Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2025 Nov 15;21(6):171.
doi: 10.1007/s11306-025-02360-x.

Analytical practices, use and needs of standard and reference materials in the German-speaking metabolomics community: results of an online survey

Carsten Jaeger #  1 , Jutta Lintelmann #  2 , Raimo Franke #  3 , Anna Artati  2 , Alexander Cecil  2 , Frank Broda  4 , Frank Klawonn  3   5 , Alexander Erban  6 , Joachim Kopka  6 , Beate Fuchs  7 , Ulf Sommer  8 , Meina Neumann-Schaal  9 , Gavin O'Connor  10 ; Standards and Reference Materials Working Group of the Deutsche Gesellschaft für Metabolomforschung (DGMet)
Affiliations

Analytical practices, use and needs of standard and reference materials in the German-speaking metabolomics community: results of an online survey

Carsten Jaeger et al. Metabolomics. .

Abstract

Introduction: Since the early 2000s, metabolomics has grown rapidly, becoming integral to fields like life sciences, health, and environmental research. This expansion has led to the formation of national and international societies, such as Germany's DGMet, to tackle emerging challenges. One of DGMet's goals is to improve measurement quality by assessing community needs for harmonization and standardization. A recent survey within the German-speaking community aimed to identify current practices and gaps in the use of chemical standards and reference materials, to guide future standardization efforts and collaborative initiatives.

Methods: An online survey was conducted between June 2023 and April 2024. The survey consisted of 38 key questions and was open to research institutions from Germany, Austria, and Switzerland.

Results: The survey was accessed by 68 laboratories, with 23 institutes providing complete or partial responses (34% response rate), which is comparable to rates reported in similar surveys within the metabolomics and lipidomics communities. Respondents were mainly experienced researchers from Germany, focusing mainly on health-related ("red") metabolomics, as indicated by 78% of the respondents, followed by microbial ("grey", 48%) and plant ("green", 39%) metabolomics (multiple answers possible). The use of targeted methods was reported more frequently (91%) than that of non-targeted methods (78%), whereas metabolite fractions studied were equally split between polar, midpolar and lipid fractions (83% each). Human (74%), mouse (61%) and Arabidopsis (30%) were the most frequently studied organisms. Most participants used synthetic chemical standards for instrument qualification (83%), calibration (78%), and metabolite identification (74%), while matrix reference materials were mainly applied for quality control (52%) and method validation (44%). There was a strong demand for more standards, especially for metabolite identification and quantification, with cost being a major barrier, particularly for isotopically labelled standards and certified reference materials.

Conclusions: Valuable insights into the use of standards and reference materials within the German-speaking metabolomics community were obtained. Moving forward, the community should address critical gaps in metabolomics standardization. To achieve this, it must share its knowledge, articulate its needs clearly, and actively engage in joint efforts with national metrology institutes and international standardization initiatives.

Keywords: Harmonization; Metabolomics; QA/QC; Reference materials; Standardization.

PubMed Disclaimer

Conflict of interest statement

Declarations. Competing interests: The authors declare no competing interests.

Figures

Fig. 1
Fig. 1
Focus and goals of the DGMet survey. The online survey consisted of 38 questions addressing the use and need of standards and reference materials in metabolomics. The number of visitors and active participants is indicated
Fig. 2
Fig. 2
Metabolomics strategies used (a), and metabolite fractions investigated (b) by the respondents. Multiple answers possible
Fig. 3
Fig. 3
Research areas in which the respondents are active (a) and organisms they study (b). Multiple answers possible. 100% = 23 participants
Fig. 4
Fig. 4
Analytical platforms (a), LC-MS instrument types (b) and chromatography systems (c) used by the respondents. Multiple answers possible. For GC-MS instrument types and chromatography systems, see Supplementary Material SM2, p. 23
Fig. 5
Fig. 5
Use of synthetic chemical standards (left) and matrix reference materials (right) in metabolomics protocols. Participants were asked to select all options that applied to their lab’s use of chemical standards and reference materials, respectively. Multiple answers possible, 100% = 23 participants
Fig. 6
Fig. 6
Perceived lack of chemical standards and reference materials. Participants were asked if they missed any standards, standard mixtures or reference materials that could support their metabolomics tools (a). Needs should be rated from 1 (no need) to 5 (strong need), multiple answers possible. In addition, they were asked to indicate the type of new standards or reference materials that are needed (b). RGTM, research grade testing material. 100% = 23 participants, % missing from 100: no answer
See this image and copyright information in PMC

References

    1. Alseekh, S., Aharoni, A., Brotman, Y., Contrepois, K., D’Auria, J., Ewald, J., Ewald, C., Fraser, J., Giavalisco, P. D., Hall, P., Heinemann, R. D., Link, M., Luo, H., Neumann, J., Nielsen, S., Perez, J., de Souza, L., Saito, K., Sauer, U., Schroeder, F. C., ..., Fernie, A. R. (2021). Mass spectrometry-based metabolomics: A guide for annotation, quantification and best reporting practices. Nature Methods,18(7), 747–756. 10.1038/s41592-021-01197-1
    1. Bowden, J. A., Ulmer, C. Z., Jones, C. M., Koelmel, J. P., & Yost, R. A. (2018). NIST lipidomics workflow questionnaire: An assessment of community-wide methodologies and perspectives. Metabolomics,14(5), 53. 10.1007/s11306-018-1340-1 - DOI - PMC - PubMed
    1. Dunn, W. B., Broadhurst, D. I., Edison, A., Guillou, C., Viant, M. R., Bearden, D. W., & Beger, R. D. (2017). Quality assurance and quality control processes: Summary of a metabolomics community questionnaire. Metabolomics,13(5), 50. 10.1007/s11306-017-1188-9 - DOI - PMC - PubMed
    1. Dunn, W. B., Erban, A., Weber, R. J. M., Creek, D. J., Brown, M., Breitling, R., Hankemeier, T., Goodacre, R., Neumann, S., Kopka, J., & Viant, M. R. (2013). Mass appeal: Metabolite identification in mass spectrometry-focused untargeted metabolomics. Metabolomics,9(1), 44–66. 10.1007/s11306-012-0434-4 - DOI
    1. Evans, A. M., O’Donovan, C., Playdon, M., Beecher, C., Beger, R. D., Bowden, J. A., Broadhurst, D., Clish, C. B., Dasari, S., Dunn, W. B., Griffin, J. L., Hartung, T., Hsu, P.-C., Huan, T., Jans, J., Jones, C. M., Kachman, M., Kleensang, A., Lewis, M. R., …, Metabolomics Quality Assurance, Quality Control Consortium (mQACC). (2020). Dissemination and Analysis of the Quality Assurance (QA) and Quality Control (QC) practices of LC-MS based untargeted metabolomics practitioners. Metabolomics,16(10), 113. 10.1007/s11306-020-01728-5

LinkOut - more resources