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

MD Simulations of Peptide-Containing Electrospray Droplets: Effects of Parameter Settings on the Predicted Mechanisms of Gas Phase Ion Formation

Electrospray ionization (ESI) mass spectrometry is widely used for interrogating peptides, proteins, and other biomolecular analytes. A growing number of laboratories use molecular dynamics (MD) simulations for uncovering ESI mechanisms by modeling the behavior of highly charged nanodroplets. The outcome of any MD simulation depends on certain assumptions and parameter settings, and it is desirable to optimize these factors by benchmarking computational data against experiments. Unfortunately, benchmarking of ESI simulations is difficult because experimentally generated gaseous ions do not generally retain any features that would reveal their formation pathway [e.g., the charged residue mechanism (CRM) or the ion evaporation mechanism (IEM)]. Here, we tackle this problem by examining the effects of various MD settings on the ESI behavior of the 9-residue peptide bradykinin in acidic aqueous droplets. Several parameters were found to significantly affect the kinetic competition between peptide IEM and CRM. By systematically probing the droplet behavior, we uncovered problems associated with certain settings, including peptide/solvent temperature imbalances, unexpected peptide deceleration during IEM, and a dependence of the ESI mechanism on the water model. We also noted different simulation outcomes for different force fields. On the basis of comprehensive tests, we propose a set of "best practice" parameter settings for MD simulations of ESI droplets. The strategies used here should be transferable to other types of droplet simulations, paving the way toward a more solid understanding of ESI mechanisms.

Comprehensive Analysis of Coupled Proline Cis-Trans States in Bradykinin Using ωBP-REMD Simulations

It is well-known that proline (Pro) cis-trans isomerization plays a decisive role in the folding and stabilization of proteins. The conformational coupling between isomerization states of different Pro residues in proteins during conformational adaptation processes is not well understood. In the present work, we investigate the coupled cis-trans isomerization of three Pro residues using bradykinin (BK), a partially unstructured nonapeptide hormone, as a model system. We use a recently developed enhanced-sampling molecular dynamics method (ω-bias potential replica exchange molecular dynamics; ωBP-REMD) that allows us to exhaustively sample all combinations of Pro isomer states and obtain converged probability densities of all eight state combinations within 885 ns ωBP-REMD simulations. In agreement with experiment, the all-trans state is seen to be the preferred isomer of zwitterionic aqueous BK. In about a third of its structures, this state presents the characteristic C-terminal β-turn conformation; however, other isomer combinations also contribute significantly to the structural ensemble. Unbiased probabilities can be projected onto the peptide bond dihedral angles of the three Pro residues. This unveils the interdependence of the individual Pro isomerization states, i.e., a possible coupling of the different Pro isomers. The cis/trans equilibrium of a Pro residue can change by up to 2.5 kcal·mol-1, depending on the isomerization state of other Pro residues. For example, for Pro7, the simulations indicate that its cis state becomes favored compared to its trans state when Pro2 is switched from the trans state to the cis state. Our findings demonstrate the efficiency of the ωBP-REMD methodology and suggest that the coupling of Pro isomerization states may play an even more decisive role in larger folded proteins subject to more conformational restraints.

Using Density Functional Theory for Testing the Robustness of Mobile-Proton Molecular Dynamics Simulations on Electrosprayed Ions: Structural Implications for Gaseous Proteins

Current experiments only provide low-resolution information on gaseous protein ions generated by electrospray ionization (ESI). Molecular dynamics (MD) simulations can yield complementary insights. Unfortunately, conventional MD does not capture the mobile nature of protons in gaseous proteins. Mobile-proton MD (MPMD) overcomes this limitation. Earlier MPMD data at 300 K indicated that protein ions generated by "native" ESI retain solution-like structures with a hydrophobic core and zwitterionic exterior [Bakhtiari, M.; Konermann, L. J. Phys. Chem. B 2019, 123, 1784-1796]. MPMD redistributes protons using electrostatic and proton affinity calculations. The robustness of this approach has never been scrutinized. Here, we close this gap by benchmarking MPMD against density functional theory (DFT) at the B3LYP/6-31G* level, which is well suited for predicting proton affinities. The computational cost of DFT necessitated the use of small peptides. The MPMD energetic ranking of proton configurations was found to be consistent with DFT single-point energies, implying that MPMD can reliably identify favorable protonation sites. Peptide MPMD runs converged to DFT-optimized structures only when applying 300-500 K temperature cycling, which was necessary to prevent trapping in local minima. Temperature cycling MPMD was then applied to gaseous protein ions. Native ubiquitin converted to slightly expanded structures with a zwitterionic core and a nonpolar exterior. Our data suggest that such inside-out protein structures are intrinsically preferred in the gas phase, and that they form in ESI experiments after moderate collisional excitation. This is in contrast to native ESI (with minimal collisional excitation, simulated by MPMD at 300 K), where kinetic trapping promotes the survival of solution-like structures. In summary, this work validates the MPMD approach for simulations on gaseous peptides and proteins.

