Amino acid composition and wavelength effects in matrix‐assisted laser desorption/ionization

Abstract

Ion yields were investigated in matrix-assisted laser desorption/ionization (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 or polar amino acid residues. The lack of basic residues led to diminishing ion formation at 337 nm. Increasing the chain length led to enhanced ionization even for peptides with non-polar side chains. In contrast to the liquid phase basicities the basic residues showed Arg > His > Lys order in their affinity to protons. Variations in the average ion yield showed decreasing trend with increasing basicity of the residues pointing to potential differences in the matrix incorporation of different guest molecules. Dye laser excitation at 280 nm resulted in extensive fragmentation and enhanced ion formation from peptides containing aromatic side chains indicating the possible role of analyte excited states in ion formation. Semi-empirical quantum chemical calculations were used to explore the sites of protonation. Heat of formation diagrams 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 these intermolecular bonds, in the case of His-His an intramolecular hydrogen bond was also formed within the analyte molecule. Proton affinity values were calculated for every dipeptide while the site of protonation was varied. The results seemed to indicate that for every dipeptide the amino terminus was more susceptible to protonation than the peptide bond. Due to increased stabilization effects in homo-oligomers (Gly,), increasing the number of residues led to an increase in proton affinity. For basic diopeptides (e.g., His-His), the side chains bad the highest proton affinity, underlining their role in MALDI of proteins.

Protonation of Glyn Homologues in Matrix-Assisted Laser Desorption Ionization

“…Detailed description of the system can be found elsewhere. 7 Briefly, the MALDI-generated ions were accelerated to 10-30 kV and ejected into the field-free region of a time-of-flight (TOF) mass spectrometer. The ions were detected by a dual-microchannel plate (Galileo Electro-Optics Co., Sturbridge, MA) that was biased to 1900 V. The ion currents were amplified (×10) and recorded by a 200 MHz transient recorder (TR8828D, LeCroy, Albuquerque, NM).…”

A density functional theory (DFT) study on gas-phase proton transfer reactions of derivatized and underivatized peptide ions generated by matrix-assisted laser desorption ionization

“…Strong evidence for proton transfer reactions between protonated matrix and analyte was recently reported using mixtures of conventional matrices and various amino acids varying in gas phase basicity [6]. In peptide analysis it was shown that the type of amino acid incorporated in the peptide backbone affects the abundance of the corresponding ions generated [14]. In particular, MALDI spectra of peptides derived from proteolytic digestion of proteins with trypsin indicated that the proton affinity of Cterminus amino acids governs the MALDI response of the resulting peptide ions and lysine containing peptides generated by tryptic digestion of proteins produce ions detected in lesser abundance than those incorporating arginine [15].…”

Algorithm for accurate similarity measurements of peptide mass fingerprints and its application

“…This allowed for tests of various hypotheses that were put forward in recent literature e.g., about influence of peptide hydrophobicity on signal intensity [13]. To elucidate how the amino acids are distributed at every position in the peptide sequence, we calculated the relative entropy [14,15] of each amino acid at every position and the potential of the peptides to form secondary structures as described by Williams et al [16] and Wilmot and Thornton [17].…”