Assessment of Gas Phase Basicities of Protonated Peptides by the Kinetic Method

Weak Acid-Base Interactions of Histidine and Cysteine Affect the Charge States, Tertiary Structure, and Zn(II)-Binding of Heptapeptides

Zinc fingers are proteins that are characterized by the coordination of zinc ions by an amino acid sequence that commonly contains two histidines and two cysteines (2His-2Cys motif). Investigations of oligopeptides that contain the 2His-2Cys motif, e.g., acetyl-His₁-Cys₂-Gly₃-Pro₄-Tyr₅-His₆-Cys₇, have discovered they exhibit pH-dependent Zn(II) chelation and have redox activities with Cu(I/II), forming a variety of metal complexes. To further understand how these 2His-2Cys oligopeptides bind these metal ions, we have undertaken a series of ion mobility-mass spectrometry and B3LYP/LanL2DZ computational studies of structurally related heptapeptides. Starting with the sequence above, we have modified the potential His, Cys, or C-terminus binding sites and report how these changes in primary structure affect the oligopeptides positive and negative charge states, conformational structure, collision-induced breakdown energies, and how effectively Zn(II) binds to these sequences. The results show evidence that the weak acid-base properties of Cys-His are intrinsically linked and can result in an intramolecular salt-bridged network that affects the oligopeptide properties.

Ion mobility spectrometry-hydrogen deuterium exchange mass spectrometry of anions: part 1. Peptides to proteins

Ion mobility spectrometry (IMS) coupled with hydrogen deuterium exchange (HDX)-mass spectrometry (MS) has been used to study the conformations of negatively-charged peptide and protein ions. Results are presented for ion conformers of angiotensin 1, a synthetic peptide (SP), bovine insulin, ubiquitin, and equine cytochrome c. In general, the SP ion conformers demonstrate a greater level of HDX efficiency as a greater proportion of the sites undergo HDX. Additionally, these ions exhibit the fastest rates of exchange. Comparatively, the angiotensin 1 ions exhibit a lower rate of exchange and HDX level presumably because of decreased accessibility of exchange sites by charge sites. The latter are likely confined to the peptide termini. Insulin ions show dramatically reduced HDX levels and exchange rates, which can be attributed to decreased conformational flexibility resulting from the disulfide bonds. For the larger ubiquitin and protein ions, increased HDX is observed for larger ions of higher charge state. For ubiquitin, a conformational transition from compact to more elongated species (from lower to higher charge states) is reflected by an increase in HDX levels. These results can be explained by a combination of interior site protection by compact conformers as well as decreased access by charge sites. The elongated cytochrome c ions provide the largest HDX levels where higher values correlate with charge state. These results are consistent with increased exchange site accessibility by additional charge sites. The data from these enhanced IMS-HDX experiments are described in terms of charge site location, conformer rigidity, and interior site protection.

The applicability of the kinetic method for measuring relative affinities of macromolecules for polyatomic substrates

This paper is a review of the kinetic method for the determination of thermochemical values for gas-phase molecules. In addition, we have explored the utility of the kinetic method to obtain meaningful relative binding energies of macromolecules for polyatomic substrates using a system comprising poly(methylmethacrylate) (PMMA) oligomers and doubly protonated diaminoalkanes. The major factors which determined the suitability of the kinetic method for this system were identified as (i) the structural arrangement of the parent ion complex, (ii) possible reverse activation barriers, and (iii) the evaluations of Δ(ΔS‡). Molecular mechanics/molecular dynamics (MM/MD) simulations, together with ion mobility spectrometry, suggests the parent ion complexes represent a relatively equal sharing of the substrate between two the PMMA oligomers within the complex and that the two PMMA oligomers interact almost exclusively with the substrate, and not with each other. MS/MS of the trimeric parent complexes resulted in one PMMA unit leaving as a neutral which suggests very limited coulombic repulsion (that would contribute to a reverse activation barrier). The drift times of PMMA-diaminoalkane complexes that were generated directly by ESI-MS or by dissociation of a trimeric PMMA-diaminoalkane-PMMA complex were found to be identical, and when combined with MM/MD simulations suggested that the product PMMA-diaminoalkane dication has the same conformation as it does when part of a trimeric complex. This is evidence for Δ(ΔS‡) ≃ Δ(ΔS) and using a statistical mechanics approach, Δ(ΔS) ≃ 0. The effective temperature variable in the kinetic method expression was found to decrease as a function of the size of the trimeric complex, suggesting that the population distribution of the dissociating ensemble of complexes narrows as size increases.

