Vapor treatment of electrospray droplets: evidence for the folding of initially denatured proteins on the sub-millisecond time-scale

Probing Acid-Induced Compaction of Denatured Proteins by High-Pressure Electrospray Mass Spectrometry

Further increase in the acidity in the most denaturing acidic solution is known to induce compaction of the fully unfolded protein into a compact molten globule. The phenomenon of "acid-induced folding of proteins" takes place at pH ∼1 in strong acid aqueous solutions with high electrical conductivity and surface tension, a condition that is difficult to handle using conventional electrospray ionization methods for mass spectrometry. Here, high-pressure electrospray ionization (HP-ESI) is used to produce well-resolved mass spectra for proteins in strong acids with pH as low as 1. The compaction of protein conformation is indicated by a large shift in the charge state from high charges to native-like low charges. The addition of salt to the protein in the most denaturing condition also reproduces the compaction effect, thereby supporting the role of anions in this phenomenon. Similar compaction of proteins is also observed in organic solvent/acid mixtures. The charge state of the compacted protein depends on the type of anions that formed ion pairs with a positive charge on the protein. The dissociation of ion pairs during the ionization process forms neutral acids that can be observed by HP-ESI using a soft ion introduction configuration.

Variable Mixing with Theta Emitter Mass Spectrometry: Changing Solution Flow Rates with Emitter Position

Two solutions can be rapidly mixed using theta glass emitters, with products measured using electrospray ionization mass spectrometry. The relative flow rates of the two emitter channels can be measured using different calibration compounds in each channel, or the flow rates are often assumed to be the same. The relative flow rates of each channel can be essentially the same when the emitters are positioned directly in front of the capillary entrance of a mass spectrometer, but the relative flow rates can be varied by up to 3 orders of magnitude by moving the position of the emitter tip ±1 cm in a direction that is perpendicular to the inner divider. Results of the emitter position on the different concentrations of reagents in the initially formed electrospray droplets are demonstrated through protein denaturation using a supercharging reagent as well as two different bimolecular reactions. The average charge state of myoglobin changed from +7.8 to +13.8 when 2.5% sulfolane was mixed with a 200 mM ammonium acetate solution containing the protein when the position of the emitter was scanned in front of the mass spectrometer inlet. The conversion ratio of a bimolecular reaction was changed from 0.98 to 0.04 with varying emitter positions. These results show that the relative flow rates must be carefully monitored because the droplet composition depends strongly on the position of the theta glass emitters. This method can be used to measure the dependence of reaction kinetics on different solution concentrations by using a single emitter and only two solutions.

Top-Down Analysis of In-Source HDX of Native Protein Ions

Hydrogen/deuterium exchange (HDX) is used in protein biophysics to probe folding dynamics, intermolecular interactions, epitope and other mapping. A typical procedure often involves HDX in buffered D₂O solution followed by pepsin digestion, and liquid chromatography/electrospray ionization mass spectrometry analysis. In this work, HDX of protein ions was conducted in the ESI source. Both native electrospray droplets of ubiquitin and denatured myoglobin were exposed to D₂O vapor in the source region of a Bruker SolariX 12T FTICR-mass spectrometer. Electron capture dissociation was used to assess deuterium incorporation at the residue level. This in-source HDX, on the millisecond-time scale, exchanges side-chain hydrogens and fast-exchanging amides compared to conventional minutes-to-hours HDX of backbone hydrogens in solution with less sample preparation (i.e., no D₂O/protein mixing and incubation, no quenching, protein digestion, or LC separation).

