Influence of amino acid composition and phosphorylation on the ion yields of peptides in MALDI-MS.

The influence of arginine (Arg), lysine (Lys), and phenylalanine (Phe) residues and phosphorylation on the molecular ion yields of model peptides have been quantitatively studied using matrix-assisted laser desorption/ionization (MALDI) mass spectrometry in both positive- and negative-ion mode. The results obtained from these experiments have been interpreted from the standpoint of two different components, namely, desorption and ionization, on the basis of the physicochemical properties of constituent amino acids of the model peptides. The presence of basic residues such as Arg and Lys enhanced the ion yields of protonated molecules [M + H](+). An N-terminal rather than a C-terminal Arg residue was advantageous for the formation of both [M + H](+) and [M - H](-). The presence of the Phe residue resulted in the increase of the ion yields of both [M + H](+) and [M - H](-). In contrast, the presence of phosphate group(s) contributed to the suppression of the yields of both [M + H](+) and [M - H](-) due to the loss of phosphate group. The detection limits for both [M + H](+) and [M - H](-) of model peptides have been evaluated. © American Society for Mass Spectrometry, 2011