Matrix-assisted laser desorption/ionisation mass spectrometric response factors of peptides generated using different proteolytic enzymes

Matrix-assisted laser desorption/ionisation (MALDI) mechanisms and the factors that influence the intensity of the ion signal in the mass spectrum remain imperfectly understood. In proteomics, it is often necessary to maximise the peptide response in the mass spectrum, especially for low abundant proteins or for proteolytic peptides of particular significance. We set out to determine which of the common proteolytic enzymes give rise to peptides with the best response factors under MALDI conditions. Standard proteins were enzymatically digested using four common proteases. We assessed relative response factors by coanalyzing the resulting digests. Thus, when tryptic peptides were added in equimolar quantities to their corresponding Asp-N, chymotrypsin and Glu-C digests, tryptic peptide signals were always predominant in the resulting MALDI mass spectra. Observable peaks attributable to non-tryptic peptides generally contained a terminal basic residue. It was proposed that a terminal basic residue has a disproportionate influence upon gas-phase basicity, and this hypothesis was supported by experiments with model isotopically labelled peptides. Experiments applying Cook's kinetic method showed that the peptide with a C-terminal arginine residue was more basic than the equivalent peptide with an N-terminal arginine, which was more basic than the peptide in which the arginine was mid-chain. Thus, the observation of the higher MALDI mass spectrometry response factors of tryptic peptides in comparison with peptides derived using other proteolytic enzymes corresponds with higher gas-phase basicities and may, along with other factors such as the complexity of the digest, influence the choice of enzyme in "bottom-up" proteomic experiments.

Leucine enkephalin--a mass spectrometry standard

The present article reviews the mass spectrometric fragmentation processes and fragmentation energetics of leucine enkephalin, a commonly used peptide, which has been studied in detail and has often been used as a standard or reference compound to test novel instrumentation, new methodologies, or to tune instruments. The main purpose of the article is to facilitate its use as a reference material; therefore, all available mass spectrometry-related information on leucine enkephalin has been critically reviewed and summarized. The fragmentation mechanism of leucine enkephalin is typical for a small peptide; but is understood far better than that of most other compounds. Because ion ratios in the MS/MS spectra indicate the degree of excitation, leucine enkephalin is often used as a thermometer molecule in electrospray or matrix-assisted laser desorption ionization (ESI or MALDI). Other parameters described for leucine enkephalin include collisional cross-section and energy transfer; proton affinity and gas-phase basicity; radiative cooling rate; and vibrational frequencies. The lowest-energy fragmentation channel of leucine enkephalin is the MH(+)  → b(4) process. All available data for this process have been re-evaluated. It was found that, although the published E(a) values were significantly different, the corresponding Gibbs free energy change showed good agreement (1.32 ± 0.07 eV) in various studies. Temperature- and energy-dependent rate constants were re-evaluated with an Arrhenius plot. The plot showed good linear correlation among all data (R(2)  = 0.97), spanned over a 9 orders of magnitude range in the rate constants and yielded 1.14 eV activation energy and 10(11.0)  sec(-1) pre-exponential factor. Accuracy (including random and systematic errors, with a 95% confidence interval) is ±0.05 eV and 10(±0.5)  sec(-1), respectively. The activation entropy at 470 K that corresponds to this reaction is -38.1 ± 9.6 J mol(-1)  K(-1). We believe that these re-evaluated values are by far the most accurate activation parameters available at present for a protonated peptide and can be considered as "consensus" values; results on other processes might be compared to this reference value.