High-Resolution Mass Spectrometry Study of the Bio-Oil Samples Produced by Thermal Liquefaction of Microalgae in Different Solvents

We have performed a comparative analysis of the bio-oil produced by thermal liquefaction of microalgae in different solvents using high-resolution Orbitrap mass spectrometry and GC-MS approach. Water, methanol, ethanol, butanol, isopropanol, acetonitrile, toluene, and hexane were used as solvents in which the liquefaction was performed. It was observed that all resulting oils demonstrate a considerable degree of similarity. For all samples, compounds containing 1 and 2 nitrogen atoms dominated in the positive ESI spectra, while a relative contribution of other compounds was small. In negative ESI mode, compounds having 2 to 7 oxygens were observed. Statistical analysis revealed that products can be combined in two groups depending on the solvent used for the liquefaction. To the first group, we can attribute the products obtained by using protic (alcohols) and to the second by using aprotic (acetonitrile, toluene) solvents. Nevertheless, based on our results, we concluded that solvent possesses a minor impact on molecular composition of bio-oil. We suggested that the driving force of the liquefaction reaction is the thermal dehydration of the carbohydrate in algae, resulting in water formation, which could be the trigger of the producing of bio-oil. To prove this hypothesis, we performed the reaction with the dry algae in the absence of the solvent and observed the formation of bio-oil. Graphical Abstract.

Investigation of bio-oil produced by hydrothermal liquefaction of food waste using ultrahigh resolution Fourier transform ion cyclotron resonance mass spectrometry

Recent research has revealed that more than 1.3 billion tons of food is wasted globally every year. The disposal of such huge biomass has become a challenge. In the present paper, we report the production of the bio-oil by hydrothermal liquefaction of three classes of food waste: meat, cheese and fruits. The highest yield of the bio-oil was observed for meat (∼60%) and cheese (∼75%), while for fruits, it was considerably low (∼10%). The molecular composition of the obtained bio-oil was investigated using ultrahigh resolution Fourier Transform Ion Cyclotron Resonance mass spectrometry and was found to be similar to that obtained from algae. Several thousand heteroatom compounds (N, N₂, ON₂, etc. classes) were reliably identified from each sample. It was found that bio-oils produced from meat and cheese have many compounds (∼90%) with common molecular formulas, while bio-oil produced from fruits differs considerably (∼30% of compounds are unique).

Joule Heating and Thermal Denaturation of Proteins in Nano-ESI Theta Tips

Electro-osmotically induced Joule heating in theta tips and its effect on protein denaturation were investigated. Myoglobin, equine cytochrome c, bovine cytochrome c, and carbonic anhydrase II solutions were subjected to electro-osmosis in a theta tip and all of the proteins were denatured during the process. The extent of protein denaturation was found to increase with the applied square wave voltage and electrolyte concentration. The solution temperature at the end of a theta tip was measured directly by Raman spectroscopy and shown to increase with the square wave voltage, thereby demonstrating the effect of Joule heating through an independent method. The electro-osmosis of a solution comprised of myoglobin, bovine cytochrome c, and ubiquitin demonstrated that the magnitude of Joule heating that causes protein denaturation is positively correlated with protein melting temperature. This allows for a quick determination of a protein's relative thermal stability. This work establishes a fast, novel method for protein conformation manipulation prior to MS analysis and provides a temperature-controllable platform for the study of processes that take place in solution with direct coupling to mass spectrometry. Graphical Abstract ᅟ.

CID fragmentation, H/D exchange and supermetallization of Barnase-Barstar complex

The barnase-barstar complex is one of the most stable protein-protein complexes and has a very wide range of possible applications. Here we report the use of top-down mass spectrometry for the investigation of the structure of this complex, its ionization via ESI, isolation and fragmentation. It was found that the asymmetry of the resulting charge state distributions of the protein monomer product ions increased as the charge state of the precursor ions increased. For the investigation of the 3D structure of the complex, the gas phase H/D exchange reaction was used. In addition, supermetallized ions of the complex with Zn were produced and investigated. It was observed that an increase in the number of metals bound to the complex results in a change in complex stability and the charge distribution between protein fragment. Analysis of the fragmentation pattern of the supermetallized complex [bn-b* + 5Zn]¹⁰⁺ indicated that this ion is present in different conformations with different charges and Zn distributions. Since Zn cannot migrate, such structures must be formed during ionization.

