Observation and implications of high mass-to-charge ratio ions from electrospray ionization mass spectrometry

High mass-to-charge ratio ions (> 4000) from electrospray ionization (ESI) have been observed for several proteins, including bovine cytochrome c (M _r 12,231) and porcine pepsin (M _r 34,584), by using a quadrupole mass spectrometer with an m/z 45,000 range. The ESI mass spectrum for cytochrome c in an aqueous solution gives a charge state distribution that ranges from 12 + to 2 +, with a broad, low-intensity peak in the mass-to-charge ratio region corresponding to the [M + H]⁺ ion. the negative ion ESI mass spectrum for pepsin in 1% acetic acid solution shows a charge state distribution ranging from 7? to 2?. To observe the [M - H]^? ion, harsher desolvation and interface conditions were required. Also observed was the abundant aggregation of the protens with average charge states substantially lower than observed for their monomeric counterparts. The negative ion ESI mass spectrum for cytochrome c in 1–100 mM NH₄OAc solutions showed greater relative abundances for the higher mass-to-charge ratio ions than in acuidic solutions, with an [M - H]^? ion relative abundance approximately 50% that of the most abundant charge state peak. The observation that protein aggregates are formed with charge states comparable to monomeric species (at fower mass-to-charge ratios) suggests that the high mass-to-charge ratio monomers may be formed by the dissociation of aggregate species. The observation of low charge state and aggregate molecular ions concurrently with highly charged species may serve to support a variation of the charged residue model, originally described by Dole and co-workers (Dole, M., et al. J. Chem. Phys. 1968, 49, 2240; Mack, L. L., et al. J. Chem. Phys. 1970, 52, 4977) which involves the Coulombically driven formation of either very highly solvated molecular ions or lower ananometer-diameter droplets.     

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.     

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.     

Molecular complexes of iodine with metal acetylacetonates

The ability of metal acetylacetonates to act as electron donors and form molecular complexes with I₂ was studied by examining the electronic, vibrational, and NMR spectra of the complexes. The specific compounds used in the study were Al(acac)₃ Sc(acac)₃ Zr(acac)₄, and Th(acac)₄. The electronic spectra of mixtures of the metal acetylacetonates with I₂ in CHCl₃ had, in addition to the absorption peaks characteristic of the free components, two peaks that were due to the charge transfer complexes. For each complex, the highest wavelength peak (near 360 nm) was assigned to the blue shifted I₂ band, while the lower peak (between 270 nm and 305 nm) was attributed to the intermolecular charge transfer. In the i.r. spectra of each complex, the major effect of complexation was to cause the I₂ stretching frequency to appear between 145 cm⁻¹ and 160 cm⁻¹. The positions of the absorption peaks in both the electronic and vibrational spectra led to the conclusion that in these complexes, I₂ had received a large amount of charge from the donors. Complex formation had little effect on the NMR spectra of the donors. Association constants of 1:1 complexes were determined from the concentration dependence of the absorbance of the blue shifted I₂ bands. Values of ΔHdg and ΔS°₂₉₈ for the complex formation were obtained from the temperature variation of the association constants. The data indicate that the complexes are extremely stable species. Both the stability of the complexes and the high degree of charge transfer were rationalized by considering a model for the intermolecular interactions that involved two M(acac) rings simultaneously transferring charge from one donor to an I₂ molecule.     

Automated deconvolution and deisotoping of electrospray mass spectra

Electrospray ionization (ESI) of peptides and proteins produces a series of multiply charged ions with a mass/charge (m/z) ratio between 500 and 2000. The resulting mass spectra are crowded by these multiple charge values for each molecular mass and an isotopic cluster for each nominal m/z value. Here, we report a new algorithm simultaneously to deconvolute and deisotope ESI mass spectra from complex peptide samples based on their mass-dependent isotopic mean pattern. All signals corresponding to one peptide in the sample were reduced to one singly charged monoisotopic peak, thereby significantly reducing the number of signals, increasing the signal intensity and improving the signal-to-noise ratio. The mass list produced could be used directly for database searching. The developed algorithm also simplified interpretation of fragment ion spectra of multiply charged parent ions.     

