Sponsored Content by EvotecReviewed by Ify IsiborAug 3 2026
Biology is underpinned by complex and dynamic molecular networks that regulate cellular function, disease progression, and cellular adaptation.
Image Credit: Shutterstock.com/angellodeco
Metabolomics and lipidomics provide the most direct snapshot of biological activity among the different omics technologies currently available. These techniques work by measuring the small molecules that represent the final products of cellular processes.
These benefits have seen untargeted metabolomics and lipidomics become influential tools in the fields of mechanism-of-action studies, disease characterization, biomarker discovery, and translational research.
While targeted approaches focus on a predefined compound list, the aim of untargeted analyses is to capture as many metabolites and lipids as possible in one analysis.
This unbiased strategy results in a unique opportunity for discovery, new hypothesis generation, and the exploration of new pathways. However, it also presents considerable computational and analytical challenges.
Biological samples include thousands of molecules with extremely diverse physicochemical properties and chemical structures. The concentration of these molecules can also span several orders of magnitude, ranging from trace-level metabolites to highly abundant compounds.
Biological systems feature numerous isomeric and isobaric species that can be difficult to distinguish analytically. Reliable identification after data acquisition remains challenging because available databases remain incomplete, and not every detected signal corresponds to a known metabolite.
As a result, one of the most significant bottlenecks in untargeted metabolomics continues to stem from the annotation of unknown compounds.
Evotec has developed a comprehensive untargeted metabolomics and lipidomics platform to help address these challenges. This platform leverages a combination of advanced analytical technologies, proprietary bioinformatics tools, and extensive annotation resources in a fully integrated workflow.
Image Credit: Evotec
A robust analytical foundation from sample to data
Proper, careful sample preparation underpins reliable metabolomics data. Evotec’s untargeted metabolomics and lipidomics platform employs semi-automated workflows designed to simultaneously maximize throughput and reproducibility while minimizing handling errors.
The workflow’s all-in-one extraction strategy is one of its key benefits, allowing simultaneous access to complex lipids, metabolites, and proteins from the same biological sample.
This approach maximizes the information acquired from valuable biological material while also supporting future multi-omics investigations.
Evotec’s platform is designed to be suitable for a diverse range of sample types, including biofluids, tissues, microorganisms, cell cultures, and other biological matrices typically employed in preclinical and translational research.
Data acquisition is underpinned by state-of-the-art mass spectrometry instrumentation. This enables comprehensive molecular profiling with high sensitivity and accuracy through high-performance liquid chromatography coupled to high-resolution mass spectrometry.
In this workflow, a Thermo Scientific Vanquish liquid chromatography system is coupled to an Exploris 120 mass spectrometer. This powerful setup offers high resolution, high mass accuracy, and excellent analytical sensitivity, capabilities that are key to successful untargeted workflows.
These mass spectrometry acquisition and chromatographic separation methods have been specifically optimized for metabolomics and lipidomics applications, further improving molecular coverage and identification confidence.
Moving beyond feature detection with annotation
The detection of molecular features is just the first step in any untargeted study. Metabolomics’ real value lies in its capacity to transform analytical signals into biologically meaningful information via a process of compound annotation.
Evotec has developed a wide range of proprietary annotation resources to support this work, covering a range of key metabolite and lipid classes implicated in cellular metabolism.
These include carbohydrates, amino acids, organic acids, vitamins, nucleic acid building blocks, steroids, cofactors, hormones, xenobiotics, and complex lipids.
Evotec’s annotation process follows internationally recognized confidence levels, ranging from tentative structural assignments to confirmed identification via authentic reference standards.
The platform relies on a continuously growing database at the highest confidence level, containing over 1850 experimentally characterized reference compounds that have been measured under standardized conditions.
A lipidomics database of around 555,000 MS/MS spectra supports putative identification of all major classes of lipid species. A structural database containing around 350,000 entries is also available, enabling broader tentative annotation of molecular features that cannot yet be confidently identified.
The combination of these resources considerably extends annotation coverage while affording researchers a more in-depth understanding of complex biological samples’ molecular composition.
Quality-driven bioinformatics
Contemporary metabolomics applications generate large, complex datasets that necessitate the use of advanced computational methods. Evotec has developed proprietary bioinformatics tools to meet these demands, tailoring them specifically to the requirements of untargeted metabolomics and lipidomics.
The workflow starts with raw data conversion, followed by feature detection, the correction of instrumental deviations, alignment across samples, and metabolite identification and annotation. Consistency and full control over data quality are assured by integrating these processes into a single pipeline.
Quality assurance is implemented throughout the analytical process. Repeated injections of a complex reference material are used for continuous monitoring of instrument performance as part of every measurement sequence.
Key parameters are systematically evaluated to ensure analytical reproducibility and stability, including mass accuracy, retention time, and signal intensity of hundreds to thousands of ions.
The resulting datasets are subjected to a range of additional post-processing steps, including normalization, quality filtering, and the handling of missing values. This comprehensive approach ensures that only features meeting predefined quality criteria are preserved for downstream analysis.
Transforming data into discovery
Untargeted metabolomics aims not only to generate data, but to facilitate biological discovery.
A wide range of bioinformatics and statistical approaches can be applied following data processing to highlight meaningful biological patterns. Exploratory methods such as hierarchical clustering and principal component analysis offer a useful overview of data structure and sample relationships.
Differential analysis identifies metabolites linked to specific biological conditions, while multivariate approaches, including LASSO, PLS-DA, sparse PLS-DA, and elastic net, support predictive modeling and biomarker discovery.
Pathway mapping and enrichment help to place molecular changes into their biological context, allowing researchers to better link metabolic alterations to underlying cellular mechanisms.
Metabolomics and lipidomics data can also be integrated with other omics layers via advanced platforms such as PanHunter. This integration is key to developing a truly systems-level understanding of biology.
Evotec's untargeted metabolomics and lipidomics platform helps accelerate discovery across biomedical research and drug development by leveraging advanced sample preparation, proprietary bioinformatics, cutting-edge instrumentation, and extensive annotation resources to transform molecular complexity into actionable biological insights.
Acknowledgments
Produced from materials originally authored by Michaël Méret, Senior Research Scientist of Metabolomics at Evotec.
About Evotec
Evotec is a life science company that is pioneering the future of drug discovery and development. By integrating breakthrough science with AI-driven innovation and advanced technologies, we accelerate the journey from concept to cure - faster, smarter, and with greater precision.
Our expertise spans small molecules, biologics, cell therapies and associated modalities, supported by proprietary platforms such as Molecular Patient Databases, PanOmics and iPSC-based disease modeling.
With flexible partnering models tailored to our customers’ needs, we work with all Top 20 Pharma companies, over 800 biotechs, academic institutions, and healthcare stakeholders. Our offerings range from standalone services to fully integrated R&D programs and long-term strategic partnerships, combining scientific excellence with operational agility.
Through Just – Evotec Biologics, we redefine biologics development and manufacturing to improve accessibility and affordability.
With a strong portfolio of over 100 proprietary R&D assets, most of them being co-owned, we focus on key therapeutic areas including oncology, cardiovascular and metabolic diseases, neurology, and immunology.
Evotec’s global team of more than 4,800 experts operates from sites in Europe and the U.S., offering complementary technologies and services as synergistic centers of excellence.
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