Current Instrumentation

The Metabolomics Core is located across several laboratories within building 221, with all relevant installations. Our current instrumentation include: 

Mass spectrometry

• Bruker timsTOF fleX high resolution MS/MS system with an Agilent 1290 (UHPLC-DAD), capable of both LC-MS and MALDI applications. Especially used for MALDI based mass spectrometry imaging (MSI) as well as accurate mass and automated-MS/MS screening of microbial secondary metabolites
• Bruker Impact II QTOF high resolution MS/MS system with an Agilent 1290 (UHPLC-DAD) system for untargeted secondary metabolite metabolomics. e.g. for microbial chemical ecology studies
• Agilent UHPLC-QqQ (G6490) triple quadrupole MS/MS used for targeted quantification of various small molecules

Gas chromatography mass spectrometry 

• Thermo ISQ 7000 with CTC PAL autosampler

Semi-Preparative Liquid chromatography

• Agilent 1260 with both DAD and MS detectors as well as automated fraction collector for bioassays and semi-preparative chromatography
• Agilent 1290 with DAD and automated fraction collector for bioassays and semi-preparative chromatography 

Analytical Liquid chromatography

• Agilent 1100 HPLC systems with diode array detection (DAD), fluorescence detection (FLD) for standard reversed phase separations. This system is used extensively in chemotaxonomic applications

Software and data-analysis

For analysing data, we have several solutions:

• DataAnalysis 5.2 to analyse data from Bruker mass spectrometers. We also create custom scripts for automated processing of data within DataAnalysis
• SCiLs for analysing MALDI base mass spectrometry images
• For untargeted metabolomics workflows we often rely of MZMine, and GNPS
• For dereplication of natural products extracts we a large in-house library of microbial secondary metabolite reference standards as well as an extensive fragmentation database for annotations

Sample preparation

• Several centrifuges for up to 50 ml samples 
• Freeze driers 
• N2 Evaporation facilities for falcon tubes, vials and microtiter plates  
• All types of SPE columns (ion exchange, mixed mode, NP, size exclusion) 
• Additional supporting instrumentation includes vacuum concentrators, ultrasonicators, instrument network server for automated data-backup
• All instruments can be remotely controlled from the office as well as home
• Cryotome, microscope and matrix-sprayer for MALDI MSI sample preparation