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Software tools, databases and resources in metabolomics: updates from 2018 to 2019

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Abstract

Metabolomics has evolved as a discipline from a discovery and functional genomics tool, and is now a cornerstone in the era of big data-driven precision medicine. Sample preparation strategies and analytical technologies have seen enormous growth, and keeping pace with data analytics is challenging, to say the least. This review introduces and briefly presents around 100 metabolomics software resources, tools, databases, and other utilities that have surfaced or have improved in 2019. Table 1 provides the computational dependencies of the tools, categorizes the resources based on utility and ease of use, and provides hyperlinks to webpages where the tools can be downloaded or used. This review intends to keep the community of metabolomics researchers up to date with all the software tools, resources, and databases developed in 2019, in one place.

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Abbreviations

CE:

Capillary electrophoresis

DB:

Database

GC:

Gas chromatography

GUI:

Graphical user interface

HRMS:

High-resolution mass spectrometry

HR MS/MS:

High-resolution tandem mass spectrometry

Q-ToF:

Hybrid quadrupole orthogonal time-of-flight

IMS:

Ion-mobility mass spectrometry

KEGG:

Kyoto encyclopedia of genes and genomes

LC:

Liquid chromatography

MSI:

Mass spectrometry imaging

MS:

Mass spectrometry

m/z :

Mass-to-charge

NMR:

Nuclear magnetic resonance

QC:

Quality control

R:

R-statistical programming

MS/MS:

Tandem mass spectrometry

UPLC-TOF:

Ultra performance liquid chromatography time-of-flight mass spectrometry

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Acknowledgements

We acknowledge the extensive efforts of the informatics and computational resource developers who help drive the field forward with their codes, packages, tools, and resources and enable biologists and analytical chemists to keep pace with the volume and complexity of the metabolomics data generated. We apologize to those developers and creators whose tools and resources have been missed in this review, either inadvertently or due to space limitations.

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Authors and Affiliations

  1. Institute of Biological, Environmental, and Rural Studies, Aberystwyth University, Ceredigion, Wales, SY23 3DA, UK

    Keiron O’Shea

  2. Center for Precision Medicine, Department of Internal Medicine, Section of Molecular Medicine, Wake Forest School of Medicine, Medical Center Boulevard, Winston-Salem, NC, 27157, USA

    Biswapriya B. Misra

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  1. Keiron O’Shea
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Contributions

BBM conceived and designed the review manuscript. Both KOS and BBM conducted literature search of the tools, KOS prepared the figure, BBM prepared the tables, and both KOS and BBM wrote the manuscript. Both authors read and approved the final manuscript.

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Correspondence to Biswapriya B. Misra.

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O’Shea, K., Misra, B.B. Software tools, databases and resources in metabolomics: updates from 2018 to 2019. Metabolomics 16, 36 (2020). https://doi.org/10.1007/s11306-020-01657-3

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