Aom² S: A new web-based application for DNA/RNA tandem mass spectrometry data interpretation

Area of Science:

• Biochemistry
• Bioinformatics
• Analytical Chemistry

Background:

• Oligonucleotide analysis using mass spectrometry is crucial for understanding nucleic acid modifications.
• Existing software tools may lack comprehensive analysis of oligonucleotide fragments from high-resolution tandem mass spectrometry (HR-MS/MS) data.

Purpose of the Study:

• To introduce a novel, open-source web-based application, Analysis of Oligonucleotide Modifications from Mass Spectra (Aom2S).
• To provide a user-friendly and flexible tool for comprehensive analysis of oligonucleotide fragments from HR-MS/MS data.

Main Methods:

• Mass spectrometry (MS) measurements were performed on modified DNA and RNA oligonucleotides using an LTQ Orbitrap FT-MS instrument.
• The Aom2S open-source package was developed and utilized for analyzing the MS data, accessible via a web browser.
• The tool identifies product ions and localizes modifications by matching theoretical isotopic patterns to experimental mass spectra.

Main Results:

• The Aom2S tool features a user-friendly interface for analyzing HR-MS/MS data of modified oligonucleotides.
• Analysis parameters, workflow, and result visualization/export options are clearly explained.
• Product ion assignment and modification localization are achieved rapidly, with results exportable in various formats.

Conclusions:

• Aom2S is a new, open-source tool for analyzing HR-MS/MS data of modified DNA and RNA oligonucleotides.
• The software is fast, flexible, and versatile, enabling automatic precursor and product ion assignment.
• It facilitates comprehensive analysis, including internal fragments and variable modification localization, with clear graphical output.