Molecular and macromolecular structure analysis by high resolution and accurate mass spectrometry (MS) is indispensable for a number of fundamental and applied research areas, including health and energy domains. Comprehensive structure analysis of molecules and macromolecules present in the extremely complex samples and performed under time-constrained experimental conditions demands a substantial increase in the acquisition speed of high resolution MS data. We demonstrate here that signal processing based on the filter diagonalization method (FDM) provides the required resolution for shorter experimental transient signals in ion cyclotron resonance (ICR) MS compared to the Fourier transform (FT) processing. We thus present the development of a FDM-based MS (FDM MS) and demonstrate its implementation in ICR MS. The considered FDM MS applications are in bottom-up and top-down proteomics, metabolomics, and petroleomics.