LC-MS-Based Targeted Metabolomics for FACS-Purified Rare Cells

Schönberger, Katharina; Mitterer, Michael; Glaser, Katharina; Stecher, Manuel; Hobitz, Sebastian; Schain-Zota, Dominik; Schuldes, Konrad; Lämmermann, Tim; Rambold, Angelika; Cabezas-Wallscheid, Nina; Büscher, Jörg Martin

doi:10.1021/acs.analchem.2c04396

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LC-MS-Based Targeted Metabolomics for FACS-Purified Rare Cells

MPS-Authors

Schönberger, Katharina
Department of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, Max Planck Society;

Mitterer, Michael
Max Planck Institute of Immunobiology and Epigenetics, Max Planck Society;

Glaser, Katharina
Max Planck Institute of Immunobiology and Epigenetics, Max Planck Society;

Stecher, Manuel
Max Planck Institute of Immunobiology and Epigenetics, Max Planck Society;

Hobitz, Sebastian
Max Planck Institute of Immunobiology and Epigenetics, Max Planck Society;

Schain-Zota, Dominik
Max Planck Institute of Immunobiology and Epigenetics, Max Planck Society;

Schuldes, Konrad
Max Planck Institute of Immunobiology and Epigenetics, Max Planck Society;

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Lämmermann, Tim
Max Planck Institute of Immunobiology and Epigenetics, Max Planck Society;

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Rambold, Angelika
Department of Developmental Immunobiology, Max Planck Institute of Immunobiology and Epigenetics, Max Planck Society;

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Cabezas-Wallscheid, Nina
Department of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, Max Planck Society;

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Büscher, Jörg Martin
Max Planck Institute of Immunobiology and Epigenetics, Max Planck Society;

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https://pubs.acs.org/doi/10.1021/acs.analchem.2c04396
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Citation

Schönberger, K., Mitterer, M., Glaser, K., Stecher, M., Hobitz, S., Schain-Zota, D., et al. (2023). LC-MS-Based Targeted Metabolomics for FACS-Purified Rare Cells. Analytical Chemistry, 95, 4325-4334. doi:10.1021/acs.analchem.2c04396.

Cite as: https://hdl.handle.net/21.11116/0000-000D-0DBE-0

Abstract

Metabolism plays a fundamental role in regulating cellular functions and fate decisions. Liquid chromatography-mass spectrometry (LC-MS)-based targeted metabolomic approaches provide high-resolution insights into the metabolic state of a cell. However, the typical sample size is in the order of 10⁵-10⁷ cells and thus not compatible with rare cell populations, especially in the case of a prior flow cytometry-based purification step. Here, we present a comprehensively optimized protocol for targeted metabolomics on rare cell types, such as hematopoietic stem cells and mast cells. Only 5000 cells per sample are required to detect up to 80 metabolites above background. The use of regular-flow liquid chromatography allows for robust data acquisition, and the omission of drying or chemical derivatization avoids potential sources of error. Cell-type-specific differences are preserved while the addition of internal standards, generation of relevant background control samples, and targeted metabolite with quantifiers and qualifiers ensure high data quality. This protocol could help numerous studies to gain thorough insights into cellular metabolic profiles and simultaneously reduce the number of laboratory animals and the time-consuming and costly experiments associated with rare cell-type purification.