Thermal dissociation of ions limits the degree of the gas-phase H/D exchange at the atmospheric pressure

We present the application of the extended desolvating capillaries for increasing the degree of the gas-phase hydrogen/deuterium exchange reaction at atmospheric pressure. The use of the extended capillaries results in the increase of the time that ions spend in the high pressure region, what leads to the significant improvement of the efficiency of the reaction. For the small protein ubiquitin, it was observed that for the same temperature, the number of exchanges increases with the decrease of the charge state so that the lowest charge state can exchange twice the number of hydrogen than the highest one. With the increase of the temperature, the difference decreases, and eventually, the number of exchanges equalizes for all charge states. The value of this temperature and the corresponding number of exchanges depend on the geometric parameters of the capillary. Further increase of the temperature leads to the thermal dissociation of the protein ion. The observed b/y fragments are identical to those produced by collision-induced dissociation performed in the ion trap. Copyright © 2017 John Wiley & Sons, Ltd.

The investigation of the bio-oil produced by hydrothermal liquefaction of Spirulina platensis using ultrahigh resolution Fourier transform ion cyclotron resonance mass spectrometry

We report the investigation of the hydrothermal liquefaction products of the Spirulina platensis microalgae by using the Fourier transform ion cyclotron resonance mass spectrometry. The hydrothermal liquefaction produced two fractions: one with boiling temperature below 300℃ and the dense residue that remained in the reactor. It was observed that N₂ and N classes of compounds that dominate in the positive ESI Fourier transform ion cyclotron resonance spectra for both fractions, and that the light fraction is considerably more saturated then the heavy one. The performed hydrogen/deuterium exchange reaction indicated the presence of the onium compounds in the bio-oil.

Isolating Protein Charge State Reduction in Electrospray Droplets Using Femtosecond Laser Vaporization

Charge state distributions are measured using mass spectrometry for both native and denatured cytochrome c and myoglobin after laser vaporization from the solution state into an electrospray (ES) plume consisting of a series of solution additives differing in gas-phase basicity. The charge distribution depends on both the pH of the protein solution prior to laser vaporization and the gas-phase basicity of the solution additive employed in the ES solvent. Cytochrome c (myoglobin) prepared in solutions with pH of 7.0, 2.6, and 2.3 resulted in the average charge state distribution (Z_avg) of 7.0 ± 0.1 (8.2 ± 0.1), 9.7 ± 0.2 (14.5 ± 0.3), and 11.6 ± 0.3 (16.4 ± 0.1), respectively, in ammonium formate ES solvent. The charge distribution shifted from higher charge states to lower charge states when the ES solvent contained amines additives with higher gas-phase basicity. In the case of triethyl ammonium formate, Z_avg of cytochrome c (myoglobin) prepared in solutions with pH of 7.0, 2.6, and 2.3 decreased to 4.9 (5.7), 7.4 ± 0.2 (9.6 ± 0.3), and 7.9 ± 0.3 (9.8 ± 0.2), respectively. The detection of a charge state distribution corresponding to folded protein after laser vaporized, acid-denatured protein interacts with the ES solvent containing ammonium formate, ammonium acetate, triethyl ammonium formate, and triethyl ammonium acetate suggests that at least a part of protein population folds within the electrospray droplet on a millisecond timescale. Graphical Abstract ᅟ.

Re-configurable, multi-mode contained-electrospray ionization for protein folding and unfolding on the millisecond time scale

Contained-electrospray ionization enables online selection of protein charge states by a direct infusion of reactive vapors and liquids into charged micro-droplets.

Ion Mobility-Mass Spectrometry Reveals Highly-Compact Intermediates in the Collision Induced Dissociation of Charge-Reduced Protein Complexes

Protocols that aim to construct complete models of multiprotein complexes based on ion mobility and mass spectrometry data are becoming an important element of integrative structural biology efforts. However, the usefulness of such data is predicated, in part, on an ability to measure individual subunits removed from the complex while maintaining a compact/folded state. Gas-phase dissociation of intact complexes using collision induced dissociation is a potentially promising pathway for acquiring such protein monomer size information, but most product ions produced are possessed of high charge states and elongated/string-like conformations that are not useful in protein complex modeling. It has previously been demonstrated that the collision induced dissociation of charge-reduced protein complexes can produce compact subunit product ions; however, their formation mechanism is not well understood. Here, we present new experimental evidence for the avidin (64 kDa) and aldolase (157 kDa) tetramers that demonstrates significant complex remodeling during the dissociation of charge-reduced assemblies. Detailed analysis and modeling indicates that highly compact intermediates are accessed during the dissociation process by both complexes. Here, we present putative pathways that describe the formation of such ions, as well as discuss the broader significance of such data for structural biology applications moving forward.

