Yong Jin Bae

Degree of Ionization in MALDI of Peptides: Thermal Explanation for the Gas-Phase Ion Formation

Degree of ionization (DI) in matrix-assisted laser desorption ionization (MALDI) was measured for five peptides using α-cyano-4-hydroxycinnanmic acid (CHCA) as the matrix. DIs were low 10−4 for peptides and 10−7 for CHCA. Total number of ions (i.e., peptide plus matrix) was the same regardless of peptides and their concentration, setting the number of gas-phase ions generated from a pure matrix as the upper limit to that of peptide ions. Positively charged cluster ions were too weak to support the ion formation via such ions. The total number of gas-phase ions generated by MALDI, and that from pure CHCA, was unaffected by the laser pulse energy, invalidating laser-induced ionization of matrix molecules as the mechanism for the primary ion formation. Instead, the excitation of matrix by laser is simply a way of supplying thermal energy to the sample. Accepting strong Coulomb attraction felt by cations in a solid sample, we propose three hypotheses for gas-phase peptide ion formation. In Hypothesis 1, they originate from the dielectrically screened peptide ions in the sample. In Hypothesis 2, the preformed peptide ions are released as part of neutral ion pairs, which generate gas-phase peptide ions via reaction with matrix-derived cations. In Hypothesis 3, neutral peptides released by ablation get protonated via reaction with matrix-derived cations.

A Simple Method for Quantification of Peptides and Proteins by Matrix-Assisted Laser Desorption Ionization Mass Spectrometry

Even though matrix-assisted laser desorption ionization (MALDI) is a powerful technique for mass spectrometry of peptides and proteins, it is not quite useful for their quantification that is one of the outstanding problems in quantitative proteomics. The main difficulty lies in the poor reproducibility of MALDI spectra. In this work, a simple method to circumvent this problem has been developed. The method is based on a previous observation that the reaction quotient for the matrix-to-peptide proton transfer evaluated in temperature-selected MALDI was nearly constant regardless of the peptide concentration in the solid sample. This implied a direct proportionality between the relative abundance of an analyte ion in a temperature-selected MALDI spectrum and the concentration of the corresponding neutral in the solid sample. This relation has been confirmed by calibration curves obtained for some peptides. Another characteristic of the relation is that it holds even when other analytes are present. This has been demonstrated for mixtures containing peptides and proteins. This and the fact that the method does not require the addition of internal standards allow rapid and inexpensive quantification of any analyte amenable to MALDI.

Quantitative reproducibility of mass spectra in matrix-assisted laser desorption ionization and unraveling of the mechanism for gas-phase peptide ion formation.

In a previous study on matrix-assisted laser desorption ionization (MALDI) of peptides using α-cyano-4-hydroxycinnamic acid (CHCA) as a matrix, we found that the patterns of single-shot spectra obtained under different experimental conditions became similar upon temperature selection. In this paper, we report that absolute ion abundances are also similar in temperature-selected MALDI spectra, even when laser fluence is varied. The result that has been obtained using CHCA and 2,5-dihydroxybenzoic acid as matrices is in disagreement with the hypothesis of laser-induced ionization of matrix as the mechanism for primary ion formation in MALDI. We also report that the total number of ions in such a spectrum is unaffected by the identity, concentration and number of analytes, i.e. it is the same as that in the spectrum of pure matrix. We propose that the generation of gas-phase ions in MALDI can be explained in terms of two thermal reactions, i.e. the autoprotolysis of matrix molecules and the matrix-to-analyte proton transfer, both of which are in quasi-equilibrium in the early matrix plume.