Differential interactions of isomeric amino sugars with insulin studied under electrospray ionisation mass spectrometry

Protein-ligand interactions were studied for bovine insulin-amino sugar systems under electrospray ionisation mass spectrometry conditions. The isomeric amino sugars showed differences in the relative abundance of 1:1 protein-ligand complex formation. The electrospray ionisation and tandem mass spectrometry results of the complex clearly demonstrated that the differences in the interaction of isomeric sugars with insulin are mainly due to the differences in their gas-phase basicity. The same phenomenon is replicated in the formation of complexes between insulin and other ligands, such as amino acids, as well as in the binding of the amino sugars with amyloid β 1-40 peptide.

Gas-phase acid-base properties of melamine and cyanuric acid

The thermochemical properties of melamine and cyanuric acid were characterized using mass spectrometry measurements along with computational studies. A triple-quadrupole mass spectrometer was employed with the application of the extended Cooks kinetic method. The proton affinity (PA), gas-phase basicity (GB), and protonation entropy (Δ(p)S) of melamine were determined to be 226.2 ± 2.0 kcal/mol, 218.4 ± 2.0 kcal/mol, and 26.2 ± 2.0 cal/mol K, respectively. The deprotonation enthalpy (Δ(acid)H), gas-phase acidity (Δ(acid)G), and deprotonation entropy (Δ(acid)S) of cyanuric acid were determined to be 330.7 ± 2.0 kcal/mol, 322.9 ± 2.0 kcal/mol, and 26.1 ± 2.0 cal/mol K, respectively. The geometries and energetics of melamine, cyanuric acid, and related ionic species were calculated at the B3LYP/6-31+G(d) level of theory. The computationally predicted proton affinity of melamine (225.9 kcal/mol) and gas-phase deprotonation enthalpy of cyanuric acid (328.4 kcal/mol) agree well with the experimental results. Melamine is best represented as the imide-like triazine-triamine form and the triazine nitrogen is more basic than the amino group nitrogen. Cyanuric acid is best represented as the keto-like tautomer and the N-H group is the most probable proton donor.

Evidence for a quasi-equilibrium distribution of states for bradykinin [M + 3H]3+ ions in the gas phase

Multidimensional ion mobility spectrometry coupled with mass spectrometry (IMS-IMS-MS) techniques are used to select and activate six different gas-phase conformations of bradykinin [M + 3H](3+) ions. Drift time distributions as a function of activation voltage show that at low voltages selected structures undergo conformational transitions in what appears to be a pathway dependent fashion. Over a relatively wide range of intermediate activation voltages a distribution of states that is independent of the initial conformation selected for activation (as well as the activation voltage in this intermediate region) is established. This distribution appears to represent an equilibrium distribution of gas-phase structures that is reached prior to the energy required for dissociation. Establishment of a quasi-equilibrium prior to dissociation results in identical dissociation patterns for different selected conformations. A discussion of the transition from solution-like to gas-phase structures is provided.

Gas-phase acidities of cysteine-polyglycine peptides: the effect of the cysteine position

