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Study Design

Chapter 0 — Your Guide to a Successful Metabolomic Study

What is This Guide?

Studies document the connection between metabolites and an array of disease states, making the comprehensive analysis of metabolomics data important for research in both diagnostics and therapeutics.1,2 In particular, research over the past decade increasingly demonstrates the impact of cellular-level analysis on characterizing the pathogenesis of various disorders.3,4 As such, incorporating metabolomics into research workflows can offer insights for research indications throughout the life sciences, including atherosclerosis, Alzheimer’s disease, cardiovascular diseases, diabetes, age-related macular degeneration, infertility, osteoporosis, multiple sclerosis, Niemann-Pick disease type C, Parkinson’s disease, and cancers.5,6

Who Should Read This?

Recent growth in omics-driven studies has created opportunities for principal investigators and laboratory directors to explore the benefits of leveraging metabolomics assays and phenotypic data. As metabolomics studies become more accessible to a wider range of study objectives, this guide should be beneficial to individuals across the life sciences continuum, from seasoned metabolomics researchers to geneticists, pharmacologists, to cancer researchers. The growing importance of metabolomics to independent research and multi-omics outcomes makes a fundamental understanding of how to develop a successful metabolomics study important for all analytical scientists.

What will you learn?

Your Guide to a Successful Metabolomic Study will equip researchers to leverage metabolomics in their labs and workflows for a variety of indications throughout the life sciences. In particular, we will cover how to select metabolites, targeted versus untargeted analysis, appropriate technology and instrumentation, study design, control versus variant analysis, sample types, sample preparation, and effective analysis of metabolomics results.

Chapters at a Glance

  1. Top 8 Questions to Ask Your Metabolomics Provider: The most important questions you need to ask to find the right vendor and complete your metabolomics study with confidence.
  2. Metabolomics Study Workflow: A discussion of key considerations for study design, sample preparation, and data analysis and interpretation.
  3. Building Your Metabolomic Study: A deep dive into designing your study — including defining your aims, study power, controls, and study size — to ensure your protocol delivers high-quality results for drawing actionable insights.
  4. Sample Types for Metabolomics: A closer look at the most common types of samples used in metabolomic studies and collection, transportation, and storage considerations and best practices for each.
  5. Metabolomics Sample Preparation, Storage, and Transportation: Best practices for sample collection, shipping, and preparation to preserve sample integrity and reduce the risk of data variability, instrument interference, and metabolite degradation.
  6. Metabolomics Study Analysis, Interpretation, and Insights: An in-depth look at the data analysis and interpretation tools and support you’ll have access to when performing your metabolomics study with Metabolon.
  7. The End of This Guide, The Beginning of Your Own Metabolomics Studies: Here’s a quick review of the main points of discussion in each chapter that you can use to find what you need quickly.

Implications of Metabolites for Research

Given the efficacy of metabolomics in successful disease state research, companies are increasingly applying metabolite tooling in their studies. Metabolon offers several methodologies to support metabolomic analysis for research endeavors throughout the life sciences, including targeted panels and assays that cover more than 1,000 metabolites and lipids across a wide range of biochemical classes, metabolic pathways, and physiological processes, and these can be customized to best fit any application.

Ready to see what new insights metabolomics can help your research reveal? Contact us today to learn more.

metabolomics study design success guide

Continue to Chapter 1 - Top 8 Questions to Ask Your Metabolomics Provider

In Chapter 1 of this guide, we arm you with the most important questions you need to ask to select the right vendor and complete your metabolomics study with confidence.

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References

  1. Surendran P, Stewart ID, Au Yeung VPW, et al. Rare and common genetic determinants of metabolic individuality and their effects on human health. Nat Med 28, 2321–2332 (2022). https://doi.org/10.1038/s41591-022-02046-0
  2. Lotta LA, Pietzner M, Stewart ID, et al. A cross-platform approach identifies genetic regulators of human metabolism and health. Nat Genet 53, 54–64 (2021). https://doi.org/10.1038/s41588-020-00751-5
  3. Biringer RG. The Role of Eicosanoids in Alzheimer’s Disease. Int J Environ Res Public Health. 2019 Jul 18;16(14):2560. doi: 10.3390/ijerph16142560. PMID: 31323750; PMCID: PMC6678666.
  4. Solito E, Sastre M. Microglia function in Alzheimer’s disease. Front. Pharmacol. 2012;3 doi: 10.3389/fphar.2012.00014.
  5. Samadi A, Sabuncuoglu S, Samadi M, Isikhan SY, Chirumbolo S, Peana M, Lay I, Yalcinkaya A, Bjørklund G. A Comprehensive Review on Oxysterols and Related Diseases. Curr Med Chem. 2021; 28(1): 110-136. doi: 10.2174/0929867327666200316142659.
  6. de Freitas FA, Levy D, Reichert CO, Cunha-Neto E, Kalil J, Bydlowski SP. Effects of Oxysterols on Immune Cells and Related Diseases. Cells. 2022; 11(8): 1251. https://doi.org/10.3390/cells11081251

Table of Contents

Chapter 0 — Your Guide to a Successful Metabolomic Study

Chapter 1 — Top 8 Questions to Ask Your Metabolomics Provider

Chapter 2 — Metabolomics Study Workflow

Chapter 3 — Building Your Metabolomic Study

Chapter 4 — Sample Types for Metabolomics

Chapter 5 — Metabolomics Sample Preparation, Storage, and Transportation

Chapter 6 — Metabolomics Study Analysis, Interpretation, and Insights

Chapter 7 — The End of This Guide, The Beginning of Your Own Metabolomics Studies

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References

1. Zgoda-Pols, J.R., et al., Metabolomics analysis reveals elevation of 3-indoxyl sulfate in plasma and brain during chemically-induced acute kidney injury in mice: investigation of nicotinic acid receptor agonists. Toxicol Appl Pharmacol, 2011. 255(1): p. 48-56.

