Selective isotopic exchange of polyfimctional ions in tandem mass spectrometry: Methodology,applications and mechanism

Isotopic exchange of mass-selected odd- and even-electron molecular ions of aromatic compounds upon collision with deuterated gases was investigated as a function of reagent gas, interaction time and collision energy. Use of ND₃ as reagent allows exchange of all active hydrogens for the compound types studied, providing a count of the total number of active hydrogens present in the analyte. CH₃OD exchanges specific types of active hydrogens, such as phenolic and carboxylic hydrogens, without exchanging amino hydrogens. This selectivity assists in the identification and enumeration of different types of active hydrogens present in polyfunctional compounds. The H–D exchange patterns serve to differentiate isomeric aromatic compounds containing methoxy, amino, hydroxy and carboxylic acid substituents. Trapping of mass-selected ions in the collision region of a triple quadrupole mass spectrometer greatly enhances the degree of H–D exchange, thereby facilitating determination of the number of active hydrogens in the analyte. Triple stage mass spectrometric experiments, performed in a pentaquadrupole mass spectrometer, help elucidate the exchange process. Isotopic exchange in the collision region of a tandem mass spectrometer also provides insights into the site of protonation in molecules containing several functional groups. The proximity of the functional groups and the proton affinity difference between the analyte and the reagent gas are important factors in site-specific H–D exchange in polyfunctional compounds. An investigation of the effects of collision energy reveals that cluster ion formation plays a major role in the exchange mechanism operating in the triple quadrupole and that H–D exchange, ion-molecule adduct formation and endothermic fragmentation are competitive reaction channels.     

Site specificity in the H–D exchange reactions of gas-phase protonated amino acids with CH3OD

H–D exchange reactions of methanol-d₁ with protonated amino acids were performed in an external-source Fourier transform mass spectrometer. Absolute rate constants were determined for the group which included glycine, alanine, valine, leucine, isoleucine and proline. By comparing reactivities with selected methyl esters, it was found that exchange on the carboxylic acid occurs 3–10 times faster than exchange on the amino group. No simple correlation is observed between the rates of H–D exchange on the acid group and the size of the alkyl group. However, the rates of exchange on the amine decrease with increasing gas-phase basicity. Glycine, the least basic amino acid, exchanges its amine hydrogens the fastest. These results are useful for determining the interaction of methanol with protonated amino acids and can provide insight into the H–D exchange reactions observed with polyprotonated proteins produced by electrospray ionization.     

Gas phase RNA and DNA ions 2. Conformational dependence of the gas-phase H/D exchange of nucleotide-5′-monophosphates

The conformational dependence of the gas-phase hydrogen/deuterium (H/D) exchange of nucleotide-5-monophosphate anions with the H/D exchange reagent D2S is reported here. The electrospray-generated [M-H]- anions of adenosine-5'-monophosphate, adenosine-5'-carboxylic acid, ribitol-5-phosphate, and 2-deoxy-ribitol-5-phosphate were reacted with D2S in the gas phase. Their reactivity (adenosine-5'-monophosphate exchanged 2 of 5 labile hydrogens, adenosine-5'-carboxylic acid exchanged 1 of 4, ribitol-5-phosphate exchanged 2 of 3, and 2-deoxy-ribitol-5-phosphate exchanged 1 of 2) suggests that the hydroxyl group in the 2 position of the ribose sugar and the amino hydrogen on the nucleobase do not exchange readily with D2S. Semiempirical molecular orbital calculations suggest that the labile hydrogens in these positions are thermodynamically facile to exchange but as a conformation inaccessible to the presumed phosphate anion, consistent with a mechanism in which the phosphate anion complexes with the exchange reagent and assists H/D exchange at a neighboring site.     

Gas-phase structure of protonated histidine and histidine methyl ester: combined experimental mass spectrometry and theoretical ab initio study