The sequence and conformational effects on the gas-phase acidities of peptides have been studied by using two pairs of isomeric cysteine-polyglycine peptides, CysGly(3,4)NH(2) and Gly(3,4)CysNH(2). The extended Cooks kinetic method was employed to determine the gas-phase acidities using a triple quadrupole mass spectrometer with an electrospray ionization source. The ion activation was achieved via collision-induced dissociation experiments. The deprotonation enthalpies (Delta(acid)H) were determined to be 323.9 +/- 2.5 kcal/mol (CysGly(3)NH(2)), 319.2 +/- 2.3 kcal/mol (CysGly(4)NH(2)), 333.8 +/- 2.1 kcal/mol (Gly(3)CysNH(2)), and 321.9 +/- 2.8 kcal/mol (Gly(4)CysNH(2)), respectively. The corresponding deprotonation entropies (Delta(acid)S) of the peptides were estimated. The gas-phase acidities (Delta(acid)G) were derived to be 318.4 +/- 2.5 kcal/mol (CysGly(3)NH(2)), 314.9 +/- 2.3 kcal/mol (CysGly(4)NH(2)), 327.5 +/- 2.1 kcal/mol (Gly(3)CysNH(2)), and 317.4 +/- 2.8 kcal/mol (Gly(4)CysNH(2)), respectively. Conformations and energetic information of the neutral and anionic peptides were calculated through simulated annealing (Tripos), geometry optimization (AM1), and single point energy calculations (B3LYP/6-31+G(d)), respectively. Both neutral and deprotonated peptides adopt many possible conformations of similar energies. All neutral peptides are mainly random coils. The two C-cysteine anionic peptides, Gly(3,4)(Cys-H)(-)NH(2), are also random coils. The two N-cysteine anionic peptides, (Cys-H)(-)Gly(3,4)NH(2), may exist in both random coils and stretched helices. The two N-cysteine peptides, CysGly(3)NH(2) and CysGly(4)NH(2), are significantly more acidic than the corresponding C-terminal cysteine ones, Gly(3)CysNH(2) and Gly(4)CysNH(2). The stronger acidities of the former may come from the greater stability of the thiolate anion resulting from the interaction with the helix-macrodipole, in addition to the hydrogen bonding interactions.

Blackbody infrared radiative dissociation of bradykinin and its analogues: energetics, dynamics, and evidence for salt-bridge structures in the gas phase

Blackbody infrared radiative dissociation (BIRD) spectra of singly and doubly protonated bradykinin and its analogues are measured in a Fourier-transform mass spectrometer. Rate constants for dissociation are measured as a function of temperature with reaction delays up to 600 s. From these data, Arrhenius activation parameters in the zero-pressure limit are obtained. The activation parameters and dissociation products for the singly protonated ions are highly sensitive to small changes in ion structure. The Arrhenius activation energy (E(a)) and pre-exponential (or frequency factor, A) of the singly protonated ions investigated here range from 0.6 to 1.4 eV and 10(5) to 10(12) s(-1), respectively. For bradykinin and its analogues differing by modification of the residues between the two arginine groups on either end of the molecule, the singly and doubly protonated ions have average activation energies of 1.2 and 0.8 eV, respectively, and average A values of 10(8) and 10(12) s(-1), respectively, i.e., the presence of a second charge reduces the activation energy by 0.4 eV and decreases the A value by a factor of 10(4). This demonstrates that the presence of a second charge can dramatically influence the dissociation dynamics of these ions. The doubly protonated methyl ester of bradykinin has an E(a) of 0.82 eV, comparable to the value of 0.84 eV for bradykinin itself. However, this value is 0.21 +/- 0.08 eV greater than that of singly protonated methyl ester of bradykinin, indicating that the Coulomb repulsion is not the most significant factor in the activation energy of this ion. Both singly and doubly protonated Lys-bradykinin ions have higher activation energies than the corresponding bradykinin ions indicating that the addition of a basic residue stabilizes these ions with respect to dissociation. Methylation of the carboxylic acid group of the C-terminus reduces the E(a) of bradykinin from 1.3 to 0.6 eV and the A factor from 1012 to 105 s(-1). This modification also dramatically changes the dissociation products. Similar results are observed for [Ala(6)]-bradykinin and its methyl ester. These results, in combination with others presented here, provide experimental evidence that the most stable form of singly protonated bradykinin is a salt-bridge structure.