Formation of Gaseous Peptide Ions from Electrospray Droplets: Competition between the Ion Evaporation Mechanism and Charged Residue Mechanism

The transfer of peptide ions from solution into the gas phase by electrospray ionization (ESI) is an integral component of mass spectrometry (MS)-based proteomics. The mechanisms whereby gaseous peptide ions are released from charged ESI nanodroplets remain unclear. This is in contrast to intact protein ESI, which has been the focus of detailed investigations using molecular dynamics (MD) simulations and other methods. Under acidic liquid chromatography/MS conditions, many peptides carry a solution charge of 3+ or 2+. Because of this pre-existing charge and their relatively small size, prevailing views suggest that peptides follow the ion evaporation mechanism (IEM). The IEM entails analyte ejection from ESI droplets, driven by electrostatic repulsion between the analyte and droplet. Surprisingly, recent peptide MD investigations reported a different behavior, that is, the release of peptide ions via droplet evaporation to dryness which represents the hallmark of the charged residue mechanism (CRM). Here, we resolved this conundrum by performing MD simulations on a common model peptide (bradykinin) in Rayleigh-charged aqueous droplets. The primary focus was on pH 2 conditions (bradykinin solution charge = 3+), but we also verified that our MD strategy captured pH-dependent charge state shifts seen in ESI-MS experiments. In agreement with earlier simulations, we found that droplets with initial radii of 1.5-3 nm predominantly release peptide ions via the CRM. In contrast, somewhat larger radii (4-5 nm) favor IEM behavior. It appears that these are the first MD data to unequivocally demonstrate the viability of peptide IEM events. Electrostatic arguments can account for the observed droplet size dependence. In summary, both CRM and IEM can be operative in peptide ESI-MS. The prevalence of one over the other mechanism depends on the droplet size distribution in the ESI plume.

Sub-ambient pressure IR-MALDI ion mobility spectrometer for the determination of low and high field mobilities

A new ion mobility (IM) spectrometer, enabling mobility measurements in the pressure range between 5 and 500 mbar and in the reduced field strength range E/N of 5-90 Td, was developed and characterized. Reduced mobility (K₀) values were studied under low E/N (constant value) as well as high E/N (deviation from low field K₀) for a series of molecular ions in nitrogen. Infrared matrix-assisted laser desorption ionization (IR-MALDI) was used in two configurations: a source working at atmospheric pressure (AP) and, for the first time, an IR-MALDI source working with a liquid (aqueous) matrix at sub-ambient/reduced pressure (RP). The influence of RP on IR-MALDI was examined and new insights into the dispersion process were gained. This enabled the optimization of the IM spectrometer for best analytical performance. While ion desolvation is less efficient at RP, the transport of ions is more efficient, leading to intensity enhancement and an increased number of oligomer ions. When deciding between AP and RP IR-MALDI, a trade-off between intensity and resolving power has to be considered. Here, the low field mobility of peptide ions was first measured and compared with reference values from ESI-IM spectrometry (at AP) as well as collision cross sections obtained from molecular dynamics simulations. The second application was the determination of the reduced mobility of various substituted ammonium ions as a function of E/N in nitrogen. The mobility is constant up to a threshold at high E/N. Beyond this threshold, mobility increases were observed. This behavior can be explained by the loss of hydrated water molecules.

Competition between salt bridge and non-zwitterionic structures in deprotonated amino acid dimers

The effect of side chain functional groups on salt bridge structures in deprotonated amino acid homodimers is investigated using both infrared multiple photon dissociation spectroscopy between 650 and 1850 cm⁻¹ and theory.

