4D-Metabolomics Enables Advances in Disease Research
Discover the impact of 4D-Metabolomics, hybrid workflows and dual ionization in disease research.
As metabolomics continues to mature and establish itself as a cornerstone of systems biology and drug discovery research, scientists are pushing for deeper molecular coverage and more actionable insights from increasingly complex datasets. Advances in mass spectrometry (MS), particularly those that expand the capabilities for differentiating analytes with similar chromatographic retention times, or for combining targeted and untargeted analysis, are central to this evolution.
At the 74th ASMS Conference on Mass Spectrometry and Allied Topics (ASMS) 2026, Bruker Daltonics announced a portfolio of new technology advancements targeting the fields of proteomics, metabolomics, lipidomics and exposomics, including the new timsMRMS™ mass spectrometer, AI-enabled software enhancements, and other updates to their range of trapped ion mobility spectrometry (TIMS) solutions.
Technology Networks spoke with Dr. Matthew Lewis, vice president of metabolomics & lipidomics at Bruker, at the conference to learn more about Bruker’s latest innovations in metabolomics research, including their advancements in 4D-Metabolomics and hybrid metabolomics workflows.
Bringing another dimension to metabolomics
What is meant by the term "4D-Metabolomics" and how does this differ from conventional metabolomics workflows?
Conventional discovery workflows combine a chromatographic separation with high resolution mass analysis for two dimensions of analyte selection. Additional tandem mass spectrometry (MS/MS) can be performed on so-called "precursor" analytes to yield their characteristic fragmentation patterns ("products"), assisting in their correct annotation as distinct chemicals.
"4D-Metabolomics contributes substantially more data by combining these conventional chromatographic and mass analyses with TIMS. TIMS, the enabling technology behind the timsMetaboTM and our timsTOF series, adds an additional dimension of separation and selectivity to every analysis, separating analyte ions in an electric field that opposes a push of gas from the ion source," Lewis explained. "Modulating the electric field allows for the trapping and separation of analyte ions, and their gradual release from the TIMS tunnel according to their mobility."
An ion’s mobility is related to its collision cross section (CCS), a physical property which reflects the ion’s size and three-dimensional shape. By separating and measuring analytes based on CCS values, TIMS can separate interferences and distinguish between biologically distinct structural isomers with the same chemical formula but different 3D structures.
"The four-dimensional dataset provides key characteristic information for metabolite measurements. Chromatographic retention time, mass-to-charge ratio separation and MS/MS fragmentation define the first three dimensions, while TIMS provides an additional fourth dimension for each analyte," Lewis said. "TIMS enhances the speed, sensitivity and selectivity of MS/MS fragmentation, avoiding the occurrence of what we call ‘chimeric’ MS/MS spectra, that is, mixed fragmentation spectra from more than one co-isolated precursor. In 4D-Metabolomics, all fragmentation data is mass and ion mobility-linked to the respective precursor, ensuring accurate interpretation of the signals produced. We refer to the comprehensive data produced as the "digital metabolome archive" of each sample."
The benefits of 4D metabolomics:
- 4D metabolomics combines chromatographic retention time, CCS, and both MS and MS/MS information.
- CCS provides an additional molecular identifier that improves annotation confidence and data transferability.
- The resulting 4D-dataset, a "digital metabolome archive," enhances both discovery and comparability.
- Data richness supports long-term reuse.
Bridging discovery and precision: The rise of hybrid metabolomics workflows
Can you tell us more about hybrid metabolomics and the challenge of combining targeted and untargeted metabolomics?
At ASMS 2026, Bruker announced the launch of an early access program for a new hybrid metabolomics capability on the timsMetabo, which builds on quantitative metabolomics solutions from biocrates to enable simultaneous quantitation and discovery experiments.
"For the past 25 years, untargeted metabolomics has approached discovery from the premise that the most important findings are often those we do not anticipate," Lewis said. "But, in reality, we do know a lot of what to expect – maybe not everything, but we know a lot about the pathways we want to explore from what has been described in previous experiments by the metabolomics community."
Advancing NPS Screening With Chromatography-Free Mass Spectrometry
Download this eBook to learn how a forensic research program is using integrated DART-MS/MS and LC-MS/MS workflows to support faster, more flexible NPS detection and method development.View eBook
"Previously, proceeding with some knowledge was the domain of targeted approaches. The benefit of targeted analyses in mass spectrometry is that you can perform accurate quantitation. In untargeted discovery approaches, you can potentially see more of the metabolome, but it is hard to quantify what you don’t expect to see, and so we are bringing those two approaches together in a single workflow."
While having separate exploratory and quantitation workflows has worked well in the past to conduct broad discovery experiments before focusing in on quantitation, this split has increasingly limited the scope of metabolomics experiments. "This is an artificial limitation based on workflow weaknesses," Lewis argues, "which can be overcome."