Investigation of deprotonation reactions on globular and denatured proteins at atmospheric pressure by ESSI-MS

Deprotonation reactions of multiply charged protein ions have been studied by introducing volatile reference bases at atmospheric pressure between an electrosonic spray ionization (ESSI) source and the inlet of a mass spectrometer. Apparent gas-phase basicities (GB(app)) of different charge states of protein ions were determined by a bracketing approach. The results obtained depend on the conformation of the protein ions in the gas phase, which is linked to the type of buffer used (denaturing or nondenaturing). In nondenaturing buffer, the GB(app) values are consistent with values predicted by the group of Kebarle using an electrostatic model (J. Mass Spectrom.2002, 38, 618) based on the crystal structures, but taking into account salt bridges between ionized basic and acidic sites on the protein surface. A new basicity order for the most basic sites was therefore obtained. An excellent agreement with the charge residue model (CRM) is obtained when comparing the observed and calculated maximum charge state. Decharging of the proteins in the electrosonic spray process could be also useful in the study on noncovalent complexes, by decreasing repulsive electrostatic interactions. A unified mechanism of the ESSI process is proposed.

Rapid and precise measurements of gas-phase basicity of peptides and proteins at atmospheric pressure by electrosonic spray ionization-mass spectrometry

Deprotonation reactions of peptide and protein ions have been studied by introducing volatile reference bases at atmospheric pressure between an electrosonic spray ionization (ESSI) source and the inlet of a hybrid quadrupole time-of-flight mass spectrometer. This new setup offers the unique possibility to measure the apparent gas-phase basicity GBapp of multiply charged ions by a bracketing approach. A very good agreement has been obtained with reference values obtained by Fourier transform-ion cyclotronic resonance (FT-ICR), validating our approach. The measurements were then extended to larger biomolecules such as insulin and myoglobin in native and denaturing buffers. The main advantages of this methodology are measurements at atmospheric pressure with good sensitivity (for concentrations less than 10 microM in denaturing or nondenaturing buffer), very good precision (less than 2%), and in a short time (less than 30 min to screen up to 23 volatile reference bases).

Gaseous bradykinin and its singly, doubly, and triply protonated forms: a first-principles study

The conformers of gaseous bradykinin, BK, (Arg(1)-Pro(2)-Pro(3)-Gly(4)-Phe(5)-Ser(6)-Pro(7)-Phe(8)-Arg(9)) and its protonated forms, [BK + H](+), [BK + 2H](2+), and [BK + 3H](3+), were examined theoretically using a combination of the Merck molecular force field, Hartree-Fock, and density functional theory. Neutral BK, [BK + H](+), and [BK + 2H](2+) exist in zwitterionic forms that are stabilized by internal solvation and have compact structures; [BK + 3H](3+) differs by the absence of a salt bridge and adopts an elongated form. The common structural feature in all four BK species is a beta-turn in the Ser(6)-Pro(7)-Phe(8)-Arg(9) sequence. The gas-phase basicity of [BK + H](+) estimated from the calculated protonation energy is in accord with published experimental basicity; population-weighted collision cross-sections of the three ionic forms are in agreement with experimental cross-sections in the literature.

Ion formation mechanisms in UV-MALDI

Matrix Assisted Laser Desorption/Ionization (MALDI) is a very widely used analytical method, but has been developed in a highly empirical manner. Deeper understanding of ionization mechanisms could help to design better methods and improve interpretation of mass spectra. This review summarizes current mechanistic thinking, with emphasis on the most common MALDI variant using ultraviolet laser excitation. A two-step framework is gaining acceptance as a useful model for many MALDI experiments. The steps are primary ionization during or shortly after the laser pulse, followed by secondary reactions in the expanding plume of desorbed material. Primary ionization in UV-MALDI remains somewhat controversial, the two main approaches are the cluster and pooling/photoionization models. Secondary events are less contentious, ion-molecule reaction thermodynamics and kinetics are often invoked, but details differ. To the extent that local thermal equilibrium is approached in the plume, the mass spectra may be straightforwardly interpreted in terms of charge transfer thermodynamics.

Prediction of Low-Energy Collision-Induced Dissociation Spectra of Peptides

A kinetic model, based on the "mobile proton" model of peptide fragmentation, was developed to quantitatively simulate the low-energy collision-induced dissociation (CID) spectra of peptides dissociated in a quadrupole ion trap mass spectrometer. The model includes most fragmentation pathways described in the literature, plus some additional pathways based on the author's observations. The model was trained by optimizing parameters within the model for predictions of CID spectra of known peptides. A best set of parameters was optimized to obtain best match between the simulated spectra and the experimental spectra in a training data set. The performance of the mathematical model and the associated optimized parameter set used in the CID spectra simulation was evaluated by generating predictions for a large number of known peptides, which were not included in the training data set. It was shown that the model is able to predict peptide CID spectra with reasonable accuracy in fragment ion intensities for both singly and doubly charged peptide parent ions up to 2000 u in mass. The optimized parameter set was evaluated to gain insight into the collision-induced peptide fragmentation process.

Chiral analysis using the kinetic method with optimized fixed ligands: applications to some antibiotics

A new version of the kinetic method for chiral analysis, which employs a fixed (nondissociating) ligand as well as the usual analyte and chiral reference ligands, is introduced to simplify the kinetics of this experiment. Singly charged clusters containing the divalent transition metal ion MnII, a peptide which serves as a fixed ligand, an amino acid chiral reference, and the analyte 4-benzyl-2-oxazolidinone were generated by electrospray ionization (ESI). The cluster ion of interest was mass-selected, and the kinetics of its competitive unimolecular dissociations was investigated in an ion trap mass spectrometer. The chiral selectivity (R(fixed)chiral), the ratio of the two fragment ion abundances when the cluster contains one pure enantiomer of the analyte expressed relative to that for the other enantiomer, varies with increasing size of the fixed peptide ligands. The metal-ligand and the ligand-ligand interactions that produce chiral discrimination are optimized in the tetrapeptide fixed ligand Gly-Gly-Ala-Gly, as shown by data for 15 fixed ligands. The difference in the free energies of activation for the two competitive reactions is estimated to be approximately 7 kJ/mol for this particular fixed ligand. The sensitive nature of the methodology and the linear relationship between the logarithm of the fragment ion abundance ratio and the optical purity (intrinsic to the kinetic method) allows mixtures to be analyzed for as little as 1% enantiomeric excess (ee), by simply recording the ratios of fragment ion abundances in a tandem mass spectrum. These features are demonstrated in the case of the pharmacologically important 4-benzyl-2-oxazolidinones and in the case of penicillamine.

Ionization energies of multiply protonated polypeptides obtained by tandem ionization in Fourier transform mass spectrometers

Ionization energies (IE) of [M + zH](z+) (z+) electrospray-produced polypeptides were determined by electron ionization in a Penning cell of 4.7 and 9.4 T Fourier transform mass spectrometers. For z = 1+ and substance P, the found IE value of 11.0 +/- 0.4 eV is in agreement with that obtained earlier for ions generated with matrix-assisted laser desorption/ionization. For higher z, the following values were found: 11.7 +/- 0.3 eV for 2+ of [Arg-8]-vasopressin, 11.1 +/- 0.6 eV for 2+ of substance P, 12.2 +/- 0.7 eV for 2+ of renin substrate, 13.3 +/- 0.4 eV for 3+ of B-chain of insulin and 14.6 +/- 0.6 eV for 4+ and 15.1 +/- 0.4 eV for 5+ of melittin. It was found that 90% of existing IE data on polypeptides in the 1.0-3.5 kDa mass range are described with <or=0.5 eV uncertainty by the empirical equation IE(z) = 9.8 + 1.1z. The average IE increase of 1.1 eV/charge is attributed to Coulombic repulsion. The deduced ionization energy of a neutral polypeptide molecule, 9.8 +/- 0.3 eV, is consistent with literature expectations.

Gas-phase basicities for ions from bradykinin and its des-arginine analogues

Apparent gas-phase basicities (GB(app)s) for [M + H]+ of bradykinin, des-Arg1-bradykinin and des-Arg9-bradykinin have been assigned by deprotonation reactions of [M + 2H]2+ in a Fourier transform ion cyclotron resonance mass spectrometer. With a GB(app) of 225.8 +/- 4.2 kcal x mol(-1), bradykinin [M + H]+ is the most basic of the ions studied. Ions from des-Arg1-bradykinin and des-Arg9-bradykinin have GB(app) values of 222.8 +/- 4.3 kcal x mol(-1) and 214.9 +/- 2.3 kcal x mol(-1), respectively. One purpose of this work was to determine a suitable reaction efficiency 'break point' for assigning GB(app) values to peptide ions using the bracketing method. An efficiency value of 0.1 (i.e. approximately 10% of all collisions resulting in a deprotonation reaction) was used to assign GB(app)s. Support for this criterion is provided by the fact that our GB(app) values for des-Arg1-bradykinin and des-Arg9-bradykinin are identical, within experimental error, to literature values obtained using a modified kinetic method. However, the GB(app)s for bradykinin ions from the two studies differ by 10.3 kcal x mol(-1). The reason for this is not clear, but may involve conformation differences produced by experimental conditions. The results may be influenced by salt-bridge conformers and/or by conformational changes caused by the use of a proton-bound heterodimer in the kinetic method. Factors affecting the basicities of these peptide ions are also discussed, and molecular modeling is used to provide information on protonation sites and conformations. The presence of two highly basic arginine residues on bradykinin results in its high GB(app), while the basicity of des-Arg1-bradykinin ions is increased by the presence of two proline residues at the N-terminus. The proline residue in the second position folds the peptide chain in a manner that increases intramolecular hydrogen bonding to the protonated N-terminal amino group of the proline at the first position.

Thermochemical aspects of proton transfer in the gas phase

The beginning of the twentieth century saw the development of new theories of acidity and basicity, which are currently well accepted. The thermochemistry of proton transfer in the absence of solvent attracted much interest during this period, because of the fundamental importance of the process. Nevertheless, before the 1950s, few data were available, either from lattice energy evaluations or from calculations using the emerging molecular orbital theory. Advances in mass spectrometry during the last 40 years allowed studies of numerous systems with better accuracy. Thousands of accurate gas-phase acidities or basicities are now available, for simple atomic and molecular systems and for large biomolecules. The intrinsic effect of structure on the Brønsted basic or acidic properties of molecules and the influence of solvents have been unravelled. In this tutorial, the basics of the thermodynamic principles involved are given, and the mass spectrometric techniques are briefly reviewed. Advances in the design and measurements of gas-phase superacids and superbases are described. Recent studies concerning biomolecules are also evoked.

Low-mass ions observed in plasma desorption mass spectrometry of high explosives

The low-mass ions observed in both positive and negative plasma desorption mass spectrometry (PDMS) of the high explosives HMX, RDX, CL-20, NC, PETN and TNT are reported. Possible identities of the most abundant ions are suggested and their presence or absence in the different spectra is related to the properties of the explosives as matrices in PDMS. The detection of abundant NO+ and NO2- ions for HMX, RDX and CL-20, which are efficient matrices, indicates that explosive decomposition takes place in PDMS of these three substances and that a contribution from the corresponding chemical energy release is possible. The observation of abundant C2H4N+ and CH2N+ ions, which have high protonation properties, might also explain the higher protein charge states observed with these matrices. Also, the observation of NO2-, possibly formed by electron scavenging which increases the survival probability of positively charged protein molecular ions, completes the pattern. TNT does not give any of these ions and it is thereby possible to explain why it does not work as a PDMS matrix. For NC and PETN, decomposition does not seem to be as pronounced as for HMX, RDX and CL-20, and also no particularly abundant ions with high protonation properties are observed. The fact that NC works well as a matrix might be related to other properties of this compound, such as its high adsorption ability.

Determining the gas-phase properties and reactivities of multiply charged ions

Approaches for analyzing kinetic and thermochemical data from the reactions of multiply charged ions are presented. A method for estimating the electrostatic repulsion in a multiply charged ion is described followed by examples of the potential energy surfaces for two representative reactions of multiply charged ions, proton transfer and nucleophilic substitution (S(N)2). The effect of electrostatic repulsion on reaction barriers is discussed and approaches for extracting thermochemical data from kinetic results are described. For reactions with small intrinsic barriers (i.e. proton transfer), considerable internal electrostatic repulsion is released at the transition state and multiply charged ions exhibit much greater reactivity than singly charged analogs. In contrast, relatively little electrostatic repulsion is released at the transition states of reactions with large intrinsic barriers (i.e. S(N)2) and multiply charged ions with moderate charge separations (>10 A) can exhibit reactivity that is very similar to that of singly charged analogs.

Ion-molecule reactions as probes of gas-phase structures of peptides and proteins

A review with over 100 references describes the recent applications of ion-molecule reactions to the study of gas-phase protonated peptides and proteins. The topic is focused specifically on the proton transfer and hydrogen-deuterium exchange reactions of amino acids, peptides, and proteins. A brief background is given of the various methods used for assigning proton affinities and gas-phase basicities. The methods used for measuring the kinetics of deuterium incorporation of charged ion in the presence of a background pressure of deuterating reagents are also described. Ion-molecule reactions are used to determine, among other things, the gas-phase basicities and proton affinities of amino acids, peptides, and proteins, the sites of protonation, intra- and intermolecular interactions, and conformational differences and changes in gas-phase ionic species. Singly charged and multiply charged ions are both covered.

Apparent gas-phase acidities of multiply protonated peptide ions: Ubiquitin, insulin B, and renin substrate

The gas-phase deprotonation reactions of multiply protonated bovine ubiquitin, insulin chain B, and renin substrate tetradecapeptide ions have been studied in a Fourier transform ion cyclotron resonance mass spectrometer coupled with an external electrospray source. Rate constants were measured for the reactions of these peptide ions with a series of reference compounds of known gas-phase basicities ranging from 195.6 to 232.6 kcal/mol. The apparent gas-phase acidities (GAapp) of the multiply protonated peptide ions [M + nH](n+) were determined with deprotonation reactions. The deduced values of GAapp show a strong dependence on the charge states of the multiply protonated peptide ions. In general, the values decrease as the charge states of the peptide ions increase. For ubiquitin ions, the determined GAapps values decrease from >232.6 to 205.0 kcal/mol for n=4-13; for insulin B ions, the GAapps decrease from >232.6 to 198.2 kcal/mol for n=2-5; for renin substrate ions, the GAapps decrease from 221.6 to <195.6 kcal/mol for n=2-4. Interestingly, at a given mass-to-charge ratio, the GAapps of these peptide ions agree within 10 kcal/mol despite large differences in their mass and charge. The ubiquitin and insulin B ions generated under the present conditions reveal multiple isomers at certain charge states, n=4, 5, 6, 12 for ubiquitin and n=4, 5 for insulin B, as evidenced by the fact that the isomers display distinctively different deprotonation reaction rates with certain reference compounds.

The importance of charge-separation reactions in tandem mass spectrometry of doubly protonated angiotensin II formed by electrospray ionization: Experimental considerations and structural implications

The occurrence of charge-separation reactions in tandem mass spectrometry of doubly protonated angiotensin II is demonstrated by the use of mass-analyzed ion kinetic energy spectrometry (MIKES) and kinetic energy release distributions (KERDs). Linked scans at a constant B/E severely discriminate against product ions formed by charge-separation reactions. Although the products are significantly more abundant in MIKES experiments, instrumental discrimination still makes quantitation of relative product ion abundances highly inaccurate. The most probable KERs (T m. p.) and the average KERs (T ave.) of the reactions are determined from the KERDs, and these values are compared to the KERs determined from the peak widths at half-height (T 0. 5). The measurement of T 0. 5 is a poor approximation to T m. p. and T ave.. The T m. p. is used to calculate a most probable intercharge distance, which is compared to results from molecular dynamics calculations. The results provide evidence with regard to the mechanisms of fragmentation of multiply charged ions and the location of the charge site in relation to the decomposition reactions.