Equipment and Facilities

The Mayo Clinic Metabolomics Core has 13 mass spectrometers divided into the following categories:

  • Isotope ratio mass spectrometers (IR/MS)
  • Single quadrupole gas chromatography mass spectrometers
  • LC tandem mass spectrometers

Isotope ratio mass spectrometer (IR/MS)

  • Thermo Scientific Delta V Advantage
  • This IR/MS system has two inlets: A gas bench inlet that has a 96-port carousel plus Leap autosampler and gas chromatograph (GC) for analyzing 13CO2 in expired air and 18O in water (by equilibration with CO2), and a gas chromatograph and online combustion unit.
  • This equipment permits the combustion of compounds separated by gas chromatography, such as amino acids, to CO2 and N2, enabling the analysis of low enrichment levels of [13C]-labeled compounds, such as [13C6] phenylalanine (which is converted to13CO2). For [15N]-labeled amino acids, online reduction (NO to N2) allows the measurement of isotopic enrichments of nitrogen.
Images
  • Thermo Delta V Advantage IR/MS, used for analyzing 13CO2 in expired air

Single quadrupole gas chromatography mass spectrometers

  • Agilent Technologies 5973N MSD
  • This bench-top quadrupole gas chromatograph/mass spectrometer (GC/MS) is fitted with both electron impact (EI) and chemical ionization (CI) ion sources. It is used mainly for the measurement of enrichment levels of [1-13C] glucose and [6,6-2H2] glucose from plasma.
  • Agilent Technologies 5975C MSD
  • This GC/MS instrument, a newer version of the 5973N, is used for the measurement of low-level analytes, such as amino acids in tissue fluid, tRNA and dialysate samples. TCA metabolites also are measured on this instrument, both for concentration and isotopomer distribution.
  • Agilent Technologies 5977A MSD
  • This is a newer GC/MS system that is used for measuring plasma [1-13C] glucose and [6,6-2H2] glucose enrichment as well as TCA metabolites and short-chain fatty acids (SCFA).
Images
  • Agilent 5973N GC/MS, used for measuring glucose enrichment
  • Agilent 5975C GC/MS, used for measuring glucose enrichment and TCA cycle metabolites
  • Agilent 5977 GC/MS, used for measuring TCA cycle analytes and SCFA

LC tandem mass spectrometers

  • AB Sciex Triple Quad 6500 (LC/MS/MS)
  • The AB Sciex 6500 is a triple quadrupole instrument coupled with a SelexIon differential mobility system and a Cohesive TX2 liquid chromatograph system. This instrument allows separation of otherwise challenging analytes such as isobaric lipid species.
  • Agilent Technologies 6460 (LC/MS/MS)
  • The Agilent 6460 triple quadrupole is attached to an Agilent 1290 Infinity liquid chromatograph in the front end.  It is used to quantify various lipid classes such as nonesterified free fatty acids, diacylglycerides and long-chain acyl coenzyme As.
  • ThermoFisher Scientific TSQ Quantum Ultra (LC/MS/MS)
  • The Quantum Ultra is a highly sensitive, LC-based triple quadrupole mass spectrometer. It is coupled with a Waters Acquity UPLC. There are two of this configuration in the Metabolomics Core, used for isotope enrichment and a wide variety of targeted metabolite measurements.
  • ThermoFisher Scientific TSQ Quantiva (LC/MS/MS)
  • The TSQ Quantiva is the newer generation of the Quantum Ultra. It is also coupled with a Waters Acquity UPLC. There are two of these systems in the core, also used for isotope enrichment and a wide variety of targeted metabolite measurements.
  • ThermoFisher Scientific Q-Exactive Plus (LC/MS/MS)
  • The Q-Exactive Plus (QE+) is a high-resolution (up to 140,000 FWHM at m/z 200), high-mass accuracy (less than 1 parts per million) Orbitrap system that utilizes very narrow (0.4 amu) quad isolation in the first sector. Its fast scanning and high resolution capture excellent data for identification of unknowns as well as for low isotopic enrichment measurement of multiple labeled compounds. It has an Ultimate 3000 Rapid Separation LC system on the front end.
  • Agilent Technologies 6550iFunnel Q-TOF (LC/Q-TOF)
  • There are two Agilent 6550iFunnel Q-TOF LC/MS systems in the Metabolomics Core; both are equipped with Agilent 1290 Infinity LC systems. Both systems are used for large-scale metabolomics profiling. Each system is set up to acquire data in both positive and negative electrospray ionization modes after LC separation in either C18-reverse phase or hydrophilic interaction column (HILIC) phase conditions. The profiles obtained are then compared using principal component analysis software to discover metabolites that are either up-regulated or down-regulated.
Images
  • Agilent 5977 GC/MS, used for measuring TCA cycle analytes and SCFA
  • Agilent 6460 LC/MS/MS
  • ThermoFisher Scientific TSQ Quantum Ultra (LC/MS/MS). The core has two of these instruments.
  • Thermo Scientific TSQ Quantiva (LC/MS/MS). The core has two of these instruments.
  • ThermoFisher Scientific Q-Exactive Plus (LC/MS/MS)
  • Agilent Technologies 6550iFunnel Q-TOF. The core has two of these instruments used for untargeted metabolite profiling.

Facilities

The Metabolomics Core facilities occupy approximately 3,500 square feet, comprising two instrument rooms, a work-up laboratory and office space, and a conference room with videoconference capabilities.

Images
  • One of the two separate instrument rooms housing the core's mass spectrometers.
  • The core's second instrument room.
  • The core has extensive wet lab space with benches and equipment for sample accession and processing.
  • The other side of the wet lab.
  • A dedicated conference room is used for meeting with investigators locally and remotely by videoconferencing or teleconferencing.

Acknowledgment

National Institutes of Health (NIH) Public Access Policy requires that all publication that results from NIH funding be uploaded to PubMed Central. Review the process for uploading publications.

All users of the core must cite the Mayo Clinic Metabolomics Resource Core grant as a funding source in any resulting publications. Use this language:

This publication was made possible by Mayo Clinic Metabolomics Resource Core through grant number U24DK100469 from the National Institute of Diabetes and Digestive and Kidney Diseases and originates from the National Institutes of Health Director's Common Fund.