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.

 

ON THIS PAGE

Services  |  Instruments

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

Services

Expand All
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.  

Lorem ipsum

Instruments

Expand All
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
TSQ Vantage

The Thermo Scientific TSQ Vantage is a triple quadrupole mass spectrometer. The TSQ contains hyperbolic quadrupole rods for high ion transmission. It also contains an S-lens for thorough desolvation of ions resulting in increased signal. This instrument uses an electrospray ionization source and it is capable of multiple scan functions, such as selective ion monitoring, or SIM, selective/multiple reaction monitoring, or S/MRM, and precursor ion scanning. This instrument is coupled to a Thermo Scientific Accela 600 with an Open AS autosampler for performing liquid chromatography mass spectrometry, or LC-MS, at flowrates ranging from 50 µL/minute to 500 µL/minute.

Recommended uses: The primary use of this system is for targeted metabolite quantification with SRM-based mass spectrometry detection. 

TSQ Vantage Mass Spectrometer
Photo by Robert Hood / Fred Hutch News Service

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