We request funds for the purchase of an electrospray-ionization ion trap mass spectrometer for protein and proteome analysis. The specific instrument is a Thermo Finnigan LTQ linear quadrupole ion trap mass spectrometry system coupled to a Surveyor HPLC system capable of 100 nL to uL flow rates and a nano or electrospray source. No instrument with comparable capabilities is available at the University of Rochester. There is a need for this instrument as demonstrated by eight major users and at least two minor users, all of whom are funded by NIH. Alan V. Smrcka (Principal Investigator) has been using hydrogen/deuterium exchange MALDI-TOF mass spectrometry for analysis of signal transduction proteins. Acquiring this instrumentation would greatly advance the level of this analysis. Other major users propose to use the system to study global protein modifications in yeast (E. Phizicky), proteins involved in nuclear transport of histones (J. Hayes), analysis of transcription factor interactions in Drosophila (D. Bohmann), proteins involved in histone transport (J .Hayes), proteomic analysis ofneurodegenerative diseases (D. Pearce), Posttranslational modifications of G protein coupled receptors (P. Hinkle), comprehensive analysis of the human salivary proteome (J. Melvin), and tubulin and histone modifications in Tetrahymena (M. Gorovsky). The LC/ESI ion trap mass spectrometer will be incorporated into a functional genomics core facility that also contains a MALDI-TOF and microarray instrumentation. A Masters level mass spectrometrist will be responsible for the day to day operation of the instrument. A Mass Spectrometry Committee has been named, that includes an outside advisory member who directs a mass spectrometry core facility at Vanderbilt University that will provide long-term guidance about the use of the instrument. The institutional commitment will provide salary support for the Masters level mass spectrometrist for three (3) years and will pay the service contract for three (3) years. A cost recovery plan will be implemented that will cover costs in future years.