KOL VOICES | CORE FACILITY SERVICE

Making absolute proteomics accessible through a core facility service

Core facilities help translate advanced analytical workflows into accessible research services. In this Q&A, Carina Sihlbom Wallem, who leads the Proteomics Core Facility (PCF) at the University of Gothenburg, discusses how standardized ProteomEdge panels can lower the barrier to robust targeted protein quantification for translational and clinical research projects.

Stakeholder lens	Core facility and research infrastructure service provider.
ProteomEdge technology used	ProteomEdge qRePS™-based panels integrated into PCF research support for absolute protein quantification.
Application area	Biomarker verification, patient stratification, longitudinal cohort analyses and translational proteomics support.

Q: Can you briefly introduce yourself and the Proteomics Core Facility at the University of Gothenburg?

A: Carina Sihlbom Wallem is an analytical chemist and mass spectrometry specialist who leads the Proteomics Core Facility at the University of Gothenburg. Her background includes work in biological mass spectrometry at places such as the University of California San Francisco, the NIH MS facility in Tallahassee, and AstraZeneca in Mölndal.

The Proteomics Core Facility (often abbreviated PCF) is an open-access research infrastructure that supports scientists with mass spectrometry-based proteomics, glycoproteomics and glycomics. The facility assists researchers with experimental planning, sample preparation strategies, protein identification and quantification, biomarker discovery, and protein interaction studies.

Q: What types of researchers and projects typically come to the facility for mass spectrometry-based proteomics support?

A: A wide range of researchers come to the facility for mass spectrometry-based proteomics support, typically when they need deeper biological insights than standard methods can provide. Many are academic life scientists, such as molecular biologists, cell biologists, and biochemists, who want to understand protein expression, protein interactions, or signaling pathways in their systems.

A large proportion also comes from translational and clinical research, including clinicians and biomedical researchers working on biomarker discovery, disease mechanisms, or patient stratification studies. These projects often involve complex samples like plasma or tissue and require robust, reproducible measurements across cohorts.

In addition, pharma and biotech teams use proteomics to support drug development, such as identifying targets, understanding mechanisms of action, and monitoring treatment response.

Q: For non-specialist readers, what is the overall value of mass spectrometry-based proteomics in modern life science and medical research?

A: Mass spectrometry-based proteomics provides a powerful way to measure proteins directly, which is essential because proteins are the molecules that actually carry out most biological functions in the body. While genes tell us what could happen, proteins show what is happening in real time.

For non-specialists, its value lies in turning complex biology into measurable, actionable information. In modern life science and medicine, this means proteomics helps bridge the gap between basic research and patient care.

“Mass spectrometry-based proteomics provides a powerful way to measure proteins directly, which is essential because proteins are the molecules that actually carry out most biological functions in the body.“

Q: What are the most common bottlenecks for researchers who want robust quantitative protein measurements but do not have specialized targeted MS expertise in-house?

A: Researchers without in-house targeted MS expertise typically struggle with a combination of technical and practical hurdles. Designing robust assays is difficult because selecting suitable, proteotypic peptides requires specialized knowledge, and many targets lack pre-validated methods.

Method development itself is complex and time-consuming, involving careful optimization of transitions, collision energies, and acquisition parameters that are highly instrument-specific. Reproducibility is often compromised by variability in sample preparation, especially digestion efficiency and cleanup steps.

Finally, reliance on shared core facilities or external providers slows iteration and prevents the development of internal expertise, collectively making robust quantitative protein measurement difficult to achieve without specialized support.

Q: Why did PCF decide to extend its service offering with ProteomEdge panels?

A: PCF extended its service offering with ProteomEdge panels to address a clear gap between discovery proteomics and truly robust, reproducible protein quantification for end users.

In practice, many researchers generate candidate protein lists from discovery workflows but then get stuck when they need reliable, high-quality quantification. Targeted MS can solve this, but as outlined earlier, it requires specialized expertise, significant method development, and careful standardization, capabilities that most labs do not have in-house.

By introducing ProteomEdge panels, PCF aimed to lower this barrier by providing pre-developed, standardized, and quality-controlled targeted assays. Instead of each research group having to design and validate their own methods, they can access ready-to-use panels that deliver consistent, reproducible measurements.

“PCF extended its service offering with ProteomEdge panels to address a clear gap between discovery proteomics and truly robust, reproducible protein quantification for end users.“

Q: From a workflow perspective, what is valuable about multiplexed panels in a standardized format?

A: Instead of developing and optimizing assays protein by protein, researchers can measure many pre-selected targets simultaneously in a single run, which greatly increases throughput and efficiency. Because the panel is already standardized, covering peptide selection, transitions, internal standards, and QC criteria, it ensures consistency across samples, batches, and even different projects or users. This reduces the risk of technical variation and makes results more reproducible and comparable over time.

Q: Which types of projects or user groups do you think could benefit most from access to this service?

A: This includes translational and clinical research groups, where reproducibility, comparability, and turnaround time are critical, such as biomarker verification studies, patient stratification, and longitudinal cohort analyses. These projects benefit from consistent assays that can be applied across many samples and timepoints without re-optimization.

They are also highly useful for academic labs transitioning from discovery to validation, where candidate proteins have already been identified but need robust, quantitative follow-up. Here, panels remove the bottleneck of building targeted assays from scratch.

Pharma and biotech teams working in drug development can benefit as well, particularly in areas like target engagement, pathway monitoring, and pharmacodynamic studies, where standardized, high-throughput measurements are needed to support decision-making.

Q: How can core facilities help bridge advanced proteomics technology and broader precision medicine or translational research needs in the clinical setting?

A: Core facilities can play a pivotal role in bridging advanced proteomics and clinical/translational needs by acting as both technology enablers and workflow coordinators that connect all the steps of a complex process into a smooth, usable end-to-end workflow.

Core facilities lower the expertise barrier by providing access to instruments, validated assays, and analysis pipelines, while aligning experiments with clinical questions like biomarker validation or patient stratification. By ensuring data quality, consistency, and scalability across large cohorts, they make proteomics outputs more comparable, interpretable, and actionable in real-world precision medicine settings.

Q: What are your hopes for this collaboration and service offering over the next year?

A: Over the next year, the hope is that this collaboration will make high-quality, quantitative proteomics much more accessible and actionable for a broader range of researchers. By combining ProteomEdge panels with the research support offering, the aim is to deliver a more streamlined, reliable workflow that reduces complexity and shortens time from question to result.

A key goal is to see wider adoption in translational and clinical projects, where standardized, multiplexed measurements can directly support biomarker validation and patient-focused studies. At the same time, there is an expectation that the collaboration will improve consistency and scalability across projects, enabling larger cohorts and more comparable data over time.

Ultimately, we hope to strengthen the role of the platform as a bridge between advanced proteomics technology and real-world research or clinical impact, while continuously refining the panels and workflows based on user needs and feedback.