Nucleo-SAFARI:\nAutomated Identification of Fragment\nIons in Top-Down MS/MS Spectra of Nucleic Acids

Recent progress in top-down mass spectrometry analysis\nof progressively\nlarger nucleic acids has enabled in-depth characterization of intact,\nmodified RNA molecules. Development of methods for desalting and MS/MS\nfragmentation allows rapid acquisition of high-quality top-down MS/MS\nspectra of nucleic acids up to 100 nt, which has spurred the need\nfor development of software approaches to identify and validate nucleic\nacid fragment ions. We have implemented an R-based approach to aid\nin analysis of MS/MS spectra of nucleic acids based on fragment ions\nobserved directly in the <i>m</i>/<i>z</i> domain.\nThis program, entitled Shiny Application for Fragment Assignment by\nRelative Isotopes (Nucleo-SAFARI), utilizes the Shiny HTML framework\nfor deployment of a user-friendly application for automated annotation\nof top-down MS/MS spectra of nucleic acids recorded on Orbitrap mass\nspectrometer platforms. This approach proceeds through <i>in\nsilico</i> generation of fragment ions and their isotopic distributions,\nfollowed by algorithmic assessment of the experimental isotopic distributions.\nNucleo-SAFARI is available for download at https://github.com/mblanzillotti/Nucleo-SAFARI.