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Navigating the Mass Spectrometry-Based Proteomic Data Using Free Computational Tools
Published on: August 19, 2025
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Punc'data: A Versatile Tool for Molecular Formula Assignment, Interactive Visualization, and Comparison of Data from
Théo Voellinger1, Sébastien Schramm1, Pierre Pacholski1,2
1Université de Lorraine, LCP-A2MC (Laboratoire de Chimie et Physique-Approche Multi-échelles des Milieux Complexes), F-57000 Metz, France.
Journal of the American Society for Mass Spectrometry
|July 25, 2025
Summary
Punc'data is a new JavaScript tool for mass spectrometry (MS) data analysis. It aids in molecular formula attribution, visualization, and comparison of complex organic mixtures, accelerating research.
Area of Science:
- Analytical Chemistry
- Computational Chemistry
Background:
- Nontargeted analysis of complex organic mixtures using ultrahigh-resolution mass spectrometry (MS) demands advanced computational tools.
- Direct infusion MS is commonly used for analyzing complex organic mixtures, necessitating efficient data processing and calibration methods.
Purpose of the Study:
- To develop a specialized software tool, Punc'data, for accelerating calibration, data processing, and analysis of MS data.
- To provide a user-friendly web-based platform for molecular formula attribution, visualization, and comparison of complex organic mixtures.
Main Methods:
- Developed Punc'data, a JavaScript tool for web-based MS data analysis.
- Employed a network approach for molecular formula attribution, allowing user-defined or de novo mass difference determination.
- Integrated interactive visualization tools including class histograms, van Krevelen diagrams, and Kendrick maps.
Main Results:
- Punc'data facilitates efficient molecular formula attribution for complex organic mixtures.
- The tool provides interactive visualization of MS data, aiding in the identification of chemical trends.
- Enables comparison of different datasets through principal component analysis and imported data visualization.
Conclusions:
- Punc'data addresses the need for specialized software in nontargeted MS analysis.
- The tool enhances the speed and accuracy of data processing and analysis for complex organic mixtures.
- Facilitates deeper insights into chemical composition and comparative analysis of MS datasets.
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