Mass and charge state assignment for proteins and peptide mixtures via noncovalent adduction in electrospray mass spectrometry

A method has been developed that takes advantage of the formation of noncovalent compounds in electrospray mass spectrometry. Mixtures of proteins and peptides are shown to produce an intense ion that corresponds to a 1:1 complex with a crown ether (18-crown-6). Although the crown ether may be added directly to the solution, for the current experiments it is introduced via the methanol liquid sheath. The spacing of these complexed species in the mass spectrum allows unambiguous determination of the charge state of the ions and their actual mass. Through constant neutral loss scans, charge state may be determined, mass assigned, spectra simplified, and chemical noise may be reduced for the analysis of complex peptide samples without chromatographic separation. Finally, the prevalence of single complexation permits mass assignments based on the mass difference of a single protein ion and its complexed form at any charge state. In essence, the method performs a separation based on charge state. It can be used to complement chromatographic separation and deconvolution algorithms for the electrospray mass spectrometry analysis of peptide-protein mixtures.     

Mass determination of megadalton-DNA electrospray ions using charge detection mass spectrometry

Charge detection mass spectrometry (CD-MS) has been used to determine the mass of double-stranded, circular DNA and single-stranded, circular DNA in the range of 2500 to 8000 base pairs (1.5–5.0 MDa). Simultaneous measurement of the charge and velocity of an electrostatically accelerated ion allows a mass determination of the ion, with instrument calibration determined independently of samples. Positive ion mass spectra of electrosprayed commercial DNA samples supplied in tris(hydroxymethyl)ethylenediaminetetraacetic acid buffer, diluted in 50 vol. % acetonitrile, were obtained without cleanup of the sample. A CD mass spectrum constructed from 3000 ion measurements takes 10 min to acquire and yields the DNA molecular mass directly (mass resolution = 6). The data collected represent progress toward a more automatable alternative to sizing of DNA by gel electrophoresis. In addition to the mass spectra, CD-MS generates charge versus mass plots, which provide another means to investigate the creation and fate of large electrospray ions.     

Heuristic charge assignment for deconvolution of electrospray ionization mass spectra

We propose a new algorithm for deconvolution of electrospray ionization mass spectra based on direct assignment of charge to the measured signal at each mass-to-charge ratio (m/z). We investigate two heuristics for charge assignment: the entropy-based heuristic is adapted from a deconvolution algorithm by Reinhold and Reinhold;10 the multiplicative-correlation heuristic is adapted from the multiplicative-correlation deconvolution algorithm of Hagen and Monnig.6 The entropy-based heuristic is insensitive to overestimates of z(max), the maximum ion charge. We test the deconvolution algorithm on two single-component samples: the measured spectrum of human beta-endorphin has two prominent and one very weak line whereas myoglobin has a well-developed quasi-gaussian envelope of 17 peaks. In both cases, the deconvolution algorithm gives a clean deconvoluted spectrum with one dominant peak and very few artefacts. The relative heights of the peaks due to the parent molecules in the deconvoluted spectrum of a mixture of two peptides, which are expected to ionize with equal efficiency, give an accurate measure of their relative concentration in the sample.     

Correct charge state assignment of native electrospray spectra of protein complexes

Correct charge state assignment is crucial to assigning an accurate mass to supramolecular complexes analyzed by electrospray mass spectrometry. Conventional charge state assignment techniques fall short of reliably and unambiguously predicting the correct charge state for many supramolecular complexes. We provide an explanation of the shortcomings of the conventional techniques and have developed a robust charge state assignment method that is applicable to all spectra.     

Modeling the maximum charge state of arginine-containing peptide ions formed by electrospray ionization

A model for the gas-phase proton transfer reactivity of multiply protonated molecules is used to quantitatively account for the maximum charge states of a series of arginine-containing peptide ions measured by Downard and Biemann (Int. J. Mass Spectrom. Ion Processes 1995, 148, 191-202). We find that our calculations account exactly for the maximum charge state for 7 of the 10 peptides and are off by one charge for the remaining 3. These calculations clearly predict the trend in maximum charge states for these peptides and provide further evidence that the maximum charge state of ions formed by electrospray ionization is determined by their gas-phase proton transfer reactivity.     