A multichannel rotating electrospray ionization mass spectrometry (MRESI): instrumentation and plume interactions

A multichannel rotating electrospray ionization (MRESI) mass spectrometry method is described. Plume interactions are also systematically studied.

Electroosmotically driven solution mixing in borosilicate theta glass nESI emitters

The use of borosilicate theta glass capillaries as nanoelectrospray ionization emitters has recently been demonstrated as a method for mixing two solutions as they are sprayed into the mass spectrometer for analysis. All previous experiments resulted in a solution mixing timescale limited to the time the analytes spend in the Taylor cone and subsequent droplets (i.e. sub-millisecond timescale). In an effort to extend the solution mixing timescale to the milliseconds regime, we demonstrate that solution can be moved from one channel of the theta tip to the opposite channel via electroosmosis by applying a potential difference between the two wire electrodes inserted into each channel of the theta tip. First, we establish that electroosmosis is responsible for solution movement using fluorescence microscopy to track fluorescent tracer dyes. We then demonstrate the utility of this technique in varying the extent of denaturation of holomyoglobin to apomyoglobin on the millisecond timescale just prior to analysis by mass spectrometry. Finally, we induce additional turbulence for better mixing by applying a square wave potential to one of the wire electrodes while holding the opposite wire at a constant voltage between the low and high potentials of the square wave. This experiment was found to provide nearly complete mixing after a single cycle of the square wave. The use of electroosmosis significantly expands the flexibility of theta tips for altering solutions prior to nESI without the need for off-line sample manipulation. Copyright © 2015 John Wiley & Sons, Ltd.

Solvent-induced structural transitions of lysozyme in an electrospray ionization source

The structural characterization of proteins using electrospray ionization mass spectrometry (ESI-MS) has become an important method for understanding protein structural dynamics. The correlation between the structures of proteins in solution and gas phase needs to be understood for the application of ESI-MS to protein structural studies. Hen egg white lysozyme (Lyz) is a small protein with a stable compact structure in solution. Although it was known that denatured Lyz in solution undergoes compaction during transfer into the gas phase via ESI, detailed characterization of the process was not available. In the present study, we show that the organic cosolvent, which denatures Lyz in solution, induces the collapse of the extended Lyz structure into compact structures during ESI. This process is further facilitated by the presence of acids, whose conjugate bases can interact with Lyz to reduce its charge state and the electrostatic repulsion between its charged residues (Analyst, 2015, 140, 661-669). Exposure of ESI droplets to acid and solvent vapors confirms that the overall process most probably occurs in the charged droplets from ESI. This study provides a detailed understanding of the possible influence of the solvent environment on protein structure during transfer into the gas phase.

Letter: Analytical potential of the in-electrospray ionization source hydrogen/deuterium exchange for the investigation of oligonucleotides

It has previously been reported that different conformations of oligonucleotides may be detected using a gas-phase hydrogen/deuterium (H/D) exchange performed in the collision cell of a mass spectrometer. The presence of different conformers was postulated based on the bimodal shape of the deuterium distribution and on the ion mobility spectrometry data. Here we implement an in-electrospray ionization source H/D exchange to detect the different conformations of oligonucleotides in the region of ion formation. We observed that the number of H/D exchanges depends considerably on the temperature of the desolvating capillary and varies from 25% at 50°C to 80% at 450°C, but no bimodality in the shape of the deuterium distribution was observed. Such results indicate that in the region of ion formation different conformations of oligonucleotide ions rapidly interconvert one into another.

