Electrochemically induced pH changes resulting in protein unfolding in the ion source of an electrospray mass spectrometer

On the Chemistry of Aqueous Ammonium Acetate Droplets during Native Electrospray Ionization Mass Spectrometry

Ammonium acetate (NH4Ac) is a widely used solvent additive in native electrospray ionization (ESI) mass spectrometry. NH4Ac can undergo proton transfer to form ammonia and acetic acid (NH4+ + Ac- → NH3 + HAc). The volatility of these products ensures that electrosprayed ions are free of undesired adducts. NH4Ac dissolution in water yields pH 7, providing "physiological" conditions. However, NH4Ac is not a buffer at pH 7 because NH4+ and Ac- are not a conjugate acid/base pair (Konermann, L. J. Am. Soc. Mass Spectrom. 2017, 28, 1827-1835.). In native ESI, it is desirable that analytes experience physiological conditions not only in bulk solution but also while they reside in ESI droplets. Little is known about the internal milieu of NH4Ac-containing ESI droplets. The current work explored the acid/base chemistry of such droplets, starting from a pH 7 analyte solution. We used a two-pronged approach involving evaporation experiments on bulk solutions under ESI-mimicking conditions, as well as molecular dynamics simulations using a newly developed algorithm that allows for proton transfer. Our results reveal that during droplet formation at the tip of the Taylor cone, electrolytically generated protons get neutralized by Ac-, making NH4+ the net charge carriers in the weakly acidic nascent droplets. During the subsequent evaporation, the droplets lose water as well as NH3 and HAc that were generated by proton transfer. NH3 departs more quickly because of its greater volatility, causing the accumulation of HAc. Together with residual Ac-, these HAc molecules form an acetate buffer that stabilizes the average droplet pH at 5.4 ± 0.1, as governed by the Henderson-Hasselbalch equation. The remarkable success of native ESI investigations in the literature implies that this pH drop by ∼1.6 units relative to the initially neutral analyte solution can be tolerated by most biomolecular analytes on the short time scale of the ESI process.

Tuning oxidative modification by a strong electric field using nanoESI of highly conductive solutions near the minimum flow rate

Oxidative modification is usually used in mass spectrometry (MS) for labeling and structural analysis. Here we report a highly tunable oxidation that can be performed in line with the nanoESI-MS analysis at the same ESI emitter without the use of oxidative reagents such as ozone and H₂O₂, and UV activation. The method is based on the high-pressure nanoESI of a highly conductive (conductivity >3.8 S m^-1) aqueous solution near the minimum flow rate. The ion source is operated under super-atmospheric pressure (0.5 MPa gauge pressure) to avoid the contribution of electric discharge. The analyte at the tip of the Taylor cone or in the emitter droplet can be locally oxidized in an on-demand manner by varying the nanoflow rate. With an offline nanoESI, the degree of oxidation, i.e., the average number of incorporated oxygen atoms, can be finely tuned by voltage modulation using spray current as the feedback signal. Oxidations of easily oxidized residues present in peptides/proteins and the double bonds of the unsaturated phosphatidylcholine occur at low flow rate operation (<5 nL min^-1) when the electric field at the tip of the Taylor cone and the initially produced charged droplet reaches approximately 1.3 V nm^-1. The oxidized ion signal responds instantaneously to changes in flow rate, indicating that the oxidation is highly localized. Using isotope labeling, it was found that the incorporated oxygen primarily originates from the gas phase, suggesting a direct oxidation pathway for the analyte enriched on the liquid surface via the reactive oxygen atoms formed by the strong electric field.

Free-flow biomolecular concentration and separation of proteins and nucleic acids using teíchophoresis

