A Direct Comparison of "First" and "Second" Gas Phase Basicities of the Octapeptide RPPGFSPF

Exploiting Charge State Distribution To Probe Intramolecular Interactions in Gas-Phase Phosphopeptides and Enhance Proteomics Analyses

Charging of analytes is a prerequisite for performing mass spectrometry analysis. In proteomics, electrospray ionization is the dominant technique for this process. Although the observation of differences in the peptide charge state distribution (CSD) is well-known among experimentalists, its analytical value remains underexplored. To investigate the utility of this dimension, we analyzed several public data sets, comprising over 250,000 peptide CSD profiles from the human proteome. We found that the dimensions of the CSD demonstrate high reproducibility across multiple laboratories, mass analyzers, and extensive time intervals. The general observation was that the CSD enabled effective partitioning of the peptide property space, resulting in enhanced discrimination between sequence and constitutional peptide isomers. Next, by evaluating the CSD values of phosphorylated peptides, we were able to differentiate between phosphopeptides that indicate the formation of intramolecular structures in the gas phase and those that do not. The reproducibility of the CSD values (mean cosine similarity above 0.97 for most of the experiments) qualified CSD data suitable to train a deep-learning model capable of accurately predicting CSD values (mean cosine similarity - 0.98). When we applied the CSD dimension to MS1- and MS2-based proteomics experiments, we consistently observed around a 5% increase in protein and peptide identification rate. Even though the CSD dimension is not as effective a discriminator as the widely used retention time dimension, it still holds the potential for application in direct infusion proteomics.

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.

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).

Charge location directs electron capture dissociation of peptide dications

The effect of peptide dication charge location on electron capture dissociation (ECD) fragmentation pattern is investigated. ECD fragmentation patterns are compared for peptides with amide and free acid C-terminal groups. ECD of free acid compared with C-terminally amidated peptides with basic residues near the N-terminus demonstrates increased formation of a-type ions. Similarly, ECD of free acid compared with C-terminally amidated peptides with basic residues near the C-terminus exhibits increased formation of y-type ions. Alteration of the peptide sequence to inhibit the formation of charged side chains (i.e., amino acid substitution and acetylation) provides further evidence for charge location effect on ECD. We propose that formation of zwitterionic peptide structures increases the likelihood of amide nitrogen protonation (versus basic side chains), which is responsible for the increase in a- and y-type ion formation.

Gas-phase ionization/desolvation processes and their effect on protein charge state distribution under matrix-assisted laser desorption/ionization conditions

The charge state distribution of proteins was studied as a function of experimental conditions, to improve the understanding of the matrix-assisted laser desorption/ionization (MALDI) mechanisms. The relative abundances of the multiply-charged ions appear to be a function of the matrix chosen, the laser fluence and the matrix-to-analyte molar ratio. A correlation is found between the matrix proton affinity and the yield of singly- versus multiply-charged ions. These results are in good agreement with a model in which gas-phase intracluster reactions play a significant role in analyte ion formation. A new model for endothermic desolvation processes in ultraviolet/MALDI is presented and discussed. It is based upon the existence of highly-charged precursor clusters and, complementary to the ion survivor model of Karas et al., assumes that two energy-dependent processes exist: (i) a soft desolvation involving consecutive losses of neutral matrix molecules, leading to a multiply-charged analyte and (ii) hard desolvation leading to a low charge state analyte, by consecutive losses of charged matrix molecules. These desolvations pathways are discussed in terms of kinetically limited processes. The efficiency of the two competitive desolvation processes seems related to the internal energy carried away by clusters during ablation.

Contact regions in the dimer of Alzheimer beta-amyloid domain [1-28] studied by mass spectrometry

Information is provided about the amino acid residues in the [1-28] domain of the Alzheimer b- amyloid protein, which participate in interstrand pairing and initiate fibillogenesis. The study was carried out using electrospray ionization on a four sector mass spectrometer, measuring kinetic energy release for a fragmentation process, and modeling the transition state with molecular dynamics calculations. The results eliminate the sequence [11-24] proposed earlier as the central core, and are consistent with, but do not distinguish between, residues [17-28] and [17-23] proposed by others based on biochemical studies.

