Nucleo-SAFARI: Automated Identification of Fragment Ions in Top-Down MS/MS Spectra of Nucleic Acids

Recent progress in top-down mass spectrometry analysis of progressively larger nucleic acids has enabled in-depth characterization of intact, modified RNA molecules. Development of methods for desalting and MS/MS fragmentation allows rapid acquisition of high-quality top-down MS/MS spectra of nuclei...

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Bibliographic Details
Published in:Analytical chemistry (Washington) 2024-10, Vol.96 (41), p.16115-16120
Main Authors: Lanzillotti, Michael B., Brodbelt, Jennifer S.
Format: Article
Language:English
Subjects:
Acids
Algorithms
Annotations
Automation
Ions
Ions - analysis
Ions - chemistry
Isotopes
Mass spectrometry
Mass spectroscopy
Nucleic acids
Nucleic Acids - analysis
Nucleic Acids - chemistry
RNA - analysis
RNA - chemistry
Software
Spectra
Tandem Mass Spectrometry - methods
Wildlife tourism
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Summary:Recent progress in top-down mass spectrometry analysis of progressively larger nucleic acids has enabled in-depth characterization of intact, modified RNA molecules. Development of methods for desalting and MS/MS fragmentation allows rapid acquisition of high-quality top-down MS/MS spectra of nucleic acids up to 100 nt, which has spurred the need for development of software approaches to identify and validate nucleic acid fragment ions. We have implemented an R-based approach to aid in analysis of MS/MS spectra of nucleic acids based on fragment ions observed directly in the m/z domain. This program, entitled Shiny Application for Fragment Assignment by Relative Isotopes (Nucleo-SAFARI), utilizes the Shiny HTML framework for deployment of a user-friendly application for automated annotation of top-down MS/MS spectra of nucleic acids recorded on Orbitrap mass spectrometer platforms. This approach proceeds through in silico generation of fragment ions and their isotopic distributions, followed by algorithmic assessment of the experimental isotopic distributions. Nucleo-SAFARI is available for download at https://github.com/mblanzillotti/Nucleo-SAFARI.
ISSN:0003-2700
1520-6882
1520-6882
DOI:10.1021/acs.analchem.4c03201