Method Development Metabolomics

Precision Metabolomics Services


Some research questions go beyond standard metabolomics workflows. Method development provides tailored analytical solutions for projects that require specific compound detection, specialized matrices, or custom assays. Whether expanding existing panels or creating new ones from the ground up, Biogenity supports flexible and scientifically robust solutions that meet your research needs.

We offer advanced method development services covering custom target design, assay optimization, and isotope tracing for pathway analysis. These approaches enable researchers to measure unique metabolites, adapt existing workflows, or explore dynamic metabolic fluxes with precision and reproducibility.

If you’d like to learn more, we are happy to discuss your project and help you get the most out of your metabolomics analysis.


Let’s discuss your project


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Guiding you from sample to biology

Each method development project begins with a consultation to understand your research objectives, target compounds, and analytical requirements. Together, we evaluate feasibility, expected performance, and project scope to design the most effective strategy.



Get a Project Estimate

We provide transparent cost estimates and timelines based on method complexity, development phases, and material requirements. Projects are divided into clear stages with Go/No-Go decision points, allowing you to evaluate progress and outcomes before moving forward.


Sample preparation and sample analysis

Sample preparation developed for the method

Sample preparation is adapted to the chemical characteristics of your target compounds. Our workflows are optimized for compound stability, recovery, and compatibility with LC–MS or GC–MS detection, ensuring high data quality from pilot development through full validation.

Supported matrices include

  • Biological fluids: plasma, serum, urine, saliva, cerebrospinal fluid
  • Cells and tissues: cell cultures, tissue biopsies, microbial and plant extracts
  • Specialized matrices: feces/gut content, food and feed samples, fermentation media, and supernatants
  • Model systems: nutritional, clinical, and environmental studies

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Targeted panels for detailed metabolic profiling

Our method development services allow you to go beyond standard panels and tailor your analysis to unique research questions. Whether adding a few new targets or designing a dedicated assay, we optimize chromatographic conditions, detection parameters, and validation strategies to ensure accurate and reproducible results.

All methods are developed using high-resolution LC-MS or GC-MS systems compatible with a broad range of compound classes. Each project includes testing, optimization, and validation phases to achieve the required performance in terms of sensitivity, selectivity, and reproducibility.


Our metbolomics method development panels

Custom Targets

Not all studies fit neatly into predefined panels. Many focus on specific metabolites that fall outside standard workflows. We offer services to develop and validate custom targets, either by expanding existing panels or establishing dedicated assays for unique compounds. This allows you to combine precise target measurements with broader metabolic searches, ensuring your analysis is tailored to your project's exact needs.



Custom Method Development

For compounds or matrices requiring specialized approaches, we provide custom LC-MS or GC-MS method development. Suitability depends on analyte properties such as molecular weight, ionization potential, and sample concentration. Organic compounds between 70-2000 Da with ionizable functional groups (-NH₂, -COOH, -OH, -PO₄, -SO₃H) are generally ideal. Costs are based on reagent acquisition, standard sourcing, and instrument setup, with phased project evaluation to ensure transparency and efficiency.

Isotope Tracing

Isotope tracing enables detailed exploration of metabolic fluxes by tracking labelled substrates through biochemical pathways. Our workflows quantify isotope distributions in key metabolites across major metabolic routes, including bile acid synthesis, lipid metabolism, amino acid turnover, and energy metabolism. By combining targeted assays with isotope tracing, we deliver sensitive and precise insights into nutrient utilization and pathway activity.

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Data analysis, including report, figures, and tables

From method development to data analysis by metabolomics experts

Data from method development and isotope tracing studies are processed by our experienced bioinformatics and biostatistics team. We evaluate signal reproducibility, isotope ratios, and dynamic patterns to ensure robust interpretation.



Reporting and documentation

Each project is delivered with a detailed report including development rationale, validation results, and recommended next steps for routine implementation or further optimization.

Delivery and discussion

Delivery, post-consultation and discussion

At the conclusion of our method developed metabolomics analysis, we ensure a seamless transition from discovery to application. We deliver detailed reports and data, followed by a post-delivery consultation to discuss your study's insights and findings.


What to expect during post-consultation

  • Explanation of the different steps in the sample analysis
  • Discussion of the data
  • Explanation of the different steps in the data analysis
  • Q&A to the report(s)

Together, we ensure that you have the best prerequisite for your further research. The consultation can also be used to explore the next step, whether you are looking to expand the project with additional omics studies or validate the results.


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