Temperature-dependent H/D exchange of compact and elongated cytochrome c ions in the gas phase

Isotopic exchange reactions of compact and elongated conformations of gaseous cytochrome c ions (+5 and +9 states) with D2O have been measured as a function of temperature (from 300 to approximately 440 K) using ion mobility techniques. Rate constants for those sites that exchange at high temperatures (>400 K) are about an order of magnitude smaller than rate constants for sites that exchange at 300 K. Although the exchange rates decrease, the maximum exchange levels for rapidly exchanging sites increase with temperature. At 300 K, exchange levels of 53 +/- 3 and 63 +/- 3 are measured for the compact and elongated states, respectively. From 300 to 335 K, the exchange levels increase slightly to approximately 60 to 70 hydrogens. Above 335 K, the levels increase to a value of approximately 200 for the +5 state and approximately 190 for the +9 state, near the maximum possible levels, 200 and 204 for these respective charge states. Molecular dynamics simulations have been carried out on structures having calculated cross sections that are near the experimental values in order to explore the exchange process. Overall, it appears that charge site and exchange site proximities are important factors in the exchange profiles for the elongated +9 ion and the compact +5 ion.

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.

Kinetic energy release distributions in mass spectrometry

Kinetic energy releases (KERs) in unimolecular fragmentations of singly and multiply charged ions provide information concerning ion structures, reaction energetics and dynamics. This topic is reviewed covering both early and more recent developments. The subtopics discussed are as follows: (1) introduction and historical background; (2) ion dissociation and kinetic energy release: kinematics; potential energy surfaces; (3) the kinetic energy release distribution (KERD); (4) metastable peak observations: measurements on magnetic sector and time-of-flight instruments; energy selected results by photoelectron photoion coincidence (PEPICO); (5) extracting KERDs from metastable peak shapes; (6) ion structure determination and reaction mechanisms: singly and multiply charged ions; biomolecules and fullerenes; (7) theoretical approaches: phase space theory (PST), orbiting transition state (OTS)/PST, finite heat bath theory (FHBT) and the maximum entropy method; (8) exit channel interactions; (9) general trends: time and energy dependences; (10) thermochemistry: organometallic reactions, proton-bound clusters, fullerenes; and (11) the efficiency of phase space sampling.

Large anhydrous polyalanine ions: evidence for extended helices and onset of a more compact state

Ion mobility measurements and molecular modeling calculations have been used to examine the conformations of large multiply charged polyalanine peptides. Two series of [Ala(n)+3H](3+) conformations which do not interconvert during the 10 to 30 ms experimental timescales are observed: a family of elongated structures for n = 18 to 39 and a series of more compact conformations for n = 24 to 41. The more compact state becomes the dominant conformer type for n > 32. Molecular modeling studies and comparisons of calculated collision cross sections with experiment indicate that the elongated ions have extended helical conformations. We suggest that the more compact state corresponds to a new conformer type: a folded hinged helix-coil state in which helical and coil regions have similar physical dimensions. The competition between extended and compact states is rationalized by considering differences in charge stabilization and entropy.

Studies on the dephosphorylation of phosphotyrosine-containing peptides during post-source decay in matrix-assisted laser desorption/ionization

Phosphorylation of tyrosine residues in proteins is a common regulatory mechanism, although it accounts for less than 1% of the total O-phosphate content in proteins. Whereas aromatic phosphorylation sites can be identified by a number of different analytical techniques, sequence analysis of phosphotyrosine-containing proteins at the low picomole or even femtomole level is still a challenging task. This paper describes the post-source decay in matrix-assisted laser desorption/ionization mass spectrometry of phosphotyrosine-containing model peptides by comparing their fragmentation behavior with sequence-homologous unphosphorylated peptides. Whereas the parent ions showed significant losses of HPO3, all phosphorylated fragment ions of the b- and y-series displayed only minor dephosphorylated signals, which often were not detectable. Surprisingly, one of the studied phosphotyrosine-containing sequences displayed, in addition to the [M + H - 80]+ ion, a more abundant [M + H - 98]+ ion, which could be explained by elimination of phosphoric acid. This dephosphorylation pattern was very similar to the patterns obtained for phosphoserine- and phosphothreonine-containing peptides. Because the dephosphorylation pattern of the parent ion is often used to identify modified amino acids in peptides, we investigated possible dephosphorylation mechanisms in detail. Therefore, we substituted single trifunctional amino acid residues and incorporated deuterated phosphotyrosine residues. After excluding direct elimination of phosphoric acid from tyrosine, we could show that the obtained loss of H3PO4 depends on aspartic acid and arginine residues. Most likely the HPO3 group is transferred to aspartic acid followed by cleavage of phosphoric acid forming a succinimide. On the other hand, arginine appears to induce the H3PO4 loss by protonation of phosphotyrosine leaving a phenyl cation.