Fast and Effective Ion Mobility-Mass Spectrometry Separation of d-Amino-Acid-Containing Peptides

Despite often minute concentrations in vivo, d-amino acid containing peptides (DAACPs) are crucial to many life processes. Standard proteomics protocols fail to detect them as d/l substitutions do not affect the peptide parent and fragment masses. The differences in fragment yields are often limited, obstructing the investigations of important but low abundance epimers in isomeric mixtures. Separation of d/l-peptides using ion mobility spectrometry (IMS) was impeded by small collision cross section differences (commonly ∼1%). Here, broad baseline separation of DAACPs with up to ∼30 residues employing trapped IMS with resolving power up to ∼340, followed by time-of-flight mass spectrometry is demonstrated. The d/l-pairs coeluting in one charge state were resolved in another, and epimers merged as protonated species were resolved upon metalation, effectively turning the charge state and cationization mode into extra separation dimensions. Linear quantification down to 0.25% proved the utility of high resolution IMS-MS for real samples with large interisomeric dynamic range. Very close relative mobilities found for DAACP pairs using traveling-wave IMS (TWIMS) with different ion sources and faster IMS separations showed the transferability of results across IMS platforms. Fragmentation of epimers can enhance their identification and further improve detection and quantification limits, and we demonstrate the advantages of online mobility separated collision-induced dissociation (CID) followed by high resolution mass spectrometry (TIMS-CID-MS) for epimer analysis.

Two-Dimensional Folding of Polypeptides into Molecular Nanostructures at Surfaces

Herein we report the fabrication of molecular nanostructures on surfaces via two-dimensional (2D) folding of the nine amino acid peptide bradykinin. Soft-landing electrospray ion beam deposition in conjunction with high-resolution imaging by scanning tunneling microscopy is used to fabricate and investigate the molecular nanostructures. Subnanometer resolved images evidence the large conformational freedom of the molecules if thermal motion is inhibited and the formation of stable uniform dimers of only one specific conformation when diffusion can take place. Molecular dynamics modeling supported by density functional theory calculations give atomically precise insight into the induced-fit binding scheme when the folded dimer is formed. In the absence of solvent, we find a hierarchy of binding strength from polar to nonpolar, manifested in an inverted polar-nonpolar segregation which suppresses unspecific interactions at the rim of the nanostructure. The demonstrated 2D-folding scheme resembles many key properties of its native 3D counterpart and shows that functional, molecular nanostructures on surfaces fabricated by folding could be just as versatile and specific.

Achieving High Resolution Ion Mobility Separations Using Traveling Waves in Compact Multiturn Structures for Lossless Ion Manipulations

We report on ion mobility (IM) separations achievable using traveling waves (TW) in a Structures for Lossless Ion Manipulations (SLIM) module having a 44 cm path length and 16 90° turns. The performance of the TW-SLIM module was evaluated for ion transmission and IM separations with different RF, TW parameters, and SLIM surface gaps in conjunction with mass spectrometry. In this work, TWs were created by the transient and dynamic application of DC potentials. The module demonstrated highly robust performance and, even with 16 closely spaced turns, achieving IM resolution performance and ion transmission comparable to a similar straight path module. We found an IM peak capacity of ∼31 and peak generation rate of 780 s(-1) for TW speeds of ∼80 m/s using the current multi-turn TW-SLIM module. The separations achieved for isomers of peptides and tetrasaccharides were found to be comparable to those from a ∼0.9-m drift tube-based IM-MS platform operated at the same pressure (4 Torr). The combined attributes of flexible design, low voltage requirements and lossless ion transmission through multiple turns for the present TW-SLIM module provides a basis for SLIM devices capable of achieving much greater IM resolution via greatly extended ion path lengths and using compact serpentine designs.

Stereoselective recognition of the Ac-Glu-Tyr-OH dipeptide by pseudopeptidic cages

Pseudopeptidic molecular cages are appealing receptors since they can display different polar and non-polar interaction sites in a modular framework and a controlled disposition. Inspired by previous host-guest knowledge, two pseudopeptidic molecular cages based on serine and threonine (CySer and CyThr, respectively) were designed and synthesized as hosts for the binding of the four possible stereoisomers of the Ac-Glu-Tyr-OH dipeptide, a target sequence of tyrosine kinases. The careful NMR titration experiments in aqueous acetonitrile allowed the determination of the binding constants and reflected a difference in the stability of the corresponding diastereomeric host-guest complexes. The CySer cage proved to be slightly more efficient than the CyThr counterpart, although both showed similar stereoselectivity trends: LL > DD ≥ LD > DL. This stereoselective binding was retained in the gas phase, as shown by ESI-MS competition experiments using the enantiomer-labelled method (EL), as well as CID experiments. Thus, the MS-determined discriminations follow the same trends observed by NMR, suggesting that the stereoselectivity observed for these systems must be mainly dictated by the polar host-guest interactions. Despite the stereoselective binding of short peptide sequences in competitive media being a challenging issue in supramolecular chemistry, our results demonstrate the power of pseudopeptidic cages in molecular recognition with foreseen implications in chemical biology.