Gas-phase H/D exchange experiments with CD3OD and D2O and quantum chemical ab initio G3(MP2) calculations were carried out on protonated histidine and protonated histidine methyl ester in order to elucidate their bonding and structure. The H/D exchange experiments show that both ions have three equivalent fast hydrogens and one appreciably slower exchangeable hydrogen assigned to the protonated amino group participating in a strong intramolecular hydrogen bond (IHB) with the nearest N(sp2) nitrogen of the imidazole fragment and to the distal ring NH-group, respectively. It is taken for granted that the proton exchange in the IHB is much faster than the H/D exchange. Unlike in other protonated amino acids (glycine, proline, phenylalanine, tyrosine, and tryptophan) studied earlier, the exchange rate of the carboxyl group in protonated histidine is slower than that of the amino group. The most stable conformers and the enthalpies of neutral and protonated histidine and its methyl ester are calculated at the G3(MP2) level of theory. It is shown that strong intramolecular hydrogen bonding between the amino group and the imidazole ring nitrogen sites is responsible for the stability and specific properties of the protonated histidine. It is found that the proton fluctuates between the amino and imidazole groups in the protonated form across an almost vanishing barrier. Proton affinity (PA) of histidine calculated by the G3(MP2) method is 233.2 and 232.4 kcal mol(-1) for protonation at the imidazole ring and at the amino group nitrogens, respectively, which is about 3-5 kcal mol(-1) lower than the reported experimental value.     

The role of acidic residues and of sodium ion adduction on the gas-phase H/D exchange of peptides and peptide dimers

Gas-phase H/D exchange is widely used for characterizing the structure of ions. However, many structural parameters that affect the rate of H/D exchange are poorly understood, which complicates the interpretation of experimental data. Here, the effects of sodium ion adduction on the rate of H/D exchange with D₂O for a series of peptides and peptide dimers with varying numbers of acidic residues are described. The maximum number of sodium ion adducts that can be accommodated by the peptides and peptide dimers in this study is N + 1, where N is the number of free carboxylic acid groups. The formation of methyl-esters at all carboxylic acid groups, or the replacement of all the acidic hydrogens with sodium ions, effectively shuts down H/D exchange with D₂O. In contrast, both the rate and the extent of H/D exchange with D₂O are increased for most of the peptides and peptide dimers by the adduction of an intermediate number of sodium ions. These results are consistent with the H/D exchange occurring via a salt-bridge mechanism and show that the presence of two carboxylic acid groups is much better than one. The results with peptide dimers also indicate that surface accessibility may not be a dominant factor in the extent of H/D exchange for these ions.     

A new method for the accurate determination of the isotopic state of single amide hydrogens within peptides using Fourier transform ion cyclotron resonance mass spectrometry

A new method is presented to accurately determine the probability of having a deuterium or hydrogen atom on a specific amide position within a peptide after deuterium/hydrogen (D/H) exchange in solution. Amide hydrogen exchange has been proven to be a sensitive probe for studying protein structures and structural dynamics. At the same time, mass spectrometry in combination with physical fragmentation methods is commonly used to sequence proteins based on an amino acid residue specific mass analysis. In the present study it is demonstrated that the isotopic patterns of a series of peptide fragment ions obtained with capillary-skimmer dissociation, as observed with a 9.4 T Fourier transform ion cyclotron resonance (FTICR) mass spectrometer, can be used to calculate the isotopic state of specific amide hydrogens. This calculation is based on the experimentally observed isotopic patterns of two consecutive fragments and on the isotopic binomial distributions of the atoms in the residue constituting the difference between these two consecutive fragments. The applicability of the method is demonstrated by following the sequence-specific D/H exchange rate in solution of single amide hydrogens within some peptides.     

Photoactivated h/d exchange in tyrosine: involvement of a radical anion intermediate

The aromatic hydrogen nuclei of tyrosine are photochemically labile and exchange with deuterons in neutral D(2)O solution. The site meta to the ring hydroxyl substituent is preferentially deuterated, exhibiting a meta/ortho deuteration rate of approximately 4:1. In contrast with acid-catalyzed H/D exchange and with nearly all of the reported photoactivated H/D exchange studies, the UV-induced H/D exchange of tyrosine is optimal at pH 9 and is effectively quenched at acid pH. Photochemical H/D exchange is strongly stimulated by the alpha-amino group (the aromatic hydrogens of p-cresol are far less subject to exchange) and by imidazole or phosphate buffers. On the basis of the results obtained here and on the previously identified cyclohexadienyl radical (Bussandri, A.; van Willigen, H. J. Phys. Chem. A 2002, 106, 1524-1532), we conclude that the exchange reaction involves a radical intermediate and results from two distinct roles of tyrosine: (1) as a phototransducer of light energy into solvated electrons (e(aq)(-)), and (2) as an acceptor of an electron to create a radical anion intermediate which is rapidly protonated, yielding a neutral cyclohexadienyl radical. Regeneration of the tyrosine can occur via a bimolecular redox reaction of the cyclohexadienyl and phenoxyl radicals to yield a carbocation/phenoxide pair, followed by deprotonation of the carbocation. The oxidation step is pH dependent, requiring the deprotonated form of the cyclohexadienyl radical. The H/D exchange thus results from a cyclic one-electron (Birch) reduction/protonation/reoxidation (by phenoxyl radical)/deprotonation cycle. Consistent with these mechanistic conclusions, the aromatic hydrogens of tyrosine O-methyl ether are photochemically inert, but become labile in the presence of tyrosine at high pH. The deuteration rate of O-methyl tyrosine is lower than that of tyrosine and shows a preference for the ortho positions. This difference is proposed to result from a variation in the oxidation step, characterized by a preferential oxidation of a cyclohexadienyl resonance structure with the unpaired electron localized on the oxygen substituent.     

