Mission of the Facility:

The VGN Proteomics Facility at the University of Vermont is a core facility funded by the Vermont Genetics Network and UVM to serve the Lead Institution and research throughout the state as part of the IDeA Program mission of building research infrastructure. The facility provides a central resource of mass spectrometry-based proteomics technologies to identify, characterize and quantify target proteins in various biological and biomedical samples. The goals of the facility are to provide expertise and the latest proteomics technology to researchers at different institutions within and outside Vermont and to establish a highly efficient research and educational environment for sharing ideas, experiences, and knowledge of proteomics application in biological, biomedical, and clinically relevant studies. 

Facility Description:

The VGN Proteomics Facility is directed by Dr. Ying Wai Lam and managed by Dr. Bin Deng and technician Bethany Ahlers. It enables investigators to use an array of state-of-the-art mass spectrometry-based techniques for proteomics experiments, ranging from routine protein identification, to post-translational modification characterization, and large-scale quantitative proteomic analyses using stable isotopes. Since its inception in 2006, the facility has analyzed over 15,000 samples and facilitated data acquisition to support 100+ publications. The proteomics facility is equipped with standard laboratory equipment, analytical HPLC systems, electrophoresis systems, a Sutter P-2000 laser puller, a Savant SpeedVac concentrator, and four mass spectrometers equipped with electrospray and nanospray ionization interfaces:

  • Q-Exactive Hybrid Quadrupole-Orbitrap Mass Spectrometer (Thermo Scientific) that can perform accurate mass measurements at 140,000 FWHM. The Q-Exactive is coupled to an EASY-nLC 1000 Liquid Chromatograph (Thermo Scientific).
  • Two Thermo-Finnigan LTQ Linear Ion Trap mass spectrometers (Thermo Scientific) for mass separation (m/z = 50-2000 mass range). These instruments are coupled to either a Prominence (Shimadzu) or a Surveyor (Thermo Finnigan) HPLC system.
  • LTQ Orbitrap Discovery (Thermo Scientific) mass spectrometer for mass separation using a linear ion trap (m/z = 50–2000 mass range). This instrument can obtain accurate mass measurement data (~1–3 ppm with lock mass function activated) at high resolution (30,000 FWHM at m/z 400). The LTQ-Orbitrap is coupled to a Surveyor HPLC system (Thermo Scientific).

The Proteomics Facility Data Processing Center offers a suite of software, including Proteome Discover with SEQUEST and MASCOT, SCAFFOLD, SIEVE, PEAKS, and SimGlycan to evaluate the datasets generated from MS-based experiments for peptide quantification and peptide-modification mapping. Working closely with the VGN bioinformatics core, Proteomics Facility staff provide “tailored” bioinformatic solutions to investigators. The facility also trains investigators in experimental design and proteomics methods, and assists with data interpretation, manuscript preparation, and grant submission.

The Proteomics Facility is located in the Marsh Life Science Building and occupies 1,408 ft2 of lab and office space. It is supported by INBRE funding (P20GM103449; //

The Proteomics Facility now offers consultations to help plan research activities. Sign up for a consultation below and meet with the full Proteomics Facility and Bioinformatics Core staff in one convenient meeting.

These meetings will help you plan successful, efficient research.

New to the VGN Proteomics Facility

We are excited to announce that, with the support from VGN, a new state-of-the-art mass spectrometer, the Q-Exactive, was just recently installed and is up and running in the facility!    

Since its inception, the VGN Proteomics Facility has been providing excellent service to our network with our three mass spectrometers, which are functioning at a very high capacity.  The additional instrumentation will address the increasing user base and meet investigators’ various proteomics needs. 

Proteomics technologies have evolved significantly over the past few years, and large-scale multiplexed quantitative proteomics made feasible by sophisticated isotope tagging reagents, is becoming the critical component in many of our investigators’ projects. With the enhanced capabilities of the Q-Exactive, many biological samples can be isotopically labeled and several thousands of proteins can be simultaneously identified and quantified in one single experiment, overcoming the limitations associated with other quantitative approaches (e.g. duplex or triplex comparisons with typical SILAC studies).  Moreover, the high speed and sensitivity of the Q-Exactive allow the opportunity to investigate very low abundant proteins (e.g. transcription factors) in complex mixtures, and proteins from samples that can only be obtained in limited amounts.    

Our goals are to continue providing cutting-edge expertise to network investigators and strengthening our interactions with BPI faculty.  We have already been designing experiments with a number of researchers taking advantage of the new instrumentation.  As we are exploring new collaboration opportunities, we would love to hear from you about your research project!  We look forward to working with you soon!

Proteomics Success Stories
Spring 2013


Please double check with your PI before submitting samples.

Our facility is supported by NIH-funded Vermont Genetics Network (P20GM103449). Investigators who use our services are therefore required to cite our facility and grant number in their further publications that use the data we provide (//  Samples will not be accepted if investigators do not agree to do so.  If you have cited our facility and grant number in published papers, please notify us. 


Contact Information:

Vermont Genetics Network
University of Vermont
120A Marsh Life Science Building
Burlington, VT 05405-0086
(802) 656-9119
(802) 656-2914 - FAX

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