Eugene Nikolaev

Initial Experimental Characterization of a New Ultra-High Resolution FTICR Cell with Dynamic Harmonization

A new Fourier transform ion cyclotron resonance (FTICR) cell based on completely new principles of formation of the effective electric potential distribution in Penning type traps, Boldin and Nikolaev (Proceedings of the 58th ASMS Conference, 2010), Boldin and Nikolaev (Rapid Commun Mass Spectrom 25:122–126, 2011) is constructed and tested experimentally. Its operation is based on the concept of electric potential space-averaging via charged particle cyclotron motion. Such an averaging process permits an effective electric force distribution in the entire volume of a cylindrical Penning trap to be equal to its distribution in the field created by hyperbolic electrodes in an ideal Penning trap. The excitation and detection electrodes of this new cell are shaped for generating a quadratic dependence on axial coordinates of an averaged (along cyclotron motion orbit) electric potential at any radius of the cyclotron motion. These electrodes together with the trapping segments form a cylindrical surface like in a conventional cylindrical cell. In excitation mode this cell being elongated behaves almost like an open cylindrical cell of the same length. It is more effective in ion motion harmonization at larger cyclotron radii than a Gabrielse et al.-type (Int J Mass Spectrom Ion Processes 88:319–332, 1989) cylindrical cell with four compensation sections. A mass resolving power of more than twenty millions of reserpine (m/z 609) and more than one million of highly charged BSA molecular ions (m/z 1357) has been obtained in a 7T magnetic field.

Fourier transform ion cyclotron resonance cell with dynamic harmonization of the electric field in the whole volume by shaping of the excitation and detection electrode assembly

A new principle of formation of the effective electric field distribution in a Penning trap is presented. It is based on the concept of electric potential space averaging via charged particle cyclotron motion. The method of making hyperbolic-type field distribution in the whole volume of a cylindrical Penning trap is developed on the basis of this new principal. The method is based on subdividing the cell cylindrical surface into segments with shapes producing quadratic dependence on axial coordinate of an averaged (along cyclotron motion orbit) electric potential at any radius of cyclotron motion. The cell performance is compared in digital experiments with the performance of a Gabrielse-type cylindrical cell with four compensation electrodes and is shown to be more effective in ion motion harmonization at higher cyclotron radii and axial oscillation amplitude.

Simple atmospheric hydrogen/deuterium exchange method for enumeration of labile hydrogens by electrospray ionization mass spectrometry.

A simple method for hydrogen/deuterium exchange in a standard electrospray (ESI) ionization source is presented. In this method, a D₂O droplet is placed between the ESI needle and the entrance of the mass spectrometer and thus saturation of the atmosphere with deuterated vapor in the ESI region is achieved. It was shown that full exchange of up to 23 labile acidic hydrogens with a minimal back exchange with the surrounding atmospheric water can be performed by this method.

Isomerization of the Asp7 Residue Results in Zinc-Induced Oligomerization of Alzheimer’s Disease Amyloid β(1–16) Peptide

Alzheimer’s disease (AD)—a fatal neurodegenerative disorder that primarily affects the elderly—is pathophysiologically characterized by the extracellular deposition of a 40/42-aminoacid-long protein, referred to as amyloid-b peptide (Ab), in the brains of AD victims. Although the molecular mechanism of AD onset is unknown, the transformation of Ab from its native monomer conformation via soluble dimers and higher oligomers into insoluble fibrillar b-sheet aggregates, which finally accumulate into the amyloid plaques, is believed to be a key event in AD pathogenesis. One plausible hypothesis suggests that the amyloid neuropathology of AD depends on zinc ions released during neurotransmission, and so it is assumed that binding of zinc to Ab might play an important role in initiating pathogenic amyloid deposition, as well as some additional still unidentified proteinaceous factors. The Ab molecules isolated from AD brain lesions have numerous endogenous post-translational modifications (PTMs), which should profoundly affect both the Ab conformation and its oligomeric state and make up a pool of potential pathogenic agents in AD. The most abundant PTM of Ab is isomerization of the Asp7 residue; this results in the formation of an lisoAsp7 isoform (isoaspartate). This nonenzymatic modification occurs spontaneously in polypeptides through an intramolecular rearrangement of aspartate or asparagine residues and is generally regarded as a degradation reaction that occurs in vivo during tissue ageing. In the case of isomerized Ab (isoAb) it is still unclear whether the isoaspartyl residues are the cause or the result of the pathological accumulation of Ab. Nevertheless, recent in vitro experimental evidence indicates that isoAb might potentially be involved in the onset of AD. To investigate the role of the Asp7 isomerization in zinc-induced oligomerization of Ab we have studied the thermodynamics of zinc binding and the oligomeric states of two synthetic model peptides that correspond to region 1–16 in Ab and in isoAb : Ab16 and isoAb16, respectively. Earlier, this region was identified as the zinc-binding domain of Ab, which binds Zn with 1:1 stoichiometry and a 6 mm dissociation constant. Both Ab16 and its complex with Zn 2+ were found to be monomeric under physiological conditions for at least six months over a wide concentration range, and so were used as monomer reference standards throughout this work. The isoAb16 was also shown to possess zinc-binding ability; [11] however, the properties of the Zn–isoAb16 complex have not been studied previously. To compare Zn binding to Ab16 and to isoAb16 (in 50 mm Tris buffer at pH 7.3), isothermal titration calorimetry (ITC) was used. The thermodynamic data demonstrate that Ab16 binds one zinc ion with an association constant of 1.7ACHTUNGTRENNUNG( 0.4)A10m 1 (Figure 1), which corresponds to previously published da ACHTUNGTRENNUNGta.

