Launch of the Mass Spectrometry Facility

IIMCB Mass Spectrometry Facility celebrates major milestone with installation of first state-of-the-art instrument

Warsaw, Poland – The International Institute of Molecular and Cell Biology in Warsaw (IIMCB) has taken a key step in establishing its new Mass Spectrometry Facility (MSF) with the arrival and installation of its first cutting-edge instrument setup. The new technologies open unprecedented possibilities for advanced proteomics, metabolomics, and lipidomics research, strengthening the resources available to the Polish life science community.

The newly installed instrument setup comprises the Bruker timsUltra AIP mass spectrometer – the first of its kind in Poland – coupled to the UltiMate 3000 nano-liquid chromatography system. Together, this setup offers both exceptional sensitivity and high throughput, enabling high-resolution analyses across a wide range of biological applications. A second high-resolution LC-MS system is expected to be installed later this year, creating a unique synergistic environment for cutting-edge mass spectrometry in Poland. 

The delivery and installation of the new instrumentation was a complex logistical endeavor, including the removal of a window frame on the sixth floor of the institute and the use of a crane to bring the equipment into the building.

These state-of-the-art acquisitions, financed through the Polish Recovery and Resilience Plan (KPO), situate the MSF as one of ten core facilities within IN-MOL-CELL, IIMCB’s integrated infrastructure that provides access to advanced technologies for both academic and industrial users. 

The Mass Spectrometry Facility is led by Dr. Vanessa Linke, an analytical chemist from Germany with extensive expertise in proteomics and metabolomics. Before joining IIMCB, she held research positions at the University of Wisconsin–Madison (USA), the International Institute of Molecular Mechanisms and Machines (Poland), and Utrecht University (Netherlands). She has built a strong track record in developing methods at the intersection of biology, chemistry, and technology. 

The initial planning and setup of the Mass Spectrometry Facility benefited from the scientific expertise of VIB (Flemish Institute for Biotechnology, Belgium), the advanced partner of IIMCB within the RACE project. In particular, the input of Dr. Simon Devos, Head of the VIB Proteomics Core, played a key role in defining the technical specifications and facility design to support advanced mass spectrometry workflows.

Mass spectrometry is a powerful technique that measures the mass of molecules with high accuracy. For example, the new instruments will make it possible to analyze the protein composition of a single biopsy, or to detect subtle changes in cellular metabolism in response to drug exposure. This level of precision and sensitivity means that discoveries that previously required months of work with large amounts of material can now be achieved much faster and with minimal sample input. This makes mass spectrometry indispensable for modern life sciences, biotechnology, and biomedical research.

“The instruments are extremely sensitive and suitable for very low-input or precious samples. They are also very fast, allowing high-throughput analyses, which together enable unprecedented depth in protein identification,” said Dr. Linke. “Importantly, the ion mobility capabilities provide an additional level of separation, especially valuable for challenging post-translational modifications, crosslinked peptides, or specialized metabolite classes.”

The Mass Spectrometry Facility will begin offering services in early 2026, starting with bottom-up proteomics (label-free and labeled). Over time, it will expand to provide a broad range of services across multiple application areas, including interactomics, crosslinking proteomics,  protein identification and purity analysis, post-translational modification (PTM) analysis, and metabolomics and lipidomics, including metabolic flux analysis.

“We encourage both academic and industrial partners to reach out during the early stages of their project planning,” Dr. Linke added. “This allows us to advise on optimal approaches and, where necessary, to develop custom workflows that make full use of these advanced technologies.”