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Ultra-high-performance liquid chromatography high-resolution mass spectrometry variants for metabolomics research


Ultra-high-performance liquid chromatography high-resolution mass spectrometry (UHPLC–HRMS) variants currently represent the best tools to tackle the challenges of complexity and lack of comprehensive coverage of the metabolome. UHPLC offers flexible and efficient separation coupled with high-sensitivity detection via HRMS, allowing for the detection and identification of a broad range of metabolites. Here we discuss current common strategies for UHPLC–HRMS-based metabolomics, with a focus on expanding metabolome coverage.

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Fig. 1: Comparison of data generated by analyzing the same extract from Arabidopsis thaliana leaves in two different systems.
Fig. 2: The relationship between resolution and cycle time in an ion trap-based mass spectrometer.
Fig. 3: Diagram of a hypothetical ion mobility mass spectrometer with different types of ion mobility cells.
Fig. 4: Conceptual differences characterizing the process and results obtained from different tandem mass fragmentation strategies.
Fig. 5: Strategies used to increase the coverage of metabolome analyses.


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A.R.F. and S.A. are supported by the European Union’s Horizon 2020 research and innovation program, project PlantaSYST (SGA-CSA 739582 under FPA 664620). L.P.d.S. is supported by the European Union’s Horizon 2020 research and innovation program, project INCREASE (GA 862862).

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L.P.d.S. and A.R.F. planned and conceptualized the manuscript and wrote the first draft. L.P.d.S. created the figures. F.S. created the figures and prepared Box 1. All authors proofread, corrected and approved the final version.

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Correspondence to Leonardo Perez de Souza or Alisdair R. Fernie.

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Peer review information Nature Methods thanks Warwick Dunn, Albert Fornace and the other, anonymous, reviewer(s) for their contribution to the peer review of this work. Allison Doerr was the primary editor on this article and managed its editorial process and peer review in collaboration with the rest of the editorial team.

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Perez de Souza, L., Alseekh, S., Scossa, F. et al. Ultra-high-performance liquid chromatography high-resolution mass spectrometry variants for metabolomics research. Nat Methods (2021).

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