Mass Spectrometry and Proteomics

Mass Spectrometry and Proteomics
Since 2003, the Biomolecular Mass Spectrometry and Proteomics Group (BioMS), embedded in the department of Chemistry and Pharmaceutical Sciences has formed the core of the Netherlands Proteomics Centre (NPC) a strategic collaboration of proteomics research groups throughout the Netherlands. At Utrecht University, access is provided for large scale proteomics experiments as well as native MS for structural analysis of proteins and protein complexes. Access is provided to 19 state-of-the-art high resolution mass spectrometers, extensive wet labs for sample preparation, enrichment and fragmentation, and data analysis infrastructure. Among others, we support projects focused on quantitative proteomics, post-translational modifications (including phosphorylation, lipidation, glycosylation and more), immunopeptidomics and analysis of intact proteins. 

Links with other infrastructures
The NPC has been involved in several major international infrastructure projects, most notably PRIME-XS (2011-2015) and EPIC-XS (2019-2024). Currently, the NPC is involved in the recently awarded follow-up project, the EASI-OMICS initiative (2026), funded by the current Horizon Europe program. The EASI-OMICS proposal builds on two advanced communities which join some of the major European genomics and proteomics infrastructures in Europe. It directly evolved from two infrastructure projects: EASIGenomics and EPIC-XS. 

The NPC is also linked to Instruct-ERIC, the European research infrastructure for structural biology (https://instruct-eric.org/) and has provided mass spectrometry services through Instruct-ERIC as part of the Dutch Instruct Centre, Instruct-NL (in which the Bijvoet Center, together with the NKI and Leiden University forms the Dutch access node).

 Available technologies
The facility at the BioMS group provides access to 19 mass spectrometers, of which 10 are equipped for LC-MS/MS proteomics-type experiments. The instruments include state-of-the-art technologies like high-resolution Orbitrap mass spectrometry (Thermo Eclipse, Thermo Fusion, 3x Thermo Exploris), time-of-flight mass spectrometry (2 Bruker Tim-sTOF) and triple-quadrupole mass spectrometry (Thermo TSQ). Together, these instruments cover the full spectrum of needs from high throughput proteome analysis to lower throughput structural proteomics experiments, as well as targeted MS-based approaches, selected reaction monitoring (SRM), and data independent acquisition (DIA). It is equipped with extensive laboratory premises to allow sample preparation, SDS gel electrophoresis and sample pre-fractionation at both the protein and peptide level by multidimensional chromatography, including ion-exchange (SCX, SAX), high-pH fractionation (HpH), size-exclusion (SEC) and gel-free fractionation. These experimental capabilities are complemented by dedicated computing infrastructure for storing and analysing the large datasets typically generated in proteomics. In addition, a specialized bioinformatics group supports the research activities, developing software tools to facilitate, among others, PTM analysis, protein quantification, data visualization and integration, statistical evaluation, protein structure analysis, and network analysis. 

For more information, procedures for access to the facility and for contact details, please visit the website of the Netherlands Proteomics Centre.