UVM Mass Spectrometry Facility home page

We tackle difficult problems in proteomics and metabolomics

Mission Statement:

The UVM Mass Spectrometry Facility is a core facility funded by the Vermont Center for Immunobiology and Infectious Diseases (VCIID) COBRE and the College of Medicine. The primary goal of the Facility is to provide investigators with support for experiments based on mass spectrometry analyses in the areas of proteomics and metabolomics. We provide support for experimental design, sample preparation, data acquisition, data analysis, and interpretation of data obtained. Services include proteomic analyses with a focus on quantification of proteins and posttranslational modifications, small molecule quantification, metabolite pattern identification, and measurement of rates and kinetics using stable isotopes of both metabolites and proteins.

Specific Goals:

Provide state-of-the-art mass spectrometry, cutting-edge techniques, and experienced personnel to enhance the research of the investigators in the VCIID-COBRE and in the College of Medicine. Current foci include:
- Development of a broad-based platform for metabolomics measurements and measurement of metabolite kinetics and pathways using stable isotopically labeled tracers.
- Identification and quantification using stable isotope labels of difficult to define posttranslational modifications and rates of protein turnover.
Provide an infrastructure of consultative services to investigators in the design, conduct, and interpretation of experiments to facilitate their research.

Services Offered:

Facility Location & contact:

Discovery Hall room W312B

mail to: massspec@uvm.edu

Sample Submission

New projects:

Prior to generating or submitting any samples, please arrange for a consultation with Dwight Matthews. The initial contact may be by e-mail or phone. The 1st step is to discuss the nature of the project. The 2nd step is to have a formal meeting with the investigator and key students/associates with the appropriate Mass Spectrometry Facility people. This meeting will define feasibility, time frame for the analyses, number of analyses expected for the project, approach, sensitivity requirements, special problems and issues, and division of labor for sample acquisition and processing. Another key purpose of this meeting is to be sure samples will be obtained and treated in a manner compatible with the mass spectrometry measurements (e.g. limiting use or removal of detergents).
A contact person and location for receiving samples will be decided, as well as a schedule.
This initial meeting will define any development work that needs to be performed.
Priorities are given to VCIID investigators, samples that fall within an existing protocol and do not require development, and samples for time-sensitive projects, including preliminary data needed for timely grant submissions and additional experiments needed for resubmission of manuscripts.
Priority is also given to samples that have been prepared in investigators labs, as sample preparation can be a very time consuming process. Or conversely, the amount of time the Facility will spend on sample preparation becomes part of the formula for both cost and time needed to complete the analyses.
Effort in terms of time of personnel to develop methods will be estimated at or after this first meeting and costs estimated.

On-going projects:

Contact the Facility person for your project to make arrangements for receiving additional samples.
The Facility person will be able to estimate the schedule for completing the analyses.
The Facility person will also confirm the method for delivery of the samples and any sample preparation details that need to be performed.

Costs for Sample Analyses:

Costs depends upon several factors, and these factors vary by year depending upon institutional and core grant support. Fees for sample analyses depend upon:

Amount of time per sample on the instrument. Instrument set up time is included in these costs. For these reasons, samples are typically group by assay type on a weekly basis to limit instrument and UPLC change over between assays.
Amount of time required by Facility personnel to analyze the samples. Instrument setup and change over are part of this component, as is sample preparation time and data analysis time. Investigators and their associates that have repeating submissions of samples are encouraged to learn the data processing skills needed to analyze their data. Facility personnel are happy to train and assist users in this process.
Underwriting of Facility costs by grant support. Currently the VCIID COBRE provides support for the Facility for VCIID investigators.

The Facility also stocks several stable isotopically labeled compounds for use by investigators

Doing so, allows us to gain quantity discounts and pass the savings on to users. Users are only billed for the amount of materials they need.

Examples of stable isotopically labeled substrates available from the facility:

D-[U-¹³C]glucose for glycolysis flux measurements
L-[U-¹³C]glutamine for oxidative metabolism flux measurements
Other ¹³C- and ²H-labeled glucose molecules, including D-[6,6-²H₂]glucose, for glycolytic process analysis
a variety of ¹³C- and ¹⁵N- labeled L-amino acids
a variety of ²H-labeled metabolites as internal standards for quantification
²H-water and ¹⁸O-water for metabolite flux measurements

Facility History:

The Facility started as a core laboratory of the NIH-funded General Clinical Research Center (GCRC) at UVM.
- Prof. Matthews became the director when he arrived at UVM from the Cornell Medical College in 1996.
- Bruce O'Rourke was one of two core laboratory personnel performing GCMS analyses for quantification of metabolites and stable isotope tracer enrichment measurement for in vivo kinetic measurement of metabolites.
- The Core Laboratory contained GCMS and IRMS instrumentation.
- The GCRC grant ended in 2011 with the close of the NIH program. Mass spectrometry instrumentation was transferred to the Mass Spectrometry Facility. Mr. O'Rourke moved to the Department of Chemistry as manager of the facility with Dr. Matthews.
In 2003 Dr. Matthews received an NIH shared instrument grant (SIG) for the purchase of a Thermo-Finnigan LCQ ion trap LCMS to initiate the Mass Spectrometry Facility funded by the UVM College of Medicine.
In 2005 Dr. Matthews received funding under the Vermont Genetics Network (VGN) grant to purchase a Thermo-Finnigan LTQ linear ion trap LCMS, initiating the VGN Proteomics Facility.
In 2006 the VCIID INBRE grant was funded and the Mass Spectrometry Facility became part of this grant to support VCIID investigators.
In 2008 an ABI-Sciex 4000 QTRAP TSQ LCMS was funded through the NSF SIG grant program adding SRM assays.
In 2015 a Waters Xevo G2-XS QTOF high resolution mass spectrometer with a Waters Nanoacquity UPLC, funded by a 2014 NIH SIG award to Dr. Matthews was installed.
- Shown above is the newly installed Waters Xevo G2-XS QTOF
Dr. Matthews is the Pomeroy Professor of Chemistry in the College of Arts & Sciences and a Professor of Medicine in the College of Medicine. Information about Dr. Matthews and his research group can be found in the links on the left.
The mass spectrometry takes several forms at UVM. Besides the UVM Mass Spectrometry Facility that offers both measurements of small molecules and metabolomics along with proteomics measurements of difficult problems, VGN Proteomics Facility offers general proteomics measurments including identification and quantification of proteins.

Abbreviations:

CID	collision-induced dissociation
ESI	electrospray ionization
GCMS	gas chromatography-mass spectrometry
HPLC	high-performance liquid chromatography
IRMS	isotope ratio-mass spectrometry
LCMS	liquid chromatography-mass spectrometry
MS	mass spectrometer
MS/MS	CID-obtained tandem mass spectrum
PRM	parallel reaction-ion monitoring
PTM	posttranslational modification
SIM	selected ion monitoring
SRM	selected reaction-ion monitoring
TSQ	triple sector quadrupole MS
UPLC	ultra-high performance liquid chromatography
QTOF	quadrupole-time of flight MS

Mass Spectrometry Core Laboratory

Vermont Center for Immunobiology and Infectious Disease (VCIID) Center for Biological Research Excellence (COBRE)