Mass Spectrometry

Access to most advanced mass spectrometers operated by MS experts


The Mass Spectrometry Facility is focused on the identification and characterization of proteins and peptides.

Mass spectrometry has emerged as the dominating technology for the characterization and quantification of proteins. However, the high price of LC-MS instrumentation makes it difficult for individual laboratories or even institutes to keep pace with the progress in state-of-the-art technology in protein analysis.

The Mass Spectrometry Facility is operated as an instrument park and supports research groups by providing a pool of advanced mass spectrometers, maintenance and quality control of the diverse LC-MS set-ups and expert advice. LC-MS requires expert operators; therefore, samples from the research groups are measured by the core facilities of the respective institutes.

Interested in using one of our LC-MS set-ups? Need additional information? Got a specific project question?


IMP, IMBA or GMI customers

For more information on available services, sample submission procedure and usage policy, interested customers from IMP, IMBA or GMI should click here or contact Karl Mechtler.

Max Perutz Labs and all external customers

Interested customers from Max Perutz Labs and all external customers can find more information on available services, sample submission procedure and usage policy here. Please contact exclusively Markus Hartl.


The Mass Spectrometry Facility operates 4 OrbiTrap Exploris 480 mass spectrometer (ThermoFisher), which are used to analyze the major part of the submitted samples. This mass spectrometer uses a high-capacity transfer tube for maximum ion loading, an electrodynamic ion funnel that accommodates and transmits ions over a broader mass range, and a high-field Orbitrap mass analyzer with a resolution of 480000 (FWHM) at m/z 200. The Advanced Peak Determination (APD) algorithm significantly increases the number of precursors available for data-dependent analysis, which in turn results in more MS/MS spectra, and peptide identifications.

Most importantly, the FAIMS-PRO device adds a new dimension of selectivity. The application of FAIMS leads to a reduction of chemical noise, leading to better signal to noise ratios. The interval of instrument cleaning is so far minimum 6-month period. FAIMS-PRO device will be cleaned in a interval of 3 weeks.

The Orbitrap Eclipse Tribrid mass spectrometer (ThermoFisher) includes 3 mass analyzers, i.e. a quadrupole mass filter, a linear ion trap and an Orbitrap mass analyzer and 2 detectors. The instrument allows different and partially complementary fragmentation techniques, which are collision induced dissociation (CID), higher-energy collisional dissociation (HCD), electron transfer dissociation (ETD) and a combination of ETD and HCD called EThcD.

One application of this instrument is multiplex quantitation of TMT-labelled samples as this instrument offers a novel method called MultiNotch MS3 combined with real time search option, which provides a higher accuracy of TMT quantification. Additionally, we use the instrument for the analysis of peptides with labile post-translational modifications such as arginine phosphorylation.

The timsTOF Pro (Bruker) is a time-of -flight instrument coupled to a dual Trapped Ion Mobility Spectrometry (TIMS) analyser. Here, ions are separated in the gas phase based on their ion mobility which adds a 3rd dimension of separation in addition to retention time and m/z. The design of the dual TIMS device allows for ions to be accumulated in the first part of the analyser, while they are sequentially released dependent on their ion mobility from the second section (PASEF; Parallel Accumulation and Serial Fragmentation). Thereby a duty cycle of nearly 100% is achieved resulting in nearly no ion loss. The design of the instrument offers a high sequencing speed (up to 100Hz) by synchronizing the quadrupole isolation mass window with the elution time of the specific peptide packages from the TIMS funnel. This design allows to reach new depths in shotgun proteomics and phosphoproteomics, using low sample amounts.

MS instruments used for shotgun proteomics require cleaning when run 24 hours a day on large sample numbers, and performance degradation can be noticeable over short time periods. The superior robustness of the timsTOF Pro allows the instrument to be run 24/7 over many days or weeks without noticeable loss of sensitivity or other performance metrics.

This mass spectrometer is used for the characterization of intact proteins. The Q-TOF Synapt G2 (Waters) employs a quadrupole for the selection of precursor ions, a second quadrupole for fragmention and a time-of-flight tube for the mass analysis. The instrument is coupled to a chromatography system using a microscale C4 column, which allows chromatographic separation of proteins before being ionized in a microspray source and entering the MS.

The instrument is equipped with a high-efficiency T-Wave ion mobility technology, which gives access to an additional dimension of separation, based on molecular size and shape. As Ion mobility experiments are time consuming and challenging, they are offered as individual projects. The acquisition and operation of this instrument is a joint initiative with the MPL mass spectrometry facility.