Suppression of peptide ion dissociation under electron capture: role of backbone amide hydrogen

RATIONALE

The electron capture dissociation (ECD) of proteins/peptides is affected by the nature and sequence of amino acid residues. Electron capture/transfer with no dissociation is an intriguing phenomenon that has occasionally been observed. We have previously identified that diarginated peptides enriched with glutamic acid residues were found to show suppression of backbone fragmentation. In this paper, we report the effect of geometrical parameters of a peptide, including chain length, conformation and amide hydrogen, on the suppression of ECD fragmentation using synthetic model peptides.

METHODS

Glycine containing model polypeptides were used to probe the mechanism. Molecular-mechanics was used to obtain the conformation of the precursor ions. The ECD experiments were performed on a Bruker APEX III 4.7 T Fourier transform ion cyclotron resonance (FTICR) mass spectrometer.

RESULTS

Significant decreases in the intensities of the fragment ions were observed for the 23-mer polypeptide with only one E residue. This implied that the E:R ratio was no longer the sole determining factor for the occurrence of suppression effects. Results of conformational searches showed that there was a hydrogen-bonding 'ladder' formed in the 23-mer polypeptide, which was not found in the 15-mer peptide. Substituting the normal amino acid residues by the corresponding N-methylated amino acid residues in the model peptide, the suppression effect disappeared.

CONCLUSIONS

Our results indicate that survival of the intact reduced peptide ion after electron capture depends also on the length of the peptide. The amide hydrogen was critical in forming the resonance structure that suppressed the ECD fragmentation.

The use of chromium(III) to supercharge peptides by protonation at low basicity sites

The addition of chromium(III) nitrate to solutions of peptides with seven or more residues greatly increases the formation of doubly protonated peptides, [M + 2H](2+), by electrospray ionization. The test compound heptaalanine has only one highly basic site (the N-terminal amino group) and undergoes almost exclusive single protonation using standard solvents. When Cr(III) is added to the solution, abundant [M + 2H](2+) forms, which involves protonation of the peptide backbone or the C-terminus. Salts of Al(III), Mn(II), Fe(III), Fe(II), Cu(II), Zn (II), Rh(III), La(III), Ce(IV), and Eu(III) were also studied. Although several metal ions slightly enhance protonation, Cr(III) has by far the greatest ability to generate [M + 2H](2+). Cr(III) does not supercharge peptide methyl esters, which suggests that the mechanism involves interaction of Cr(III) with a carboxylic acid group. Other factors may include the high acidity of hexa-aquochromium(III) and the resistance of Cr(III) to reduction. Nitrate salts enhance protonation more than chloride salts and a molar ratio of 10:1 Cr(III):peptide produces the most intense [M + 2H](2+). Cr(III) also supercharges numerous other small peptides, including highly acidic species. For basic peptides, Cr(III) increases the charge state (2+ versus 1+) and causes the number of peptide molecules being protonated to double or triple. Chromium(III) does not supercharge the proteins cytochrome c and myoglobin. The ability of Cr(III) to enhance [M + 2H](2+) intensity may prove useful in tandem mass spectrometry because of the resulting overall increase in signal-to-noise ratio, the fact that [M + 2H](2+) generally dissociate more readily than [M + H](+), and the ability to produce [M + 2H](2+) precursors for electron-based dissociation techniques.

An IMS-IMS threshold method for semi-quantitative determination of activation barriers: Interconversion of proline cis↔trans forms in triply protonated bradykinin

Collisional activation of selected conformations by multidimensional ion mobility spectrometry (IMS-IMS), combined with mass spectrometry (MS), is described as a method to determine semi-quantitative activation energies for interconversion of different structures of the nonapeptide bradykinin (BK, Arg-Pro-Pro-Gly-Phe-Ser-Pro-Phe-Arg). This analysis is based on a calibration involving collision-induced dissociation measurements of ions with known dissociation energies (i.e., "thermometer" ions) such as leucine enkephalin, BK, and amino acid-metal cation systems. The energetic barriers between six conformations of [BK+3H]3+ range from 0.23 ±0.01 to 0.55 ±0.03 eV. Prior results indicate that the major peaks in the IMS distributions correspond to specific combinations of cis and trans configurations of the three proline residues in the peptide sequence. The analysis allows us to directly assess pathways for specific transitions. The combination of structural assignments, experimentally determined barrier heights, onset of the quasi-equilibrium region, and dissociation threshold are used to derive a semi-quantitative potential energy surface for main features of [BK+3H]3+.

