Changes in dissociation efficiency and kinetics of peptide ions induced by basic residues and their mechanistic implication

Formation of gas-phase peptide ions and their dissociation in MALDI: insights from kinetic and ion yield studies

Insights on mechanisms for the generation of gas-phase peptide ions and their dissociation in matrix-assisted laser desorption ionization (MALDI) gained from the kinetic and ion yield studies are presented. Even though the time-resolved photodissociation technique was initially used to determine the dissociation kinetics of peptide ions and their effective temperature, it was replaced by a simpler method utilizing dissociation yields from in-source decay (ISD) and post-source decay (PSD). The ion yields for a matrix and a peptide were measured by repeatedly irradiating a region on a sample and collecting ion signals until the sample in the region was completely depleted. Matrix- and peptide-derived gas-phase cations were found to be generated by pre-formed ion emission or by ion-pair emission followed by anion loss, but not by laser-induced ionization. The total number of ions, that is, matrix plus peptide, was found to be equal to the number of ions emitted from a pure matrix. A matrix plume was found to cool as it expanded, from around 800-1,000 K to 400-500 K. Dissociation of peptide ions along b/y channels was found to occur statistically, that is, following RRKM behavior. Small critical energy (E0  = 0.6-0.7 eV) and highly negative critical entropy (ΔS(‡)  = -30 to -25 eu) suggested that the transition structure was stabilized by multiple intramolecular interactions.

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.

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.

Ion yields for some salts in MALDI: mechanism for the gas-phase ion formation from preformed ions

Preformed ion emission is the main assumption in one of the prevailing theories for peptide and protein ion formation in matrix-assisted laser desorption ionization (MALDI). Since salts are in preformed ion forms in the matrix-analyte mixture, they are ideal systems to study the characteristics of preformed ion emission. In this work, a reliable method to measure the ion yield (IY) in MALDI was developed and used for a solid salt benzyltriphenylphosphonium chloride and two room-temperature ionic liquids 1-butyl-3-methylimidazolium hexafluorophosphate and trihexyltetradecylphosphonium bis(2,4,4-trimethylpentyl)phosphinate. IY for the matrix (α-cyano-4-hydroxycinnamic acid, CHCA) was also measured. Taking 1 pmol salts in 25 nmol CHCA as examples, IYs for three salts were similar, (4-8) × 10(-4), and those for CHCA were (0.8-1.2) × 10(-7). Even though IYs for the salts and CHCA remained virtually constant at low analyte concentration, they decreased as the salt concentrations increased. Two models, Model 1 and Model 2, were proposed to explain low IYs for the salts and the concentration dependences. Both models are based on the fact that the ion-pair formation equilibrium is highly shifted toward the neutral ion pair. In Model 1, the gas-phase analyte cations were proposed to originate from the same cations in the solid that were dielectrically screened from counter anions by matrix neutrals. In Model 2, preformed ions were assumed to be released from the solid sample in the form of neutral ion pairs and the anions in the ion pairs were assumed to be eliminated via reactions with matrix-derived cations.

Expansion cooling in the matrix plume is under-recognized in MALDI mass spectrometry

Time-of-flight (TOF) mass spectra for a peptide (Y(6)) were obtained by utilizing matrix-assisted infrared laser desorption ionization (IR-MALDI) with glycerol as the matrix and by ultraviolet MALDI with α-cyano-4-hydroxycinnamic acid (CHCA), sinapinic acid (SA), and 2,5-dihydroxybenzoic acid (DHB). Collisional activation during ion extraction and exothermicity in the gas-phase proton transfer were found to be unimportant as the driving forces for in-source (ISD) and post-source (PSD) decays, indicating that the thermal energy acquired during photo-ablation is responsible for their occurrence. The temperatures of [Y(6) + H](+) in the 'early' and 'late' matrix plumes were estimated by the kinetic analysis of the ISD and PSD yields, respectively. The order of the temperatures was glycerol < DHB ≈ SA < CHCA in the early plume and glycerol < DHB < SA < CHCA in the late plume. For each matrix, the temperature in the late plume was lower than in the early plume by 300-400 K, which was attributed to expansion cooling. The model (thermalization followed by expansion cooling) proposed to explain the occurrence of both rapid ISD and slow PSD is not only in sharp contrast with but also mutually exclusive with the prevailing explanation that the exothermicity in proton transfer and in-plume collisional activation are the driving forces for ion fragmentation in MALDI. The model also explains why MALDI is more successful for mass spectrometry of labile molecules than other desorption techniques that do not utilize a matrix. Factors affecting the plume temperature are also discussed.