2. Bryant, J.A., et al., The impact of an oral purified microbiome therapeutic on the gastrointestinal microbiome. Nat Med, 2026. 32(1): p. 186-196

3. McGovern, B .H., et al., SER-109, an Investigational Microbiome Drugto Reduce Recurrence After Clostridioides difficile Infection: Lessons Learned From a Phase 2 Trial. Clin Infect Dis, 2021. 72(12): p. 2132-2140.

4. Feuerstadt, P., et al., SER-109, an Oral Microbiome Therapy for Recurrent Clostridioides difficile Infection. N Engl J Med, 2022. 386(3): p. 220-229.

5. Hu, Z., et al., Targeted metabolomics reveals novel diagnostic biomarkers for colorectal cancer. Mol Oncol, 2025. 19(6): p. 1737-1750.

6. Butler, F.M., et al., Vegetarian Dietary Patterns and Diet-Related Metabolites Are Associated With Kidney Function in the Adventist Health Study-2 Cohort. J Ren Nutr, 2025.

7. Stanford, J., et al., Metabolomic Profiling and Diet Quality Scoring in a Randomized Crossover Trial of Healthy and Typical Dietary Patterns. Mol Nutr Food Res, 2025 . 69(23): p. e70271.

8. O’Connor, L.E., et al., Metabolomic Profiling of an Ultraprocessed Dietary Pattern in a Domiciled Randomized Controlled Crossover Feeding Trial. J Nutr, 2023. 153(8): p. 2181-2192.

9. Fritsch, D.A., et al., Microbiome function underpins the efficacy of a fiber-supplemented dietary intervention in dogs with chronic large bowel diarrhea. BMC Vet Res, 2022. 18(1): p. 245.

10. Leal, L.N., et al., Preweaning nutrient supply improves lactation productivity and reduces the risk of culling in Holstein cows. J Dairy Sci, 2025. 108(6): p. 5875-5888.

11. Ahsin, M., et al., Soil and pasture health underlie improved beef nutrient density determined by untargeted metabolomics in Southern US grass finished beef systems. NPJ Sci Food, 2025. 9(1): p. 151.

12. Yin, W., et al., Plasma lipid profiling across species for the identification of optimal animal models of human dyslipidemia. J Lipid Res, 2012. 53(1): p. 51-65.

13. Porter, F .D., et al., Cholesterol oxidation products are sensitive and specific blood-based biomarkers for Niemann-Pick C1 disease. Sci Transl Med, 2010. 2(56): p. 56ra81.

14. Needham, B .D., et al., Plasma and Fecal Metabolite Profiles in Autism Spectrum Disorder. Biol Psychiatry, 2021. 89(5): p. 451-462

15. Li, C., et al., Estradiol and mTORC2 cooperate to enhance prostaglandin biosynthesis and tumorigenesis in TSC2-deficient LAM cells. J Exp Med, 2014. 211(1): p. 15-28.

16. Green, P.G., et al., Metabolic flexibility and reverse remodelling of the failing human heart. Eur Heart J, 2025. 46(25): p. 2422-2433.

17. Maekawa, H., et al., SGLT2 inhibition protects kidney function by SAM-dependent epigenetic repression of inflammatory genes under metabolic stress. J Clin Invest, 2025. 135(19).

18. Wu, D., et al., Integrated screens reveal that guanine nucleotide depletion, which is irreversible via targeting IMPDH2, inhibits pancreatic cancer and potentiates KRAS inhibition. Gut, 2026.

19. Schwerdtfeger, L.A., et al., Gut microbiota and metabolites are linked to disease progression in multiple sclerosis. Cell Rep Med, 2025. 6(4): p. 102055.

20. Wu, H., et al., Microbiome-metabolome dynamics associated with impaired glucose control and responses to lifestyle changes. Nat Med, 2025. 31(7): p. 2222-2231.

21. Jacobs, J.P., et al., Cognitive behavioral therapy for irritable bowel syndrome induces bidirectional alterations in the brain-gut-microbiome axis associated with gastrointestinal symptom improvement. Microbiome, 2021. 9(1): p. 236.

22. Pietzner, M., et al., Plasma metabolites to profile pathways in noncommunicable disease multimorbidity. Nat Med, 2021. 27(3): p. 471-479.

23. Faquih, T.O., et al., Robust Metabolomic Age Prediction Based on a Wide Selection of Metabolites. J Gerontol A Biol Sci Med Sci, 2025. 80(3).

24. Scherer, N., et al., Coupling metabolomics and exome sequencing reveals graded effects of rare damaging heterozygous variants on gene function and human traits. Nat Genet, 2025. 57(1): p. 193-205.

25. Holmes, Z.C., et al., Untargeted metabolomic analysis of human milk from healthy mothers reveals drivers of metabolite variability. Sci Rep, 2024. 14(1): p. 20827.

26. Titz, B., et al., Implications of Ocular Confounding Factors for Aqueous Humor Proteomic and Metabolomic Analyses in Retinal Diseases. Transl Vis Sci Technol, 2024. 13(6): p. 17.

27. Bloom, S.M., et al., Cysteine dependence of Lactobacillus iners is a potential therapeutic target for vaginal microbiota modulation. Nat Microbiol, 2022. 7(3): p. 434-450.

28. Leimer, E.M., et al., Lipid profile of human synovial fluid following intra-articular ankle fracture. J Orthop Res, 2017. 35(3): p. 657-666.