Effects of solvent on the maximum charge state and charge state distribution of protein ions produced by electrospray ionization

The effects of solvent composition on both the maximum charge states and charge state distributions of analyte ions formed by electrospray ionization were investigated using a quadrupole mass spectrometer. The charge state distributions of cytochrome c and myoglobin, formed from 47%/50%/3% water/solvent/acetic acid solutions, shift to lower charge (higher m/z) when the 50% solvent fraction is changed from water to methanol, to acetonitrile, to isopropanol. This is also the order of increasing gas-phase basicities of these solvents, although other physical properties of these solvents may also play a role. The effect is relatively small for these solvents, possibly due to their limited concentration inside the electrospray interface. In contrast, the addition of even small amounts of diethylamine (<0.4%) results in dramatic shifts to lower charge, presumably due to preferential proton transfer from the higher charge state ions to diethylamine. These results clearly show that the maximum charge states and charge state distributions of ions formed by electrospray ionization are influenced by solvents that are more volatile than water. Addition of even small amounts of two solvents that are less volatile than water, ethylene glycol and 2-methoxyethanol, also results in preferential deprotonation of higher charge state ions of small peptides, but these solvents actually produce an enhancement in the higher charge state ions for both cytochrome c and myoglobin. For instruments that have capabilities that improve with lower m/z, this effect could be taken advantage of to improve the performance of an analysis.     

Automated assignment of charge states from resolved isotopic peaks for multiply charged ions

The recent proliferation of electrospray as an ionization method has greatly increased the ability to perform analyses of large biomolecules by using mass spectrometry. The major advantage of electrospray is the ability to produce multiply charged ions, which brings large molecules down to a mass-to-charge ratio range amenable to most instruments. Multiple charging is also a disadvantage because mass (m) becomes ambiguous unless charge (z) can be assigned. This is typically performed with simple algorithms that use multiple peaks of the same m and different z, but these methods are difficult to apply to complex mixtures and not applicable when only one z appears for each m. The use of mass analyzers with higher resolving powers, like the Fourier transform mass spectrometer, allows resolution of isotopic peaks, providing an internal 1-Da mass scale that can be used for unambiguous charge assignment. Manual assignment of charge state from the isotopic peaks is time consuming and becomes inaccurate when either the signal level or resolving power are low. For these cases, computer algorithms based on pattern recognition techniques have been developed to assist in assignment of charge states to isotopic clusters. These routines provide for more rapid analysis with higher accuracy than available manually.     

On the maximum charge state and proton transfer reactivity of peptide and protein ions formed by electrospray ionization

A relatively simple model for calculation of the energetics of gas-phase proton transfer reactions and the maximum charge state of multiply protonated ions formed by electrospray ionization is presented. This model is based on estimates of the intrinsic proton transfer reactivity of sites of protonation and point charge Coulomb interactions. From this model, apparent gas-phase basicities (GB^app) of multiply protonated ions are calculated. Comparison of this value to the gas-phase basicity of the solvent from which an ion is formed enables a maximum charge state to be calculated. For 13 commonly electrosprayed proteins, our calculated maximum charge states are within an average of 6% of the experimental values reported in the literature. This indicates that the maximum charge state for proteins is determined by their gas-phase reactivity. Similar results are observed for peptides with many basic residues. For peptides with few basic residues, we find that the maximum charge state is better correlated to the charge state in solution. For low charge state ions, we find that the most basic sites Arg, Lys, and His are preferentially protonated. A significant fraction of the less basic residues Pro, Trp, and Gln are protonated in high charge state ions. The calculated GB^app of individual protonation sites varies dramatically in the high charge state ions. From these values, we calculate a reduced cross section for proton transfer reactivity that is significantly lower than the Langevin collision frequency when the GB^app of the ion is approximately equal to the GB of the neutral base.     