Analysis and elimination of systematic errors originating from coulomb mutual interaction and image charge in Fourier transform ion cyclotron resonance precise mass difference measurements.

The effect of mutual Coulomb-mediated interactions between ions of two different mass-to-charge ratios (but equal ion cyclotron orbital radii) on their Fourier transform ion cyclotron resonance (FT/ICR) mass spectral frequency difference is derived analytically and measured experimentally. For a cylindrical ion trap, ion packets are modeled theoretically as infinitely extended lines of charge, and contributions to cyclotron frequency difference due to direct Coulomb repulsion between the lime charges as well as the forces arising from image charge induced on the trap electrodes by each line charge are calculated. A striking theoretical prediction is that the effect on ICR frequency difference of mutual Coulomb repulsion between ions in a mass doublet may be compensated by the image-charge effect. As a result, there is an optimal (calculable) ion cyclotron orbital radius at which the measured cyclotron orbital frequency difference between ions of two different mass-to-charge ratios is independent of mutual Coulomb-mediated interactions between the two components of the mass doublet! Moreover, if the two mass-doublet component ions are present in equal numbers, then the measured ion cyclotron orbital frequency difference is also independent of all Coulomb-mediated interactions between the two types of ions! Thus, the single largest systematic error in measurement of mass difference in a mass doublet by FT/ICR mass spectrometry may be virtually eliminated by appropriate control of ICR orbital radius and/or by performing measurements at various relative abundance ratios and extrapolating to equal relative abundance of the two mass-doublet components. We report experimental tests and verification of these predictions for two different mass doublets: 3He+/3H+ (cylindrical trap at 4.7 Tesla) and 12C1H2+/14 N+ (cubic trap at 7.0 Tesla). From the latter measurement, we determine the mass of atomic nitrogen as m(14N)=14.003 074 014(19) u.

Conformational changes of ubiquitin during electrospray ionization as determined by in-ESI source H/D exchange combined with high- resolution MS and ECD fragmentation

In the paper, we have demonstrated the possibility of performing hydrogen/deuterium (H/D) exchange of proteins in the region of gas-phase ion formation in an electrospray ion source by saturating the electrospray ionization source with vapors of a deuterating agent (D(2)O or MeOD). In this region, charged droplets are shrinking and the protein ions transfer into the gas phase. As a model protein, we have used ubiquitin whose ion mobility spectrometry and gas-phase H/D exchange in the vacuum part of a mass spectrometer demonstrated the presence of gas-phase conformers with different cross sections and H/D exchange rates. In our experiments, we observed monomodal deuterium distributions for all solvents, charge states, desolvating capillary temperature and types of deuterating agent. Also, we found that the number of H/D exchanges increases with an increasing desolvating capillary temperature and decreasing charge state. We observed that solution composition (49 : 50 : 1 H(2)O : MeOH : formic acid or 99 : 1 H(2)O : formic acid) influences the charge-state distribution but did not change the degree of H/D exchange for the same charge state. Electron-capture dissociation fragmentation shows that higher charge states contain a segment that is protected from access by the deuterating agent.