Simple setup for gas-phase H/D exchange mass spectrometry coupled to electron transfer dissociation and ion mobility for analysis of polypeptide structure on a liquid chromatographic time scale

Gas-phase hydrogen/deuterium exchange (HDX) is a fast and sensitive, yet unharnessed analytical approach for providing information on the structural properties of biomolecules, in a complementary manner to mass analysis. Here, we describe a simple setup for ND3-mediated millisecond gas-phase HDX inside a mass spectrometer immediately after ESI (gas-phase HDX-MS) and show utility for studying the primary and higher-order structure of peptides and proteins. HDX was achieved by passing N2-gas through a container filled with aqueous deuterated ammonia reagent (ND3/D2O) and admitting the saturated gas immediately upstream or downstream of the primary skimmer cone. The approach was implemented on three commercially available mass spectrometers and required no or minor fully reversible reconfiguration of gas-inlets of the ion source. Results from gas-phase HDX-MS of peptides using the aqueous ND3/D2O as HDX reagent indicate that labeling is facilitated exclusively through gaseous ND3, yielding similar results to the infusion of purified ND3-gas, while circumventing the complications associated with the use of hazardous purified gases. Comparison of the solution-phase- and gas-phase deuterium uptake of Leu-Enkephalin and Glu-Fibrinopeptide B, confirmed that this gas-phase HDX-MS approach allows for labeling of sites (heteroatom-bound non-amide hydrogens located on side-chains, N-terminus and C-terminus) not accessed by classical solution-phase HDX-MS. The simple setup is compatible with liquid chromatography and a chip-based automated nanoESI interface, allowing for online gas-phase HDX-MS analysis of peptides and proteins separated on a liquid chromatographic time scale at increased throughput. Furthermore, online gas-phase HDX-MS could be performed in tandem with ion mobility separation or electron transfer dissociation, thus enabling multiple orthogonal analyses of the structural properties of peptides and proteins in a single automated LC-MS workflow.

Separation of protein conformers by differential ion mobility in hydrogen-rich gases

Proteins in solution or the gas phase tend to exhibit multiple conformational families, each comprising distinct structures. Separation methods have generally failed to resolve these, with their convolution producing wide peaks. Here, we report full separation of >10 conformers for most ubiquitin charge states by the new approach of differential ion mobility spectrometry (field asymmetric waveform ion mobility spectrometry, FAIMS) employing H2/N2 gas mixtures with up to 85% H2. The resolving power (up to 400) is five times the highest previously achieved (using He/N2 buffers), greatly increasing the separation specificity. The peak widths match the narrowest obtained by FAIMS for any species under the same conditions and scale with the protein charge state (z) and ion residence time (t) as z(-1/2) and t(-1/2), as prescribed for instrumental (diffusional) broadening. This suggests resolution of specific geometries rather than broader ensembles.

Cis-trans isomerizations of proline residues are key to bradykinin conformations

A recent ion mobility-mass spectrometry (IM-MS) study of the nonapeptide bradykinin (BK, amino acid sequence Arg(1)-Pro(2)-Pro(3)-Gly(4)-Phe(5)-Ser(6)-Pro(7)-Phe(8)-Arg(9)) found evidence for 10 populations of conformations that depend upon the solution composition [J. Am. Chem. Soc. 2011, 133, 13810]. Here, the role of the three proline residues (Pro(2), Pro(3), and Pro(7)) in establishing these conformations is investigated using a series of seven analogue peptides in which combinations of alanine residues are substituted for prolines. IM-MS distributions of the analogue peptides, when compared to the distribution for BK, indicate the multiple structures are associated with different combinations of cis and trans forms of the three proline residues. These data are used to assign the structures to different peptide populations that are observed under various solution conditions. The assignments also show the connectivity between structures when collisional activation is used to convert one state into another.