Hydration of gas-phase ions formed by electrospray ionization

The hydration of gas-phase ions produced by electrospray ionization was investigated. Evidence that the hydrated ions are formed by two mechanisms is presented. First, solvent condensation during the expansion inside the electrospray source clearly occurs. Second, some solvent evaporation from more extensively solvated ions or droplets is apparent. To the extent that these highly solvated ions have solution-phase structures, then the final isolated gas-phase structure of the ion will be determined by the solvent evaporation process. This process was investigated for hydrated gramicidin S in a Fourier-transform mass spectrometer. Unimolecular dissociation rate constants of isolated gramicidin S ions with between 2 and 14 associated water molecules were measured. These rate constants increased from 16 to 230 s-1 with increasing hydration, with smaller values corresponding to magic numbers.     

Manipulation of charge states of biopolymer ions by atmospheric pressure ion/molecule reactions implemented in an extractive electrospray ionization source

A home-made extractive electrospray ionization source is coupled to an linear quadrupole ion trap mass spectrometer to investigate ion/molecule reactions of biopolymers at ambient pressure. Multiply charged biopolymers such as peptides and proteins generated in an electrospray are easily reduced to a low charge state by the atmospheric pressure ion/molecule reactions occurring between the multiply charged ions and a strong basic reagent sprayed in neutral form into the electrospray plume. The charge state of the biopolymer ions can be manipulated by controlling the amount of the basic reagent. The production of biopolymer ions with low charge states results in a substantial improvement of sensitivity and reduced spectral congestion in ESI-MS. This is of importance for biopolymer mixture analysis and could have promising applications in proteomics.     

Primary and secondary locations of charge sites in angiotensin II (M + 2H)2+ ions formed by electrospray ionization

High-energy tandem mass spectrometry and molecular dynamics calculations are used to determine the locations of charge in metastably decomposing (M + 2H)2+ ions of human angiotensin II. Charge-separation reactions provide critical information regarding charge sites in multiple charged ions. The most probable kinetic energy released (Tm.p.) from these decompositions are obtained using kinetic energy release distributions (KERDs) in conjunction with MS/MS (MS2), MS/MS/MS (MS3), and MS/MS/MS/MS (MS4) experiments. The most abundant singly and doubly charged product ions arise from precursor ion structures in which one proton is located on the arginine (Arg) side chain and the other proton is located on a distal peptide backbone carbonyl oxygen. The MS3 KERD experiments show unequivocally that neither the N-terminal amine nor the aspartic acid (Asp) side chain are sites of protonation. In the gas phase, protonation of the less basic peptide backbone instead of the more proximal and basic histidine (His) side chain is favored as a result of reduced coulomb repulsion between the two charge sites. The singly and doubly charged product ions of lesser abundance arise from precursor ion structures in which one proton is located on the Arg side chain and the other on the His side chain. This is demonstrated in the MS3 and MS4 mass-analyzed ion kinetic energy spectrometry experiments. Interestingly, (b7" + OH)2+ product ions, like the (M + 2H)2+ ions of angiotensin II, are observed to have at least two different decomposing structures in which charge sites have a primary and secondary location.     

Mass spectral evidence for the hydroxymethylene radical cation

Collisionally-activated decompositions show that ·CHO⁺H ions are stable, confirming theoretical predictions.     

Cyclic transmembrane charge transport mediated by pyrylium and thiopyrylium ions

Transient spectroscopy revealed that 2,4,6-trimethylpyrylium, 2,4,6-triphenylpyrylium, and 2,4,6-triphenylthiopyrylium ions oxidatively quench excited triplet [5,10,15,20-tetrakis(4-sulfonatophenyl)porphinato]zinc(II) to form the corresponding neutral radicals and the zinc porphyrin pi-cation. The measured quenching rate constants were proportional to the pyrylium one-electron reduction potentials, that is, the reaction driving force. In the presence of anionic dihexadecyl phosphate vesicles, only the fraction of pyrylium not bound to the vesicle was capable of reacting with the photoexcited zinc porphyrin. Nonetheless, the pyrylium radicals mediated highly efficient transmembrane reduction of tris(2,2'-bipyridine)cobalt(III) contained within the inner aqueous core of the vesicles with apparent quantum yields that approached unity. Permeability coefficients (P) determined for the pyrylium radicals, pyrylium cations, and the proton were 10(-4)-2 x 10(-5) cm/s, 10(-10) cm/s, and < 5 x 10(-7) cm/s, respectively, so that only the neutral radicals are membrane-permeable on the time scale of the transmembrane redox reactions. However, each electron carrier was demonstrated to transport up to 200 electrons, at which point the internal pool of electron acceptors was exhausted. Since the cations are membrane-impermeable, a reaction cycle is proposed that includes hydrolysis of the pyrylium cations formed within the aqueous core to the corresponding 1,5-diketones which, as neutral molecules, can diffuse across the bilayer. According to this mechanism, while undergoing redox cycling the pyrylium ions function as cyclical antiporters of OH(-) and the electron, thereby maintaining electroneutrality in the reaction compartments.     

