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. 2022 Aug 8;13:4619. doi: 10.1038/s41467-022-32016-6

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© The Author(s) 2022

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

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Fig. 1 — a Native metabolomics setup. A crude extract is separated by µ-flow UHPLC. The pH is adjusted after chromatography with ammonium acetate to native-like conditions via the make-up pump. Orthogonally, the protein of interest is infused, and the resulting protein-binder complexes are measured by MS. The procedure is repeated as a metabolomics run (high-resolution UHPLC-MS/MS acquisition without protein infusion). For the data analysis (b) the Δ m/z and retention time of the native MS run are correlated with m/z values and retention time of the metabolomics (LC-MS/MS) run and subsequently visualized using molecular networking and retention time pairing that links the observed mass differences of the protein in the native state vs bound states with the parent mass of MS/MS spectra of the small molecule.