Department of Chemistry, University of Texas at Austin, Austin, Texas 78712 United States.
Anal Chem. 2024 Oct 15;96(41):16115-16120. doi: 10.1021/acs.analchem.4c03201. Epub 2024 Oct 4.
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 / 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 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.
最近，自上而下的质谱分析技术在分析越来越大的核酸方面取得了进展，使人们能够深入了解完整的、修饰的 RNA 分子。脱盐和 MS/MS 碎裂方法的发展允许对长达 100 个核苷酸的核酸进行快速采集高质量的自上而下 MS/MS 谱，这刺激了开发用于识别和验证核酸片段离子的软件方法的需求。我们已经实施了一种基于 R 的方法，以帮助分析基于在 / 结构域中直接观察到的片段离子的核酸 MS/MS 谱。这个名为 Shiny Application for Fragment Assignment by Relative Isotopes (Nucleo-SAFARI) 的程序，利用 Shiny HTML 框架，部署了一个用户友好的应用程序，用于自动注释在轨道阱质谱仪平台上记录的核酸自上而下的 MS/MS 谱。该方法通过生成片段离子及其同位素分布，然后通过算法评估实验同位素分布来进行。Nucleo-SAFARI 可在 https://github.com/mblanzillotti/Nucleo-SAFARI 下载。
