The Whitehead Proteomics Core Facility provides Proteomics Resources to the Whitehead and MIT communities as well as other Institutions. We utilize high resolution mass spectrometry and liquid chromatography for protein identification, comparative proteomics and quantitative proteomics as well as the identification of post-translational modifications. The facility is run by Eric Spooner with assistance from Ed Dudek and is located in Rm327 of the Whitehead Institute at 455 Main St, Cambridge, MA 02142. (spooner@wi.mit.edu or 617-324-1805: office or 617-584-7784: cell)

Our technology is based on "bottom-up" proteomics technology where proteins are digested with trypsin or other appropriate proteases and the resulting peptides are chromatographically separated and analyzed by tandem mass spectrometry on a Thermo Orbitrap Elite or Thermo Exploris 480 mass spectrometer operated in conjunction with nanoflow HPLC systems. Protein identification and quantitative information are obtained from the acquired data through the use of database search engines and species specific databases. The results are presented in a spreadsheet format generated from commercially available software. We can also provide Project files which can be viewed through the use of Free Viewers available from our software vendors.

The facility performs both quantitative proteomics analysis, post translational modification identification and simple protein identifications. We work with both gel-based and solution-based samples. We can perform stable isotope labeling analytical methods including SILAC, TMT and iTRAQ and routinely perform two dimensional chromatographic separations for TMT/iTRAQ based samples and other samples as needed.