The ability to preconcentrate, separate, and purify biomolecules, such as proteins and nucleic acids, is an important requirement for the next generation of portable diagnostic tools for environmental monitoring and disease detection. Traditionally, such pretreatment has been accomplished using large, centralized liquid- or solid-phase extraction equipment, which can be time-consuming and requires many processing steps. Here, we present a newly developed electrokinetic concentration technique, teíchophoresis (TPE), to concentrate and separate proteins, and to concentrate nucleic acids. In TPE, a free-flowing sample is exposed to a perpendicular electric field in the vicinity of a mass-impermeable conductive wall and a conductive terminating electrolyte (TE), which creates a high electric field strength zone between the lower mobility sample and the no-flux barrier. Unlike a similar electrokinetic concentration method, isotachophoresis (ITP), TPE does not require a leading electrolyte (LE), yet still enables a continuous field-driven electrophoretic ion migration across the channel and a free-flowing biomolecular concentration at the conductive wall. Here, we demonstrate the use of free-flow TPE (FFTPE) to manipulate biomolecular samples containing proteins or nucleic acids. We first use TPE to drive a 6.6-fold concentration increase of avidin-FITC, and also demonstrate protein separation and stacking between ovalbumin-fluorescein and BSA-AlexaFluor 555, both without the use of a conventional LE. Further, we utilize TPE to perform a 21-fold concentration increase of nucleic acids. Our results show that TPE is biocompatible with both proteins and nucleic acids, requires only 10 V DC, produces no significant sample pH changes during operation, and demonstrates that this method can be used as an effective sample pretreatment to prepare biological samples for downstream analysis in a continuous free-flowing microfluidic channel.

Application of Multiple Length Cross-linkers to the Characterization of Gaseous Protein Structure

The speed, sensitivity, and tolerance of heterogeneity, as well as the kinetic trapping of solution-like states during electrospray, make native mass spectrometry an attractive method to study protein structure. Increases in the resolution of ion mobility measurements and in mass resolving power and range are leading to the increase of the information content of intact protein measurements and an expanded role of mass spectrometry in structural biology. Herein, a suite of different length noncovalent (sulfonate to positively charged side chain) cross-linkers was introduced via gas-phase ion/ion chemistry and used to determine distance restraints of kinetically trapped gas-phase structures of native-like cytochrome c ions. Electron capture dissociation allowed for the identification of cross-linked sites. Different length linkers resulted in distinct pairs of side chains being linked, supporting the ability of gas-phase cross-linking to be structurally specific. The gas-phase lengths of the cross-linkers were determined by conformational searches and density functional theory, allowing for the interpretation of the cross-links as distance restraints. These distance restraints were used to model gas-phase structures with molecular dynamics simulations, revealing a mixture of structures with similar overall shape/size but distinct features, thereby illustrating the kinetic trapping of multiple native-like solution structures in the gas phase.

Surface Activity of Amines Provides Evidence for the Combined ESI Mechanism of Charge Reduction for Protein Complexes

Charge reduction reactions are important for native mass spectrometry (nMS) because lower charge states help retain native-like conformations and preserve noncovalent interactions of protein complexes. While mechanisms of charge reduction reactions are not well understood, they are generally achieved through the addition of small molecules, such as polyamines, to traditional nMS buffers. Here, we present new evidence that surface-active, charge reducing reagents carry away excess charge from the droplet after being emitted due to Coulombic repulsion, thereby reducing the overall charge of the droplet. Furthermore, these processes are directly linked to two mechanisms for electrospray ionization, specifically the charge residue and ion evaporation models (CRM and IEM). Selected protein complexes were analyzed in solutions containing ammonium acetate and selected trialkylamines or diaminoalkanes of increasing alkyl chain lengths. Results show that amines with higher surface activity have increased propensities for promoting charge reduction of the protein ions. The electrospray ionization (ESI) emitter potential was also found to be a major contributing parameter to the prevalence of charge reduction; higher emitter potentials consistently coincided with lower average charge states among all protein complexes analyzed. These results offer experimental evidence for the mechanism of charge reduction in ESI and also provide insight into the final stages of the ESI and their impact on biological ions.

Temperature Regulates Stability, Ligand Binding (Mg2+ and ATP), and Stoichiometry of GroEL-GroES Complexes

