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Primary Metabolism and Untargeted Metabolomics

compound identification, complex lipids, HILIC, target assays

Fiehn laboratory of Advanced Metabolomics

The Fiehn research laboratory develops improved methods in analytical chemistry and bioinformatics to capture and utilize metabolomic data. These tools are employed to understand, which parts of larger biochemical networks respond to genetic perturbation or environmental stress.

Currently funded research projects are targeting  cardiovascular metabolism (PIs Hazen, Wilson, Lefer, Fiehn), mammalian mitochondrial metabolism (PIs Adams, Hockenbery, Fiehn), drug response phenotyping (PIs Kaddurah-Daouk, Fiehn), algae metabolism (PIs Arita, Fiehn, Kind, Wikoff, VanderGheyst, Labavitch), metabolomic methods (PI Fiehn), metabolomic databases (PIs Subramaniam, Fiehn) and repair metabolism (PIs Hanson, Crecy-Lagard, Henry, Fiehn).

mimi swe at hoodcarlos leon at fridge

wikoff+cajka at qtof

Staff researcher Mimi Swe                                 Dr. Bill Wikoff (front) and Dr. Tomas Cajka (middle) discuss QTOF                         Dr. Carlos Leon checks
prepares samples.                                            MS results. Back: Dr. Dmitry Grapov, specialist Elizabeth Axton.                            quality control samples.

Compound Identification

kumari et al workflowRoutine metabolomic profiling for primary metabolism or complex lipids (see Core Services) yields relative quantitative data for 300-500 identified compounds. With these lists of compounds, a range of biological questions can be answered. However, over the past years we have routinely found that the most dramatic differences, both in magnitude and in statistical significance levels, were observed for metabolic peaks with unidentified chemical structure. We offer collaborative projects with the Fiehn research laboratory to engage in identification of such unknown peaks, either via collaborative grant submissions or through pilot and feasibility studies. One aspect of our research is to increase metabolite mass spectral libraries, including acquiring mass spectra for novel metabolite standards with accurate mass MS/MS analysis, accurate mass GC-QTOF MS and accurate mass ion tree fragmentations (MS^n). Another aspect of such research is to improve algorithms for modeling mass spectra from virtual compound libraries, to implement and develop methods for retention time prediction, and to utilize workflows that integrate multiple steps for compound identification.

If interested, please contact Professor Oliver Fiehn ( for more information, and visit the Fiehn research website.

Untargeted metabolomics by LC-accurate mass MS/MS analysis

Using targeted assays, e.g. by LC-QTRAP mass spectrometers, yields high confidence data on a range of metabolites from different biochemical pathways. However, this view assumes we already know everything there is to know about cellular and physiological metabolism! This assumption is certainly false. We routinely detect hundreds of novel metabolic signals in liquid chromatography-mass spectrometry profiling. Unlike gas chromatography, such LC-based methods are much more selective in terms of the compounds that can be seen in any specific method. For example, our lipidomic assays (see Core Services) have been implemented as routine tools for blood plasma or blood serum analysis, detecting over 300 identified complex lipids from a range of different lipid classes. However, such method is blind for hydrophilic compounds, including compounds that are critical in cardiovascular diseases (e.g. carnitine, creatinine, choline, betaine), gut microbial metabolites (such as sulfates) or polysaccharides and glucuronidated metabolites. Many transformations are carried out by mammalian endogenous enzymes due to substrate (or reaction) unspecificity, and, equally important, many biochemical reactions are performed by microbes living within the human super-organism. In addition, humans eat plants.... All such biochemicals can therefore be found as 'unknowns' in LC-MS or GC-MS profiling scans, and these compounds are certainly not yet covered by databases like HMDB or KEGG.

We therefore engage with interested biological or clinical scientists to develop LC-methods, including sample preparation, to better address this chemical complexity. We use a range of different columns, including hydrophilic interaction chromatography, to look for polar compounds; we devise novel ways to acquire and process such complex MS and MS/MS data, and we test different mass spectrometers in conjunction with instrument vendors. These projects should lead to collaborative research papers and NIH grant submissions.

If interested, please contact Professor Oliver Fiehn ( for more information, and visit the Fiehn research website.


Fiehn research and WCMC service core lab:

7 LCMS instruments

2x Agilent 6530 QTOF mass spectrometer with 1290 UHPLC
1x Agilent 6550 QTOF mass spectrometer with 1290 UHPLC
1x AB Sciex QTRAP 4000 mass spectrometer with Waters UPLC
1x AB Sciex Triple TOF mass spectrometer with Eksigent microLC
2x ThermoFisher ion trap LTQ
with Advion NanoMate robotic nanoelectrospray or 1290 UHPLC

7 GCMS instruments

1x Agilent GC-QTOF mass spectrometer for chemical or electron ionization
2x Agilent GC-quadrupole mass spectrometer with autosampler and s/sl injector or APEX large volume injector
LECO Pegasus IV GC-time of flight mass spectrometer with Gerstel automatic liner exchange and cold injection system, plus Gerstel Twister thermodesorption unit for profiling of volatile compounds, plus GCxGC option



fiehnlab 2015

This photo (Jan 2015) shows Fiehn research and metabolomics core service lab members.
Photo: Jeannette Martins


Director: Oliver Fiehn, PhD, Professor (Molecular and Cellular Biology, Genome Center, College of Biological Sciences at UC Davis)

Laboratory manager: Mine Palazoglu
staff research associate: Mimi Swe (service core)
staff research associate: Stephanie Samra (service core)
staff research associate: Ingrid Gennity, PhD (service core)
staff research associate: Carol Tran (service core)
staff research associate: Luis Valdiviez (service core)
junior specialist: Benjamin Wancewicz (service core)
junior specialist: Lana Amerie (service core)

WCMC Program Coordinator: Bill Wikoff, PhD (Project Scientist)
WCMC study design, statistics: open
WCMC communication specialist: Kristine Sales
WCMC outreach core, courses: Jeannette Martins
stem cell and biochemistry research: Megan Showalter, graduate student
pharmacology and repair metabolism research: Mona El-Badawi, graduate student

Cheminformatics and compound ID team leader: Tobias Kind, PhD (Project Scientist)
MS software / algae metabolism: Yan Ma, graduate student
MS ion trees / repair metabolism: Arpana Vaniya, graduate student
GC-QTOF MS: Zijuan Lai, graduate student

Novel technologies team leader: Tomas Cajka, PhD (Project Scientist)
flux analysis, cancer metabolism: Johannes Fahrmann, PhD
metabolic imaging: Brian Defelice, graduate student
genomics integration: Kwanjeera Wanichthanarak, PhD
chemotaxonomy: Dominique Ardura, graduate student

Software development team leader: Gert Wohlgemuth
programmer: Sajjan Mehta
programmer: Diego Pedrosa

Visiting scientists

Emma Sherman, New Zealand
Haishan Deng, China
Yang Bo, China
Yan-Ping Zhou, China
Yufeng Liu, China

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