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Reactomics: Using mass spectrometry as a chemical reaction detector

View ORCID ProfileMiao Yu, Lauren Petrick
doi: https://doi.org/10.1101/855148
Miao Yu
1Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, United States
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Lauren Petrick
1Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, United States
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  • For correspondence: lauren.petrick@mssm.edu
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Abstract

Chemical reactions among small molecules enable untargeted metabolomics analysis, in which small molecules within tissue samples are identified through high-throughput assays. In standard mass spectrometry-based metabolomics, first significant small molecules are identified, then their biochemical relationships are probed to reveal biological fate (environmental studies) or biological impact (physiological response). However, we propose that biochemical relationships could be directly retrieved through untargeted high-resolution paired mass distance (PMD), which investigates chemical pairs in the samples without a priori knowledge of the identities of those participating compounds. We present the potential for this chemical reaction detector, or ‘reactomics’ approach, linking PMD from the mass spectrometer to biochemical reactions obtained via data mining of known small molecular metabolites/compounds and reaction databases. This approach encompasses both quantitative and qualitative analysis of reaction by mass spectrometry, and its potential applications include PMD network analysis, source appointment of unknown compounds, and biomarker reaction discovery instead of compound discovery. Such applications may promote novel biological discoveries that are not currently possible with classical chemical analysis.

Significance Statement Chemical reactions can describe the relationships among molecules. If we could directly measure chemical reactions, the identification of unknown molecules in the living system could be bypassed in metabolomics studies. In this work we propose “reactomics”, a concept that uses a paired mass distances (PMD) profile among mass spectrometry measured peaks to perform quantitatively and qualitatively analysis of reactions in the samples. For example, peaks involved in a PMD 15.995 Da imply an oxidation process, and changes in levels of these reactions can be used to investigate living processes. We developed the pmd package to perform reactomics analysis including screening unknown metabolites linked with exposure, source appointment of unknown peaks, and biomarker reaction discovery for lung cancer.

Footnotes

  • add Significance Statement

  • https://yufree.github.io/pmd/

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission.
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Posted December 24, 2019.
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Reactomics: Using mass spectrometry as a chemical reaction detector
Miao Yu, Lauren Petrick
bioRxiv 855148; doi: https://doi.org/10.1101/855148
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Reactomics: Using mass spectrometry as a chemical reaction detector
Miao Yu, Lauren Petrick
bioRxiv 855148; doi: https://doi.org/10.1101/855148

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