Chaperonins are nanomachines that harness ATP hydrolysis to power and catalyze protein folding, a chemical action that is directly linked to the maintenance of cell function through protein folding/refolding and assembly. GroEL and the GroEL-GroES complex are archetypal examples of such protein folding machines. Here, variable-temperature electrospray ionization (vT-ESI) native mass spectrometry is used to delineate the effects of solution temperature and ATP concentrations on the stabilities of GroEL and GroEL-GroES complexes. The results show clear evidence for destabilization of both GroEL₁₄ and GroES₇ at temperatures of 50 and 45 °C, respectively, substantially below the previously reported melting temperature (T_m ∼ 70 °C). This destabilization is accompanied by temperature-dependent reaction products that have previously unreported stoichiometries, viz. GroEL₁₄-GroES_y-ATP_n, where y = 1, 2, 8 and n = 0, 1, 2, 8, that are also dependent on Mg²⁺ and ATP concentrations. Variable-temperature native mass spectrometry reveals new insights about the stability of GroEL in response to temperature effects: (i) temperature-dependent ATP binding to GroEL; (ii) effects of temperature as well as Mg²⁺ and ATP concentrations on the stoichiometry of the GroEL-GroES complex, with Mg²⁺ showing greater effects compared to ATP; and (iii) a change in the temperature-dependent stoichiometries of the GroEL-GroES complex (GroEL₁₄-GroES₇ vs GroEL₁₄-GroES₈) between 24 and 40 °C. The similarities between results obtained by using native MS and cryo-EM [Clare et al. An expanded protein folding cage in the GroEL-gp31 complex. J. Mol. Biol. 2006, 358, 905-911; Ranson et al. Allosteric signaling of ATP hydrolysis in GroEL-GroES complexes.Nat. Struct. Mol. Biol. 2006, 13, 147-152] underscore the utility of native MS for investigations of molecular machines as well as identification of key intermediates involved in the chaperonin-assisted protein folding cycle.

New insights into the metal-induced oxidative degradation pathways of transthyretin

The amyloidogenic mechanism of transthyretin is still debated but understanding it fully could lend insight into disease progression and potential therapeutics. Transthyretin was investigated revealing a metal-induced (Cr/Cu) oxidation pathway leading to N-terminal backbone fragmentation and oligomer formation; previously hidden details were revealed only by FT-IM-Orbitrap MS and surface-induced dissociation.

Distinct Stabilities of the Structurally Homologous Heptameric Co-Chaperonins GroES and gp31

The GroES heptamer is the molecular co-chaperonin that partners with the tetradecamer chaperonin GroEL, which assists in the folding of various nonnative polypeptide chains in Escherichia coli. Gp31 is a structural and functional analogue of GroES encoded by the bacteriophage T4, becoming highly expressed in T4-infected E. coli, taking over the role of GroES, favoring the folding of bacteriophage proteins. Despite being slightly larger, gp31 is quite homologous to GroES in terms of its tertiary and quaternary structure, as well as in its function and mode of interaction with the chaperonin GroEL. Here, we performed a side-by-side comparison of GroES and gp31 heptamer complexes by (ion mobility) tandem mass spectrometry. Surprisingly, we observed quite distinct fragmentation mechanisms for the GroES and gp31 heptamers, whereby GroES displays a unique and unusual bimodal charge distribution in its released monomers. Not only the gas-phase dissociation but also the gas-phase unfolding of GroES and gp31 were found to be very distinct. We rationalize these observations with the similar discrepancies we observed in the thermal unfolding characteristics and surface contacts within GroES and gp31 in the solution. From our data, we propose a model that explains the observed simultaneous dissociation pathways of GroES and the differences between GroES and gp31 gas-phase dissociation and unfolding. We conclude that, although GroES and gp31 exhibit high homology in tertiary and quaternary structure, they are quite distinct in their solution and gas-phase (un)folding characteristics and stability. Graphical Abstract.

Hydrogen/deuterium exchange in mass spectrometry

The isotopic exchange approach is in use since the first observation of such reactions in 1933 by Lewis. This approach allows the investigation of the pathways of chemical and biochemical reactions, determination of structure, composition, and conformation of molecules. Mass spectrometry has now become one of the most important analytical tools for the monitoring of the isotopic exchange reactions. Investigation of conformational dynamics of proteins, quantitative measurements, obtaining chemical, and structural information about individual compounds of the complex natural mixtures are mainly based on the use of isotope exchange in combination with high resolution mass spectrometry. The most important reaction is the Hydrogen/Deuterium exchange, which is mainly performed in the solution. Recently we have developed the approach allowing performing of the Hydrogen/Deuterium reaction on-line directly in the ionization source under atmospheric pressure. Such approach simplifies the sample preparation and can accelerate the exchange reaction so that certain hydrogens that are considered as non-labile will also participate in the exchange. The use of in-ionization source H/D exchange in modern mass spectrometry for structural elucidation of molecules serves as the basic theme in this review. We will focus on the mechanisms of the isotopic exchange reactions and on the application of in-ESI, in-APCI, and in-APPI source Hydrogen/Deuterium exchange for the investigation of petroleum, natural organic matter, oligosaccharides, and proteins including protein-protein complexes. The simple scenario for adaptation of H/D exchange reactions into mass spectrometric method is also highlighted along with a couple of examples collected from previous studies.