Intrinsic Ca2+ affinities of peptides: application of the kinetic method to analogs of calcium-binding site III of rabbit skeletal troponin C

We extended the kinetic method to determine the intrinsic affinities of nonvolatile organic molecules with divalent metal ions and then applied the amended method to determine the calcium affinities of peptide analogs of the calcium-binding site III of rabbit skeletal troponin C. Metal-bis(peptide) complexes of the composition ([H2Pi + H2Pii] - H + Ca)+, where H2P is a neutral peptide, were introduced into the gas phase by fast atom bombardment. The extended kinetic method recognizes that the dissociation characteristics of a singly charged, bis(peptide) complexes of divalent metal ions are determined by not only the metal-ion affinity but also the proton affinities of the neutral and deprotonated peptides. The modified method requires one to measure the relative abundances of [H2P - H + Ca]+, [H2P + H]+, and [H2P - H]- ions that form upon collisional activation of mixed peptide/metal complexes, proton-bound peptide dimers, and deprotonated peptide dimers, respectively. We found, by using the modified method, that the set of peptides has a different affinity order than that in solution. Peptides with one aspartic acid have a higher intrinsic Ca2+ affinity than those with two aspartates. The location of the aspartic acid (Asp) residues at various positions also affects the Ca2+ affinity. Those peptides with one Asp in the middle of the chain have higher Ca2+ affinities than those with Asp on the end because the former peptides offer greater polarizability to stabilize the charge. Peptides with two Asp's located in close proximity have higher intrinsic calcium affinities than those with aspartates positioned further apart.

Proteins in vacuo: a molecular dynamics study of the unfolding behavior of highly charged disulfide-bond-intact lysozyme subjected to a temperature pulse

Molecular dynamics simulations were used to interpret a variety of experimental data on highly charged disulfide-bond-intact lysozyme in vacuo. The simulation approach involved submitting a model of the protein [Reimann, Velázquez, and Tapia, J. Phys. Chem. B 102, 9344 (1998)] in a given charge state to a 3-ns-long heat pulse (usually at 500 K) followed by cooling or relaxation for 1 ns back to room temperature (293 K). This treatment yielded a charge threshold around Q(0)=8+ for obtaining significant unfolding, as indicated by an enhancement in collision cross section and conformer length. The collision cross sections and lengths theoretically obtained, along with the threshold charge state for initiating unfolding, were compatible with experimental results on lysozyme in vacuo. The unfolded, highly elongated conformations obtained for Q> or = 9+ displayed a significant level of non-native beta-sheet content which appeared to be additionally stabilized by charge self-solvation.

A database of 660 peptide ion cross sections: use of intrinsic size parameters for bona fide predictions of cross sections

An ion trap/ion mobility/time-of-flight mass spectrometry technique has been used to measure collision cross sections for 660 peptide ions generated by tryptic digestion of 34 common proteins. Measured cross sections have been compiled into a database that contains peptide molecular weight and sequence information. The database is used to generate average intrinsic contributions to cross section (size parameters) for different amino acid residues by solving systems of equations that relate the unknown contributions of individual residues to the sequences and cross sections of database peptides. Size parameters are combined with information about amino acid composition to calculate cross sections for database peptides. Bona fide cross section predictions (made prior to measurement) for peptides observed in tryptic digests of sperm whale myoglobin and yeast enolase are made. Eight of 10 predicted cross sections are within 2% of the experimental values and all 10 are within 3.2%. The utility of size parameters for cross section prediction is explored and discussed.

