Funds are requested to purchase a Thermo Finnigan LTQ linear ion trap mass spectrometer, accompanying micro HPLC system and computer cluster for the Institutional Mass Spectrometry Laboratory (MSL) of the University of Texas Health Science Center at San Antonio, under the direction of Dr. Susan Weintraub, who has over 30 years experience in biomedical mass spectrometry. At the present time, capillary HPLC-ESI/ MS/MS analyses are conducted on a Thermo Finnigan LCQ-Classic that was installed in 1997, and MALDI-TOF mass spectra are acquired on an Applied Biosystems Voyager-DE STR. These instruments have been extraordinarily powerful tools for identification and characterization of proteins and peptides for a large number of investigators. The 2003 user group consisted of 36 individual faculty members from 14 departments at UTHSCSA in addition to a number of researchers from other institutions in Texas and elsewhere in the U.S. Several technological limitations of the LCQ-Classic along with concerns about its operating lifetime prompted efforts to seek funding for a new instrument for the MSL. Regarding the performance of the instrument, improvements in detection limits, scan speed and sample through-put would benefit a large proportion of the user group. Advantages of the LTQ related to routine maintenance would enhance efficiency of day-to-day usage. Dr. Weintraub evaluated the LTQ during a trip to San Jose in February 2004 at which time she analyzed representative samples prepared in her laboratory. The results clearly demonstrated the significant benefits to the user group of the MSL that will result from acquisition of an LTQ in the following areas: (1) identification of low levels of protein in a gel; (2) identification of a low level of protein in a complex mixture in a gel; and (3) detection of a phosphopeptide at low stoichiometry. Project descriptions for 9 major users, 4 minor users and 3 future users are presented.