Untargeted metabolomics provides a broad view of the small molecules present in biological samples, helping researchers explore metabolic changes associated with disease, treatment, environmental conditions and other biological processes. But detecting molecular features is only the beginning. The greater challenge is determining what those features represent and how confidently they can be annotated.

At Novogene Europe, our untargeted metabolomics service provides broad metabolite profiling with confidence-ranked annotation to support discovery and biological interpretation. Delivered from our Cambridge Omics Centre, the workflow combines LC-MS/MS analysis with extensive metabolite annotation resources and MS/MS spectral information to support the interpretation of complex metabolomics data.

Detection is only the first step

LC-MS/MS can detect thousands of molecular features within a complex biological sample. Accurate mass can help narrow the range of possible compounds, while MS/MS fragmentation provides additional structural information that can distinguish between potential candidates.

However, a detected signal does not automatically correspond to a confirmed metabolite identity. Different compounds may have similar masses, structural isomers can be difficult to distinguish, and the evidence available for different metabolites varies considerably.

This is why metabolite annotation depends not only on sensitive detection, but also on the breadth and quality of the reference information available for comparison.

Broad chemical coverage for untargeted discovery

Untargeted studies can encounter a highly diverse range of molecules, from lipids and organic acids to nucleotides, alkaloids and plant-derived compounds. Broad reference coverage therefore increases the chemical space that can be explored during annotation.

Novogene’s metabolite annotation resources encompass more than 500,000 entries, spanning a wide range of chemical classes. The table below highlights this breadth and examples of representative compounds within each class.

This breadth is particularly valuable for discovery-driven studies where the metabolites of interest may not be known in advance. It enables the annotation workflow to search across diverse areas of chemical space rather than focusing on a predefined group of compounds.

Adding experimental evidence to broad coverage

Breadth, however, is only one part of the annotation story.

Within these overall resources, Novogene maintains an in-house library of approximately 20,000 authentic reference standards. These are purchased chemical standards that have been experimentally measured under Novogene laboratory conditions to generate reference data for metabolite identification.

This distinction is important. The 500,000+ entries represent the combined breadth of the annotation resources used in the workflow, while the approximately 20,000 in-house reference standards provide experimentally measured reference information for compounds represented within the in-house library.

Our workflow combines this reference information with accurate mass, MS/MS fragmentation and spectral matching to support confidence-ranked metabolite annotation, rather than treating every database match as equivalent.

Why annotation confidence matters

Untargeted metabolomics is frequently used for discovery, where hundreds or thousands of features may be investigated without a predefined target list. These annotations can subsequently contribute to pathway analysis, biomarker discovery, treatment-response studies or investigations linking molecular changes with phenotype.

The biological interpretation is therefore only as useful as the evidence supporting the underlying metabolite annotations. Understanding the level of confidence behind an assignment helps researchers prioritise findings, interpret pathways more carefully and identify metabolites that may require further targeted validation.

From molecular features to biological insight

The value of untargeted metabolomics is not simply in detecting as many molecular features as possible. It lies in turning those signals into interpretable information that can help answer biological questions.

Novogene Europe’s untargeted metabolomics service combines broad LC-MS/MS profiling with extensive annotation resources, experimentally measured reference standards and confidence-ranked annotation. By bringing together broad chemical coverage and multiple layers of supporting evidence, our workflow helps researchers move from molecular feature detection towards meaningful biological insight.

For a closer look at the workflow, analytical platform and data analysis used in Novogene Europe’s untargeted metabolomics service, explore our Untargeted Metabolomics Technical Note.