Core Facility Proteomics & Mass Spectrometry

Equipment

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

We operate three orbitrap LC-MS systems (ThermoFisher Scientific) and a timsTOF Pro with PASEF (Bruker). Each system is composed of a nano-UPLC and a high resolution mass spectrometer. The orbitrap instruments can acquire data with resolutions up to 500'000 and accurate mass within <±5 ppm, the timsTOF with 60’000 resolution and <±15 ppm. The Fusion Lumos ETD is a versatile instrument with two mass filters (quadrupole and iontrap), and two detectors (orbitrap and iontrap). It is capable of fragmenting ions in different modes, namely low energy CID, higher energy CID (HCD), electron transfer dissociation (ETD), and mixed modes of ETD and CID or HCD. The two QExactives (first generation and HF) have a quadrupole mass filter before the orbitrap detector and an HCD fragmentation cell. The TOF instrument has a trapped ion mobility cell in front of the Q-TOF enabling together with the PASEF algorithm an unprecedented usage of all incoming ions for mass detection and fragmentation at an acquisition rate of 100 Hz. All instruments can be used for targeted protein quantification assays at high sensitivity and specificity, while the Fusion Lumos and timsTOF have their strength in deep proteome mining and PTM characterization.

For all mass spectrometers we have nano electrospray sources (nano-ESI) available in order to connect to UPLC separation instruments (two EASY-nLC 1000, and two Ultimate 3000). The Swiss National Science Foundation, the University of Bern, and the Faculty of Medicine of the University of Bern had jointly sponsored all LC-MS equipment.

We can process MS data on a total of two 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 commercial software (Proteome Discoverer, PEAKS Studio, Spectronaut). Furthermore, the laboratory is equipped with one analytical HPLC, one OFFGEL Fractionator (Agilent Technologies), and SDS-PAGE/Westernblot equipment (Biorad), and as of June 2022 one AssayMAP Bravo (Agilent Technologies).