Having state-of-the-art in-house facilities is a strong asset for research at the Perutz. The Mass Spectrometry facility processes more than 1500 samples per year, providing a tailored service that supports the research activities of over 50 groups, mainly at the Perutz, but also from other institutes on and off the Vienna BioCenter campus. What’s more, in recent years the Perutz MS facility has established itself as a sought-after partner within the entire Vienna proteomics community. Facility head Markus Hartl explains their role as a provider of state-of-the-art technology, as well as scientific consultation: “We are all scientists at heart - we want to understand the scientific question and contribute to finding a solution. For our clients, this means that the service consists of more than just submitting a sample and receiving results without much feedback. Our goal is to provide guidance throughout the research project, from discussing the research question and experimental design to data analysis.”
In 2023, the MS facility team co-authored eight publications and was acknowledged repeatedly. The facility is also part of the Special Research Program ‘HDACs as regulators of T cell-mediated immunity in health and disease’. Senior scientist Wolfgang Reiter, together with the facility team, investigates the impact of histone deacetylases (HDACs) on T cell function and development. Wolfgang uses mass spectrometry to map the interactomes and post-translational modifications of HDACs and their substrates.
Service and research intertwined
While the most frequently requested service is interaction proteomics, aimed at identifying protein-protein interactions, the facility offers a range of services including quantitative whole proteome analyses, intact protein mass determination and cross-linking MS. “The whole process from sample to report involves more steps than just the MS itself and takes – depending on sample and research question – from a couple of days up to six weeks. On average, our most frequently requested services take two to three weeks”, Markus Hartl explains.
Clients receive not only a sophisticated report, but also data files in a ready-to-use format for the web-based software ‘Amica’ which was developed in a collaborative project together with Sebastian Didusch from the Baccarini lab. The platform streamlines data analysis for biologists. Featuring a user-friendly interface, Amica not only facilitates data inspection, but also enables scientists to visualize and interpret their findings. The platform incorporates quality control and provides exportable graphics suitable for both publications and presentations.
Decoding molecules: Understanding mass spectrometry
Mass spectrometry is used to identify and quantify substances based on their mass. Every molecule has a particular molecular weight defined by its chemical composition. By ionizing molecules and manipulating them in electric and/or magnetic fields, the mass spectrometer is capable of precisely determining their masses, which can then be used to deduce the chemical composition of each molecule. In proteomics this analytical technique enables scientists to identify proteins, their substrates and interaction partners, to quantify post-translational modifications, or perform essential quality control on their recombinant proteins.
The mass spectrometer basically consists of an ion source, a mass analyzer, and a detector. The molecules are ionized and vaporized in the ion source before they enter the mass spectrometer where the mass analyzer separates the ions according to their mass and charge. The mass analyzers differ in the way they discriminate the different ions which results in different data quality (e.g., mass precision and resolution), acquisition speed, as well as quantitative accuracy and sensitivity. The resulting mass spectra provide a unique fingerprint of the sample's composition, which is then used to identify and quantify the individual molecules.