Statistical analysis of ion mobility spectrometry. II. Adaptively biased methods and shape correlations

Following a recent effort [J. Am. Soc. Mass Spectrom. 23, 386-396 (2012)], we continue to explore computational methodologies for generating molecular conformations to support collisional cross sections suggested by ion mobility measurements. Here, adaptively biased molecular dynamics (ABMD) simulations are used to sample the configuration space and to achieve flat-histogram sampling along the reaction coordinates of the first two moments of the gyration tensor. The method is tested and compared with replica-exchange simulations on triply-protonated bradykinin and on a larger 25-residue peptide. It is found to have a much higher efficiency for producing large sets of conformations in a broad range of diffusion cross-sections, whereas it does not compete with conventional replica-exchange molecular dynamics in locating the lowest-energy structure. Nevertheless, the broad sampling obtained from the ABMD method allows to quantitatively correlate the diffusion cross-section Ω with other geometric order parameters that have simpler interpretation. The strong correlations found between the diffusion cross-section and the radius of gyration, the surface area and the volume of the convex hull suggest an optimal template for accurately mimicking the variations of Ω in a broad range of conformations, using only geometrical information and doing so at a very moderate computational cost. The existence of such a correlation is confirmed on the much larger protein α-lactalbumin.

Statistical analysis of ion mobility spectrometry. I. Unbiased and guided replica-exchange molecular dynamics

Achieving (bio)macromolecular structural assignment from the interpretation of ion mobility spectrometry (IMS) experiments requires successful comparison with computer modeling. Replica-exchange molecular dynamics simulations with suitable force fields not only offer a convenient framework to locate relevant conformations, especially in the case of multiple-funnel energy landscapes, but they are also well suited to statistical analyses. In the present paper, we discuss two extensions of the method used to improve its efficiency in the context of IMS. Two doubly-protonated polyalanines [RA(4)XA(4)K + 2H](2+) with X=V and D appear as favorable cases for which the calculated collision cross-section distributions naturally agree with the measurements, providing reliable candidate structures. For these compounds, a careful consideration of other order parameters based on the weighted histogram method resolves several otherwise hidden underlying conformational families. In the case of a much larger peptide exhibiting bistability, assignment is more difficult but could be achieved by guiding the sampling with an umbrella potential using the square gyration radius as the biasing coordinate. Applied to triply protonated bradykinine, the two presented methods indicate that different conformations compatible with the measurements are very close in energy.

Separation of a set of peptide sequence isomers using differential ion mobility spectrometry

Protein identification in bottom-up proteomics requires disentangling isomers of proteolytic peptides, a major class of which are sequence inversions. Their separation using ion mobility spectrometry (IMS) has been limited to isomeric pairs. Here we demonstrate baseline separation of all seven 8-mer tryptic peptide isomers using differential IMS. Evaluation of peak capacity implies that even larger libraries should be resolved for heavier peptides with higher charge states.

Doubly charged protonated a ions derived from small peptides

Protonated a(2) and a(3) (therefore doubly charged) ions in which both charges lie on the peptide backbone are formed in collision-induced dissociations of [La(III)(peptide)(CH(3)CN)(m)](3+) complexes. Abundant (a(3)+H)(2+) ions are formed from triproline (PPP) and peptides with a proline residue at the N-terminus; these peptides are the most effective in producing ions of the type (a(2)+H)(2+) and (a(3)+H)(2+). A systematic study of the effect of the location of the proline residue and other residues of aliphatic amino acids on the generation of protonated a ions is reported. Density functional theory calculations at B3LYP/6-311++G(d,p) gave the proton affinity of the a(3) ion derived from PPP to be 167.6 kcal mol(-1), 2.6 kcal mol(-1) higher than that of water. The protonated a(2) ions of diglycine and diproline and a(3) ions of triglycine have lower proton affinities and are only observed in lower abundances, possibly due to proton transfer to water in ion-molecule reactions.

Ion mobility separation of isomeric phosphopeptides from a protein with variant modification of adjacent residues

Ion mobility spectrometry (IMS), and particularly differential or field asymmetric waveform IMS (FAIMS), was recently shown capable of separating peptides with variant localization of post-translational modifications. However, that work was limited to a model peptide with Ser phosphorylation on fairly distant alternative sites. Here, we demonstrate that FAIMS (coupled to electrospray/mass spectrometry (ESI/MS)) can broadly baseline-resolve variant phosphopeptides from a biologically modified human protein, including those involving phosphorylation of different residues and adjacent sites that challenge existing tandem mass spectrometry (MS/MS) methods most. Singly and doubly phosphorylated variants can be resolved equally well and identified without dissociation, based on accurate separation properties. The spectra change little over a range of infusion solvent pH; hence, the present approach should be viable in conjunction with chromatographic separations using mobile phase gradients.

