The BOKU Core Facility Mass Spectrometry (CFMS) provides high-end separation science and mass spectrometry for proteomics, glycomics, metabolomics as well as elemental and isotopic analysis in life, environmental and food sciences.

The CFMS equipment and services enables research and applications in several “-omics” fields at one location. Nano-LC-MS/MS is used for studies requiring proteomics and glycoproteomics data, while LC-MS/MS, GC-MS/MS, and high-resolution molecular mass spectrometry platforms are applied to the analysis of small molecules using targeted (quantitative) and non-targeted approaches. The non-targeted approaches allow differential analysis, mass spectrometric fingerprinting and compound discovery using advanced identity confirmation workflows.

In addition to the molecular mass spectrometric platforms, the CFMS contains three ICP-MS systems situated in a clean room. Two systems are used for quantitative analysis, and one multi-collector system for isotope ratio analysis.  

Besides providing instruments, we offer professional training of entire analytical workflows, comprising experimental design, sampling, sample preparation, analysis, and data evaluation. Moreover, we offer analytical services for all described methods and applications.

Proteomics and glycomics

In the fields of proteomics and glycomics, we provide electrospray time-of-flight and Orbitrap mass spectrometers with different tuning configurations as well as various source options to address a broad variety of research questions. The combination of on-line liquid chromatography as a separation technique allows for in-depth identification and quantification of complex sample mixtures. The analysis of glycosylated peptides as well as free glycans and many other post translational modifications is one of our core competences.

For on-line LC-ESI-MS we are employing Dionex Ultimate 3000 / Thermo Vanquish UHPLC systems directly linked to

In addition, the CFMS is equipped with an off-line MALDI-ToF spectrometer to further increase our range of applications:

Rudolf Figl
Email: rudolf.figl(at)
Phone: +43 1 47654-35053

Small molecules

We provide LC and GC separations in combination with triple quadrupole mass spectrometry systems for quantification of a broad range of small organic molecules covering a wide base of applications. One of our specializations is metabolomics for biotechnology applications. In this context we provide technology and methods delivering high quality data for cellular metabolism studies.

Our high-resolution time of flight instruments allow non-targeted analysis and support identity confirmation and screening workflows using accurate mass, ion mobility, and fragmentation-supported workflows. Methods covering a range of sample types and research questions can be developed upon request.

Daniel Maresch, BSc
Email: daniel.maresch(at)
Phone: +43 1 47654-35054

Elemental and isotope ratio analysis

We provide sector-field and quadrupole-based ICP-MS systems for quantification of almost all elements of the periodic system in various matrices. An additional focus lies on elemental speciation analysis, i.e. the on-line combination of separation techniques (LC, GC, CE) with ICP-MS for investigation of elemental species and element/biomolecule interaction. In this context we provide technologies delivering information of metal/protein stoichiometry or binding efficiency.

Our high-end MC ICP-MS enables accurate isotope ratio analysis of stable isotopes of strontium, sulfur, and lead. Methods for other elements can be developed upon request.

Dipl.-Ing. Dr. Clemens Grünwald-Gruber
Email: clemens.gruber(at)
Phone: +43 1 47654-35052


Muthgasse 11 (MUG3), Bauteil B, 1. Stock


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