The mass spectrometric method of DNA analysis promises to be very productive since it eliminates the time-consuming stages of DNA analysis, namely band identification and interpretation by traditional methods of gel electrophoresis and fluorescent analysis. We propose to develop an infrared (IR) matrix-assisted laser desorption/ ionization (MALDI) ion trap mass spectrometer (ITMS) for DNA analysis in contrast to the time-of-flight (TOF) mass spectrometer (MS) commonly used with MALDI ion sources. The presence of fragments is very common in MALDI spectra of biomolecules, making analysis of even simple DNA mixtures extremely complicated especially when automated systems are considered. This proposal is focused towards improving the yield of the molecular DNA ions in MALDI process, increasing the sensitivity and reliability of the method, and allowing for automation of DNA MS analysis. The proposed ITMS will operate at several frequencies to extend the mass range up to m/z 30,000 and over. The interface of the instrument with the MALDI ion source will be optimized to achieve better sensitivity and lower fragmentation. The use of the miniature tunable infrared laser that has already been tested in the experiments on our TOFMS will allow us to choose the best matrix-wavelength combinations. In addition, an automated system for high throughput DNA analysis will be built using a cooled 2D chip sample array probe. PROPOSED COMMERCIAL APPLICATIONS: A number of medical and clinical applications including Nucleic Acid (DNA & RNA) analysis and diagnostics, PCR fragment analysis, protein and peptide analysis are envisaged. Military applications such as identifications of biological agents are also expected.