Metabolon Logo
Metabolon Logo

Study Design

Chapter 1 — Top 8 Questions to Ask Your Metabolomics Provider

Before you embark on a metabolomics study, there are several important considerations you should make—especially if you are going to work with a vendor to complete your study. Here, we arm you with the most important questions you need to ask in order to find the right vendor and complete your metabolomics study with confidence.

1. How Many Metabolites Can You Detect?

When it comes to metabolomics research, not all data are created equal. The success of your study is directly related to the number of metabolites you can detect and whether those metabolites are appropriate for your research question.

Whether you are interested in using global, untargeted metabolomics to obtain a broad picture of all metabolites present in your samples or targeted metabolomics to detect particular metabolites of interest for your research question, it’s important to work with a vendor that has a wide range of appropriate, readily available assays that are capable of detecting a vast number of metabolites. Depending on your research, you may also want to work with a vendor that facilitates custom assay design.

With a comprehensive in-house database of over 5,400 biologically relevant metabolites, Metabolon is unmatched when it comes to the number of compounds—including microbial metabolites—that you can accurately identify in your studies. Additionally, our targeted and custom panels can support any research question you want to explore. Our PhD-trained metabolomics experts work with you to identify and, if necessary, develop the appropriate panel(s) to advance your research.

2. What Metabolomics Technology Do You Use?

Two main technologies are used to obtain metabolite data: nuclear magnetic resonance (NMR) and liquid chromatography-mass spectrometry (LC-MS). The approach you use directly impacts your results.

While NMR is a great approach for untargeted metabolomics efforts, LC-MS is a much more sensitive method than NMR, and is especially well-suited for targeted metabolomics analyses.1 LC-MS can measure thousands of metabolites at a time and is often used to analyze different classes of metabolites from the same sample, achieving wider coverage of the metabolome.2 Currently available LC-MS techniques are incredibly sensitive and accurate and offer high mass resolution, meaning that more than 80% of the pathways present in the KEGG database can be detected using this method.3 The sensitivity of LC-MS also makes it an exceptional tool for precision medicine research, which often requires precise and accurate identification and quantification of specific biomarkers (including microbiome-derived metabolites) and characterization of metabolite-drug interactions.

Metabolon’s proprietary LC-MS technology is best-in-class, detecting more unique metabolites than any other technology available. Our products have been used by several customers to advance precision medicine research. For example, a leading pharmaceutical company used this technology to develop a more efficacious dosing strategy and redesign their clinical trial to bring their microbiome-based therapeutic (SER-109) that had failed Phase II clinical trials through a successful Phase III trial. SER-109 is now poised to be the first microbiome-based therapeutic to receive FDA approval.

3. What Is Your Metabolomics Workflow?

All metabolomics studies follow the same basic workflow: study design, sample preparation and handling, data production, and data interpretation and visualization. How the vendor you work with approaches each individual aspect can make or break your study. Additionally, how a vendor delivers your data is a critical consideration, along with communication across the entire process.

4. Do You Help With Metabolomics Study Design?

A controlled and insightful research outcome is highly dependent on the quality of your study preparation. Every study at Metabolon begins with a one-on-one consultation to fully assess the client’s research goals. Then, the Metabolon team works to ensure three main components: a clearly defined objective, strong study design elements, and adequate study power.

Our 20+ years of experience optimizing protocols and working with hundreds of sample types combined with our reference library containing over 5,400 metabolites means that we are fully equipped to help you design your study, collect the right samples the right way, and obtain the highest quality data possible with meaningful, definitive answers to your research questions.

5. How Should Metabolomics Samples Be Prepared?

As we discuss in greater detail in Chapter 4 of this guide, there are several different sample types that can be analyzed using metabolomics protocols. The sample source you used depends on your research goal, and each sample type requires different handling and preparation. It is critical that the vendor you work with has worked with your sample type(s) before to ensure accurate handling and processing and high-quality data generation.

Metabolon simplifies this step for you with our free Study Success Sample Handling Kit customized specifically for your study. With the kit, we include barcoded tubes specific to your matrix (ie, biofluids, solid samples, or cell pellets) with instructions for mailing your samples to us to ensure they arrive safely.

We’ve performed over 10,000 metabolomics studies with samples collected from over 100 species and 500 disease states. No matter what sample type you send us, we have the expertise to extract the highest quality data possible.