Organic Reactions in Microdroplets: Reaction Acceleration Revealed by Mass Spectrometry

The striking finding that reaction acceleration occurs in confined-volume solutions sets up an apparent conundrum: Microdroplets formed by spray ionization can be used to monitor the course of bulk-phase reactions and also to accelerate reactions between the reagents in such a reaction. This Minireview introduces droplet and thin-film acceleration phenomena and summarizes recent methods applied to study accelerated reactions in confined-volume, high-surface-area solutions. Conditions that dictate either simple monitoring or acceleration are reconciled in the occurrence of discontinuous and complete desolvation as the endpoint of droplet evolution. The contrasting features of microdroplet and bulk-solution reactions are described together with possible mechanisms that drive reaction acceleration in microdroplets. Current applications of droplet microreactors are noted as is reaction acceleration in confined volumes and possible future scale-up.

Time-resolved method to distinguish protein/peptide oxidation during electrospray ionization mass spectrometry

Electrospray ionization mass spectrometry (ESI-MS) is one of the most prevalent techniques used to monitor protein/peptide oxidation induced by reactive oxygen species (ROSs). However, both corona discharge (CD) and electrochemistry (EC) can also lead to protein/peptide oxidation during ESI. Because the two types of oxidation occur almost simultaneously, determining the extent to which the two pathways contribute to protein/peptide oxidation is difficult. Herein, a time-resolved method was introduced to identify and differentiate CD- and EC-induced oxidation. Using this approach, we separated the instantaneous CD-induced oxidation from the hysteretic EC-induced oxidation, and the effects of the spray voltage and flow rate of the ESI source on both oxidation types were investigated with a homemade ESI source. For angiotensin II analogue (b-DRVYVHPF-y), the dehydrogenation and oxygenation species were the detected EC-induced oxidation products, while the oxygenation species were the major CD-induced oxidation products. This time-resolved approach was also applicable to a commercial HESI source, in which both CD and EC were responsible for hemoglobin and cytochrome c oxidation with upstream grounding while CD dominated the oxidation without upstream grounding.

Unexpected Reduction of Iminoquinone and Quinone Derivatives in Positive Electrospray Ionization Mass Spectrometry and Possible Mechanism Exploration

Unexpected reduction of iminoquinone (IQ) and quinone derivatives was first reported during positive electrospray ionization mass spectrometry. Upon increasing spray voltage, the intensities of IQ and quinone derivatives decreased drastically, accompanying the increase of the intensities of the reduction products, amodiaquine (AQ) and phenol derivatives. To gain more insight into the mechanism of such reduction, we explored the experimental factors that are influential to corona discharge (CD). The results show that experimental parameters that favor severe CD, including metal spray emitter, using water as spray solvent, sheath gas with low dielectric strength (e.g., nitrogen), and shorter spray tip-to-mass spectrometer inlet distance, facilitated the reduction of IQ and quinone derivatives, implying that the reduction should be closely related to CD in the gas phase. Graphical Abstract ᅟ.

Addressing a Common Misconception: Ammonium Acetate as Neutral pH "Buffer" for Native Electrospray Mass Spectrometry

Native ESI-MS involves the transfer of intact proteins and biomolecular complexes from solution into the gas phase. One potential pitfall is the occurrence of pH-induced changes that can affect the analyte while it is still surrounded by solvent. Most native ESI-MS studies employ neutral aqueous ammonium acetate solutions. It is a widely perpetuated misconception that ammonium acetate buffers the analyte solution at neutral pH. By definition, a buffer consists of a weak acid and its conjugate weak base. The buffering range covers the weak acid pK_a ± 1 pH unit. NH₄⁺ and CH₃-COO^- are not a conjugate acid/base pair, which means that they do not constitute a buffer at pH 7. Dissolution of ammonium acetate salt in water results in pH 7, but this pH is highly labile. Ammonium acetate does provide buffering around pH 4.75 (the pK_a of acetic acid) and around pH 9.25 (the pK_a of ammonium). This implies that neutral ammonium acetate solutions electrosprayed in positive ion mode will likely undergo acidification down to pH 4.75 ± 1 in the ESI plume. Ammonium acetate nonetheless remains a useful additive for native ESI-MS. It is a volatile electrolyte that can mimic the solvation properties experienced by proteins under physiological conditions. Also, a drop from pH 7 to around pH 4.75 is less dramatic than the acidification that would take place in pure water. It is hoped that the habit of referring to pH 7 solutions as ammonium acetate "buffer" will disappear from the literature. Ammonium acetate "solution" should be used instead. Graphical Abstract ᅟ.