Automated charge state determination of complex isotope-resolved mass spectra by peak-target Fourier transform

This study describes a new algorithm for charge state determination of complex isotope-resolved mass spectra. This algorithm is based on peak-target Fourier transform (PTFT) of isotope packets. It is modified from the widely used Fourier transform method because Fourier transform may give ambiguous charge state assignment for low signal-to-noise ratio (S/N) or overlapping isotopic clusters. The PTFT algorithm applies a novel "folding" strategy to enhance peaks that are symmetrically spaced about the targeted peak before applying the FT. The "folding" strategy multiplies each point to the high-m/z side of the targeted peak by its counterpart on the low-m/z side. A Fourier transform of this "folded" spectrum is thus simplified, emphasizing the charge state of the "chosen" ion, whereas ions of other charge states contribute less to the transformed data. An intensity-dependent technique is also proposed for charge state determination from frequency signals. The performance of PTFT is demonstrated using experimental electrospray ionization Fourier transform ion cyclotron resonance mass spectra. The results show that PTFT is robust for charge state determination of low S/N and overlapping isotopic clusters, and also useful for manual verification of potential hidden isotopic clusters that may be missed by the current analysis algorithms, i.e., AID-MS or THRASH.     

High-resolution accurate mass measurements of biomolecules using a new electrospray ionization ion cyclotron resonance mass spectrometer

A novel electrospray ionization/Fourier transform ion cyclotron resonance mass spectrometer based on a 7-T superconducting magnet was developed for high-resolution accurate mass measurements of large biomolecules. Ions formed at atmospheric pressure using electrospray ionization (ESI) were transmitted (through six differential pumping stages) to the trapped ion cell maintained below 10^?9 torr. The increased pumping speed attainable with cryopumping (> 10⁵ L/s) allowed brief pressure excursions to above 10^?4 torr, with greatly enhanced trapping efficiencies and subsequent short pumpdown times, facilitating high-resolution mass measurements. A set of electromechanical shutters were also used to minimize the effect of the directed molecular beam produced by the ES1 source and were open only during ion injection. Coupled with the use of the pulsed-valve gas inlet, the trapped ion cell was generally filled to the space charge limit within 100 ms. The use of 10–25 ms ion injection times allowed mass spectra to be obtained from 4 fmol of bovine insulin (M_r 5734) and ubiquitin (M_r 8565, with resolution sufficient to easily resolve the isotopic envelopes and determine the charge states. The microheterogeneity of the glycoprotein ribonuclease B was examined, giving a measured mass of 14,898.74 Da for the most abundant peak in the isotopic envelope of the normally glycosylated protein (i.e., with five mannose and two N-acetylglucosamine residues (an error of approximately 2 ppm) and an average error of approximately 1 ppm for the higher glycosylated and various H₃PO₄ adducted forms of the protein. Time-domain signals lasting in excess of 80 s were obtained for smaller proteins, producing, for example, a mass resolution of more than 700,000 for the 4⁺ charge state (m/z 1434) of insulin.     

ESIprot: a universal tool for charge state determination and molecular weight calculation of proteins from electrospray ionization mass spectrometry data

Electrospray ionization (ESI) ion trap mass spectrometers with relatively low resolution are frequently used for the analysis of natural products and peptides. Although ESI spectra of multiply charged protein molecules also can be measured on this type of devices, only average spectra are produced for the majority of naturally occurring proteins. Evaluating such ESI protein spectra would provide valuable information about the native state of investigated proteins. However, no suitable and freely available software could be found which allows the charge state determination and molecular weight calculation of single proteins from average ESI‐MS data. Therefore, an algorithm based on standard deviation optimization (scatter minimization) was implemented for the analysis of protein ESI‐MS data. The resulting software ESIprot was tested with ESI‐MS data of six intact reference proteins between 12.4 and 66.7 kDa. In all cases, the correct charge states could be determined. The obtained absolute mass errors were in a range between ?0.2 and 1.2 Da, the relative errors below 30 ppm. The possible mass accuracy allows for valid conclusions about the actual condition of proteins. Moreover, the ESIprot algorithm demonstrates an extraordinary robustness and allows spectral interpretation from as little as two peaks, given sufficient quality of the provided m/z data, without the necessity for peak intensity data. ESIprot is independent from the raw data format and the computer platform, making it a versatile tool for mass spectrometrists. The program code was released under the open‐source GPLv3 license to support future developments of mass spectrometry software. Copyright © 2010 John Wiley & Sons, Ltd.     