Ultrahigh-resolution differential ion mobility spectrometry using extended separation times

Ion mobility spectrometry (IMS), and particularly differential IMS or field asymmetric waveform IMS (FAIMS), is emerging as a versatile tool for separation and identification of gas-phase ions, especially in conjunction with mass spectrometry. For over two decades since its inception, the utility of FAIMS was constrained by resolving power (R) of less than ∼20. Stronger electric fields and optimized gas mixtures have recently raised achievable R to ∼200, but further progress with such approaches is impeded by electrical breakdown. However, the resolving power of planar FAIMS devices using any gas and field intensity scales as the square root of separation time (t). Here, we extended t from the previous maximum of 0.2 s up to 4-fold by reducing the carrier gas flow and increased the resolving power by up to 2-fold as predicted, to >300 for multiply charged peptides. The resulting resolution gain has enabled separation of previously "co-eluting" peptide isomers, including folding conformers and localization variants of modified peptides. More broadly, a peak capacity of ∼200 has been reached in tryptic digest separations.

Gas-phase structure and fragmentation pathways of singly protonated peptides with N-terminal arginine

The gas-phase structures and fragmentation pathways of the singly protonated peptide arginylglycylaspartic acid (RGD) are investigated by means of collision-induced-dissociation (CID) and detailed molecular mechanics and density functional theory (DFT) calculations. It is demonstrated that despite the ionizing proton being strongly sequestered at the guanidine group, protonated RGD can easily be fragmented on charge directed fragmentation pathways. This is due to facile mobilization of the C-terminal or aspartic acid COOH protons thereby generating salt-bridge (SB) stabilized structures. These SB intermediates can directly fragment to generate b(2) ions or facilely rearrange to form anhydrides from which both b(2) and b(2)+H(2)O fragments can be formed. The salt-bridge stabilized and anhydride transition structures (TSs) necessary to form b(2) and b(2)+H(2)O are much lower in energy than their traditional charge solvated counterparts. These mechanisms provide compelling evidence of the role of SB and anhydride structures in protonated peptide fragmentation which complements and supports our recent findings for tryptic systems (Bythell, B. J.; Suhai, S.; Somogyi, A.; Paizs, B. J. Am. Chem. Soc. 2009, 131, 14057-14065.). In addition to these findings we also report on the mechanisms for the formation of the b(1) ion, neutral loss (H(2)O, NH(3), guanidine) fragment ions, and the d(3) ion.

High-resolution differential ion mobility separations using planar analyzers at elevated dispersion fields

The ion mobility spectrometry (IMS) methods are grouped into conventional IMS, based on the absolute ion mobility, and differential or field asymmetric waveform IMS (FAIMS), based on mobility differences between strong and weak electric fields. A key attraction of FAIMS is substantial orthogonality to mass spectrometry (MS). Although several FAIMS/MS platforms were commercialized, their utility was limited by FAIMS resolving power, typically ∼10-20. Recently, gas mixtures comprising up to 75% He have enabled resolving power >100 that permits separation of numerous heretofore "coeluting" isomers. This performance opens major new proteomic and other biological applications. Here, we show that raising the separation field by ∼35% over the previous 21 kV/cm provides similar or better resolution (with resolving powers of >200 for multiply charged peptides) using only 50% He, which avoids problems due to elevated pressure and He content in the mass spectrometer. The heating of ions by the separation field in this regime exceeds that at higher He content but weaker field, inducing greater isomerization of labile species.

Natural structural motifs that suppress peptide ion fragmentation after electron capture

Series of doubly and triply protonated diarginated peptide molecules with different number of glutamic acid (E) and asparagine (N) residues were analyzed under ECD conditions. ECD spectra of doubly-protonated peptides show a strong dependence on the number of E and N residues. Both the backbone cleavages and hydrogen radical (H*) loss from the charge-reduced precursor ions ([M+2H](+*)) were suppressed as the number of E and N residues increases. A strong inhibition of the backbone cleavages and H* loss from [M+2H](+*) was found for peptides with 6E residues (or 4E + 2N residues). The results obtained using these model peptides were re-confirmed by analyzing N-arginated Fibrinopeptide-B (i.e., REGVNDNEEGFFSAR). In contrast to the N-arginated peptide, ECD of the doubly-protonated Fibrinopeptide-B and its analogues show extensive backbone cleavages leading to series of c- and z-ions ( approximately 80% sequence coverage). Based on these results, it is believed that peptide ions with all surplus protons sequestered in arginine-residues would show enhanced stability under ECD conditions as the number of acid-residue increases. The suppression of backbone cleavages and H* loss from [M+2H](+*) are presumably attributed to the low reactivity of the charge-reduced precursor ions. One of the possible hypothesis is that diarginated E-rich peptides may contain hydrogen bonds between carbonyl oxygen of E side chains and backbone amide hydrogen. These hydrogen bonds would provide extra stabilization for [M+2H](+*). This is the first demonstration of natural structural motifs in peptides that would inhibit the backbone fragmentation of the charge-reduced peptide ions under ECD conditions.

