Services
Chemoproteomics and Spatial MS-Based Omics
Chemoproteomics
Chemoproteomics is an advanced set of techniques used to study interactions between small molecule drugs and proteins within complex biological systems. By combining chemical tools, high-throughput screening, mode-of-action studies, and cheminformatics, chemoproteomics enables researchers to map drug–target interactions across the entire proteome. This approach facilitates the discovery of novel drug candidates and uncovers new therapeutic pathways.
Spatial MS-based omics
Spatial MS-based omics, on the other hand, combines spatial data with omics analysis, allowing researchers to create detailed maps of biomolecule distributions in tissues and cells. Together, these methods provide powerful tools for studying molecular interactions in depth, advancing our understanding of complex biological systems and supporting the development of targeted therapies.
Partnersites:
Three institutions have joined our consortium as official Chemoproteomics and Spatial Mass Spectrometry (MS)-Based Omics partner sites, enhancing the services we can offer to the research community in the areas of target identification and validation:
Technische Universität München (TUM) Chair of Proteomics and Bioanalytics, München, Germany
The core expertise of the Technische Universität München (TUM) Chair of Proteomics and Bioanalytics in Munich, Germany, led by Prof. Dr Bernhard Küster, lies in proteome-wide characterisation of the mechanisms of action of small molecule drugs and biologics. Some of the approaches they use include target deconvolution, pathway engagement and cellular reprogramming. Their primary aim is to understand patient tumours at the level of the proteome and repurpose existing cancer drugs for new indications.
“Because almost all therapeutic drugs act on protein, it is very important to characterise drugs at the level of the proteome,” Bernhard told us. “This helps to understand how drugs actually work and can spot potential unwanted side effects early on.”
The infrastructure at TUM comprises laboratory automation, several high-end mass spectrometers and substantial computing power, allowing them to support small and large drug characterisation studies, from experimental design to proteome mapping and post translational modification (PTM) analyses.
Alongside their extensive MS expertise, TUM offers the following capabilities:
- Advanced bioinformatics and AI integration: Use of AI-powered software tools for accurate peptide spectrum prediction
- Biochemical and cellular assay proficiency: Expertise in cell culture and various target identification techniques, such as affinity-based probes, thermal profiling, and UV cross-linking
- Proteome-wide drug characterisation technology: DecryptM technology to monitor the impact of small molecules on cell signaling pathways and DecryptE for assessing drug effects on protein expression
Visit the TUM website: https://www.mls.ls.tum.de/proteomics/home/
Hochschule Mannheim Centre for Mass Spectrometry and Optical Spectroscopy (CeMOS), Mannheim, Germany
The Centre for Mass Spectrometry and Optical Spectroscopy (CeMOS) at the Hochschule Mannheim, Germany, led by Prof. Dr Carsten Hopf, is a pioneer in the field of matrix-assisted laser desorption/ionization (MALDI) mass spectrometry cell assays and a leading centre for mass spectrometry imaging (MSI). It is recognised for co-developing novel MALDI chemistry, supporting devices, cutting-edge IT solutions and pharmaceutical applications of MSI in three core areas:
- MS bioassays and technology: Advancing MS-based bioassays for diverse research needs
- Spatialomics: Specializing in the spatial distribution of molecules within tissues to generated detailed maps of analytes for biological and medical studies and spatially restricted biomarker discovery
- MS-centric bioinformatics: Developing bioinformatics tools tailored to MS and MSI data analysis
CeMOS additionally operates an advanced untargeted LC-MS metabolomic/lipidomics platform and is at the forefront of developing innovative bioassays, 3D-cell culture disease models and corresponding IT solutions to support both chemical biology research and pharmaceutical compound profiling.
“CeMOS’ very international team,” according to Carsten, “has been a technology innovator in MALDI spatialomics, MS-based cell assays and MS-centric bioinformatics for many years. We are proud to now make our technology and expertise available for European academic and SME partners.”
Visit the CeMOS website: https://www.cemos.hs-mannheim.de/en/
Karolinska Institutet Chemical Proteomics Core Facility, Stockholm, Sweden
The Chemical Proteomics Core Facility (ChemProt) at the Karolinska Institutet in Stockholm, Sweden, led by Dr Massimiliano Gaetani, supports target deconvolution, mode-of-action elucidation and characterisation of drug-target interactions, offering end-to-end workflows from cell culture treatments to data analysis and experimental integration. They employ cutting-edge technology and optimised MS-based approaches to enable unbiased, orthogonal, multiplexed, deep and proteome-wide analysis.
ChemProt offers access to their unique Proteome Integral Solubility Alteration (PISA) assay, a leading approach invented at ChemProt to deconvolute targets and mechanisms of action. Massimiliano explained this assay to us: “The PISA assay in living cells [...] sustainably allows multiparametric experimental designs for deconvoluting targets and mechanisms of action, as the engagement of the target causing a cascade to the functional effects depends on the target protein but also on the complexes or networks in which targets are presented in living cells.”
As a new EU-OPENSCREEN partner site, ChemProt offers a range of further innovative services and technologies to our research community, in combination or integration:
- Time-resolved proteomics
- Expression proteomics for drug-specific responses
- High-throughput RedOx proteomics (proteins and peptide levels)
Affinity/activity-chemoproteomics
PTM analysis
Hydrogen-deuterium exchange (HDX)-MS
Visit the ChemProt website: https://ki.se/en/mbb/research/research-division-of-physiological-chemistry-i/chemical-proteomics-core-facility