AMINO-ACID-COMPOSITION AND WAVELENGTH EFFECTS IN MATRIX-ASSISTED LASER-DESORPTION IONIZATION

Ion yields were investigated in matrix-assisted laser desorption/ioniz ation (MALDI) as a function of amino acid composition using a variable wavelength ion source. In the case of nitrogen laser excitation (337 nm), [M+H](+) ions were abundant for short peptides containing basic o r polar amino acid residues. The lack of basic residues led to diminis hing ion formation at 337 nm. Increasing the chain length led to enhan ced ionization even for peptides with non-polar side chains. In contra st to the liquid phase basicities the basic residues showed Arg > His > Lys order in their affinity to protons. Variations in the average io n yield showed decreasing trend with increasing basicity of the residu es pointing to potential differences in the matrix incorporation of di fferent guest molecules. Dye laser excitation at 280 nm resulted in ex tensive fragmentation and enhanced ion formation from peptides contain ing aromatic side chains indicating the possible role of analyte excit ed states in ion formation. Semi-empirical quantum chemical calculatio ns were used to explore the sites of protonation. Heat of formation di agrams of the matrix-analyte complexes were examined as a function of their configuration. Investigation of the optimized geometries allowed the location of bifurcated and linear hydrogen bonds between the non- polar analyte (e.g., Gly-Gly) and matrix molecules. In addition to the se intermolecular bonds, in the case of His-His an intramolecular hydr ogen bond was also formed within the analyte molecule. Proton affinity values were calculated for every dipeptide while the site of protonat ion was varied. The results seemed to indicate that for every dipeptid e the amino terminus was more susceptible to protonation than the pept ide bond. Due to increased stabilization effects in homo-oligomers (Gl y(n)), increasing the number of residues led to an increase in proton affinity. For basic diopeptides (e.g., His-His), the side chains had t he highest proton affinity, underlining their role in MALDI of protein s.