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.

High-resolution differential ion mobility separations using helium-rich gases

Analyses of complex mixtures and characterization of ions increasingly involve gas-phase separations by ion mobility spectrometry (IMS) and particularly differential or field asymmetric waveform IMS (FAIMS) based on the difference of ion mobility in strong and weak electric fields. The key advantage of FAIMS is substantial orthogonality to mass spectrometry (MS), which makes FAIMS/MS hybrid a powerful analytical platform of broad utility. However, the potential of FAIMS has been constrained by limited resolution. Here, we report that the use of gas mixtures comprising up to 75% He dramatically increases the FAIMS separation capability, with the resolving power for peptides and peak capacity for protein digests reaching and exceeding 100. The resolution gains extend to small molecules, where previously unresolved isomers can now be separated. These performance levels open major new applications of FAIMS in proteomic and other biomolecular analyses.

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.

Differential ion mobility separations of peptides with resolving power exceeding 50

Differential ion mobility spectrometry (IMS) or field asymmetric waveform IMS (FAIMS) separates gas-phase ions by mobility differences with respect to the electric field intensity. A major emerging FAIMS application is the fractionation of proteolytic digests. Using a planar FAIMS unit with helium/nitrogen mixtures, we have increased FAIMS resolving powers for peptide analyses from the prior maximum of approximately 20-30 to approximately 50-70. The resolution improved nearly 3-fold, allowing, in particular, separation of previously unresolved conformers.

A density functional theory (DFT) study on gas-phase proton transfer reactions of derivatized and underivatized peptide ions generated by matrix-assisted laser desorption ionization

In this study, classic molecular dynamics (MD) simulations followed by density functional theory (DFT) calculations are employed to calculate the proton transfer reaction enthalpy shifts for native and derivatized peptide ions in the MALDI plume. First, absolute protonation and deprotonation enthalpies are calculated for native peptides (RPPGF and AFLDASR), the corresponding hexyl esters and three common matrices alpha-cyano-4-hydroxycinnamic acid (4HCCA), 2,5-dihydroxybenzoic acid (DHB), and 6 aza-2-thiothymine (ATT). From the proton exchange reaction calculations, protonation and deprotonation of the neutral peptides are thermodynamically favorable in the gas phase as long as the corresponding protonated/deprotonated matrix ions are present in the plume. Moreover, the gain in proton affinity shown by the ester ions suggests that the increase in ion yield is likely to be related to an easier proton transfer from the matrix to the peptide.

Optimization of Algorithms for Ion Mobility Calculations

Ion mobility spectrometry (IMS) is increasingly employed to probe the structures of gas-phase ions, particularly those of proteins and other biological macromolecules. This process involves comparing measured mobilities to those computed for potential geometries, which requires evaluation of orientationally averaged cross sections using some approximate treatment of ion-buffer gas collisions. Two common models are the projection approximation (PA) and exact hard-spheres scattering (EHSS) that represent ions as collections of hard spheres. Though calculations for large ions and/or conformer ensembles take significant time, no algorithmic optimization had been explored. Previous EHSS programs were dominated by ion rotation operations that allow orientational averaging. We have developed two new algorithms for PA and EHSS calculations: one simplifies those operations and greatly reduces their number, and the other disposes of them altogether by propagating trajectories from a random origin. The new algorithms were tested for a representative set of seven ion geometries including diverse sizes and shapes. While the best choice depends on the geometry in a nonobvious way, the difference between the two codes is generally modest. Both are much more efficient than the existing software, for example faster than the widely used Mobcal (implementing EHSS) approximately 10-30-fold.

How large is the [Fe(III)(protoporphyrin IX)]+ ion (hemin+) in the gas phase?

Comparison of the collision cross-section of the [Fe(III)-protoporphyrin IX]+ ion, hemin+, measured by means of ion-mobility experiments and the cross-sections calculated from theoretical structures based on density functional theory reveals that hemin+, in the gas phase, contains intramolecular hydrogen bonding between its two propionic acid side-chains.