Observation of the multiple halogenation of peptides in the electrospray ionization source

The chlorination of peptides and proteins is an important posttranslational modification, which is a physiological signature of an enzyme myeloperoxidase and can serve as a potential biomarker of some diseases (Parkinson's disease, Alzheimer's disease, etc.). The quantification of the chlorinated peptides has been very challenging in part due to their low levels and artifacts associated with sample preparation. One of the most convenient and promising methods to detect and investigate the chlorinated peptides in the biological samples is the electrospray ionization (ESI) mass spectrometry coupled to the fragmentation techniques (collision-induced dissociation and electron capture dissociation/electron transfer dissociation). We have shown that if the chlorine anions are present in the solution, then the peptide can undergo the chlorination during the ESI ionization. The effect was found to depend on the values of electric potentials of metal parts of the ESI interface. It was found that the grounding of ESI syringe results in the formation of an additional electric loop leading to the electrolytic production of Cl2 and as a consequence the hypochlorous acid inside the ESI needle. Hypochlorous acid reacts with amino groups of peptides and proteins producing chloramine or causing the protein cleavage. In the paper, it is shown on the example of the solution of the several peptides in the presence of HCl that by manipulating the ESI syringe potential, it is possible to create complexes with up to five Cl atoms for sample peptides when the ESI is operated in the positive mode.

Alleviation of electrochemical oxidation for peptides and proteins in electrospray ionization: obtaining more accurate mass spectra with induced high voltage

Accurate mass spectrometry (MS) signal for peptide/protein analysis, which could be affected by various MS conditions, plays an essential role in identification and quantification of biological samples. Herein, we tried to alleviate the possible interferences from electrochemical oxidations during electrospray ionization (ESI). Three most common electrochemical oxidation reactions in ESI include oxidation of analyte, solvent, and electrode. With introduction of induced electrospray ionization (IESI) (a variant form of ESI), these interferences were significantly alleviated for peptides/proteins. That effect was also tested with flow injection experiments with different solution flow rates, electrolyte concentrations and solvent compositions, which was to simulate various chromatography conditions in conventional liquid chromatography (LC) separations. For all chromatography conditions tested, electrochemical oxidation was significantly alleviated for the absence of physical contact between spray solution and electrode.

Mass spectrometric methods for monitoring redox processes in electrochemical cells

Electrochemistry (EC) is a mature scientific discipline aimed to study the movement of electrons in an oxidation-reduction reaction. EC covers techniques that use a measurement of potential, charge, or current to determine the concentration or the chemical reactivity of analytes. The electrical signal is directly converted into chemical information. For in-depth characterization of complex electrochemical reactions involving the formation of diverse intermediates, products and byproducts, EC is usually combined with other analytical techniques, and particularly the hyphenation of EC with mass spectrometry (MS) has found broad applicability. The analysis of gases and volatile intermediates and products formed at electrode surfaces is enabled by differential electrochemical mass spectrometry (DEMS). In DEMS an electrochemical cell is sampled with a membrane interface for electron ionization (EI)-MS. The chemical space amenable to EC/MS (i.e., bioorganic molecules including proteins, peptides, nucleic acids, and drugs) was significantly increased by employing electrospray ionization (ESI)-MS. In the simplest setup, the EC of the ESI process is used to analytical advantage. A limitation of this approach is, however, its inability to precisely control the electrochemical potential at the emitter electrode. Thus, particularly for studying mechanistic aspects of electrochemical processes, the hyphenation of discrete electrochemical cells with ESI-MS was found to be more appropriate. The analytical power of EC/ESI-MS can further be increased by integrating liquid chromatography (LC) as an additional dimension of separation. Chromatographic separation was found to be particularly useful to reduce the complexity of the sample submitted either to the EC cell or to ESI-MS. Thus, both EC/LC/ESI-MS and LC/EC/ESI-MS are common.

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.

