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Mass spectrometry based proteomics has matured over the last decades and has by now gained a strong position, but it clearly has not reached the required stage for large-scale biomedical and clinical applications in terms of comprehensiveness of analysis, robustness and availability.

We seek to invest into this emerging next-generation of proteomics technology, focusing on high-end applications being widely accessible to researchers in the Netherlands and abroad.

For that reason the following challenges in proteomics will be addressed by X-omics:

Higher throughput, lowering costs and sample needed, aiming at assays to support clinical decision making and other applications.

Development of faster and more sensitive mass spectrometers to improve proteome coverage and separation of proteoforms.

Development of more sensitive enrichment technologies to improve depth of analysis of post-translational protein modifications.

Development of novel cross-linking approaches and affinity-proteomics technologies to elucidate the structural organization of proteins in their natural cellular environment.


In-depth charting of the molecular interactions within the cell, and how they respond to external perturbations.

Proteomics services

The main area of expertise of the proteomics facilities, that are part of the X-omics research infrastructure, consists of quantification of cellular proteome, phosphoproteome, and protein complexes. The services offered by the facilities are described in more detail below.

Quantification of cellular proteome

  • Whole cell lysate quantitative proteomics (starting from cell pellet or sample lysate)

Quantification of phosphoproteome

  • Whole cell lysate quantitative phosphoproteomics (starting from cell pellet or sample lysate)

Quantification of protein complexes

  • LC-MS analysis of protein complexes (starting from purified samples or elution from beads/columns)

Data analysis

  • MaxQuant
  • Proteome Discoverer
  • MSFragger

Available equipment for these analyses

  • Q-Exactive Orbitrap Exploris MS
  • Orbitrap Fusion Lumos Tribrid MS
  • TimsTOF Pro MS

All services mentioned above are custom services.
Please contact our helpdesk for a quote with turnaround times and prices based on your research question.