Investigating protein folding and unfolding in electrospray nanodrops upon rapid mixing using theta-glass emitters

Theta-glass emitters are used to rapidly mix two solutions to induce either protein folding or unfolding during nanoelectrospray (nanoESI). Mixing acid-denatured myoglobin with an aqueous ammonium acetate solution to increase solution pH results in protein folding during nanoESI. A reaction time and upper limit to the droplet lifetime of 9 ± 2 μs is obtained from the relative abundance of the folded conformer in these rapid mixing experiments compared to that obtained from solutions at equilibrium and a folding time constant of 7 μs. Heme reincorporation does not occur, consistent with the short droplet lifetime and the much longer time constant for this process. Similar mixing experiments with acid-denatured cytochrome c and the resulting folding during nanoESI indicate a reaction time of between 7 and 25 μs depending on the solution composition. The extent of unfolding of holo-myoglobin upon rapid mixing with theta-glass emitters is less than that reported previously (Fisher et al. Anal. Chem.2014, 86, 4581−458824702054), a result that is attributed to the much smaller, ∼1.5 μm, average o.d. tips used here. These results indicate that the time frame during which protein folding or unfolding can occur during nanoESI depends both on the initial droplet size, which can be varied by changing the emitter tip diameter, and on the solution composition. This study demonstrates that protein folding or unfolding processes that occur on the ∼10 μs time scale can be readily investigated using rapid mixing with theta-glass emitters combined with mass spectrometry.

On-line desalting of crude oil in the source region of a Fourier transform ion cyclotron resonance mass spectrometer

The presence of dissolved metal ions in waters associated with crude oils has many negative implications for the transport, processing, and refining of petroleum. In addition, mass spectrometric analysis of sodium containing crude oil samples suffers from ionization suppression, unwanted adduct formation, and an increase in the complexity of data analysis. Here, we describe a method for the reduction/elimination of these adverse effects by modification of the source region gas-inlet system of a 12 T Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometer. Several acids were examined as part of this study, with the most suitable for on-line desalting found to have both high vapor pressure and low pK(a); 12.1 M HCl showed the strongest desalting effect for crude oil samples with a sodium removal index (SRI) of 88%-100% ± 7% for the NaOS compound class. In comparison, a SRI of only 38% ± 9% was observed for a H₂O/toluene solution-phase extraction of oil 1. These results clearly demonstrate the increased efficacy of pseudo-vapor phase desalting with the additional advantages that initial sample solution conditions are preserved and no sample preparation is required prior to analysis.

Hydrogen/deuterium exchange in parallel with acid/base induced protein conformational change in electrospray droplets

The exposure of electrospray droplets to vapors of deuterating reagents during droplet desolvation in the interface of a mass spectrometer results in hydrogen/deuterium exchange (HDX) on the sub-millisecond time scale. Deuterated water is used to label ubiquitin and cytochrome c with minimal effect on the observed charge state distribution (CSD), suggesting that the protein conformation is not being altered. However, the introduction of deuterated versions of various acids (e.g., CD3COOD and DCl) and bases (ND3) induces unfolding or refolding of the protein while also labeling these newly formed conformations. The extent of HDX within a protein CSD associated with a particular conformation is essentially constant, whereas the extent of HDX can differ significantly for CSDs associated with different conformations from the same protein. In some cases, multiple HDX distributions can be observed within a given charge state (as is demonstrated with cytochrome c) suggesting that the extent of HDX and CSDs share a degree of complementarity in their sensitivities for protein conformation. The CSD is established late in the evolution of ions in electrospray whereas the HDX process presumably takes place in the bulk of the droplet throughout the electrospray process. Back exchange is also performed in which proteins are prepared in deuterated solvents prior to ionization and exposed to undeuterated vapors to exchange deuteriums for hydrogens. The degree of deuterium uptake is easily controlled by varying the identity and partial pressure of the reagent introduced into the interface. Since the exchange occurs on the sub-millisecond time scale, the use of deuterated acids or bases allows for transient species to be generated and labeled for subsequent mass analysis.

