Will various interpretation strategies of the same ultrahigh-resolution mass spectrometry data tell different biogeochemical stories? A first assessment based on natural aquatic dissolved organic matter

Yuanbi Yi; Chen He; Katrin Klaproth; Julian Merder; Penghui Li; Yulin Qi; Pingqing Fu; Siliang Li; Thorsten Dittmar; Quan Shi; Ding He

doi:10.1002/lom3.10548

Will various interpretation strategies of the same ultrahigh-resolution mass spectrometry data tell different biogeochemical stories? A first assessment based on natural aquatic dissolved organic matter

Yuanbi Yi, Chen He, Katrin Klaproth, Julian Merder, Penghui Li, Yulin Qi, Pingqing Fu, Siliang Li, Thorsten Dittmar, Quan Shi^*, Ding He^*

^*Corresponding author for this work

Research output: Journal Publications and Reviews › RGC 21 - Publication in refereed journal › peer-review

42 Citations (Scopus)

Abstract

Fourier ion cyclotron resonance mass spectrometry (FT-ICR MS), one of the state-of-the-art ultrahigh-resolution techniques, is widely used in dissolved organic matter (DOM) research. As research that focuses on identifying DOM molecular fingerprints increases tremendously, there is and will be an urgent need to compare among studies. Different research groups usually use various types of data processing and interpretation strategies. It is critical to explore if different interpretation strategies will impact the comparability of FT-ICR MS results and their biogeochemical interpretations. To address this question, we selected DOM samples along a freshwater-to-marine continuum to be measured by negative-ion mode electrospray ionization FT-ICR MS. We interpreted the raw MS data using different strategies, compared the results and evaluated the interpretation strategy-induced effects on biogeochemical interpretations. Our results show that a total of 3827 formulas that account for 91.6% ± 4.1% (on average) of the total intensity are assigned in all interpretation strategies, while 6521 formulas for 8.4% ± 4.1% (on average) of the total intensity are not commonly assigned in all three interpretation strategies. We conclude that (i) different interpretation strategies do not significantly affect the geochemical stories relied on DOM molecular composition, and (ii) comparison based on intensity results gives more reliable results than the formular number alone. Moreover, we also provide raw and interpreted data (by our different strategies) for the community to compare their interpretation. We aim to call attention to the community for improving the comparability of FT-ICR MS results and facilitating the integration of DOM molecular composition among global studies. © 2023 Association for the Sciences of Limnology and Oceanography.

Original language	English
Pages (from-to)	320-333
Journal	Limnology and Oceanography: Methods
Volume	21
Issue number	6
Online published	10 May 2023
DOIs	https://doi.org/10.1002/lom3.10548
Publication status	Published - Jun 2023
Externally published	Yes

Funding

This work was supported by the National Science Foundation of China (42188102, 42222061, 42230509), the Research Grants Council of Hong Kong (ECS26300822), the National Key Research and Development Program of China (2018YFA0605800), Guangdong Basic and Applied Basic Research Foundation (2020A1515110194), Science and Technology Program of Guangzhou (202102021142), the open fund of State Key Laboratory of Satellite Ocean Environment Dynamics, Second Institute of Oceanography, MNR, the Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou) (SMSEGL20SC01), and funding support from the Center for Ocean Research in Hong Kong and Macau (CORE). CORE is a joint research centre for ocean research between QNLM and HKUST.

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Yi, Y., He, C., Klaproth, K., Merder, J., Li, P., Qi, Y., Fu, P., Li, S., Dittmar, T., Shi, Q., & He, D. (2023). Will various interpretation strategies of the same ultrahigh-resolution mass spectrometry data tell different biogeochemical stories? A first assessment based on natural aquatic dissolved organic matter. Limnology and Oceanography: Methods, 21(6), 320-333. https://doi.org/10.1002/lom3.10548

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title = "Will various interpretation strategies of the same ultrahigh-resolution mass spectrometry data tell different biogeochemical stories? A first assessment based on natural aquatic dissolved organic matter",

abstract = "Fourier ion cyclotron resonance mass spectrometry (FT-ICR MS), one of the state-of-the-art ultrahigh-resolution techniques, is widely used in dissolved organic matter (DOM) research. As research that focuses on identifying DOM molecular fingerprints increases tremendously, there is and will be an urgent need to compare among studies. Different research groups usually use various types of data processing and interpretation strategies. It is critical to explore if different interpretation strategies will impact the comparability of FT-ICR MS results and their biogeochemical interpretations. To address this question, we selected DOM samples along a freshwater-to-marine continuum to be measured by negative-ion mode electrospray ionization FT-ICR MS. We interpreted the raw MS data using different strategies, compared the results and evaluated the interpretation strategy-induced effects on biogeochemical interpretations. Our results show that a total of 3827 formulas that account for 91.6% ± 4.1% (on average) of the total intensity are assigned in all interpretation strategies, while 6521 formulas for 8.4% ± 4.1% (on average) of the total intensity are not commonly assigned in all three interpretation strategies. We conclude that (i) different interpretation strategies do not significantly affect the geochemical stories relied on DOM molecular composition, and (ii) comparison based on intensity results gives more reliable results than the formular number alone. Moreover, we also provide raw and interpreted data (by our different strategies) for the community to compare their interpretation. We aim to call attention to the community for improving the comparability of FT-ICR MS results and facilitating the integration of DOM molecular composition among global studies. {\textcopyright} 2023 Association for the Sciences of Limnology and Oceanography.",

