iMSC
Interfaculty Mass Spectrometry Center
The Interfaculty Mass Spectrometry Center (IMSC) is a joint research infrastructure of the University of Groningen (Faculty of Science and Engineering, Groningen Research Institute of Pharmacy, Analytical Biochemistry) and the University Medical Center Groningen (UMCG). It is dedicated to advancing research through mass spectrometry. IMSC’s mission is to provide high-level scientific services, develop innovative methodologies, and promote research in areas such as proteomics, biomarker research, lipidomics, metabolomics, glycomics, glycoproteomics, single-cell proteomics, extracellular vesicle isolation, spatial omics, multi-omics data integration and other computational mass spectrometry bioinformatics approaches.
Infrastructure and User Services
The IMSC provides fee-based access to over 15 mass spectrometers, including 10 state-of-the-art, high-resolution platforms, supported by advanced sample preparation and automated liquid handling systems.
The center offers robust computational infrastructure, including three high-performance computing clusters equipped with more than 0.5 TB RAM, over 200 TB of storage, and 48–96 CPU threads. This setup enables efficient high-throughput data analysis and multi-omics data integration. A large-scale data storage facility and dedicated bioinformatics environment further support these capabilities.
Total investments and 5-year operational costs at IMSC exceed €13 million. The center supports both clinical and fundamental research in areas such as cancer (e.g., melanoma, head and neck cancer), respiratory diseases (e.g., COPD, asthma), and biomarker discovery, qualification, and validation. IMSC is connected to major cohorts and biobanks, including OncoLife and Lifelines, under the umbrella of the Cohort and Biobank Coordination Hub (CBCH).
The IMSC team includes three principal investigators, one manager and six specialized technicians with permanent appointments, with expertise across proteomics, metabolomics, glycomics, glycoproteomics, and computational mass spectrometry.
Bioinformatics expertise spans data processing, statistical analysis, and custom software development. In-house tools include Pipelines and Systems for Threshold-Avoiding Quantification (PASTAQ), MALDIViewer, Glycogenius, MSIWarp, and a proteogenomics data integration pipeline.
Examples/description of the type of research
The IMSC performs both untargeted and targeted quantitative bioanalysis of proteins, peptides, glycans, glycopeptides, lipids, and metabolites in complex biological samples (e.g., plasma, serum, tissues, and cell lines). It has cutting-edge expertise in processing and statistically analyzing high-dimensional, multivariate datasets for comparative proteomics, glycoproteomics, and metabolomics, as well as in integrating these data with genomic, imaging, and clinical metadata.
IMSC supports biomarker research across the full pipeline—from initial discovery using untargeted mass spectrometry platforms in small cohort studies, to biomarker qualification, confirmation, and validation using targeted approaches in large clinical cohorts.
The institute is currently establishing infrastructure for spatial omics, including mass spectrometry imaging of small molecules (e.g., drugs and their metabolites), glycoproteomics, and metabolic flux analysis using stable isotope labeling. It also develops new bioinformatics methods to support the analysis of these data types.
IMSC works closely with the UMCG genomics facility to integrate next-generation sequencing data into proteogenomic and metabologenomic (systems medicine) approaches, while also advancing novel LC-MS/MS signal processing workflows.
Overall, IMSC develops innovative analytical, instrumental and computational methods to enable the translation of mass spectrometry-based research into clinical applications and advance clinical research.
How to access the infrastructure ?
IMSC provides coordinated access to its facility services based on a clear protocol on sample analysis submission process The services include:
- Consultancy on the applied analysis approaches, including feasibility, experimental design, optimal sample preparation, and analysis methods suited to answer the research questions.
- Use of mass spectrometry analytical platforms and data acquisition settings.
- Optimal data analysis, along with data stewardship, integration, and analysis following FAIR data management principles.
Virtual access is provided for raw data as well as pre-processed data. We also collaborate with users on studies requiring both dry and wet lab method development.