Development and comparison of formula assignment algorithms for ultrahigh-resolution mass spectra of natural organic matter

Fu, Qing‐Long; Fujii, Manabu; Riedel, Thomas

doi:10.1016/j.aca.2020.05.048

Cited by 133 publications

(100 citation statements)

References 63 publications

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“…3). While there is a discrepancy between these approaches, this is due to inefficient formula assignment of FTICR-MS data and will vary from dataset to dataset, and with improved formula assignment tools 60 . Detailed differences between these dendrograms are explored in the Supplement, but each resulted in different metabolite clustering patterns that help provide deeper insight into ecosystem assembly.…”

Section: Resultsmentioning

confidence: 99%

Using metacommunity ecology to understand environmental metabolomes

et al. 2020

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Environmental metabolomes are fundamentally coupled to microbially-linked biogeochemical processes within ecosystems. However, significant gaps exist in our understanding of their spatiotemporal organization, limiting our ability to uncover transferrable principles and predict ecosystem function. We propose that a theoretical paradigm, which integrates concepts from metacommunity ecology, is necessary to reveal underlying mechanisms governing metabolomes. We call this synthesis between ecology and metabolomics ‘meta-metabolome ecology’ and demonstrate its utility using a mass spectrometry dataset. We developed three relational metabolite dendrograms using molecular properties and putative biochemical transformations and performed ecological null modeling. Based upon null modeling results, we show that stochastic processes drove molecular properties while biochemical transformations were structured deterministically. We further suggest that potentially biochemically active metabolites were more deterministically assembled than less active metabolites. Understanding variation in the influences of stochasticity and determinism provides a way to focus attention on which meta-metabolomes and which parts of meta-metabolomes are most likely to be important to consider in mechanistic models. We propose that this paradigm will allow researchers to study the connections between ecological systems and their molecular processes in previously inaccessible detail.

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Section: Resultsmentioning

confidence: 99%

Using metacommunity ecology to understand environmental metabolomes

et al. 2020

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“…All these criteria have been implemented in formula assignment software packages, and other techniques and software packages, such as spectral accuracy and MassWorks, have also been employed to improve the identification of small organic compounds using MS 1,12–17 . However, there is still no standard approach to data processing.…”

Section: Resultsmentioning

confidence: 99%

“…However, there is still no standard approach to data processing. In particular, the formula assignment of a large number of peaks remains a challenging but necessary step in the interpretation of ultrahigh‐resolution MS data 17 . Therefore, one purpose of this study is to provide a method that definitively determines the chemical formulae of unknown constituents in TCMs.…”

Section: Resultsmentioning

confidence: 99%

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A simplified strategy for molecular formula determination of chemical constituents in traditional Chinese medicines based on accurate mass, A + 1 and A + 2 isotopic peaks using Fourier transform ion cyclotron resonance mass spectrometry

Zhang

Wang

et al. 2020

Rapid Comm Mass Spectrometry

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Rationale Recently, isotopic fine structures derived from Fourier transform ion cyclotron resonance mass spectrometry have been used to determine the molecular formula for unknown compounds in many complex systems. However, a simplified strategy for molecular formula determination of chemical constituents in traditional Chinese medicines (TCMs) based on accurate mass, A + 1 and A + 2 isotopic peaks is necessary. Methods Salviae miltiorrhizae was selected as a representative species. First, the chemical constituents were chromatographically separated and their accurate masses were obtained. The A + 1 and A + 2 isotopic peaks of all chemical constituents were then also acquired. Finally, the chemical formulae of the chemical constituents were determined. Results In the sample of Salviae miltiorrhizae, the formulae of 38 CHO‐containing chemical constituents were quickly determined, and all chemical constituents were identified using their tandem mass spectrometric data. Moreover, the method was validated by comparison of the A + 1 and A + 2 isotopic peaks, their fragmentation patterns and the retention times of six selected standard substances. Conclusions The results demonstrate that the described strategy performs well for molecular formula determination of chemical constituents in TCMs. This also indicates that this method will be meaningful for the structural identification of chemical constituents of TCMs.

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“…Due to the extremely diverse nature of NOM, it was challenging to elucidate their chemical composition at the molecular level until the employment of ultrahighresolution mass spectrometry (UHR-MS), particularly the Fourier-transform ion cyclotron resonance mass spectrometry (FTICR-MS) 4,5 . Since its first application to NOM study 6 , FTICR-MS has been widely adopted to characterize the complexity of NOM in the last two decades through the development of automated molecular formula assignment methods such as the inhouse code from Kujawinski and Behn 7 , MassCal 8 , Formularity software 9 , MFAssignR 10 , ICBM-OCEAN 11 , and the TRFu code 12 . Moreover, FTICR-MS with stable isotope labeling has initiated the new possibilities of quantifying the number of labile H and O and structural information such as ether O atoms, carboxyl and hydroxyl functional groups in individual molecules of NOM 1,[13][14][15] , further refining compound aromaticity 16 , and relation of NOM molecular structures with optical property 17 .…”

Section: Introductionmentioning

confidence: 99%

A New Formula Assignment Algorithm for the Deuterium Labeled Ultrahigh-Resolution Mass Spectrometry: Implications to the Formation Mechanism of Halogenated Disinfection Byproducts

Fujii

Watanabe

et al. 2021

Preprint

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The ultrahigh-resolution mass spectrometry (UHR-MS) coupled with isotope labeling is of increasing attentions in elucidating the transform mechanisms of dissolved organic matter (DOM).However, there is a paucity of automated formula assignment algorithm applicable to halogenated disinfection byproducts (Xn-DBPs), particurally for iodinated organic compounds, and deuterated DOM . Herein, for the first time, we have developed a novel formula assignment algorithm based on deuterium-labeled UHR-MS, namely FTMSDeu, and the algorithm was applied to determine precursor molecules of Xn-DBPs and evaluate the relative contribution of electrophilic addition and electrophilic substitution reactions in Xn-DBPs formation according to the hydrogen/deuterium exchange of DOM molecules. Furthermore, tandem mass spectrometry with homologous-based network analysis was employed to validate the formula assignment accuracy (41%) of FTMSDeu for iodinated disinfection byproducts (In-DBPs). And the remaining In-DBPs compounds were assigned with the empirical rule of minimum number of non-oxygen heteratoms.The electrophilic substitution accounted for 82%-98%, 71%-89%, and 43%-45% of Xn-DBPs formation for Xn-DBPs containing chlorine, bromine, and iodine, respectively, manifesting the dominant role of electrophilic substitution in chlorine disinfection under conditions of low bromine and iodine concentrations. The absence of presumed Xn-DBPs precursors in some treatments in this study also suggests that Xn-DBPs formation include secondary reactions (e.g., oxidation, hydrolysis) in addition to electrophilic addition and/or substitution of halogens. These findings highlight the significance of isotopically labeled UHR-MS techniques in revealing the transformation of DOM in natural and engineered systems.

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Development and comparison of formula assignment algorithms for ultrahigh-resolution mass spectra of natural organic matter

Cited by 133 publications

References 63 publications

Using metacommunity ecology to understand environmental metabolomes

Using metacommunity ecology to understand environmental metabolomes

A simplified strategy for molecular formula determination of chemical constituents in traditional Chinese medicines based on accurate mass, A + 1 and A + 2 isotopic peaks using Fourier transform ion cyclotron resonance mass spectrometry

A New Formula Assignment Algorithm for the Deuterium Labeled Ultrahigh-Resolution Mass Spectrometry: Implications to the Formation Mechanism of Halogenated Disinfection Byproducts

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