Funds are requested to purchase a Thermo-Finnigan liquid chromatograph-mass spectrometer (LCMS) with electrospray ionization (ESI) using a Deca XP quadrupole ion trap analyzer capable of performing MS/MS collision induced disassociation (MS2) and MSn fragmentation. The requested system is the Thermo-Finnigan Proteome X configuration that bundles HPLC equipment that will perform 2-dimensional (2D) chromatography for separating complex peptide mixtures and includes software packages specific for controlling the HPLC, the ion trap, including data dependent acquisition, and software specific to facilitate proteomics applications.The software includes critical database search algorithms (SEQUEST) for identifying proteins in mixtures on the basis of the spectra of peptides in the digest of these proteins. Although there are older triple sector quadrupole ESI-LCMS and a matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) are available, these instruments are complementary to the requested ion trap ESI-LCMS and cannot perform the necessary functions for which this instrument is required. Only the current generation ion trap ESI-LCMS ion trap technology has the sensitivity and speed to perform the necessary rapid MS/MS spectra collection of peptides in complex mixtures to identify by their sequences the SEQUEST database search the originating proteins, including modifications to these proteins. A variety of investigators from different departments and colleges at the University of Vermont (UVM), funded by several different NIH institutes, have come together to request this ion trap ESI-LCMS system configured in a versatile manner, but focused to solve proteomic and protein chemistry problems. No such instrument is available either at UVM or in the entire state. Several of the funded projects have reached successful points in their investigations that now beg new and more mechanistic questions be answered that require the requested instrument. Other investigators have already begun proteomic studies, but these initiatives are limited by constraints of external collaboration and fee-for-service arrangements. These investigators would greatly benefit from having the necessary instrumentation in-house where they, their colleagues and students could directly use and learn the techniques for which their research is becoming increasingly more dependent.
