Machine Learning in Metabolomics: Unlocking the Future of Data Analysis

A special issue of Metabolites (ISSN 2218-1989). This special issue belongs to the section "Bioinformatics and Data Analysis".

Deadline for manuscript submissions: 20 August 2025 | Viewed by 1157

Special Issue Editors


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Core Facilities, Medical University of Vienna, Spitalgasse 23, 1090 Vienna, Austria
Interests: metabolomics; mass spectrometry; single-cell; maternal immune activation; CSF
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Guest Editor
Institute for Experiential AI, Northeastern University, Boston, MA 02115, USA
Interests: mass spectrometry; proteomics; metabolomics; multi-omics integration; bioinformatics
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Machine learning (ML) is transforming the landscape of metabolomics, building on its revolutionary impact in precision medicine and other omics fields. With its ability to identify patterns and relationships in complex datasets without explicit programming, ML is driving advancements in biomarker discovery, disease and patient cohort classification, chemical composition analysis, and more.

A key breakthrough lies in the application of ML to compound annotation, where it has dramatically improved the identification of unknown small molecules. By refining fingerprinting techniques and introducing innovative algorithms, researchers are expanding the capabilities of untargeted metabolomics, uncovering new insights into the vast, unexplored universe of small molecules.

Another pivotal area is biomarker discovery. ML algorithms excel at processing large datasets, identifying specific metabolic signatures that indicate diseases. These discoveries hold enormous promise for precision medicine, enabling treatments tailored to an individual’s unique metabolic profile.

Moreover, ML is a cornerstone in multiomics integration—combining data from genomics, transcriptomics, proteomics, and metabolomics. This holistic approach provides a comprehensive view of biological systems, with ML enhancing both data interpretation and analytical precision.

However, despite significant advancements in analytical platforms and software, challenges remain in data processing and integration. These hurdles underscore the importance of developing novel ML methods tailored to the unique demands of metabolomics. As the field evolves, such innovations are critical for addressing data complexity, advancing our understanding of biological systems, and driving innovative personalized medicine solutions.

Dr. Boryana Petrova
Dr. Arzu Tugce Guler
Guest Editors

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Keywords

  • metabolomics
  • MS imaging
  • machine learning
  • AI
  • multi-omics
  • integration
  • biomarker discovery
  • compound annotation
  • spectra interpretation

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Published Papers (1 paper)

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Research

12 pages, 740 KiB  
Article
Deep Learning-Based Molecular Fingerprint Prediction for Metabolite Annotation
by Hoi Yan Katharine Chau, Xinran Zhang and Habtom W. Ressom
Metabolites 2025, 15(2), 132; https://doi.org/10.3390/metabo15020132 - 14 Feb 2025
Viewed by 897
Abstract
Background/Objectives: Liquid chromatography coupled with mass spectrometry (LC-MS) is a commonly used platform for many metabolomics studies. However, metabolite annotation has been a major bottleneck in these studies in part due to the limited publicly available spectral libraries, which consist of tandem mass [...] Read more.
Background/Objectives: Liquid chromatography coupled with mass spectrometry (LC-MS) is a commonly used platform for many metabolomics studies. However, metabolite annotation has been a major bottleneck in these studies in part due to the limited publicly available spectral libraries, which consist of tandem mass spectrometry (MS/MS) data acquired from just a fraction of known compounds. Application of deep learning methods is increasingly reported as an alternative to spectral matching due to their ability to map complex relationships between molecular fingerprints and mass spectrometric measurements. The objectives of this study are to investigate deep learning methods for molecular fingerprint based on MS/MS spectra and to rank putative metabolite IDs according to similarity of their known and predicted molecular fingerprints. Methods: We trained three types of deep learning methods to model the relationships between molecular fingerprints and MS/MS spectra. Prior to training, various data processing steps, including scaling, binning, and filtering, were performed on MS/MS spectra obtained from National Institute of Standards and Technology (NIST), MassBank of North America (MoNA), and Human Metabolome Database (HMDB). Furthermore, selection of the most relevant m/z bins and molecular fingerprints was conducted. The trained deep learning models were evaluated on ranking putative metabolite IDs obtained from a compound database for the challenges in Critical Assessment of Small Molecule Identification (CASMI) 2016, CASMI 2017, and CASMI 2022 benchmark datasets. Results: Feature selection methods effectively reduced redundant molecular and spectral features prior to model training. Deep learning methods trained with the truncated features have shown comparable performances against CSI:FingerID on ranking putative metabolite IDs. Conclusion: The results demonstrate a promising potential of deep learning methods for metabolite annotation. Full article
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