Date of Award


Degree Name

Doctor of Philosophy



First Advisor

Kinsel, Gary


The equilibrium nature of a plume of laser desorbed material was examined through the application of a previously developed thermodynamic model to the ion signals observed in 337 nm MALDI mass spectra of mixtures of the matrix sinapic acid with the amino acids alanine, valine, isoleucine, and phenylalanine. Samples were prepared using both conventional dried-droplet and solvent-free methods for comparison. The relative yield of protonated amino acid was shown to increase as the amino acid gas-phase basicity increases for both sample preparation methods. Matrix gas phase basicity values extracted from the equilibrium plots were shown to be in good agreement ([M – H+]• 876 kJ/mol and [M] 879 kJ/mol) with published experimental values supporting a mechanism wherein the protonated sinapic acid and/or the matrix radical cation act as the proton donor species. These experiments further reveal that there is a large difference in the extracted plume effective temperatures (Teff ) with the solvent-free method yielding lower plume Teff as compared to the dried-droplet sample preparation, e.g., 552 K versus 1296 K, respectively, at M:A 1:1 (mole:mole). In addition, these experiments suggest that plume Teff’s decrease as the relative amount of matrix deposited with the analyte increases, regardless of the sample preparation method. Cumulatively, these observations suggest that the crystalline solid allows more efficient transfer of the photoexcitation energy during the sample desorption step, as compared to the solvent-free sample, and/or collisional cooling is more effective for the plume of material desorbed from the solvent-free sample as compared to the conventional dried-droplet sample. Sample preparation has also been shown to have an influence on analyte ion signals observed in MALDI mass spectra. Methods to reduce matrix crystal size, control morphology, and improve sample homogeneity have yielded higher and more reproducible analyte ion yields. Explanations typically point toward increased laser heating as crystal size decreases leading to better sample ablation. The influence on crystal size on the plume Teff is not fully understood. MALDI samples prepared using the conventional dried-droplet method to plume Teff measured after the crystal size is reduced with on target grinding. The dried-droplet method for 10:1 and 20:1 (mole: mole) matrix to analyte ratios were determined to be 853 and 755 K, respectively, when the protonated matrix [SA+H+] was assumed to be the proton donor. Reduction of the matrix crystal size by grinding caused the measured plume Teff values to decrease by 20 to 40%. The plume Teff value for the ground dried-droplet sample at 10:1 was 681 K and at 20:1 was 407 K. These observations suggest the decreased plume Teff values measured when increasing the matrix-to-analyte ratio or decreasing the matrix crystal size as evidence of increased collisional cooling of the desorbed material. No amino acid fragmentation was observed in the MALDI mass spectra of samples prepared using the dried-droplet method at 2.19 mJ/cm2. However, prominent immonium ion signals were present for all amino acids studied after reducing the matrix crystal size by grinding. Lowering the laser fluence to 1.69 mJ/cm2 reduced but did not eliminate the observed fragmentation. This observation suggests that heat dissipation was limited in the small matrix crystals and led to analyte degradation. The plume Teff values measured at 1.69 mJ/cm2 were still lower than that measured at 2.19 mJ/cm2. The plume Teff value was 458 K for 10:1 and 346 K for 20:1 (mole: mole) matrix-to-analyte ratios Finally, a series of tri- and tetra- peptides were employed to explore the effects of amino acid residue position on the calculated gas phase basicities of the peptides. A notable observation is that of the gas phase basicity for the tri-peptide FAA vs that of AAF, in which the more basic residue that resides on the N-terminus has a higher gas phase basicity than that of the peptide with the residue on the C-terminus. It appears that intramolecular hydrogen bonding may also influence the gas phase basicity of the series of peptides studied.




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