Etude comparative en luminescence UV-visible du 1,1′-binaphtyle et du 2,2′-binaphtyle

The modifications of emission spectra obtained in fluid and rigid media as a function of temperature show a conformation change for 1,1′-binaphthyl in the excited state. This change is facilitated in fluid medium by the rotation of the two naphthyl groups around the C₁C_1′ bond. The molecular twisting in this excited state explains the original results for 1,1′-binaphthyl where the intensity ratio of phosphorescence to fluorescence (I_ph/I_fluo) varies with excitation wavelength. This result agrees with the charge transfer (CT) character obtained by the excited state S*₂ due to the twist of this molecule.The emission spectra of 2,2′-binaphthyl, a molecule which is practically identical in its electronic structure to 1,1′-binaphthyl, do not undergo significant modification with effects of temperature variation, and as a function of the excitation wavelength. These different effects for 1,1′-binaphthyl and 2,2′-binaphthyl agree with the difference of twist for the naphthyl rings around the single bond between these rings.     

Algorithms for automatic interpretation of high resolution mass spectra

Automated interpretation of high-resolution mass spectra in a reliable and efficient manner represents a highly challenging computational problem. This work aims at developing methods for reducing a high-resolution mass spectrum into its monoisotopic peak list, and automatically assigning observed masses to known fragment ion masses if the protein sequence is available. The methods are compiled into a suite of data reduction algorithms which is called MasSPIKE (Mass Spectrum Interpretation and Kernel Extraction). MasSPIKE includes modules for modeling noise across the spectrum, isotopic cluster identification, charge state determination, separation of overlapping isotopic distributions, picking isotopic peaks, aligning experimental and theoretical isotopic distributions for estimating a monoisotopic peak's location, generating the monoisotopic mass list, and assigning the observed monoisotopic masses to possible protein fragments. The method is tested against a complex top-down spectrum of bovine carbonic anhydrase. Results of each of the individual modules are compared with previously published work.     

Radioxenon production through neutron irradiation of stable xenon gas

The Spectral Deconvolution Analysis Tool (SDAT) software was developed to improve counting statistics and detection limits for nuclear explosion radionuclide measurements. SDAT utilizes spectral deconvolution spectroscopy techniques and can analyze both β–γ coincidence spectra for radioxenon isotopes and high-resolution HPGe spectra from aerosol monitors. The deconvolution algorithm of the SDAT requires a library of β–γ coincidence spectra of individual radioxenon isotopes to determine isotopic ratios in a sample. In order to get experimentally produced spectra of the individual isotopes, we have irradiated enriched samples of ¹³⁰Xe, ¹³²Xe, and ¹³⁴Xe gas with a neutron beam from the TRIGA reactor at The University of Texas. The samples were counted in an Automated Radioxenon Sampler/Analyzer (ARSA) style β–γ coincidence detector. The spectra produced show that this method of radioxenon production yields samples with very high purity of the individual isotopes for ^131mXe and ¹³⁵Xe and a sample with a substantial ^133mXe to ¹³³Xe ratio.     

The mass-to-charge ratio scale

Increases in the capacity for accurately measuring the mass-to-charge ratio of specific gas-phase ions justify the reconsideration and standard definition of the gas-phase mass-to-charge ratio scale and the clearly denned connection of that scale to condensed phases. We propose that the chemical mass standard for solids and the gas phase be based upon the mass of carbon-12 buckminsterfulierene (¹²C₆₀). The mass-to-charge ratio scale in the gas phase would be based upon the mass of gas-phase ¹²C₆₀, the mass of the electron, and the electron charge in atomic units. As mass measurement accuracy improves, corrections to this mass-to-charge ratio standard are anticipated for the vaporization energy of the 12C60 molecule and its ionization potential or electron affinity. We propose that the positive ion scale be set by the mass-to-charge ratio of ¹²C ₆₀ ⁺ as (+)719.9994514±0.0000004 u per electron charge. We propose that the negative ion mass scale be set by the mass-to-charge ratio of ¹²C ₆₀ ^? as (?)720.0005484±0.0000004 u per electron charge.     

