Infrastructure

Mass spectrometry

For untargeted metabolomics and lipidomics, our workhorses are the SCIEX ZenoTOF 7600 system, a Thermo Fisher Orbitrap IQ-X, and an Agilent 6550 QTOF for flow injection.

For special projects, we also have a Thermo QExactive HF-X, an Agilent 6546 QTOF (tracing studies), an Agilent 6520 QTOF (enzyme assays or analysis of salty samples)

For targeted analyses, we have an Agilent 6495C (highly sensitive applications about primary metabolism), a SCIEX 5500 QTRAP (special applications, sugar analysis, SCFAs, etc.), and an Agilent 5793 GC-MS.

Additionally, our lab hosts a variable number of loaned prototypes or commercial instruments as part of collaborations with MS vendors.

We have ca. 8 UHPLC stacks (Agilent, Thermo, Waters) to cover the full range from nano to normal flow.

Sample preparation

For project that require large scale or highly reproducible sample preparation, we have established several key protocols for e.g. polar and lipid fractions, cold (-20°C) and hot (up to 90°C) extraction, protein precipitation, lipid depletion, etc. on automated liquid handling devices such as the Hamilton Star and the Agilent Bravo systems.

Data processing and storage

Data analysis relies on workflows, methods, and algorithms that we developed to combine depth and breadth of metabolite coverage, scalability, and accuracy. Data and results and kept on a dedicated infrastructure provided by ETH IT Services. Results are delivered through Leonhardmed or directly by encrypted file transfer.