Annotation: Metabolomics atlases are emerging as powerful resources for understanding biological systems across tissues, developmental stages, diseases, and environmental or dietary interventions. Their successful construction requires close collaboration between biology, analytical chemistry, and bioinformatics laboratories, integrating experimental design, sample collection, advanced mass spectrometry workflows, data processing, and computational analysis [1]. This lecture will introduce the concept of metabolomics atlases and highlight several recently developed resources, including the Circadian Ontogenetic Metabolomics Atlas (COMA) [2], the LCNEC Metabolomics Atlas of Lung Neuroendocrine Carcinoma [3], the GTTAtlas [4], the MetaboAtlas21 [1], and the ongoing MiLiMA project focused on microbiome- and diet-modulating interventions. Particular emphasis will be placed on analytical chemistry challenges, including standardization of sample preparation, multiplatform LC–MS analysis, metabolite annotation, data harmonization, and long-term reproducibility. The presentation will further discuss how interdisciplinary collaboration enables the generation of robust, reproducible, and biologically meaningful atlas-scale metabolomics datasets.

Contact at IPHYS: Tomas Cajka (tomas.cajka@fgu.cas.cz)

References:

[1] S. Rakusanova, O. Fiehn, T. Cajka: Toward building mass spectrometry-based metabolomics and lipidomics atlases for biological and clinical research. TrAC Trends in Analytical Chemistry 158 (2023) 116825. (doi: 10.1016/j.trac.2022.116825)

[2] L. Rudl Kulhava, P. Houdek, M. Novakova, J. Hricko, M. Paucova, O. Kuda, M. Sladek, O. Fiehn, A. Sumova, T. Cajka: Circadian Ontogenetic Metabolomics Atlas: An interactive resource with insights from rat plasma, tissues, and feces. Cellular and Molecular Life Sciences 82 (2025) 264. (doi: 10.1007/s00018-025-05783-w)

[3] I. Tietzova, J. Hricko, R.C. Rancourt, M.A. Schneider, M. Allgäuer, T. Cajka: A metabolomics and lipidomics atlas of pulmonary large cell neuroendocrine carcinoma. Biomedicine & Pharmacotherapy 198 (2026) 119327. (doi: 10.1016/j.biopha.2026.119327)

[4] M. Lopes, K. Brejchova, M. Riecan, M. Novakova, M. Rossmeisl, T. Cajka, O. Kuda: Metabolomics atlas of oral 13C-glucose tolerance test in mice. Cell Reports 37 (2021) 109833. (doi: 10.1016/j.celrep.2021.109833)