High-resolution photoelectron spectroscopy through deconvolution

A new iterative deconvolution algorithm for the development of very high resolution Hc(I)-excited photoelectron spectra of gases is presented. The algorithm accepts as input a medium-resolution spectrum and an instrument function obtained by scanning intrinsically narrow line (e.g. the Ar²P_3/2 line) under conditions identical to those used to acquire the medium resolution spectrum. The deconvolved partial spectrum of an O₂H₂O mixture is presented as a test case prior to presentation of results for three nitrogen lines. For comparison purposes directly obtained high-resolution spectra of the nitrogen lines are included. The shapes of the nitrogen lines are discussed within the framework of a one-center expansion theory of photoionization. The conditions under which deconvolution can be profitably applied are briefly discussed and an attempt is made to establish the deconvolution (contrary to still popular belief) is not in any way equivalent to curve fitting.     

Determination of peptide and protein ion charge states by fourier transformation of isotope-resolved mass spectra

We report an automated method for determining charge states from high-resolution mass spectra. Fourier transforms of isotope packets from high-resolution mass spectra are compared to Fourier transforms of modeled isotopic peak packets for a range of charge states. The charge state for the experimental ion packet is determined by the model isotope packet that yields the best match in the comparison of the Fourier transforms. This strategy is demonstrated for determining peptide ion charge states from "zoom scan" data from a linear quadrupole ion trap mass spectrometer, enabling the subsequent automated identification of singly- through quadruply-charged peptide ions, while reducing the numbers of conflicting identifications from ambiguous charge state assignments. We also apply this technique to determine the charges of intact protein ions from LC-FTICR data, demonstrating that it is more sensitive under these experimental conditions than two existing algorithms. The strategy outlined in this paper should be generally applicable to mass spectra obtained from any instrument capable of isotopic resolution.     

Automated data reduction for hydrogen/deuterium exchange experiments,enabled by high-resolution fourier transform ion cyclotron resonance mass spectrometry

Mass analysis of proteolytic fragment peptides following hydrogen/deuterium exchange offers a general measure of solvent accessibility/hydrogen bonding (and thus conformation) of solution-phase proteins and their complexes. The primary problem in such mass analyses is reliable and rapid assignment of mass spectral peaks to the correct charge state and degree of deuteration of each fragment peptide, in the presence of substantial overlap between isotopic distributions of target peptides, autolysis products, and other interferant species. Here, we show that at sufficiently high mass resolving power (m/Δm_50% ≥ 100,000), it becomes possible to resolve enough of those overlaps so that automated data reduction becomes possible, based on the actual elemental composition of each peptide without the need to deconvolve isotopic distributions. We demonstrate automated, rapid, reliable assignment of peptide masses from H/D exchange experiments, based on electrospray ionization FT-ICR mass spectra from H/D exchange of solution-phase myoglobin. Combined with previously demonstrated automated data acquisition for such experiments, the present data reduction algorithm enhances automation (and thus expands generality and applicability) for high-resolution mass spectrometry-based analysis of H/D exchange of solution-phase proteins.     

Peak deconvolution in high-field asymmetric waveform ion mobility spectrometry (FAIMS) to characterize macromolecular conformations

Protonated poly(ethylene glycol), produced by electrospray ionization (ESI), with molecular weights ranging from 0.3 to 5 kDa and charge states from 1+ to 7+ were characterized using high-field asymmetric waveform ion mobility spectrometry (FAIMS). Results for all but some of the 3+ and 4+ charge states are consistent with a single gas-phase conformer or family of unresolved conformers for each of these charge states. The FAIMS compensation voltage scans resulted in peaks that could be accurately fit with a single Gaussian for each peak. The peak widths increase linearly with compensation voltage for maximum ion transmission but do not depend on m/z or molecular weight. Fitting parameters obtained from the poly(ethylene glycol) data were used to analyze conformations of oxidized and reduced lysozyme formed from different solutions. For oxidized lysozyme formed from a buffered aqueous solution, a single conformer (or group of unresolved conformers) was observed for the 7+ and 8+ charge states. Two conformers were observed for the 9+ and 10+ charge states formed from more denaturing solutions. Data for the fully reduced form indicate the existence of up to three different conformers for each charge state produced directly by ESI and a general progression from a more extended to a more folded structure with decreasing charge state. These results are consistent with those obtained previously by proton-transfer reactivity and drift tube ion mobility experiments, although more conformers were identified for the fully reduced form of lysozyme using FAIMS.     

