GNU polyxmass: a software framework for mass spectrometric simulations of linear (bio-)polymeric analytes

Area of Science:

• Biochemistry
• Computational Chemistry
• Polymer Science

Background:

• Mass spectrometry is crucial for analyzing biopolymers like DNA, RNA, saccharides, and proteins.
• Interpreting mass spectrometry data involves iterative hypothesis testing, which is time-consuming.
• Current software tools are polymer-chemistry specific, creating an overhead for researchers analyzing diverse analytes.

Purpose of the Study:

• To develop an integrated software framework for mass spectrometry data analysis.
• To address the lack of universal software for various polymer chemistries.
• To streamline the analysis of diverse (bio-)polymeric analytes.

Main Methods:

• Developed the GNU polyxmass software framework.
• Implemented three modules within a single binary program for defining polymer chemistries, performing mass calculations, and editing sequences.
• Enabled configurable mass calculations, polymer chemistry reactions, and graphical sequence editing.

Main Results:

• The GNU polyxmass framework supports common (bio-)chemical simulations and mass spectrometric calculations for linear biopolymers.
• It handles diverse polymer types including DNA, RNA, saccharides, and proteins.
• The software provides a user-friendly interface with a calculator paradigm and graphical sequence editor.

Conclusions:

• Provides a unified software framework for mass spectrometry data prediction and analysis.
• Supports scientists analyzing (bio-)polymeric analytes across different chemistries.
• Reduces the overhead associated with using multiple specialized software tools.