Serine-phosphoric acid cluster ions studied by electrospray ionization and tandem mass spectrometry

More than 310 kinds of cluster ions of S(m) P(n) H(k) (k+) are observed in a single ESI mass spectrum of a mixed solution of serine and phosphoric acid. Some typical cluster ions are selected, activated by collision in a FT ICR cell, and the dissociation pathways were deduced in detail. For large singly protonated ions, the collisions cause the ejection of subunits of serine or phosphoric acid subsequently producing the ions of S(2) P(4) H(1) (1+) , which can be further dissociated by the loss of phosphoric acid molecules in turn and form the protonated serine dimer and monomer. However, for the doubly protonated ions, the dissociation pathways change from the loss of a protonated serine dimer for the ions of S(7) P(9) H(2) (2+) to the neutral loss of H(3) PO(4) for the ions of S(7) P(12) H(2) (2+) or the neutral loss of serine or H(3) PO(4) for the larger clusters, indicating the effect of cluster sizes on the process of dissociation. The structure of S(2) P(4) H(1) (1+) is suggested based on B3LYP/6-31G(d,p) calculations. The diversity and structural orderliness of the hetero-cluster ions are mainly attributed to the network of hydrogen bonds inside the cluster ions and the extraordinary amphotericity of the components.     

Direct correlation of the crystal structure of proteins with the maximum positive and negative charge states of gaseous protein ions produced by electrospray ionization

Electrospray mass spectrometric studies in native folded forms of several proteins in aqueous solution have been performed in the positive and negative ion modes. The mass spectra of the proteins show peaks corresponding to multiple charge states of the gaseous protein ions. The results have been analyzed using the known crystal structures of these proteins. Crystal structure analysis shows that among the surface exposed residues some are involved in hydrogen-bonding or salt-bridge interactions while some are free. The maximum positive charge state of the gaseous protein ions was directly related to the number of free surface exposed basic groups whereas the maximum negative charge state was related to the number of free surface exposed acidic groups of the proteins. The surface exposed basic groups, which are involved in hydrogen bonding, have lower propensity to contribute to the positive charge of the protein. Similarly, the surface exposed acidic groups involved in salt bridges have lower propensity to contribute to the negative charge of the protein. Analysis of the crystal structure to determine the maximum charge state of protein in the electrospray mass spectrum was also used to interpret the reported mass spectra of several proteins. The results show that both the positive and the negative ion mass spectra of the proteins could be interpreted by simple consideration of the crystal structure of the folded proteins. Moreover, unfolding of the protein was shown to increase the positive charge-state because of the availability of larger number of free basic groups at the surface of the unfolded protein.     

