Metabolomics Services

Metabolite Profiling and Quantification

We have dedicated mass spectrometry instruments for metabolomics services, including assays for profiling and quantifying metabolites in a variety of sample types. We also offer expert consultation and services in sample preparation and data analysis.


Services  |  Instruments  |  Local Metabolomics Groups

Schedule With Us

To schedule metabolomics services or to get more information about how we can work with you, view our rates and scheduling page or contact our core director:

Dr. Phil Gafken
Director, Proteomics & Metabolomics shared resource

Q-Exactive HFX in action
Our Thermo Scientific Q Exactive HF-X mass spectrometer in action Photo by Robert Hood / Fred Hutch News Service


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Untargeted Metabolite Profiling

We currently offer three untargeted assays.

Polar metabolite analysis: Using HILIC, or hydrophilic interaction chromatography, this assay can identify approximately 200 known metabolites from biological samples, including cell culture extracts, tissue samples and plasma/media. The assay identifies analytes in positive or negative mode by retention time matching and accurate mass.

Phospholipid analysis: This assay utilizes C18 reverse-phase high-performance liquid chromatography, or HPLC, to identify over 230 distinct phospholipid species from positive and negative mode ionization. 

Fatty acid analysis: The assay detects saponified fatty acids using ultra high-pressure, or UHPLC, C18-based chromatography with negative ionization. Currently, our assay can detect 20 fatty acids.

Contact us for developing assays for other metabolite classes.

Targeted Metabolite Quantification

Quantification assays are available for adenosine, N6-methyladenosine, 5-hydroxymethyl-2’-deoxycitidine, and 5-methyl-2’-deoxycitidine. Assays use C18 reverse phase chromatography with selective reaction monitoring (SRM)-based mass spectrometry with positive ion detection.

Contact us for assay details — such as limits of detection, typical analysis variation and sample quantities required — and for developing other targeted metabolite analyses.

Sample Preparation

We have experience with preparing samples from cell culture extracts, tissue samples and clinical samples for each assay type. Please consult us during experiment design to ensure your samples will be compatible with downstream mass spectrometry.

Contact us for assay details — such as limits of detection, typical analysis variation and sample quantities required — and for developing other targeted metabolite analyses.

Data Analysis

We identify metabolites through retention time and accurate mass matching. We also use the Thermo Scientific Compound Discoverer 3.0 to assist with metabolite identification. For metabolite quantification, we analyze data with Thermo Scientific TraceFinder 4.1.  

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Q-Exactive HF-X

The Thermo Scientific Q Exactive HF-X mass spectrometer combines a quadrupole mass filter in-line with a high-field Orbitrap mass analyzer. The Orbitrap can obtain data at resolutions ranging from 7,500 to 240,000 (at m/z 200) and mass accuracies of < 3 ppm. When acquiring data at the 7,500-resolution setting, the Orbitrap can acquire data at 40 Hz. Polarity switching at <1 sec. is possible, and the instrument is equipped with higher-energy collision-induced dissociation, or HCD, for carrying out tandem mass spectrometry analyses. A Thermo Scientific Vanquish Horizon HPLC with autosampler is coupled via a heated electrospray ionization, or HESI, source to the HF-X. Typical flowrates during LC-MS analysis range between 50 µL/min. to 300 µL/min. 

Recommended uses: This system is used for untargeted profiling of polar metabolites using hydrophilic interaction chromatography, or HILC, and phospholipids and fatty acids using C18 reverse phase chromatography. We develop analyses for additional metabolite classes when requested.  

Q-Exactive HF-X
Photo by Robert Hood / Fred Hutch News Service


Local Metabolomics Groups

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Northwest Metabolomics Research Center (NW-MRC)

The Northwest Metabolomics Research Center (NW-MRC) is located at the University of Washington School of Medicine’s South Lake Union campus and it is directed by Dr. Dan Raftery, Professor in the Department of Anesthesiology and Pain Medicine at UW and Professor in the Public Health Sciences Division at Fred Hutch. The center provides extensive mass spectrometry and NMR based metabolomics services to support the wider scientific community. Learn more here

University of Washington Medicinal Chemistry

The University of Washington’s Department of Medicinal Chemistry Mass Spectrometry Center is a mass spectrometry-based resource with expertise to support studies in drug metabolism, toxicology, and bioanalytical chemistry.  Learn more about their services here

Questions about our metabolomics services or how to schedule with us?