require accurate analysis of extremely complex mixtures of species in a wide mass and charge state ranges. To optimize the related FTMS data analysis accuracy, parameters for data acquisition and the allied data processing should be selected rationally and their influence on the data analysis outcome is to be understood. Thus, to facilitate this selection process and to guide the experiment design and data processing workflows, we implemented the underlying algorithms in a software tool with a graphic user interface, FTMS Isotopic Simulator. This tool accurate-ly computes FTMS data via time-domain data (transient) simulations for user-defined molecular species of interest and FTMS instruments, including diverse Orbitrap FTMS models, followed by user-specified FT processing steps. Herein we describe implementation and benchmarking of this tool for analysis of a wide range of compounds, as well as compare simulated and experimentally-generated FTMS data. In particular, we discuss the use of this simulation tool for narrowband and broadband, low- and high-resolution analysis of small mol-ecules, peptides and proteins, up to the level of their isotopic fine structures. By demonstrating the allied FT processing artifacts, we raise awareness of a proper selection of FT processing parameters for modern applications of FTMS, including intact mass analysis of proteoforms and top-down proteomics. Over-all, the described transient-mediated approach to simulate FTMS data has proven useful for supporting contemporary FTMS applications. We also find its utility in fundamental FTMS studies and creating didactic materials for FTMS teaching.