Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry with Re-Engineered 2, a 5-Dihydroxypheny Acid Derivative

Matrix-assisted laser desorption ionization (MALDI) has been a mainstay in protein mass spectrometry, imaging, and proteomics. The common approach to matrix design and selection has been empirical. The most common matrices used are 2,5-dihydroxybenzoic (2,5-DHB) and alpha-cyano-4-hydroxycinnamic acid (aCCa). Using the known relationship between 2,5-phenyl carboxylic acid and tyrosine amino A 2,5-dihydroxyphenylcarboxylic acid molecule based on the hydroquinone core of 2,5-DHB was designed and synthesized (M10) by using the known relationship between 2,5-phenyl carboxylic acid and tyrosine amino acids. The two matrices (aCCa and M10) were compared and contrasted using neuronal peptide mixtures, tryptic digests from two-dimensional gel spots from culture Escherichia coli, and mature green tomato fruit. The peptide mixtures or mass fingerprints were analyzed similarly, except only a 30 s analysis time window per sample was allocated for M10, whereas 3 min per sample were allocated for aCCa. The results are that M10 generated greater ion yield, sequence coverage, and probable Mascot identification scores over aCCa, or the scores were comparable with less sample acquisition time for M10. The n-decanoic acid side chain promotes matrix-to-analyte interactions and proton transfer during crystallization. Our findings support the hypothesis of pseudo proton transfer from the excited matrix species during crystallization as a dominant mechanism for generating protonated and deprotonated analyte ions due to the lower proton affinity of M10 that is computed using density functional theory and the 6–311G** basis set for the protonated matrix species. The enhanced performance of matrix M10 will positively impact MALDI research and will extend the lifetime and operability of older instruments at hospitals, laboratories, and teaching-intensive universities where instrument budgets are stretched. By using M10 as a matrix, the sampled runtime is reduced, ion yield is increased, and potential instrument usage lifetime is increased.