Molecular Mapping of Sorbent Selectivities with Respect to Isolation of Arctic Dissolved Organic Matter as Measured by Fourier Transform Mass Spectrometry

The objectives of this study were to identify molecular features characteristic to arctic DOM from the Kolyma River basin and to elucidate structural imprints induced by a choice of the sorption technique. To achieve this goal, DOM was isolated from the Kolyma River basin with a use of three nonionic sorbents: Amberlite XAD-8 resin, PPL- and C18 - SPE cartridges, and one anion exchanging resin-diethylaminoethyl (DEAE) -cellulose. The structural studies were conducted with a use of electrospray ionization Fourier Transform Ion Cyclotron Resonance (ESI FT-ICR) mass spectrometry and liquid state (1)H NMR spectroscopy. The DOM isolates obtained with a use of PPL and C18 cartridges were characterized with higher content of aliphatic compounds as compared to XAD-8 and DEAE-isolates. In total, for all arctic DOM isolates we observed predominance of hydrogen saturated compounds with high H/C values of identified formulas from FT-ICR MS data. (1)H NMR spectroscopy studies have confirmed this trend and revealed high contribution of alkyl-chain protons into the spectral density of the arctic DOM reaching 43% for PPL isolates.

Enumeration of Labile Hydrogens in Natural Organic Matter by Use of Hydrogen/Deuterium Exchange Fourier Transform Ion Cyclotron Resonance Mass Spectrometry

A method to enumerate labile hydrogens in all constituents of molecular ensemble of natural organic matter (NOM) based on our previously developed simple hydrogen/deuterium (H/D) exchange (electrospray ionization (ESI) ion source (Kostyukevich et al. Anal. Chem. 2013, 85, 5330) and ultra-high-resolution Fourier transform ion cyclotron resonance mass spectrometry is presented. The method was applied for analysis of Suwannee River fulvic acid (SRFA), which is an International Humic Substances Society standard, as well as Siberian crude oil; and lignosulfonate. We found that SRFA and lignosulfonate molecules contain 2-5 labile hydrogens, and their number increases with the number of oxygens in the molecule. Also, we observed that compounds of Siberian crude oil ionizing in positive-ESI mode do not have labile hydrogens, while compounds ionizing in negative-ESI mode have one labile hydrogen that detaches during ESI ionization.

Fine structure in isotopic peak distributions measured using a dynamically harmonized Fourier transform ion cyclotron resonance cell at 7 T.

The fine structure of isotopic peak clusters in mass spectra of reserpine and substance P are measured using Fourier transform ion cyclotron resonance mass spectrometry at a 7 T magnetic field. The resolved peaks in the fine structure consist of (13)C, (15)N, (17)O, (18)O, (2)H, (33)S, (34)S, and combinations of them. A recently introduced high-resolution ion cyclotron resonance cell (Nikolaev, E. N.; Boldin, I. A.; Jertz, R.; Baykut, G. J. Am. Soc. Mass Spectrom. 2011, 22, 1125-1133) is used in these experiments. The positions of the experimentally obtained fine structure peaks on the mass scale agree with the isotopic distribution simulations with ≤200 ppb error. Some deviation from the theoretical isotopic distribution is observed, less abundant peaks in the fine structure patterns are a little suppressed compared to the larger ones. We present a method for atomic composition determination using accurate mass data and fine isotopic structure of the mass spectrum. Our method combines the traditional atomic composition determination from accurate mass data by enumeration of all possible formulas within constraints defined a priori with the estimation of element coefficients from resolved isotopic structures. These estimated values allow one to narrow the search space for the composition and therefore to reduce the number of candidate formulas.

In-ESI source hydrogen/deuterium exchange of carbohydrate ions.

We present the investigation of hydrogen/deuterium (H/D) exchange of carbohydrates ions occurring in the electrospray ion source. The shape of the deuterium distribution was observed to be considerably dependent on the temperature of the ion transfer tube and the solvent used. If deuterated alcohol (EtOD or MeOD) or D2O/deuterated alcohol is used as an electrospray solvent, then for high temperatures (>350 °C), intensive back exchange is observed, resulting in ∼30% depth of the deuterium exchange. At low temperatures (<150 °C), the back exchange is weaker and the depth of the deuterium exchange is ∼70%. In the intermediate temperature region (∼250 °C), the deuterium distribution is unusually wide for methanol and bimodal for ethanol. The addition of 1% formic acid results in low (∼30%) depth of the deuterium exchange for any temperature in the operating region. The bimodal distribution for the ethanol can be possibly explained by the presence of differently folded gas-phase ions of carbohydrates.