Hydrogen-deuterium exchange and selective labeling of deprotonated amino acids and peptides in the gas phase

Hydrogen-deuterium exchange reactions of deprotonated amino acids and small peptides were studied. Selective labeling can be carried out at the alpha-amino group of lysine (2 of 4 labile hydrogens undergo exchange with CF3CH2OD) and the guanidine side chain of arginine (3 of 6 labile hydrogens undergo exchange with CH3CH2OD and C6H5CH2OD). Differential labeling of peptides also was accomplished, and the extent of H/D exchange is dependent on the amino acids which are present as well as their order in the chain.     

Computational investigation and hydrogen/deuterium exchange of the fixed charge derivative tris(2,4,6-Trimethoxyphenyl) phosphonium: Implications for the aspartic acid cleavage mechanism

Aspartic acid (Asp)-containing peptides with the fixed charge derivative tris(2,4,6trimethoxyphenyl) phosphonium (tTMP-P+) were explored computationally and experimentally by hydrogen/deuterium (H/D) exchange and by fragmentation studies to probe the phenomenon of selective cleavage C-terminal to Asp in the absence of a "mobile" proton. Ab initio modeling of the tTMP-P+ electrostatic potential shows that the positive charge is distributed on the phosphonium group and therefore is not initiating or directing fragmentation as would a "mobile" proton. Geometry optimizations and vibrational analyses of different Asp conformations show that the Asp structure with a hydrogen bond between the side-chain hydroxy and backbone carbonyl lies 2.8 kcal/mol above the lowest energy conformer. In reactions with D2O, the phosphonium-derived doubly charged peptide (H+)P+LDIFSDF rapidly exchanges all 12 of its exchangeable hydrogens for deuterium and also displays a nonexchanging population. With no added proton, P+LDIFSDF exchanges a maximum of 4 of 11 exchangeable hydrogens for deuterium. No exchange is observed when all acidic groups are converted to the corresponding methyl esters. Together, these H/D exchange results indicate that the acidic hydrogens are "mobile locally" because they are able to participate in exchange even in the absence of an added proton. Fragmentation of two distinct (H+)P+LDIFSDF ion populations shows that the nonexchanging population displays selective cleavage, whereas the exchanging population fragments more evenly across the peptide backbone. This result indicates that H/D exchange can sometimes distinguish between and provide a means of separation of different protonation motifs and that these protonation motifs can have an effect on the fragmentation.     

Hydrogen exchange rates in proteins from water (1)H transverse magnetic relaxation

Access to the fast exchange kinetics of labile protein hydrogens in solution is provided by exchange broadening of the water 1H NMR line. We analyzed the chemical shift modulation contribution of labile hydrogens in bovine pancreatic trypsin inhibitor (BPTI) to the transverse 1H spin relaxation rate, R2, of the bulk solvent. Both the experimental pH dependence and the CPMG dispersion of R2 could be quantitatively accounted for on the basis of known chemical shifts, exchange rates, and ionization constants for BPTI. This analysis provided, for the first time, the hydrogen exchange rate constants for Lys and Arg side chains in a protein and pointed to an internal catalysis of the N-terminal amino protons in BPTI by a salt bridge. The method can be used for mapping the hydrogen exchange rates in protein solutions and biomaterials, which may be important for the control of relaxation-weighted contrast in biological MRI.     

