Protonation of Glyn Homologues in Matrix-Assisted Laser Desorption Ionization

Protonation reactions of Glyn homologues were studied in order to elucidate the effect of peptide chain length and matrix materials on the matrix-assisted laser desorption ionization (MALDI) mechanism. At 337 nm nitrogen laser excitation the relative ion yield-chain length relationship showed considerable variability in 3,5-dimethoxy-4-hydroxycinnamic acid (SA), 2,5-dihydroxybenzoic acid (DHB), 6-aza-2-thiothymine (ATT), and R-cyano-4-hydroxycinnamic acid (CHCA), the four matrices studied. For SA and ATT, a monotonic increase of relative ion yields (RIYs) was observed with increasing peptide length. Similar increasing pattern and significantly higher RIYs were found for the homologues of the Glyn series in the CHCA matrix with the exception of Gly. The particularly high MALDI ion yield of this amino acid in CHCA may be attributed to preferential embedding and/or more efficient condensed-phase proton transfer. To unveil the nature of the proton-transfer reactions in MALDI, the peptide length dependence of the measured RIYs was compared to the trends observed in proton affinities (PAs) of the same homologues as well as to ion-molecule reaction rates calculated using the Langevin cross section. Chain extension enhancements in MALDI RIYs of all the studied matrices cannot be explained either by the increase in ground-state ion-molecule reaction rates or by a linear dependence on gas-phase PAs. However, in SA and ATT positive correlation was observed between MALDI RIYs of Glyn homologues and their PAs. The RIYs observed in CHCA were significantly higher than in SA. This effect could be explained by the markedly lower PA of CHCA (183 ( 2 kcal/mol) compared to that of SA (204 ( 4 kcal/mol).