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/ion chemistry of high-mass multiply charged ions

Electrospray ionization has enabled the establishment of a new area of ion chemistry research based on the study of the reactions of high-mass multiply charged ions with ions of opposite polarity. The multiple-charging phenomenon associated with electrospray makes possible the generation of multiply charged reactant ions that yield charged products as a result of partial neutralization due to ion/ion chemistry. The charged products can be readily studied with mass spectrometric methods, providing useful insights into reaction mechanisms. This review presents the research done in this area, all of which has been performed within the past decade. Ion/ion chemistry has been studied at near-atmospheric pressure in a reaction region that leads to the atmospheric/vacuum interface of a mass spectrometer, and within a quadrupole ion trap operated with a bath gas at a pressure of 1 mtorr. Proton transfer has been the most common reaction type for high-mass ions, but other forms of "charge transfer," such as electron transfer and fluoride transfer, have also been observed. For some ion/ion reactions, attachment of the two reactants has been observed. Multiply charged ion/ion reactions are fast, due to the long-range Coulombic attraction, and they are universal in that any pair of oppositely charged ions is expected to react due to the high exothermicity associated with mutual neutralization. The kinetics of reaction for multiply charged ions, derived from the same molecule with a given singly charged reactant ion, follow a charge-squared dependence, at least under normal quadrupole ion trap conditions. This dependence suggests that reaction rates are determined by the long-range Coulomb attraction, and that the ions react with constant efficiency as a function of charge state. In the case of proton transfer reactions from polypeptides to even-electron perfluorocarbon anions, no fragmentation of the polypeptide product ions has, as yet, been observed. Electron transfer from small oligonucleotide anions to rare gas cations, on the other hand, results in extensive fragmentation of the nucleic acid product ions. The extent of fragmentation decreases as the size of the oligonucleotide anions increases, reflecting a decrease in fragmentation rates associated with an increase in the number of internal degrees of freedom of the oligonucleotide. When ion-cooling rates become competitive with dissociation rates, the initially formed product ions are stabilized and fragmentation is avoided. Collisional cooling, therefore, likely plays an important role in the relative lack of dissociation observed thus far as a result of ion/ion reactions for most high-mass ions. The observed dependence of ion/ion reaction rates on the square of the ion charge, the universal nature of mutual neutralization, and the relative lack of fragmentation that arises from ion/ion reactions, makes ion/ion chemistry a particularly useful means for manipulating charge states. This review emphasizes applications that take advantage of the unique characteristics of ion/ion proton transfer chemistry for manipulating charge states. These applications include mixture analysis by electrospray, precursor ion charge state manipulation for tandem mass spectrometry studies, and simplified interpretation of product ion spectra.

High-order structure and dissociation of gaseous peptide aggregates that are hidden in mass spectra

Injected-ion mobility and high-pressure ion mobility techniques have been used to examine the conformations of bradykinin, insulin chain A, and several other peptide ions in the gas phase. Under the experimental conditions employed, evidence for multimer formation in the mass spectra of peptides is minimal or absent altogether. However, ion mobility distributions show that aggregates of peptides (containing a single charge per monomer unit) are observed at the same mass-to-charge ratios as the singly charged parent ions. Collision cross sections for these clusters show that they have tightly packed roughly spherical conformations. We have bracketed the average density as 0.87 < p < 1.00 g cm-3. In some cases, specific stable aggregate forms within a cluster size can be distinguished indicating that some high order structures are favored in the gas phase. Multimer formation between different sizes of polyalanine peptides shows no evidence for size specificity in aggregate formation. Collisional and thermal excitation studies have been used to examine structural transitions and dissociation of the multimers. Aggregates appear to dissociate via loss of singly charged monomers. The observation that peptide multimers can be concealed in mass spectral data requires that fragmentation patterns and reactivity studies of singly charged monomers be undertaken with care.