Gravitational sampling electrospray ionization mass spectrometry for real-time reaction monitoring

RATIONALE

The elucidation of chemical reaction mechanisms has attracted tremendous interest in recent years. Here, gravitational sampling electrospray ionization mass spectrometry (GS-ESI-MS) is used to explore a simple method for the real-time monitoring of chemical and biochemical reactions.

METHODS

A sample solution in a stainless steel sample well is directly delivered through a fused-silica capillary due to the forces of gravity, capillary action, and electroosmotic flow (EOF). Analyte ions are continuously generated via electrospray ionization from the capillary tip when a high voltage is applied on the sample well.

RESULTS

Liquid solutions (<5 μL) of small organic compounds (e.g., crystal violet) and large biomolecules (e.g., reserpine, angiotensin II, and insulin) were directly analyzed via GS-ESI-MS. In addition, the technique was successfully applied to continuously monitor chemical [e.g. chelation of ethylenediaminetetraacetic acid (EDTA) with copper(II), and addition-elimination of aminophenol and acetic anhydride] and biochemical (e.g., unfolding of cytochrome c) reactions in real time, where chelation complexes, reaction intermediates, and protein conformation changes were observed.

CONCLUSIONS

GS-ESI-MS is a very simple modification of the ESI technique that does not require sample delivery pumps or nebulizer gases. It is particularly suitable for the analysis of liquid samples and the real-time monitoring of inorganic/organic chemical or biochemical reactions.

An improved rapid mixing device for time-resolved electrospray mass spectrometry measurements

Time series data can provide valuable insight into the complexity of biological reactions. Such information can be obtained by mass-spectrometry-based approaches that measure pre-steady-state kinetics. These methods are based on a mixing device that rapidly mixes the reactants prior to the on-line mass measurement of the transient intermediate steps. Here, we describe an improved continuous-flow mixing apparatus for real-time electrospray mass spectrometry measurements. Our setup was designed to minimize metal–solution interfaces and provide a sheath flow of nitrogen gas for generating stable and continuous spray that consequently enhances the signal-to-noise ratio. Moreover, the device was planned to enable easy mounting onto a mass spectrometer replacing the commercial electrospray ionization source. We demonstrate the performance of our apparatus by monitoring the unfolding reaction of cytochrome C, yielding improved signal-to-noise ratio and reduced experimental repeat errors.

Mass spectrometry-based approaches to protein–ligand interactions

One of the greatest current challenges in proteomics is to develop an understanding of cellular communication and regulation processes, most of which involve noncovalent interactions of proteins with various binding partners. Mass spectrometry plays an important role in all aspects of these research efforts. This article provides a survey of mass spectrometry-based approaches for exploring protein-ligand interactions. A wide array of techniques is available, and the choice of method depends on the specific problem at hand. For example, the high-throughput screening of compound libraries for binding to a specific receptor requires different approaches than structural studies on multiprotein complexes. This review is directed to readers wishing to obtain a concise yet comprehensive overview of existing experimental techniques. Specific emphasis is placed on emerging methods that have been developed within the last few years.

Noncovalent mass spectrometry for the characterization of antibody/antigen complexes

Monoclonal antibodies (mAbs) have taken on an increasing importance for the treatment of various diseases including cancers, immunological disorders, and other pathologies. These large biomolecules display specific structural features, which affect their efficiency and need therefore to be extensively characterized using sensitive and orthogonal analytical techniques. Among them, mass spectrometry (MS) has become the method of choice to study mAb amino acid sequences as well as their posttranslational modifications with the aim of reducing their chemistry, manufacturing, and control liabilities. This chapter will provide the reader with a description of the general approach allowing antibody/antigen systems to be characterized by noncovalent MS. In the present chapter, we describe how recent noncovalent MS technologies are used to characterize immune complexes involving both murine and humanized mAb 6F4 directed against human JAM-A, a newly identified antigenic protein (Ag) over-expressed in tumor cells. We will detail experimental conditions (sample preparation, optimization of instrumental parameters, etc.) required for the detection of noncovalent antibody/antigen complexes by MS. We will then focus on the type and the reliability of the information that we get from noncovalent MS data, with emphasis on the determination of the stoichiometry of antibody/antigen systems. Noncovalent MS appears as an additional supporting technique for therapeutic mAbs lead characterization and development.

