Netherlands Proteomics Center (NPC)

Advanced proteomics infrastructure and expertise

The facilities of the Biomolecular Mass Spectrometry and Proteomics group (BioMS) are organized under the name of the Netherlands Proteomics Centre (NPC).

NPC provides academic and industry partners with access to advanced mass spectrometry infrastructure, proteomics technologies and specialist support. Using state-of-the-art mass spectrometry, structural proteomics and computational tools, the facility enables the identification, quantification and structural characterization of proteins, peptides, protein complexes and post-translational modifications.

These technologies can be applied to research questions in areas including cell biology, biotherapeutics, immunology, structural biology, biomarker discovery, drug response and systems biology.

Proteomics technologies and services

NPC offers access to a broad range of proteomics technologies and expertise, including:

• Quantitative proteomics;
• Analysis of post-translational modifications, such as phosphorylation and glycosylation;
• Affinity purification mass spectrometry for studying protein interactions;
• Immune peptidomics and the identification of peptides presented by human leukocyte antigen molecules;
• Characterization of intact proteins and protein complexes.

Mass spectrometry infrastructure

The facility provides access to 19 mass spectrometers, including 10 instruments equipped for LC-MS/MS proteomics experiments. The infrastructure includes high-resolution Orbitrap mass spectrometry, timsTOF mass spectrometry and triple-quadrupole mass spectrometry.

Together, these instruments support applications ranging from high-throughput proteome analysis and targeted mass spectrometry to data-independent acquisition and lower-throughput structural proteomics experiments.

Sample preparation, data analysis and bioinformatics

Extensive laboratory facilities are available for sample preparation, SDS-PAGE and protein and peptide fractionation. Available techniques include ion-exchange chromatography, high-pH fractionation, size-exclusion chromatography and gel-free fractionation.

Dedicated computational infrastructure supports the storage and analysis of large proteomics datasets. Bioinformatics expertise is available for protein quantification, PTM analysis, data visualization and integration, statistical evaluation, protein structure analysis and network analysis.

Collaboration and access

Projects are tailored to the specific samples and research questions of each user. Support can cover experimental design, sample preparation, measurements, data analysis and interpretation.

Access is offered through a flexible model combining fee-for-service activities with scientific collaboration.