Gas phase hydrogen/deuterium exchange of arginine and arginine dipeptides complexed with alkali metals

The hydrogen/deuterium (H/D) exchange of protonated and alkali-metal cationized Arg-Gly and Gly-Arg peptides with D(2)O in the gas phase was studied using electrospray ionization quadropole ion trap mass spectrometry. The Arg-Gly and Gly-Arg alkali metal complexes exchange significantly more hydrogens than protonated Arg-Gly and Gly-Arg. We propose a mechanism where the peptide shifts between a zwitterionic salt bridge and nonzwitterionic charge solvated conformations. The increased rate of H/D exchange of the alkali metal complexes is attributed to the peptide metal complexes' small energy difference between the salt-bridge conformation and the nonzwitterionic charge-solvated conformation. Implications for the applicability of this mechanism to other zwitterionic systems are discussed.     

The complexation of protonated peptides with saccharides in the gas phase decreases the rates of hydrogen/deuterium exchange reactions

Gas-phase noncovalently bound complexes are probed by hydrogen/deuterium exchange. The complexes, composed of a protonated amino acid and a monosaccharide, are investigated to observe the effects of complexation on the rates of exchange. Rate constants are determined and compared for complexed and uncomplexed amino acids. The overall rate constant, which corresponds to exchange of a specific number of hydrogens, is deconvoluted to yield site-specific rate constants. Complexation of amino acids with saccharides significantly decreases the rate constants of the exchange. Results of molecular orbital calculations are provided to explain the decrease in the rates.     

Protonated serine octamer cluster: structure elucidation by gas-phase H/D exchange reactions

The H/D exchange kinetics of the protonated serine octamer was investigated by both flow-tube and FT-ICR experiments. The exchange was observed to be bimodal in agreement with previous observations. Quantitative analysis of the experimental results led to site-specific H/D exchange rate constants on the basis of which the structures of both ion populations were deduced. We observe the two separate conformers exchanging 33 hydrogens each-in an independent manner and at different rates. This result was achieved through a probabilistic algorithm that groups together equivalent hydrogen atoms having equal rate constants. The slower exchanging population A is assigned an all-zwitterionic structure. Its faster exchanging counterpart B is assigned an all-neutral structure. Population A was found to be more stable toward collision-induced activation than population B. All of these findings are consistent with previous experimental results, thus comprising a self-consistent picture of the protonated serine octamer and its gas-phase properties.     

Gas phase hydrogen deuterium exchange reactions of a model peptide: FT-ICR and computational analyses of metal induced conformational mutations

We utilized gas phase hydrogen/deuterium (H/D) exchange reactions and ab initio calculations to investigate the complexation between a model peptide (Arg-Gly-AspRGD) with various alkali metal ions. The peptide conformation is drastically altered upon alkali metal ion complexation. The associated conformational changes depend on both the number and type of complexing alkali metal ions. Sodium has a smaller ionic diameter and prefers a multidentate interaction that involves all three amino acids of the peptide. Conversely, potassium and cesium form different types of complexes with the RGD. The [RGD + 2Cs − H]⁺ species exhibit the slowest H/D exchange reactivity (reaction rate constant of 6 × 10⁻¹³ cm³molecule⁻¹s⁻¹ for the fastest exchanging labile hydrogen with ND₃). The reaction rate constant of the protonated RGD is two orders of magnitude faster than that of the [RGD + 2Cs − H]⁺. Addition of the first cesium to the RGD reduces the H/D exchange reaction rate constant (i.e., D₀) by a factor of seven whereas sodium reduces this value by a factor of thirty. Conversely, addition of the second alkali metal ions has the opposite effect; the rate of D₀ disappearance for all [RGD + 2Met − H]⁺ species (MetNa, K, and Cs) decreases with the alkali metal ion size.     

Fast gas-phase hydrogen/deuterium exchange observed for a DNA G-quadruplex

The gas-phase hydrogen/deuterium (H/D) exchange kinetics of DNA G-quadruplexes has been investigated using Fourier transform ion cyclotron resonance mass spectrometry (FTICRMS). The quadruplex [(TGGGGT)4 . 3NH4+] undergoes very fast H/D exchange, in both the positive and in the negative ion modes, compared to DNA duplexes and other quadruplexes tested, and compared to the corresponding single-stranded TGGGGT. Substitution of NH4+ for K+ did not alter this fast H/D exchange, indicating that the hydrogens of the ammonium ions are not those exchanged. However, stripping of the interior cations of the quadruplex by source collision-induced dissociation (CID) in the positive ion mode showed that the presence of the inner cations is essential for the fast exchange to be possible. Molecular dynamics simulations show that the G-quadruplex is very rigid in the gas phase with NH4+ ions inside the tetrads. We suggest that the fast H/D exchange is favored by this rigid quadruplex conformation. This example illustrates that the concept that compact DNA structures exchange H for D slower than unfolded ones is a misconception.     