Electrothermal supercharging in mass spectrometry and tandem mass spectrometry of native proteins

Electrothermal supercharging of protein ions formed by electrospray ionization from buffered aqueous solutions results in significant increases to both the maximum and average charge states compared to native mass spectrometry in which ions are formed from the same solutions but with lower spray potentials. For eight of the nine proteins investigated, the maximum charge states of protonated ions formed from native solutions with electrothermal supercharging is greater than those obtained from conventional denaturing solutions consisting of water/methanol/acid, although the average charging is slightly lower owing to contributions of small populations of more folded low charge-state structures. Under these conditions, electrothermal supercharging is slightly less effective for anions than for cations. Equivalent sequence coverage (80%) is obtained with electron transfer dissociation of the same high charge-state ion of cytochrome c formed by electrothermal supercharging from native solutions and from denaturing solutions. Electrothermal supercharging should be advantageous for combining structural studies of proteins in native environments with mass spectrometers that have limited high m/z capabilities and for significantly improving tandem mass spectrometry performance for protein ions formed from solutions in which the molecules have native structures and activities.

Electrospray ionization-induced protein unfolding

Electrospray ionization mass spectrometry (ESI-MS) measurements were performed under a variety of solution conditions on a highly acidic sub-fragment (B3C) of the C-terminal carbohydrate-binding repeat region of Clostridium difficile toxin B, and two mutants (B4A and B4B) containing fewer acidic residues. ESI-MS measurements performed in negative ion mode on aqueous ammonium acetate solutions of B3C at low ionic strength (I < 80 mM) revealed evidence, based on the measured charge state distribution, of protein unfolding. In contrast, no evidence of unfolding was detected from ESI-MS measurements made in positive ion mode at low I or in either mode at higher I. The results of proton nuclear magnetic resonance and circular dichroism spectroscopy measurements and gel filtration chromatography performed on solutions of B3C under low and high I conditions suggest that the protein exists predominantly in a folded state in neutral aqueous solutions with I > 10 mM. The results of ESI-MS measurements performed on B3C in a series of solutions with high I at pH 5 to 9 rule out the possibility that the structural changes are related to ESI-induced changes in pH. It is proposed that unfolding of B3C, observed in negative mode for solutions with low I, occurs during the ESI process and arises due to Coulombic repulsion between the negatively charged residues and liquid/droplet surface charge. ESI-MS measurements performed in negative ion mode on B4A and B4B also reveal a shift to higher charge states at low I but the magnitude of the changes are smaller than observed for B3C.

Basic vapor exposure for tuning the charge state distribution of proteins in negative electrospray ionization: elucidation of mechanisms by fluorescence spectroscopy

Manipulation for simplifying or increasing the observed charge state distributions of proteins can be highly desirable in mass spectrometry experiments. In the present work, we implemented a vapor introduction technique to an Agilent Jet Stream ESI (Agilent Technologies, Santa Clara, CA, USA) source. An apparatus was designed to allow for the enrichment of the nitrogen sheath gas with basic vapors. An optical setup, using laser-induced fluorescence and a pH-chromic dye, permits the pH profiling of the droplets as they evaporate in the electrospray plume. Mechanisms of pH droplet modification and its effect on the protein charging phenomenon are elucidated. An important finding is that the enrichment with basic vapors of the nitrogen sheath gas, which surrounds the nebulizer spray, leads to an increase in the spray current. This is attributed to an increase in the electrical conductivity of water-amine enriched solvent at the tip exit. Here, the increased current results in a generation of additional electrolytically produced OH(-) ions and a corresponding increase in the pH at the tip exit. Along the electrospray plume, the pH of the droplets increases due to both droplet evaporation and exposure to basic vapors from the seeded sheath gas. The pH evolution in the ESI plume obtained using pure and basic seeded sheath gas was correlated with the evolution of the charge state distribution observed in mass spectra of proteins, in the negative ion mode. Taking advantage of the Agilent Jet Stream source geometry, similar protein charge state distributions and ion intensities obtained with basic initial solutions, can be obtained using native solution conditions by seeding the heated sheath gas with basic vapors.