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The Metabolomics Knowledge Center (MKC) provides scientific expertise and instrumentation for the measurement of small molecules such as metabolites and lipids to the ChEM-H and Stanford communities.  The center leverages expertise in mass spectrometry and allied techniques to understand the biology of small molecules both metabolites and xenobiotics and to apply that understanding to advances in human health. 


For more information, contact Dr. Yuqin Dai (Head, Metabolomics Knowledge Center) at


The MKC staff is available to provide training, consultation, and collaboration to support broad ranges of small molecule applications and LC/MS method development:

  • Untargeted metabolomics and lipidomics analysis
  • Targeted metabolomics and lipidomics analysis
  • Targeted quantitation for small molecule bioanalysis (i.e. in vitro ADME and in vivo PK)
  • Qualitative targeted flux analysis
  • Small molecule structure characterization and elucidation
  • LC/MS Methodology: Reverse phase and HILIC chromatography coupled to various types of MS technology


The Metabolomics Knowledge Center (MKC) currently hosts three mass spectrometers: two high resolution accurate mass instruments for untargeted metabolomics and one triple quadrupole instrument for targeted analysis.

Agilent 6545 Q-TOF mass spectrometer with Agilent 1290 Infinity II UHPLC

A high resolution accurate mass Q-TOF instrument offers MS/MS capability and reliable isotopic fidelity.  This instrument can be applied to broad applications such as untargeted metabolomics profiling, qualitative targeted flux analysis, small molecule accurate mass determination, structure characterization and elucidation. 

Agilent 6470 triple quadrupole with Agilent 1290 Infinity II UHPLC

A workhorse for targeted quantitation applications such as targeted metabolomics analysis and small molecule bioanalysis

Thermo Orbitrap ID-X Tribrid mass spectrometer with Vanquish UHPLC

A high resolution accurate mass instrument that combines leading mass analyzer technology with Thermo Scientific AcquireX intelligent MSn data acquisition strategy.  This instrument offers broad applications such as untargeted and targeted metabolomics analyses, small molecule accurate mass determination.  The MSn capability offers great advantages to small molecule structure elucidation and identification.

Equipment access and rates are available via the Stanford iLab Knowledge Centers portal:


Instrument and vendor specific software packages are available to support data analyses and facilitate data interpretation.

Qualitative analysis software

  • Agilent MassHunter Qualitative Analysis
  • Thermo Freestyle

Quantitative analysis software

  • Agilent MassHunter Quantitative Analysis
  • Thermo TraceFinder

Metabolomics feature finding, statistical and pathway analysis, and flux analysis software

  • Agilent Profinder
  • Agilent Mass Profiler Professional
  • Agilent Lipid Annotator
  • Agilent VistaFlux
  • Thermo Compound Discoverer
  • Thermo Lipid Search