Mass Spectrometry Facility (MFPL)


The Mass Spectrometry Facility of the MFPL provides proteomics services to the research groups of MFPL and, if capacity remains, also to external customers. We use a range of state of the art LC-MS platforms and bioinformatic tools for identifying and quantifying peptides and proteins, including their post-translational modifications. Besides our pipeline for standard services, we offer consultation, training, and capacities for method development to our users to find the best analytical solution for a given problem.

The facility is run in close co-operation with the Protein Chemistry Group of the IMP (Institute of Molecular Pathology), IMBA (Institute of Molecular Biotechnology) and GMI (Gregor Mendel Institute) and performs all MS measurements using the instrument pool of the Vienna Biocenter Core Facilities (VBCF).


In the context of the Vienna Life Science Instruments (VLSI) initiative the MFPL Mass Spectrometry Facility offers proteomics services to external candidates only if capacity remains and only after prior consultation of the head of the facility. Furthermore, either a valid scientific collaboration agreement and/or the acceptance of the general terms and conditions during the submission procedure will be required.


  • Protein/peptide identification, including a range post-translation modifications (e.g. phosphorylation, acetylation, etc.)
  • Protein/peptide quantification: solutions for all major approaches, such as metabolic or chemical labeling, as well as label-free quantification are available
  • Interaction proteomics: affinity-purification/enrichment or proximity-based labeling strategies (e.g. BioID, APEX)
  • Cross-linking mass spectrometry: for obtaining low-resolution structural information of proteins and protein complexes in solution
  • Intact protein mass analysis: determination of intact proteins under denaturing conditions using ESI-TOF-MS. For example for confirming the mass of an expressed protein or monitoring modifications or stability.
  • Counseling with regards to the experimental plan and analysis choice
    Experimental plan optimization
    Selection of suitable analysis strategy
    Advice on sample preparation
    Optionally: pilot experiments
  • Further services available upon request


The MFPL Mass Spectrometry Facility has access to the VBCF instrument pool which currently hosts the following technology:

  • Q Exactive HF-X (Thermo)
  • Orbitrap Fusion Lumos (Thermo)
  • Synapt G2-Si HDMS


Whenever you use services of the MFPL Mass Spectrometry Facility you are obliged to acknowledge our service in your publications: “Proteomics analyses were performed by the MFPL Mass Spectrometry Facility in the framework of the VLSI using the VBCF instrument pool.”


Markus Hartl, Dr.
Head of Facility 
Max F. Perutz Laboratories Support GmbH
Mass Spectrometry Facility
Dr. Bohrgasse 3, A-1030 Vienna
Tel.: +43-1-79044-4291
Facility e-mail address: