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

Altering Conformational States of Dynamic Ion Populations using Traveling Wave Structures for Lossless Ion Manipulations

With its capacity to store and translate ions across considerable distances and times, traveling wave structures for lossless ion manipulations (TW-SLIM) provide the foundation to expand the scope of ion mobility spectrometry (IMS) experiments. While promising, the dynamic electric fields and consequential ion-neutral collisions used to realize extensive degrees of separation have a considerable impact on the empirical results and the fundamental interpretation of observed arrival time distributions. Using a custom-designed set of TW-SLIM boards (∼9 m) coupled with a time-of-flight mass spectrometer (SLIM-ToF), we detail the capacity to systematically alter the gas-phase distribution of select peptide conformers. In addition to discussing the role charge-transfer may play in TW-SLIM experiments that occur at extended time scales, the ability of the SLIM-ToF to perform tandem IMS was leveraged to confirm that both the compact and elongated conformers of bradykinin2+ undergo interconversion within the SLIM. Storage experiments in which ions are confined within SLIM using static potential wells suggest that factors aside from TW-induced ion motion contribute to interconversion. Further investigation into this matter suggests that the use of radio frequency (RF) fields to confine ions within SLIM may play a role in ion heating. Aside from interconversion, storage experiments also provide insight into charge transfer behavior over the course of extended periods. The results of the presented experiments suggest that considerations should be taken when analyzing labile species and inform strategies for the TW-SLIM design and method development.

Multi-component ion modifiers and arcing suppressants to enhance differential mobility spectrometry for separation of peptides and drug molecules

The optimization of ion/molecule chemistry in a differential mobility spectrometer (DMS) is shown to result in improved peak capacity, separation, and sensitivity. We have experimented with a modifier composed of multiple components, where each component accomplishes a specific task on mixtures of peptides and small drug molecules. Use of a higher proton affinity modifier (hexanol) provides increased peak capacity and separation. Analyte ion/modifier proton transfer is suppressed by adding a large excess of low proton affinity modifier (water or methanol), significantly increasing signal intensity and sensitivity for low proton affinity analytes. Finally, addition of an electrical arcing suppressant (chloroform) allows the device to operate reliably at higher separation fields, improving peak capacity and separation. We demonstrate a 20% increase in the device peak capacity without any loss of sensitivity and estimate that further optimization of the modifier composition can increase this to 50%. Use of 3-, 4-, or even 5-component modifiers offers the opportunity for the user to fine-tune the modifier performance to maximize the device performance, something not possible with a single component modifier.

Non-covalent dimers of the lysine containing protonated peptide ions in gaseous state: electrospray ionization mass spectrometric study

Study of the non-covalent molecular complexes in gas phase by electrospray ionization mass spectrometry (ESI-MS) represents a promising strategy to probe the intrinsic nature of these complexes. ESI-MS investigation of a series of synthetic octapeptides containing six alanine and two lysine residues differing only by their positions showed the formation of non-covalent dimers, which were preserved in the gas phase. Unlike the monomers, the dimers were found to show only singly protonated state. The decrease in the solvent polarity from water to alcohol showed enhanced propensity of formation of the dimer indicating that the electrostatic interaction plays a crucial role to stabilize the dimer. Selective functionalization studies showed that ε-NH(2) of lysine and C-terminal amide (-CONH(2)) facilitate the dimerization through intermolecular hydrogen bonding network.

On the zwitterionic nature of gas-phase peptides and protein ions

Determining the total number of charged residues corresponding to a given value of net charge for peptides and proteins in gas phase is crucial for the interpretation of mass-spectrometry data, yet it is far from being understood. Here we show that a novel computational protocol based on force field and massive density functional calculations is able to reproduce the experimental facets of well investigated systems, such as angiotensin II, bradykinin, and tryptophan-cage. The protocol takes into account all of the possible protomers compatible with a given charge state. Our calculations predict that the low charge states are zwitterions, because the stabilization due to intramolecular hydrogen bonding and salt-bridges can compensate for the thermodynamic penalty deriving from deprotonation of acid residues. In contrast, high charge states may or may not be zwitterions because internal solvation might not compensate for the energy cost of charge separation.

Accurate benchmark calculations on the gas-phase basicities of small molecules

Accurate benchmark calculations of gas-phase basicities of small molecules are presented and compared with available experimental results. The optimized geometries and thermochemical analyses were obtained from MP2/aug-cc-pVTZ calculations. Two different ab initio electron-correlated methods MP2 and CCSD(T) were employed for subsequent gas-phase basicity calculations, and the single-point energies were extrapolated to the complete basis set (CBS) limit. The overall accuracy for different ab initio methods is compared, and the accuracy in descending order is CCSD(T)_CBS > CCSD(T)/aug-cc-pVDZ > (MP2/aug-cc-pVQZ approximately MP2_CBS) > HF/aug-cc-pVQZ. The best root-mean-squared-error obtained was 1.0 kcal mol(-1) at the CCSD(T)_CBS//MP2/aug-cc-pVTZ level for a test set of 41 molecules. Clearly, accurate calculations for the electron correlation energy are important for the theoretical prediction of molecular gas-phase basicities. However, conformational effects were also found to be relevant in several instances when more complicated molecules were examined.

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.

Negative ion dissociation of peptides containing hydroxyl side chains

The dissociation of deprotonated peptides containing hydroxyl side chains was studied by electrospray ionization coupled with Fourier transform ion cyclotron resonance (ESI-FTICR) via sustained off-resonance irradiation collision induced dissociation (SORI-CID). Dissociation under post-source decay (PSD) conditions was performed by matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF). This work included hexapeptides with one residue of serine, threonine, or tyrosine and five inert alanine residues. During SORI-CID and PSD, dissociation of [M-H](-) yielded c- and y-ions. Side-chain losses of formaldehyde (HCHO) from serine-containing peptides, acetaldehyde (CH(3)CHO) from threonine-containing peptides, and 4-methylene-2,5-cycohexadienone (C(7)H(6)O) from tyrosine-containing peptides were generally observed in the negative ion PSD and SORI-CID spectra. Side-chain loss occurs much less from tyrosine-containing peptides than from serine- and threonine-containing peptides. This is probably due to the bulky side chain of tyrosine, resulting in steric hindrance and poor geometry for dissociation reactions. Additionally, a selective cleavage leading to the elimination of the C-terminal residue from [M-H](-) was observed from the peptides with serine and threonine at the C-terminus. This cleavage does not occur in the dissociation of peptides with an amide group at the C-terminus or peptides with neutral or basic residues at the C-terminus. It also does not occur with tyrosine at the C-terminus. Both the C-terminal carboxylic acid group and the hydroxyl side chain of the C-terminal residue must play important roles in the mechanism of C-terminal residue loss. A mechanism involving both the C-terminal carboxylic acid group and a hydroxyl side chain of serine and threonine 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.

Reagent anions for charge inversion of polypeptide/protein cations in the gas phase

Various reagent anions capable of converting polypeptide cations to anions via ion/ion reactions have been investigated. The major charge inversion reaction channels include multiple proton transfer and adduct formation. Dianions composed of sulfonate groups as the negative charge carriers show essentially exclusive adduct formation in converting protonated peptides and proteins to anions. Dianions composed of carboxylate groups, on the other hand, show far more charge inversion via multiple proton transfer, with the degree of adduct formation dependent upon both the size of the polypeptide and the spacings between carboxylate groups in the dianion. More highly charged carboxylate-containing anions, such as those derived from carboxylate-terminated polyamidoamine half-generation dendrimers show charge inversion to give anion charges as high in magnitude as -4, with the degree of adduct formation being inversely related to dendrimer generation. All observations can be interpreted on the basis of charge inversion taking place via a long-lived chemical complex. The lifetime of this complex is related to the strengths and numbers of the interactions of the reactants in the complex. Calculations with model systems are fully consistent with sulfonate groups giving rise to more stable complexes. The kinetic stability of the complex can also be affected by the presence of electrostatic repulsion if it is multiply charged. In general, this situation destabilizes the complex and reduces the likelihood for observation of adducts. The findings highlight the characteristics of multiply charged anions that play roles in determining the nature of charge inversion products associated with protonated peptides and proteins.

Ion mobility spectrometer with radial collisional focusing

An ion mobility spectrometer that has its mobility cell as a 20-segment quadrupole and functionally the q2 of a triple-quadrupole mass spectrometer has been assembled and tested. The combination of high cell pressure (maximum of 4 Torr of helium) and low axial field (20-160 V per 20.2 cm) results in negligible internal excitation of the ions despite applications of rf and axial fields. The presence of collisional focusing ensures efficient ion transmission and good sensitivity. Collision cross sections of atomic, cluster, peptide, and protein ions were measured and found comparable to literature and calculated cross sections.

Zwitterionic States in Gas-Phase Polypeptide Ions Revealed by 157-nm Ultra-Violet Photodissociation

A new method of detecting the presence of deprotonation and determining its position in gas-phase polypeptide cations is described. The method involves 157-nm ultra-violet photodissociation (UVPD) and is based on monitoring the losses of CO2 (44 Da) from electronically excited deprotonated carboxylic groups relative to competing COOH losses (45 Da) from neutral carboxylic groups. Loss of CO2 is a strong indication of the presence of a zwitterionic [(+)...(-)...(+)] salt bridge in the gas-phase polypeptide cation. This method provides a tool for studying, for example, the nature of binding within polypeptide clusters. Collision-activated dissociation (CAD) of decarboxylated cations localizes the position of deprotonation. Fragment abundances can be used for the semiquantitative assessment of the branching ratio of deprotonation among different acidic sites, however, the mechanism of the fragment formation should be taken into account. Cations of Trp-cage proteins exist preferentially as zwitterions, with the deprotonation position divided between the Asp9 residue and the C terminus in the ratio 3:2. The majority of dications of the same molecule are not zwitterions. Furthermore, 157-nm UVPD produces abundant radical cations M*+ from protonated molecules through the loss of a hydrogen atom. This method of producing M*+ ions is general and can be applied to any gas-phase peptide cation. The abundance of the molecular radical cations M*+ produced is sufficient for further tandem mass spectrometry (MS/MS), which, in the cases studied, yielded side-chain loss of a basic amino acid as the most abundant fragmentation channel together with some backbone cleavages.

Gas-phase ion/ion reactions of multiply protonated polypeptides with metal containing anions

Gas-phase reactions of multiply protonated polypeptides and metal containing anions represent a new methodology for manipulating the cationizing agent composition of polypeptides. This approach affords greater flexibility in forming metal containing ions than commonly used methods, such as electrospray ionization of a metal salt/peptide mixture and matrix-assisted laser desorption. Here, the effects of properties of the polypeptide and anionic reactant on the nature of the reaction products are investigated. For a given metal, the identity of the ligand in the metal containing anion is the dominant factor in determining product distributions. For a given polypeptide ion, the difference between the metal ion affinity and the proton affinity of the negatively charged ligand in the anionic reactant is of predictive value in anticipating the relative contributions of proton transfer and metal ion transfer. Furthermore, the binding strength of the ligand anion to charge sites in the polypeptide correlates with the extent of observed cluster ion formation. Polypeptide composition, sequence, and charge state can also play a notable role in determining the distribution of products. In addition to their usefulness in gas-phase ion synthesis strategies, the reactions of protonated polypeptides and metal containing anions represent an example of a gas-phase ion/ion reaction that is sensitive to polypeptide structure. These observations are noteworthy in that they allude to the possibility of obtaining information, without requiring fragmentation of the peptide backbone, about ion structure as well as the relative ion affinities associated with the reactants.

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.

Role of opposite charges in protein electrospray ionization mass spectrometry

The conformation dependence of protein spectra recorded by electrospray ionization mass spectrometry (ESI-MS) is an interesting and useful phenomenon, whose origin is still the object of debate. Different mechanisms have been invoked in the attempt to explain the lower charge state of folded versus unfolded protein ions in ESI-MS, such as electrostatic repulsions, solvent accessibility, charge availability, and native-like interactions. In this work we try to subject to direct experimental test the hypothesis that conformation-dependent neutralization of charges with polarity opposite to the net charge of the protein ion could play a critical role in such an effect. We present results of time-of-flight nano-ESI-MS on the peptide angiotensin II, indicating that negative charges of carboxylate groups can contribute to spectra recorded in positive-ion mode when stabilized by favorable electrostatic interactions, which is the central assumption of our hypothesis. Comparison of horse and spermwhale myoglobin (Mb) shows that changing the total number of basic residues within a given three-dimensional structure shifts the charge-state distribution (CSD) of the folded protein in positive-ion mode. This result appears to be in contrast to models in which electrostatic repulsions or availability of charges in the ESI droplets represent the limiting factor for the ionization of folded protein ions in ESI-MS. At the same time, it suggests a role of acidic residues in conformational effects in positive-ion mode. Furthermore, an attempt is made to rationalize those cases in which, in contrast, the main charge state observed in ESI-MS under non-denaturing conditions deviates considerably from the net charge expected on the basis of the amino-acid composition. These cases usually correspond to proteins with quite balanced content in basic and acidic residues, suggesting that this might be a factor influencing their charging behavior in ESI-MS. Experiments on mutants of ribonuclease Sa (RNase Sa) reveal that progressively reducing the excess of acidic residues, replacing them by lysine, causes almost no shift in the spectrum of the folded protein in negative-ion mode. Analogously, variants with an excess of three or five basic residues give similar spectra in positive-ion mode. These results indicate a lower limit to the extent of ionization observable by ESI-MS (6- or 8+ in the case of RNase Sa in water). Below such limit of net charge, changes in the relative amount of ionizable side chains do not affect the qualitative features of the observed CSDs. A progressive loss of signal intensity caused by the mutations in negative-ion mode suggests that low charge states might also be counterselected, even within the m/z range theoretically accessible to the instrument.