Equipment

Our laboratory operates as a core facility for proteomics research housed by the Department for BioMedical Research, Faculty of Medicine. We offer services with top of the line equipment and dedicated staff with decades of expertise.

We work with four nano-flow ultra-high pressure liquid chromatography high resolution mass spectrometry systems (nLC-MS) all having a mass accuracy << 20 ppm:

1. Orbitrap Fusion Lumos with an Ultimate 3000RSLC nano UPLC (ThermoFisher Scientific), featuring a high-field orbitrap (up to 500’000 resolution) and a low resolution dual pressure linear iontrap detector with scan rates of 20 Hz and three different fragmentation oprtions (CID, HCD, ETD) up to a MS¹⁰ level. This instrument is optimally suited for structural characterization work.
2. timsTOF Pro (Bruker) with an Ultimate 3000RSLC nano UPLC (ThermoFisher Scientific), featuring trapped ion-mobility hyphenated with a Time-of-Flight detector and parallel acquisition serial fragmentation (PASEF) technology with a data acquisition rate of up to 120 Hz at a resolution of 60’000. The trapped ion mobility cell together with the PASEF algorithm enable an unprecedented usage of all incoming ions for deep proteome mining.
3. timsTOF HT with a nanoElute 2 nano UPLC (Bruker) is based on the same technology as the timsTOF Pro but with improved sensitivity and a data acquisition rate of up to 300 Hz. This instrument is suited for the analysis of highly complex proteomes and samples with low amounts.
4. Orbitrap Astral with a Vanquish neo nano UPLC (ThermoFisher Scientific), featuring an ultra-high-field orbitrap detector with resolution of up to 480’000 and a data acquisition rate of 40 Hz together with a next-generation high-resolution (80’000) accurate Astral mass analyzer with a MS² acquisition rate of up to 200 Hz equipped with a dual pressure ion processor for efficient ion trapping and HCD fragmentation. The instrument comes with a FAIMS Pro Duo interface for online gas-phase fractionation based on ion mobility. This instrument is suited for the analysis of highly complex proteomes and samples with low amounts.

Furthermore, we operate an Assay-MAP BRAVO (Agilent Technologies) liquid handling robot for automated sample processing (phosphoproteomics, enrichment, fractionation on small scale). The Swiss National Science Foundation, the NCCR RNA & Disease, the University of Bern, and all life science faculties of the University of Bern jointly sponsored all LC-MS equipment.

We can process MS data on three multicore servers operating both Linux and Windows virtual machines, and two powerful Windows workstations. We use mostly open-source software for data interpretation. In addition, we do have licenses for these commercial software packages: Proteome Discoverer including xLinkx, PEAKS Studio, and Spectronaut.