Cyclic transmembrane charge transport mediated by low-potential pyrylium ions

We have investigated the capacity of a series of N-dialkylaminophenyl-substituted pyrylium and thiopyrylium ions to act as photosensitizers and redox mediators between reactants separated by bilayer membranes. These studies were prompted by earlier results indicating that simple trimethy- and triphenyl-substituted analogues could promote efficient photosensitized transmembrane redox between vectorially organized reactants by an electroneutral e(-)/OH(-) antiport mechanism. Unlike the dyes used in the earlier studies, the ions investigated herein absorb strongly throughout the visible absorption region and are therefore potentially useful in solar photoconversion processes. We demonstrate that these ions can carry out cyclic electron transport between phase-separated electron donors and occluded Co(bpy)(3)(3+) in several transversely organized vesicles. The quantum yields obtained were relatively low, but were independent of the membrane microviscosity, suggesting that transmembrane diffusion was not rate-limiting. Triphenylpyrylium and triphenylthiopyrylium ions were shown to be capable of acting as combined photosensitizers/redox relays, apparently by direct oxidation of either solvent (water) or buffer (acetate) ions from their triplet-excited state. These reactions did not require addition of separate photosensitizers and electron donors; as such, they represent a minimal photochemical scheme for effecting transmembrane charge separation. The low-potential visible-absorbing pyrylium ions were unable to function in this dual capacity, consistent with thermodynamic limitations. However, redox titrations established that the pyranyl radicals of these dyes should be capable of reducing H(+) to H(2) in weakly acidic solutions. Consistent with their strongly reducing nature, these dyes were shown to be capable of forming methyl viologen radical in photoinitiated transmembrane redox reactions.     

Detection of inorganic ions from water by electrospray ionization-ion mobility spectrometry

The results from this study illustrate the first time electrospray ionization-ion mobility spectrometry (ESI-IMS) has been used to separate inorganic cations in aqueous solutions. Using ESI-IMS nine inorganic cation solutions were analyzed. Counter ions affected both the sensitivity and the identity of the response ions. Aluminum sulfate, lanthanum chloride, strontium chloride, uranyl acetate, uranyl nitrate, and zinc sulfate produced spectra containing a single response ion. Aluminum nitrate and zinc acetate solutions produced multiple ion peaks, which increased the detection limits and the difficulty of identification. Cation detection limits ranged from 0.16 to 13 ng μl⁻¹ depending on the solution studied. The identities of the ion species detected were unconfirmed, but mass spectrometry literature suggested the detection of positively charged cation-solvent or cation-solvent-anion complexes. Finally, cations from strontium and lanthanum chloride solutions were separated with a resolution of 2.2. The results from this study suggest that ESI-IMS has potential as a field technique for the detection of metal cations and their complexes in the environment.     

Efficient charge assignment and back interpolation in multigrid methods for molecular dynamics

The assignment of atomic charges to a regular computational grid and the interpolation of forces from the grid back to the original atomic positions are crucial steps in a multigrid approach to the calculation of molecular forces. For purposes of grid assignment, atomic charges are modeled as truncated Gaussian distributions. The charge assignment and back interpolation methods are currently bottlenecks, and take up to one-third the execution time of the multigrid method each. Here, we propose alternative approaches to both charge assignment and back interpolation where convolution is used both to map Gaussian representations of atomic charges onto the grid and to map the forces computed at grid points back to atomic positions. These approaches achieve the same force accuracy with reduced run time. The proposed charge assignment and back interpolation methods scale better than baseline multigrid computations with both problem size and number of processors.     

Exploring fluorescence and fragmentation of ions produced by electrospray ionization in ultrahigh vacuum

An instrument for fluorescence spectrometry and FTICR-MS has been developed to study ions produced by a commercial ESI source.

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Tandem mass spectrometry of metal nitrate negative ions produced by electrospray ionization

M(NO(3))(x)(-) ions are generated by electrospray ionization (ESI) of metal solutions in nitric acid in negative ion mode. Collision-induced reactions of these ions are monitored in a tandem mass spectrometer (MS) of quadrupole-octopole-quadrupole (QoQ) geometry. For Group 1 and 2 elements, the M(NO(3))(x)(-) ions dissociate into NO(3)(-) and neutral metal nitrate molecules. These elements also form some M(x)(NO(3))x+1- clusters, especially Li(+). Metal nitrate ions from transition elements and Group 13 elements fragment into oxo products and also undergo internal electron transfer to leave the M atom in a lower oxidation state. To calibrate the collision energy, the dissociation energy of O-NO(2)(-) is found to be 5.55 eV, about 0.76 eV lower than a value derived from thermochemistry. The product ions from Fe(NO(3))(4)(-) ions have low formation thresholds of only 0.5 to 2 eV.