Kinetics of gas-phase hydrogen/deuterium exchange and gas-phase structure of protonated phenylalanine, proline, tyrosine and tryptophan

Site-specific rate constants for the gas-phase hydrogen/deuterium (H/D) exchange of four, three, five and five hydrogen atoms in protonated phenylalanine (Phe), proline (Pro), tyrosine (Tyr) and tryptophan (Trp), respectively, were determined from matrix-assisted laser desorption/ionization Fourier transform ion cyclotron resonance mass spectrometry (MALDI-FTICRMS) experiments with D(2)O, D(2)S, and CH(3)OD as deuterating agents. No H/D exchange was observed with D(2)S. For exchange with both CD(3)OD and D(2)O, which is about ten times slower in the latter, results indicate for all compounds protonation of the alpha-amino group in agreement with theoretical results. Also, with both reagents, all compounds exchange at the COOH site more than ten times faster than at the protonation site, with OH and NH sites of Tyr and Trp, respectively, exchanging slowest. The observation of H/D exchange despite the high differences in proton affinities between the amino acids and deuterating agent exceeding 200 kJ mol(-1) is in agreement with lowering of the barrier for proton transfer through hydrogen bonding proposed by Lebrilla and coworkers.     

Methyl guanine isomer distinction by hydrogen / deuterium exchange using a fourier transform mass spectrometer

Analytical Chemistry Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA Differentiation of the seven isomers of methyl guanine has been accomplished by monitoring gas-phase hydrogen/deuterium (H/D) exchange reactions of the protonated molecular ions with deuterium oxide (D₂O) in a Fourier transform mass spectrometer. In each case a distinctive reaction rate for the first H/D exchange was observed, and exchanges of up to three deuterium atoms occurred with characteristic ion abundances that could be used to differentiate the isomers. O⁶-Methyl guanine, for example, showed only one slow H/D exchange with D₂O, whereas l-methyl guanine exchanged two hydrogen atoms at a significantly faster rate. On comparison of the possible resonance structures of each protonated isomer with the experimental information about the number and rate of H/D exchanges observed, a reaction mechanism involving a concerted proton abstraction-deuterium cation donation was proposed.     

Deuteriation of nitrobenzoic acids in the presence of divalent platinum catalyst

The kinetic behavior of deuteriation of nitrobenzoic acids has been studied at 130 °C in the presence of homogenous platinum salt catalyst in a medium containing deuteriated acetic acid in heavy water. The quasiunimolecular H/D exchange rate constants for particular position of aromatic ring hydrogens were determined by proton NMR integration signal. The difference in the kinetics patterns of H/D exchange has been shown for the 2-nitro-, 3-nitro- and 4-nitrobenzoic acid.     

Deuteriation of bromobenzoic acids in the presence of homogeneous platinum catalyst

The kinetic behavior of deuteriation of bromobenzoic acids in the presence of homogenous platinum salt catalyst in a medium containing solution of deuteriated acetic acid in heavy water has been studied at 130°C. The quasiunimolecular H/D exchange rate constants for particular position of aromatic ring hydrogens were determined by proton NMR integration signal. The difference in the kinetics patterns of H/D exchange has been shown for the chloro- and bromo-derivatives of benzoic acid.     

Gas-phase H/D exchange reactions of polyamine complexes: (M + H)+, (M + alkali metal+), and (M + 2H)2+

Gas-phase hydrogen/deuterium exchange reactions between noncovalent polyamine complexes and D2O, CH3OD, or ND3 are undertaken in a quadrupole ion trap mass spectrometer. Structural features of the protonated polyamines can be differentiated by the rates and overall extent of exchange, specifically the presence of propylene units and/or a cyclic structure noticeably decreases exchange compared to the exchange observed for acyclic polyamines with only ethylene bridges between amino groups. Significant differences are observed for singly protonated vs. doubly protonated complexes, where the doubly protonated complexes undergo more efficient exchange at a higher rate than the analogous singly protonated complexes. Molecular modeling calculations suggest that more diffuse conformations may exist for the higher charge states, thus facilitating H/D exchange. In addition, H/D exchange reactions between the alkali metal cationized complexes and ND3 are nearly quenched, compared to the significant exchange seen for singly protonated complexes. A conformational change or the loss of a low energy reaction pathway may explain the limited exchange reactions seen when a bulky cation replaces a proton in the complex.