The VBRN Proteomics Facility at the University of Vermont is a core facility funded by the Vermont Biomedical Research 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.
The VBRN Proteomics Facility is directed by Dr. Ying Wai Lam and managed by Dr. Bin Deng and technician Clarissa Gold. 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 VBRN 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.