The Jahn-Teller effect in CH 3 Cl +(X̃E2): A combined high-resolution experimental measurement and ab initio theoretical study

The energy levels of CH(3)Cl(+)X̃(2)E showing strong spin-vibronic coupling effect (Jahn-Teller effect) have been measured up to 3500 cm(-1) above the ground vibrational state using one-photon zero-kinetic energy photoelectron and mass-analyzed threshold ionization spectroscopic method. Theoretical calculations have been also performed to calculate the spin-vibronic energy levels using a diabatic model and ab initio adiabatic potential energy surfaces (PESs). In the theoretical calculations the diabatic potential energy surfaces are expanded by the Taylor expansions up to the fourth-order including the multimode vibronic interactions. The calculated spin-orbit energy splitting (224.6 cm(-1)) for the ground vibrational state is in good agreement with the experimental data (219 ± 3 cm(-1)), which indicates that the Jahn-Teller and the spin-orbit coupling have been properly described in the theoretical model near the zero-point energy level. Based on the assignments predicted by the theoretical calculations, the experimentally measured energy levels were fitted to those from the diabatic model by optimizing the main spectroscopic parameters. The PESs from the ab initio calculations at the level of CASPT2/vq(t)z were thus compared with those calculated from the experimentally determined spectroscopic parameters. The theoretical diagonal elements in the diabatic potential matrix are in good agreement with those determined using the experimental data, however, the theoretical off-diagonal elements appreciably deviate from those determined using the experimental data for geometric points far away from the conical intersections. It is also concluded that the JT effect in CH(3)Cl(+) mainly arises from the linear coupling and the mode coupling between the CH(3) deform (υ(5)) and CH(3) rock (υ(6)) vibrations. The mode couplings between the symmetric C-Cl stretching vibration υ(3) with υ(5) and υ(6) are also important to understand the spin-vibronic structure of the molecule.

Efficient methods to generate reproducible mass spectra in matrix-assisted laser desorption ionization of peptides.

AbstractIn our previous matrix-assisted laser desorption ionization (MALDI) studies of peptides, we found that their mass spectra were virtually determined by the effective temperature in the early matrix plume, Tearly, when samples were rather homogeneous. This empirical rule allowed acquisition of quantitatively reproducible spectra. A difficulty in utilizing this rule was the complicated spectral treatment needed to get Tearly. In this work, we found another empirical rule that the total number of particles hitting the detector, or TIC, was a good measure of the spectral temperature and, hence, selection of spectra with the same TIC resulted in reproducible spectra. We also succeeded in obtaining reproducible spectra throughout a measurement by controlling TIC near a preset value through feedback adjustment of laser pulse energy. Both TIC selection and TIC control substantially reduced the shot-to-shot spectral variation in a spot, spot-to-spot variation in a sample, and even sample-to-sample variation in MALDI using α-cyano-4-hydroxycinnamic acid or 2,5-dihydroxybenzoic acid as matrix. Based on the utilization of acquired data, TIC control was more efficient than TIC selection by an order of magnitude. Both techniques produced calibration curves with excellent linearity, suggesting their utility in quantification of peptides. Figureᅟ

Matrix Suppression as a Guideline for Reliable Quantification of Peptides by Matrix-Assisted Laser Desorption Ionization

We propose to divide matrix suppression in matrix-assisted laser desorption ionization into two parts, normal and anomalous. In quantification of peptides, the normal effect can be accounted for by constructing the calibration curve in the form of peptide-to-matrix ion abundance ratio versus concentration. The anomalous effect forbids reliable quantification and is noticeable when matrix suppression is larger than 70%. With this 70% rule, matrix suppression becomes a guideline for reliable quantification, rather than a nuisance. A peptide in a complex mixture can be quantified even in the presence of large amounts of contaminants, as long as matrix suppression is below 70%. The theoretical basis for the quantification method using a peptide as an internal standard is presented together with its weaknesses. A systematic method to improve quantification of high concentration analytes has also been developed.

