Waters GC-TOF MS                                  Leco GC-TOF MS            Agilent/Frontier  pyrolysis GC-quadrupole MS

                                                     

                                           Thermo LC-ion trap MS       Leco    LC-TOF MS

Mass Spectrometers and relationship to the Metabolomics Core: 

The Fiehn laboratory hosts six different mass spectrometers, four GC/MS systems and two LC/MS systems.  All systems serve different applications and purposes. The current workhorse for metabolite profiling is a Leco Pegasus IV GCxGC-time of flight mass spectrometer which is directly connected to the Fiehnlab databases SetupX and BinBase.  It is served by a Gerstel MPS2/ALEX dual rail automatic liner exchange autosampler.
Lipid and cellulosic/lignin contents are screened by an Agilent GC/quadrupole mass spectrometer using a Frontier pyrolyzer system. Target analyses and metabolite profiling with accurate quantification is performed using an Agilent GC/quadrupole mass spectrometer in continuous SIM/scan modus. Identification of unknown compounds by accurate mass spectrometry is investigated in an arrangement with Waters using a GCT premier system under chemical ionization.
Metabolite profiling of large, thermolabile and non-volatile metabolites is performed using an Agilent 1100 HPLC / Leco Unique time of flight mass spectrometer and an Agilent 1200 UPLC / ThermoElectron LTQ ion trap.

In addition, the Fiehn laboratory has access to four further mass spectrometers for method development through the partnering Metabolomics Core which is located directly adjacent to the research lab: three LC/MS instruments and one GC/TOF mass spectrometer. Dr. Fiehn serves as faculty lead and chair of the campus advisory committee for the Metabolomics Core. However, none of the Fiehn staff is involved in the daily business of the core, and none of the core staff is involved in Fiehnlab research. Both budgets and projects are totally separate. The core's GC-TOF and LTQ ion trap instruments are identical to the mass spectrometers present in the Fiehn research lab. In addition, the core lab hosts a Waters UPLC connected to a ABI 4000 QTrap for ultra-sensitive target analysis in MRM modus, for example for hormone analysis.  Lipidomic fingerprints, specifically for membrane lipids, are pursued using an Advion NanoMate connected to a ThermoFinnigan LTQ-FTICR mass spectrometer. Core staff has access to Fiehnlab equipment if instruments are idle, and vice versa. The combined resources at the Genome Center's Metabolomics facility thus account for a total of 10 mass spectrometers.

The Fiehn laboratory has embarked on a collaboration with Genedata to use and improve Genedata's mass spectrometry data processing software Expressionist, specifically for unbiased metabolomics.

Computer Infrastructure: 

The Fiehn laboratory hosts dedicated servers and databases. The mass spectral database BinBase is a Oracle DB with 10g (1.2 TB raw). The SetupX database is stored by a Dual Intel Xeon server at 2.4 GHz - 4 GB Ram (6.4 T raw) managed by gentoo 2006. Experimental mass spectra are stored on a redundant Dual Intel Xeon storage server at 3.0GHz - 4 GB Ram running open suse linux 10.2. The Fiehnlab further provides services like WebServers, FTP-Servers, Firewalls, JBoss Application Servers, CMS, CVS, native XML Databases and different RDBMS (MySQL, Oracle). Backup is provided by attached NAS and tapedrives and is also mirrored to remote location on campus. The Lab is equipped with a dedicated high speed secured network to ensure data security and to provide fast connections between the mass spectrometers and storage servers. All staff working in Dr. Fiehn's laboratory have their own desktop PCs and printers equipped with all necessary software and hardware. Statistical assessments are performed by Statistica DataMiner.  Network analysis for systems biology approaches is performed by taking apart technical error from biological variance using Bayesian likelihood assessments. The tool is available at www.likelynet.com.

In addition, the Fiehn laboratory has access to further infrastructure through the Bioinformatics Core which currently maintains three large computer clusters: (1) Shiraz:111 nodes, dual socket dual core 2.0 GHz Opteron processor cluster.  32 nodes have 8GB RAM and 78 ones with 4GB RAM. It has 6.4 TB (raw) storage and is managed by ROCKS 4.1. (2) Apple:37 nodes, dual Dual G4 1GHz cluster.  All nodes have 2GB. It has 1.8 TB (raw) storage and is managed by OSX 10.3. (3) GenBeo:24 nodes, dual core 2.2 GHz Opteron processor cluster.  All nodes have 4GB RAM. It has 3.2 TB (raw) storage and is managed by ROCKS 4.1.  The Bioinformatics Core also maintains servers for Web sites, File Systems (NSF/AFS), DNS, DHCP, KDC, CVS/SVN, Terminal Services, Firewall.

Laboratory Infrastructure: 

The experimental Fiehn laboratory extends to 2,000 ft² on the first floor of the UC Davis Genome Center.  The Fiehn laboratory has seating for 6 reseachers and students  in a separate office next to the experimental laboratory, and seating for further 4 staff and students in the cubicle space next to the Bioinformatics Core, both on the first floor.  Adjacent to the Fiehnlab and bioinformatics core office space we have access to a dedicated meeting room for 10 persons.  The Fiehn laboratory is equipped with all the necessary equipment for analytical laboratories (benches, balances, freezers, centrifuges, vacuum concentrators, extraction and grinding devices, ultrasonicators, thermoshakers and cooling baths). It further hosts 1,000 pure reference chemicals and a controlled environmental chamber (e.g. for algae cultures).