Advantages of high-resolution and high-mass range magnetic-sector mass spectrometry for electrospray ionization

Electrospray ionization (ESI) mass spectra have been measured on a magnetic-sector double-focusing mass spectrometer for a number of proteins and peptides. It is pointed out how in theory raising the mass resolution of a mass spectrometer from 800–1000 to 2400–3000 significantly increases the precision with which the envelope of isotopic peaks of a protein ion (or other organic ion) can be defined, particularly at higher masses. Better definition of the isotopic envelope ought to lead to higher precision in the experimental determination of molecular mass, which has been demonstrated. It is shown how ESI mass spectra of high-mass molecules are significantly less congested at higher m/z values, so that for these molecules (RMM > 40 000) there is an advantage in being able to record peaks at higher m/z values (m/z > 2000) representing ions with fewer charges. Fragmentation of a small peptide in the ESI source has been found to provide sequence information.     

SPECTRAL FORMS AND ORIENTATION OF BACTERIOCHLOROPHYLLS c AND α IN CHLOROSOMES OF THE GREEN PHOTOSYNTHETIC BACTERIUM Chloroflexus aurantiacus

Spectral forms of bacteriochlorophyll (Bchl) in chlorosomes were analyzed by linear dichroism, circular dichroism (CD), and deconvolution of these spectra. Isolated chlorosomes were embedded in polyacrylamide gels and compressed unidirectionally (along the x-axis) while allowing the gel to stretch in another direction (along the z-axis). The chlorosomes were aligned three-dimensionally due to their flat oblong shape; the longest axis was presumed to parallel the z-axis, its shortest axis was presumed to parallel the x-axis, and the intermediate-length axis was presumed to parallel the y-axis. Degrees of polarization (A_I? A₁)/(A_I+ A₁) of Bchl c and a measured from the y-axis with linearly polarized light were significantly different from those measured from the x-axis. Deconvolution of spectra into components revealed the presence of two major forms of Bchl c with peaks at 744 nm and 727 nm. The degrees of polarization of the 744 and 727 nm spectral forms were 0.76 and 0.59 from the y-axis and 0.48 and 0.39 from the x-axis, respectively. The degrees of polarization of Bchl a794 were –0.21 from the y-axis and 0.12 from the x-axis. These values indicate that the direction of the Q_y transition moment of Bchl c744 is almost completely parallel to the longest axis of chlorosomes and that of Bchl c727 is also nearly, but slightly less so, parallel to the longest axis of the chlorosomes. The Q_y transition moment of the baseplate Bchl a peak at 794 nm is nearly perpendicular to the longest axis and parallel to the shortest axis: that is, it is perpendicular to the associated membrane plane in the cell. These alignments of Bchl transition moments in chlorosomes were lost after suspending the chlorosomes in a solution saturated with 1-hexanol accompanying a shift in the peak position from 742 nm to 670 nm. The alignment recovered after the hexanol concentration was decreased. The presence of two major spectral forms of Bchl c was supported by the deconvolution of CD spectra and absorption spectra.     

A one-dimensional kalman filter for peak resolution

A one-dimensional Kalman filter algorithm is presented that resolves several overlapped liquid chromatographic peaks without algebraic operations of matrices. The resolving powers or filtering reliability of the algorithm is independent of the number of peaks, but depends on both the peak overlap (resolution value R_s) and the signal-to-noise ratio more significantly than the usual multi-dimensional Kalman filter. The reliability is shown to be similar to that of the multi-dimensional filter for the resolution of overlapped Gaussian peaks with limited R_s and S/N values.