Thank you. Listen to this article using the player above. ✖
Want to listen to this article for FREE?
Complete the form below to unlock access to ALL audio articles.
Proteomics and metabolomics are entering a transformative era. As pharmaceutical research shifts from mere protein identification to deep structural and functional characterization, technologies that decode protein isoforms, post-translational modifications and metabolite profiles are becoming essential.
Combined with robust data analysis platforms, these innovations are redefining our understanding of disease mechanisms and drug development pipelines.
At the American Society for Mass Spectrometry conference 2025, Technology Networks spoke with Stefan Foser, vice president of global pharma at Bruker, to explore how the company’s latest instrument suite is empowering this shift. Foser explains how Bruker is seamlessly integrating instrumentation, software and consumables to support early-stage pharma innovation.
Jack Rudd (JR):
Can you provide an overview of the new technologies Bruker announced at ASMS?
Stefan Foser (SF):
The timsOmniTM is an enhancement, not only of speed and robustness, but also in enabling entrance into the functionality of proteomics. We are now at the edge of understanding, not only in a disease setting but also in drug development, the consequences of different protein isoforms.
Then we have the timsMetaboTM, which provides annotation confidence and can generate a digital metabolome archive. In biobanks, this can help not only with understanding of the metabolomics, but also can help ensure that the biobank samples, which are usually limited, can be high-quality and, as a consequence, also of actionable information.
Functional proteomics is the area of the timsOmni and the timsUltraTM AIP, and timsMetabo provides the opportunity to understand metabolomics with quality standard QC and TwinScapeTM. In the area of imaging, we launched the neofleXTM last year.
This means we cover all areas from lead identification to lead validation or target validation up to confirmation, which is the entire innovation area at the beginning of pharma research.
How is technology advancing our understanding of protein relevance in disease?
I joined Bruker a year ago, and before I worked for almost two decades in the pharma industry.
In pharmaceutical research, we always look to protein groups (e.g., VEGF) as a target. We’ve never had the technology to look deeper and identify the different isoforms of a protein group and the consequences. What Bruker has done now is open up an area of potential of being able to ask much more; for example, with a biomarker we can differentiate between the protein isoforms and the disease setting.
What do you see proteoforming looking like for your customers in the future?
There are two areas. In drug development, if you used an antibody drug conjugate – which is an antibody, a linker bound to the antibody and a certain kind of small molecule like a toxin – in the past, the most important part was focusing on where the antibodies were binding, to determine the efficacy of the drug. Now, we can understand the terms of glycosylation, which has a consequence on the half-life of the antibody drug conjugate in the blood. We can also understand the complexity of where to bind the most efficiently. So, we can really start to characterize and optimize drug development.
The other area is clinical or disease research. We can start to understand not only the biomarkers but different kinds of post translational modifications. Any proteins which are oxidated, glycosylated or phosphorylated in a certain area have completely different consequences in signaling pathways, for example, in disease progression or remission.
For the early adopters and the customers that you’ve been working with in developing those instrumentations, what kind of feedback have you had around that kind of work and what they’ve been able to achieve?
What we’ve heard has been tremendously positive, because now people can ask these new kinds of differentiating questions. In the last 20 years, most signaling pathways have been more or less covered by competition. Now, with opening it up to protein isoforms, there is an opportunity to be unique, differentiating in your drug development or in disease understanding.
How have you built accessibility and ease-of-use into these instruments?
We have done this by not only focusing on the instruments. The key is the combination of the instrumentation with software, because instruments generate a lot of data. The software solutions cannot only analyze these data but also illustrate the data in the context of your scientific question.
The combination of MetaboScapeTM with the QC TwinScape ensures that your instrument is in good health before you do your experiments.
Biobanks can have hundreds of thousands of samples, but these are not unlimited. So, it’s critical to get the best actionable and high-quality data from the limited volumes available.
Part of that process must also be preparing for different regulatory requirements that come at different stages of the pipeline?
We are currently focusing on the innovation area in pharma. But what you can see is that a lot of samples from clinical studies are coming into research too. I would not say that it’s a strategy to go into more regulated areas, but you have to show that your data are protected, safe and robust.
How are you handling the classic dilemma between speed and scale?
Through standardization, you can get up to 500 samples per day on the timsUltra AIP system. With our software, you cannot only collect the data, but you can bring it into perspective. But it is always important to have the assurance of the robustness of the system with your software.
How were last year’s instruments received and adopted by your customers in the area?
Last year we announced that we had 1000 timsTOFTM instruments in the field – this number has grown significantly over the past year. It’s tremendous to see that the rise in awareness, particularly in pharma with these new modalities and increased complexity, is driving the need for our solutions.
Are there any particular pieces of customer feedback that have stood out to you?
We have had requests to move further in terms of characterization of biomarkers and bringing more value, not only just having a number of protein lists, but also the consequences of that.
With the software suite we have, we can really translate this, not only to the structure, but we can also study the functional protein in a living cell, which is what people were looking for. We have now the tools that scientists can use.
What’s one emerging trend or a shift in pharma that you think could be really important over the next three to five years?
One emerging trend from my perspective is the building of new modalities and therapy types. Protein degraders and antibody drug conjugates are moving into the clinic and becoming more commercialized, and that drives the request and the need for our solutions.