Rotational state selection of a CH3I+ ion beam using vacuum ultraviolet–mass-analyzed threshold ionization spectroscopy: Characterization using photodissociation spectroscopy

The A(2)A(1)<--X(2)E(3/2) transition of CH(3)I(+) was investigated by photodissociation (PD) of the cation generated by one-photon mass-analyzed threshold ionization (MATI). Compared to the PD spectrum obtained by excitation of the cation in the main 0-0 band in the MATI spectrum, those obtained by excitation of the cations in the satellite structures showed substantially simplified rotational structures for nondegenerate vibronic bands. Spectral simplification occurred because each satellite consisted mostly of cations with one K quantum number. Spectroscopic constants in the ground vibronic state and in the 2(1)3(5), 2(1)3(8), 3(9), and 3(13) nondegenerate vibrational states in A(2)A(1) were determined via spectral fitting. Also, those in the 2(1)3(n)6(1) (n=1?) degenerate state, which had been reported previously, was improved. The K quantum number in each satellite determined by the present high resolution study was compatible with the prediction by the symmetry selection rule for photoionization. That is, the K quantum number of the ion core in high Rydberg states accessed by one-photon excitation was found to be conserved upon pulsed field ionization. This work demonstrates generation of mass-selected, vibronically selected, and K-selected ion beam by one-photon MATI.

K selection in one-photon mass-analyzed threshold ionization of CH3I and CD3I to the X̃E3∕22 state cations

One-photon mass-analyzed threshold ionization (MATI) spectra for the X (2)E(3/2) states of CH(3)I(+) and CD(3)I(+) were measured using vacuum ultraviolet radiation generated by four-wave mixing in Kr. Spin-orbit density functional theory calculations at the B3LYP/aug-cc-pVTZ level and spin-orbit/Jahn-Teller calculations were made to aid vibrational assignment. Each vibrational band consisted of several peaks due to different DeltaK transitions, which could be assigned by using molecular parameters determined in the previous high resolution photodissociation spectroscopic study. Possibility of generating mass-selected, vibronically selected and K-selected ion beam with decent intensity by one-photon MATI was demonstrated. The ionization energies to the X (2)E(3/2) states of CH(3)I(+) and CD(3)I(+) corrected for the rotational contribution were 9.5386+/-0.0006 and 9.5415+/-0.0006 eV, respectively.

A Thermal Mechanism of Ion Formation in MALDI

An important recent discovery concerning the fundamentals of matrix-assisted laser desorption/ionization (MALDI) is that the abundance of each ion appearing in a spectrum is fixed, regardless of the experimental condition, when an effective temperature associated with the spectrum is fixed. We describe this phenomenon and the thermal picture for the ion formation in MALDI derived from it. Accepting that matrix-to-analyte proton transfer is in quasi-equilibrium as supported by experimental data, the above thermal determination occurs because the primary (matrix) ion formation processes are thermally governed. We propose that the abundances of the primary ions are limited by the autoprotolysis-recombination process regardless of how they are initially produced. Finally, we note that primary ion formation, secondary (analyte) ion formation, and their dissociations occur sequentially while the effective temperature of the matrix plume falls steadily due to cooling associated with expansion.

Why do the Abundances of Ions Generated by MALDI Look Thermally Determined

AbstractIn a previous study (J. Mass Spectrom.48, 299–305, 2013), we observed that the abundance of each ion in a matrix-assisted laser desorption ionization (MALDI) spectrum looked thermally determined. To find out the explanation for the phenomenon, we estimated the ionization efficiency and the reaction quotient (QA) for the autoprotolysis of matrix, M + M → [M + H]+ + [M − H]−, from the temperature-controlled laser desorption ionization spectra of α-cyano-4-hydroxycinnamic acid (CHCA) and 2,5-dihydroxybenzoic acid (DHB). We also evaluated the equilibrium constants (KA) for the autoprotolysis at various temperatures by quantum chemical calculation. Primary ion formation via various thermal models followed by autoprotolysis-recombination was compatible with the observations. The upper limit of the effective temperature of the plume where autoprotolysis-recombination occurs was estimated by equating QA with the calculated equilibrium constant. Figureᅟ