6. What Kind of Metabolomics Data Interpretation and Visualization Do You Provide?

Data interpretation is often the most difficult part of any metabolomics project. Instruments don’t produce easy-to-read summaries with beautiful graphics; instead, you get tables with endless columns and values that you must transform into understandable insights using any one of a number of available software tools (some of which are free, others of which are not). If no one on your team is trained in analyzing metabolomics data, you may lack confidence in your interpretation and the likelihood of missing important, actionable observations is high.

Working with Metabolon, you’ll never be left in the dark when it comes to interpreting your data. Discovery Panels come with continuous access to the MyMetabolon Portal, where you can access customized interpretation by our PhD-level study directors, statistical tests they performed, and fully customizable data visualizations. And while targeted panels don’t have the same statistical analysis and visualization as global panels, we do provide a formatted data table that is ready for import and analysis with third-party tools such as R and Python.

7. How are Metabolomics Results Delivered?

Even if the vendor you work with aids in data interpretation and analysis—and especially if they don’t—you’ll want to ensure the data they send you is amenable for easy analysis. For every study you do with Metabolon, you’ll receive a client data table (CDT) containing all of the metabolite data in a format that is easy to import and export. You can readily analyze these data with R, Python, and many other programs.

Throughout the entire process, from study design to data delivery, Metabolon scientists work with you to ensure you achieve meaningful answers to your research questions. We help you design your study, work with you to create custom panels if needed, have the know-how to work with any sample type you send us, and have the scientific expertise to identify deep insights in your data and collaborate with you to analyze your data and advance your research forward.

8. What Are Your Metabolomics Quality Standards?

It’s no secret that the success of any metabolomics study is firmly rooted in the quality of the process and the data. We operate using procedures established in our Quality Management System to ensure that our complex deliverables are accurate and consistent. Abiding by our rigorous quality measures, we’ve helped researchers produce over 3,000 scientific presentations and publications. In January of 2023 alone, our data was used in 30 published studies. Publications using Metabolon’s services cover a diverse set of topics, from diabetes to the microbiome to malaria.

Over the past 20 years, we’ve optimized our internal quality standards, which we refer to as the 4Cs: Coverage, Competency, Comparability, and Capacity. By upholding the 4Cs, we guarantee our clients will detect unmatched breadth and diversity of metabolites, receive high-quality data and data interpretation, be able to cross-compare their data with hundreds of thousands of other samples from different researchers, times, geographies, patients, and matrices, and won’t wait for ages to receive their data.

At every stage, we deliver robust quality assurance and quality control with a rigorous data governance program and adherence to valued U.S. federal and international standards and regulations (including CAP/CLIA, and ISO 9001:2015). Metabolon handles your data in accordance with accepted data integrity, data privacy, and data security principles and adherence to applicable data privacy laws.

What’s Next?

In this chapter, we explored the key considerations to make around data and metabolite portfolios, technology, process, and quality as you consider who to work with on your next metabolomics study. In the next chapter, we will take a deeper dive into all the critical components of building your next metabolomics study with Metabolon.

metabolomics study design success guide

Continue to Chapter 2 - Metabolomics Study Workflow

In this chapter, we provide an overview of each step in the workflow, from study design to data analysis and interpretation, and how Metabolon can help you each step of the way.


  1. Emwas AH, Roy R, McKay RT et al. Recommendations and Standardization of Biomarker Quantification Using NMR-Based Metabolomics with Particular Focus on Urinary Analysis. J Proteome Res. 2016;15(2):360–373. doi: 10.1021/acs.jproteome.5b00885
  2. Nagana Gowda GA and Raftery D. NMR Based Metabolomics. Adv Exp Med Biol. 2021;1280:19–37. doi: 10.1007/978-3-030-51652-9_2
  3. Bedia C. Metabolomics in environmental toxicology: Applications and challenges. Trends in Env Anal Chem. 2022;34:e00161. doi: 10.1016/j.teac.2022.e00161

See how Metabolon can advance your path to preclinical and clinical insights

Contact Us

Talk with an expert

Request a quote for our services, get more information on sample types and handling procedures, request a letter of support, or submit a question about how metabolomics can advance your research.

Corporate Headquarters

617 Davis Drive, Suite 100
Morrisville, NC 27560

Mailing Address:
P.O. Box 110407
Research Triangle Park, NC 27709

+1 (919) 572-1721