author = "Yuanbi Yi and Chen He and Katrin Klaproth and Julian Merder and Penghui Li and Yulin Qi and Pingqing Fu and Siliang Li and Thorsten Dittmar and Quan Shi and Ding He",

year = "2023",

month = jun,

doi = "10.1002/lom3.10548",

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Yi, Y, He, C, Klaproth, K, Merder, J, Li, P, Qi, Y, Fu, P, Li, S, Dittmar, T, Shi, Q & He, D 2023, 'Will various interpretation strategies of the same ultrahigh-resolution mass spectrometry data tell different biogeochemical stories? A first assessment based on natural aquatic dissolved organic matter', Limnology and Oceanography: Methods, vol. 21, no. 6, pp. 320-333. https://doi.org/10.1002/lom3.10548

Will various interpretation strategies of the same ultrahigh-resolution mass spectrometry data tell different biogeochemical stories? A first assessment based on natural aquatic dissolved organic matter. / Yi, Yuanbi; He, Chen; Klaproth, Katrin et al.
In: Limnology and Oceanography: Methods, Vol. 21, No. 6, 06.2023, p. 320-333.

Research output: Journal Publications and Reviews › RGC 21 - Publication in refereed journal › peer-review

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T1 - Will various interpretation strategies of the same ultrahigh-resolution mass spectrometry data tell different biogeochemical stories? A first assessment based on natural aquatic dissolved organic matter

AU - Yi, Yuanbi

AU - He, Chen

AU - Klaproth, Katrin

AU - Merder, Julian

AU - Li, Penghui

AU - Qi, Yulin

AU - Fu, Pingqing

AU - Li, Siliang

AU - Dittmar, Thorsten

AU - Shi, Quan

AU - He, Ding

PY - 2023/6

Y1 - 2023/6

N2 - Fourier ion cyclotron resonance mass spectrometry (FT-ICR MS), one of the state-of-the-art ultrahigh-resolution techniques, is widely used in dissolved organic matter (DOM) research. As research that focuses on identifying DOM molecular fingerprints increases tremendously, there is and will be an urgent need to compare among studies. Different research groups usually use various types of data processing and interpretation strategies. It is critical to explore if different interpretation strategies will impact the comparability of FT-ICR MS results and their biogeochemical interpretations. To address this question, we selected DOM samples along a freshwater-to-marine continuum to be measured by negative-ion mode electrospray ionization FT-ICR MS. We interpreted the raw MS data using different strategies, compared the results and evaluated the interpretation strategy-induced effects on biogeochemical interpretations. Our results show that a total of 3827 formulas that account for 91.6% ± 4.1% (on average) of the total intensity are assigned in all interpretation strategies, while 6521 formulas for 8.4% ± 4.1% (on average) of the total intensity are not commonly assigned in all three interpretation strategies. We conclude that (i) different interpretation strategies do not significantly affect the geochemical stories relied on DOM molecular composition, and (ii) comparison based on intensity results gives more reliable results than the formular number alone. Moreover, we also provide raw and interpreted data (by our different strategies) for the community to compare their interpretation. We aim to call attention to the community for improving the comparability of FT-ICR MS results and facilitating the integration of DOM molecular composition among global studies. © 2023 Association for the Sciences of Limnology and Oceanography.

AB - Fourier ion cyclotron resonance mass spectrometry (FT-ICR MS), one of the state-of-the-art ultrahigh-resolution techniques, is widely used in dissolved organic matter (DOM) research. As research that focuses on identifying DOM molecular fingerprints increases tremendously, there is and will be an urgent need to compare among studies. Different research groups usually use various types of data processing and interpretation strategies. It is critical to explore if different interpretation strategies will impact the comparability of FT-ICR MS results and their biogeochemical interpretations. To address this question, we selected DOM samples along a freshwater-to-marine continuum to be measured by negative-ion mode electrospray ionization FT-ICR MS. We interpreted the raw MS data using different strategies, compared the results and evaluated the interpretation strategy-induced effects on biogeochemical interpretations. Our results show that a total of 3827 formulas that account for 91.6% ± 4.1% (on average) of the total intensity are assigned in all interpretation strategies, while 6521 formulas for 8.4% ± 4.1% (on average) of the total intensity are not commonly assigned in all three interpretation strategies. We conclude that (i) different interpretation strategies do not significantly affect the geochemical stories relied on DOM molecular composition, and (ii) comparison based on intensity results gives more reliable results than the formular number alone. Moreover, we also provide raw and interpreted data (by our different strategies) for the community to compare their interpretation. We aim to call attention to the community for improving the comparability of FT-ICR MS results and facilitating the integration of DOM molecular composition among global studies. © 2023 Association for the Sciences of Limnology and Oceanography.

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M3 - RGC 21 - Publication in refereed journal

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JO - Limnology and Oceanography: Methods

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Will various interpretation strategies of the same ultrahigh-resolution mass spectrometry data tell different biogeochemical stories? A first assessment based on natural aquatic dissolved organic matter

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