Instrumentation

Facilities and Other Resources

Space

The Fiehnlab and Metabolomics Facility space extends to 3,500 ft² for laboratory, five separate offices for 30 staff and students, plus the PI office and a dedicated meeting room for 12 persons on the same floor. In addition, we have recently opened a satellite laboratory as ThermoFisher Center of Excellence in Clinical Metabolomics at the UC Davis clinical campus in Sacramento, with additional 1,500 ft laboratory space plus ancillary rooms for offices and freezers.

The labs have all the necessary equipment such as freezers, balances, homogenizers, lyophilizers, shakers, centrifuges, speedvacs and sonicators.

The Genome Center is a research-only Center; the 150-seat auditorium and the 35-seat seminar rooms plus two 15-seat meeting rooms are reserved for Genome Center faculty, including Prof. Fiehn, through an online system.

 

Equipment

Combined, the Fiehn metabolomics research laboratories hosts 16 mass spectrometers:

11 LCMS instruments

ifunnel 3 Agilent QTOF mass spectrometers (6530, 6546, 6550 models) with 1290 UHPLC
1 Sciex QTRAP 6500+ mass spectrometer with ThermoFisher Vanquish UHPLC
1 Sciex Triple TOF mass spectrometer with with ThermoFisher Vanquish UHPLC
3 ThermoFisher Orbitrap mass spectrometers (Q-Exactive, IQX, Exploris models) with Vanquish UHPLC
2 ThermoFisher Altis triple quadrupole mass spectrometers with ThermoFisher Vanquish UHPLC
1 Bruker timsTOF mass spectrometer flex with Vanquish UHPLC

5 GCMS instruments

5 LECO Pegasus time of flight mass spectrometers with Agilent gas chromatographs + autosamplers

 

 Chemical and Informatics Resources

The Fiehn laboratory has purchased over 6,500 chemical reference standards for identification and quantifications and hosts several metabolomics databases:

Server Rack

  • MassBank of North America for more than 2m mass spectra (including LipidBlast)
  • FiehnLib with mass spectra and retention indices of more than 1,200 authentic primary compounds
  • BinBase storing data for over 300,000 samples and more than 17,000 metabolites
  • miniX as LIMS system
  • Chemical Translation Service to translate between more than 200 public databases of biochemical and chemical species.

Computer hardware Calculations are performed via the Genome Center computer clusters. The raw data file server consists of 200 TB hard drive space with 24GB Ram on 16 cores. The file backup system runs on 80 TB hard drive space with 8 cores and 8 GB Ram.

  • The Fiehnlab BinBase database runs on 8 cores with 16 GB Ram.
  • The Fiehnlab cluster environment includes a master node with 16 cores/48GB and five compute nodes with 16-48 cores and 48-256 GB Ram.
  • MassBank of North America runs on 48 Cores with 128 GB Ram.
  • The miniX study design database server uses 24 Cores with 96GB Ram.

Through the Genome Center resources, Dr. Fiehn has access to two further computer clusters: a 110-node Linux cluster with dual-socket, dual-core Opteron (including 32 nodes with 8GB RAM, rest 4GB) with a total of 440 CPU cores and 568GB of RAM and 10TB of storage; and a 104 node, 996 CPU core (mostly Opteron, some Intel) cluster with a total of 3,160GB of RAM and a total of 36TB of disk storage.

All data are automatically backed up.