Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.
Rapid Commun Mass Spectrom. 2020 Dec 15;34(23):e8927. doi: 10.1002/rcm.8927.
The Analysis of Oligonucleotide Modifications from Mass Spectra (Aom S) was created to support the analysis of oligonucleotide mass spectra. This application complements the existing software tools by providing a comprehensive analysis of oligonucleotide fragments from high-resolution tandem mass spectrometry (HR-MS/MS) data in a flexible and user-friendly manner, directly accessible through a web browser without any need for installation.
MS measurements of aminoC6-DNA and inosine-RNA were performed using an LTQ Orbitrap FT-MS instrument. The obtained data were analyzed by our newly developed open-source package Aom S accessible from the ms.epfl.ch web page or directly at https://mstools.epfl.ch/am2s/ to demonstrate the various functionalities of this tool, notably the possibility to identify different product ions from a nucleotide sequence with any fixed/variable modification by matching theoretical isotopic patterns to any experimental mass spectra with similarity scores ranking.
A detailed description of the Aom S tool with its user-friendly interface is exemplified using HR-MS/MS data of modified DNA and RNA oligonucleotides. Explanations of analysis parameters and tool workflow, as well as multiple options for viewing and exporting the results, are provided. Product ion assignment and modification localization can be achieved in seconds, and results can be exported as tables, matched mass spectra, and fragmentation maps.
A new open source tool (Aom S) for the analysis of HR-MS/MS data for modified DNA and RNA oligonucleotides is described. Aom S is fast, highly flexible, and versatile, allowing automatic precursor and product ion assignment in a comprehensive manner, including internal fragments and variable modification localization, with clear graphical representation of the results.
寡核苷酸修饰分析从质谱（Aom S）旨在支持寡核苷酸质谱分析。该应用程序通过以灵活且用户友好的方式直接通过网络浏览器提供对来自高分辨率串联质谱（HR-MS/MS）数据的寡核苷酸片段的全面分析，补充了现有的软件工具，而无需安装。
使用 LTQ Orbitrap FT-MS 仪器对氨基 C6-DNA 和肌苷-RNA 进行 MS 测量。通过我们新开发的开源软件包 Aom S 对获得的数据进行分析，该软件包可从 ms.epfl.ch 网页访问，也可直接在 https://mstools.epfl.ch/am2s/ 访问，以展示该工具的各种功能，特别是通过将理论同位素模式与任何实验质谱匹配，识别核苷酸序列中任何固定/可变修饰的不同产物离子的可能性，具有相似度评分排名。
使用修饰的 DNA 和 RNA 寡核苷酸的 HR-MS/MS 数据详细说明了 Aom S 工具及其用户友好的界面。解释了分析参数和工具工作流程，以及查看和导出结果的多种选项。产物离子分配和修饰定位可以在几秒钟内完成，结果可以以表格、匹配的质谱和碎片图谱的形式导出。
描述了一种用于分析修饰的 DNA 和 RNA 寡核苷酸的 HR-MS/MS 数据的新开源工具（Aom S）。Aom S 速度快、高度灵活且多功能，允许全面自动分配前体和产物离子，包括内部片段和可变修饰定位，并以清晰的图形表示结果。
