The ease of peptide detection by matrix-assisted laser desorption/ionization mass spectrometry: the effect of secondary structure on signal intensity.

Several structurally well-characterized model peptides were used to examine the relationship between peptide structure and signal intensity in matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS). It was found that peptides displaying stable alpha-helical and beta-sheet structures show lower signal intensities than the corresponding analogs having disturbed secondary structures caused by substitution of two adjacent amino acids by their D isomers. Since such substitutions do not affect properties other than the secondary structure propensity, the differences observed are ascribed to this phenomenon or some related effect such as association. The results indicate that the formation of stable secondary structures in peptides may be a possible source of incomplete peptide mass fingerprints resulting from protein digestion and for difficulties in the quantitative evaluation of peptide mixtures via MALDI-MS.