"Now, using the biocrates standard methods and kits, we’re able to derive two different data streams from each analysis," Lewis said. "The result combines the benefits of rigorous targeted metabolite quantitation with the peace of mind that unexpected metabolites forming a broader metabolic profile, including the exposome, are not excluded by design. So, in addition to the targeted analysis based on the biocrates kit, we can extract further biological insight from the remaining data in the same measurements. Our MetaboScape software solution provides in silico derivatization of compound libraries, which is key to the automated metabolite annotation."
By bringing targeted and untargeted workflows together, Lewis expects to simplify both clinical metabolomics research and large-scale studies, using a single instrument and a single experiment to build a more complete picture of the metabolic changes that drive disease.
Modern Methods for Faster Microbial Analysis
Rapid microbial analysis is essential for maintaining product quality, ensuring safety, and supporting efficient laboratory workflows, yet selecting the most appropriate analytical approach can be challenging.View Webinar
"We consider this an innovation that pushes in an inevitable direction of the field," said Lewis.
Hybrid metabolomics, explained:
- Untargeted workflows enable discovery but lack precise quantitation.
- Targeted workflows provide quantitative information but limit exploration.
- Hybrid workflows deliver both in a single experiment.
- Software tools enable quantitation of known and annotation of previously unknown metabolites with increasing confidence.
Dual ionization for expanded metabolome coverage
How can simultaneous chemical ionization and electronic ionization benefit metabolomics studies?
Early on in metabolomics studies, the field was more oriented around the use of GC-MS and nuclear magnetic resonance (NMR) spectroscopy, Lewis recounted. Eventually, this gave way to LC-MS. "But LC-MS is not the perfect coupling for human biochemistry," Lewis pointed out, "because human biochemicals are often small and polar."
This is why LC-MS techniques are sometimes coupled with hydrophilic interaction liquid chromatography or ion-pairing chromatography, in order to separate highly polar compounds such as oligonucleotides, peptides, and polar metabolites.
"All of these are imperfect approximations of how you would ideally tackle these very small polar analytes," Lewis said. "GC has always been good at it."
Resolving Daily Bottlenecks in Modern Liquid Chromatography
This eBook lays out solutions to almost 100 chromatographic challenges across system handling, result validation, operational efficiency, and sustainability.View eBook
GC single-quadrupole approaches have spawned widely used mass spectrum libraries based on electron ionization (EI), a type of "hard" ionization that bombards vaporized molecules with high-energy electrons to ionize and fragment them. "But I think people were maybe less able to discover new things after that, and, fundamentally, discovery is what drives omics research. Metabolomics discovery is difficult with GC-EI due to missing precursor information," Lewis considered.
Chemical ionization (CI) is a "soft" ionization technique that uses a pre-ionized reagent gas to ionize analytes with minimal fragmentation, resulting in more intense molecular or quasi-molecular MS peaks . Thus, CI can provide direct access to molecular information (sum formulas) when coupled to high-resolution MS.
At ASMS 2026, Bruker announced that its MetaboScape® data analysis software now supports the processing of EI and CI spectra simultaneously acquired on the ecTOF™, a gas chromatography-high resolution mass spectrometer with dual ionization capabilities.
"If we’re working in the exposome or we’re working in complex microbiome chemistry, these are all areas where people still want to discover new chemistry," Lewis said. "We think that combined dual ionization helps to expand coverage, and we think it will help to improve confidence in automated annotation. This is a unique discovery platform for scientists working in these areas."
"If we are very successful, we will have driven a renaissance for GC-MS in metabolomics," Lewis added.
Simultaneous ionization data provides new insights:
- GC–MS is highly effective for studying small, polar metabolites.
- EI provides rich fragmentation for library matching; CI preserves molecular ion information for discovery.
- Dual ionization expands both identification and discovery capabilities.
- Dual ionization approaches open new avenues for exposomics and microbiome studies.
DMPK Playbook: Complete Workflows Not Workarounds
This eBook explores key challenges and solutions across metabolite identification, bioanalysis, and tissue distribution, highlighting complete workflow approaches.View eBook
Toward integrated, knowledge-driven metabolomics
These innovations highlight a broader shift in metabolomics away from isolated, untargeted experiments and towards more integrated, hybrid workflows. The addition of TIMS-enabled LC-MS-based metabolomics and new capabilities in GC-based acquisition bring unprecedented metabolome coverage and depth, while hybrid workflows reduce trade-offs between dedicated discovery and quantitation experiments.
"Studies, in the end, are not done in isolation. Annotation isn’t done in isolation," Lewis concluded. "It’s leveraging past knowledge that really drives you forward."
The future of metabolomics lies in integration—of dimensions, workflows, and knowledge. New advances are bringing together quantitation and discovery workflows, as well as "hard" and "soft" ionization techniques to paint a clearer picture of how the metabolome reacts to and drives disease development.
Key takeaways:
- 4D metabolomics enhances identification confidence by integrating ion mobility.
- Hybrid workflows unify quantitation precision with untargeted discovery in a single experiment.
- Dual-ionization GC-MS expands chemical coverage while supporting unknown identification.
This content includes text that has been created with the assistance of generative AI and has undergone editorial review before publishing. Technology Networks' AI policy can be found here.
Add Technology Networks as a preferred Google source to see more of our trusted coverage.