Gas-phase reactivity and molecular modeling studies on triply protonated dodecapeptides that contain four basic residues

Gas-phase deprotonation and hydrogen/deuterium (H/D) exchange reactions for ions from three model dodecapeptides were studied by Fourier transform ion cyclotron resonance mass spectrometry. Molecular dynamics calculations were employed to provide information on conformations and Coulomb energies. The peptides, (KGG)4, (K2G4)2, and K4G8, each contain four high basicity lysine residues and eight low basicity glycine residues; however, in the present work only three lysine residues were protonated. Proton transfer reactions with a series of reference amines revealed apparent gas-phase acidities in a narrow range of 207.3-209.6 kcal/mol, with deprotonation efficiencies following the order [K4G8 + 3H]3+ > [(KGG)4 + 3H]3+ > [(K2G4)2 + 3H]3+. The three ions also react similarly with d4-methanol: each exchanged a maximum of 23-25 of their 25 labile hydrogens, with the first 15-17 exchanges occurring at rate constants of (1.6-2.6) x 10(-11) cm3 molecule-1 s-1. The experimental results agree with molecular modeling findings of similar conformations and Coulomb energies for the three peptide ions. The [M + 3H]3+ data are compared to data obtained previously in our laboratory for the "fully" protonated [M + 4H]4+ (Zhang, X.; Ewing, N. P.; Cassady, C. J. Int. J. Mass Spectrom. Ion Phys., in press). For (KGG)4 and (K2G4)2, there is a marked difference in H/D exchange reactivity between 3+ ions and 4+ ions. The 4+ ions, which have diffuse conformations, slowly exchange only 14 hydrogens, whereas their more compact 3+ counterparts exchange 23-25 hydrogens at a 5-times greater rate. In contrast, the 3+ and 4+ ions of K4G8 have similar compact conformations and exchange reactivity. The results indicate that a multiply hydrogen-bonded intermediate between the deuterating reagent and the peptide ion is necessary for facile H/D exchange. The slower, incomplete H/D exchange of [(KGG)4 + 4H]4+ and [(K2G4)2 + 4H]4+ is attributed to the inability of their protonated lysine n-butylamino groups (which extend away from the peptide backbone) to form this intermediate.

Three-dimensional ion mobility/TOFMS analysis of electrosprayed biomolecules

An ion mobility/mass spectrometry technique has been developed to record mass-resolved ion mobility distributions for multiple ions simultaneously. The approach involves a new instrument that couples an electrospray ion source to an injected-ion drift tube/time-of-flight mass spectrometer. Individual components in a mixture of ions are separated by mobility differences in a drift tube and subsequently dispersed by mass-to-charge ratios in a time-of-flight instrument. Flight times in the mass spectrometer are much shorter than residence times in the drift tube, making it possible to record mass-resolved ion mobilities for all ions simultaneously. The result is a three-dimensional spectrum that contains collision cross section, mass-to-charge, and ion abundance information. The instrument and data acquisition system are described. Examples of combined ion mobility/time-of-flight data are presented for distributions of electrosprayed bradykinin and ubiquitin ions.

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.

Stability of secondary structural elements in a solvent-free environment: the alpha helix

The stability of the alpha helix as an element of secondary structure is examined in the absence of solvation, in the gas phase. Mass-analyzed ion kinetic energy (MIKE) spectrometry was applied to measure intercharge repulsion and intercharge distance in multiply protonated melittin, a polypeptide known to possess a stable helical structure in a number of different environments. The experimental results, interpreted in combination with molecular mechanics calculations, suggest that triply charged melittin retains its secondary structure in the gas phase. The stability if the alpha-helical conformation of the polypeptide in the absence of solvent molecules reflects the fact that a network of intrinsic helical hydrogen bonds is energetically more favorable than unfolded conformations.

Counting basic sites in oligopeptides via gas-phase ion chemistry

Cations derived from oligopeptides ranging from laminin fragment (5 residues) to beta-lactoglobulin (162 residues) have been subjected to gas-phase ion/molecule reactions with hydroiodic acid. The sum of the ion charge state and the maximum number of molecules of hydroiodic acid that attach to the ion is equal to the total number of lysines, arginines, histidines, and N-termini consisting of a primary amine for ions derived from all 21 oligopeptides studied. These results suggest that ion/molecule reactions can provide useful information regarding oligopeptide basic site number, which might be used as a criterion for searching protein data bases instead of, or in conjunction with, use of proteolytic digestion or gas-phase ion dissociation procedures.

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.