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Summary

This review offers a comprehensive overview of freely available, open-source metabolomics software and tools. It aims to help researchers navigate complex data processing and analysis for mass spectrometry (MS) and nuclear magnetic resonance (NMR) based metabolomics.

Keywords:
AnnotationData analysisData processingData visualizationDatabasesMass spectrometryMetabolitesMetabolomicsNMRSoftware toolsStatistics

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Area of Science:

  • Metabolomics
  • Bioinformatics
  • Computational Biology

Background:

  • High-throughput metabolomic experiments generate complex data requiring advanced processing and interpretation.
  • Existing resources for metabolomics software and databases are fragmented and lack comprehensive overviews.
  • The increasing complexity of metabolomic datasets necessitates improved in silico approaches for data analysis.

Purpose of the Study:

  • To provide an overview of recently developed, freely available, and open-source metabolomics tools, software, and databases.
  • To raise awareness among metabolomics researchers about new developments in data processing and analysis.
  • To facilitate and advance data processing workflows in metabolomics research.

Main Methods:

  • Review and compilation of freely available, open-source tools, algorithms, and frameworks for metabolomics.
  • Focus on resources for data processing, data annotation, and data visualization.
  • Inclusion of tools applicable to both mass spectrometry (MS) and nuclear magnetic resonance (NMR) based metabolomics, with emphasis on untargeted workflows.

Main Results:

  • Identification and summarization of various open-source tools and resources for metabolomics data processing, annotation, and visualization.
  • Categorization of tools based on their application in MS and NMR-based metabolomics, including untargeted and specialist workflows.
  • A comprehensive overview table detailing the described tools and their platform dependencies is provided.

Conclusions:

  • The presented overview serves as a valuable resource for metabolomics researchers seeking efficient data processing and analysis solutions.
  • Awareness of these open-source tools can significantly advance and streamline metabolomics research workflows.
  • Facilitating access to and utilization of these computational resources is crucial for the progress of the metabolomics field.