Ascorbic acid for homogenous redox buffering in electrospray ionization-mass spectrometry

Electrospray ionization (ESI) involves the dispersion of a liquid containing analytes of interest into a fine aerosol by applying a high potential difference to the sample solution with respect to a counter electrode. Thus, from the electrochemical point of view, the ESI source represents a two-electrode controlled-current electrochemical flow cell. The electroactive compounds part of the solvent sprayed may be altered by occurring electrolysis (oxidation in positive ion mode and reduction in negative ion mode). These reactions can be troublesome in the context of unknown identification and quantification. In the search for a simple, inexpensive, and efficient way to suppress electrochemical oxidation in positive ESI, the usability of ascorbic acid, hydroquinone, and glutathione for homogenous redox buffering was tested. Performance of the antioxidants was assessed by analyzing pharmaceutical compounds covering a broad range of functional groups prone to oxidation. Different emitter setups were applied for continuous infusion, flow injection, and liquid chromatography/mass spectrometry experiments. Best performance was obtained with ascorbic acid. In comparison to hydroquinone and glutathione, ascorbic acid offered superior antioxidant activity, a relatively inert oxidation product, and hardly any negative effect on the ionization efficiency of analytes. Furthermore, ascorbic acid suppressed the formation of sodiated forms and was able to induce charge state reduction. Only in the very special case of analyzing a compound isobaric to ascorbic acid, interference with the low-abundant [ascorbic acid+H](+) signal may become a point of attention.

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.

Formation of iron complexes from trifluoroacetic acid based liquid chromatography mobile phases as interference ions in liquid chromatography/electrospray ionization mass spectrometric analysis

Two unexpected singly charged ions at m/z 1103 and 944 have been observed in mass spectra obtained from electrospray ionization mass spectrometric analysis of liquid chromatography effluents with mobile phases containing trifluoroacetic acid (TFA) that severely interfered with sample analysis. Accurate mass measurement and tandem mass spectrometry studies revealed that these two ions are composed of three components; clusters of trifluoroacetic acid, clusters of mass 159 and iron. Formation of these ions is inhibited by removing TFA from the mobile phases and using formic acid in its place, replacing the stainless steel union with a titanium union or by adding a small blank fused-silica capillary column between the chromatography column and the electrospray tip via a stainless steel union without any adverse effects to chromatographic separation, peak broadening or peptide identifications.

Compact conformations of α-synuclein induced by alcohols and copper

The intrinsically disordered protein α-synuclein aggregates into amyloid fibrils, a process known to be implicated in several neurodegenerative states. Partially folded forms of the protein are thought to trigger the aggregation process. Here, α-synuclein conformers are characterized by analysis of the charge-state distributions observed in electrospray-ionization mass spectrometry under negative-ion mode. It is found that, even at neutral pH, a small fraction of the molecular population is in a compact conformation. Several distinct partially folded forms are then identified under conditions that promote α-synuclein aggregation, such as solutions of simple and fluorinated alcohols. Specific intermediates accumulate at increasing concentrations of ethanol, hexafluoro-2-propanol, and trifluoroethanol. Finally, extensive folding induced by Cu(2+) binding is revealed by titrations in the presence of Cu(2+)-glycine. The data confirm the existence of a single, high-affinity binding site for Cu(2+). Because accumulation of this partially folded form correlates with enhancement of fibrillation kinetics, it is likely to represent an amyloidogenic intermediate in α-synuclein conformational transitions.

Protein-protein binding affinities in solution determined by electrospray mass spectrometry

Electrospray ionization (ESI) allows the transfer of multi-protein complexes into the gas phase, thereby providing a simple approach for monitoring the stoichiometry of these noncovalent assemblies by mass spectrometry (MS). It remains unclear, however, whether the measured ion abundance ratios of free and bound species are suitable for determining solution-phase binding affinities (K(d) values). Many types of mass spectrometers employ rf-only quadrupoles as ion guides. This work demonstrates that the settings used for these devices are a key factor for ensuring uniform transmission behavior, which is a prerequisite for meaningful affinity measurements. Using bovine β-lactoglobulin and hemoglobin as model systems, it is demonstrated that under carefully adjusted conditions the "direct" ESI-MS approach is capable of providing K(d) values that are in good agreement with previously published solution-phase data. Of the several ion sources tested, a regular ESI emitter operated with pressure-driven flow at 1 μL min(-1) provided the most favorable results. Potential problems in these experiments include conformationally-induced differences in ionization efficiencies, inadvertent collision-induced dissociation, and ESI-induced clustering artifacts. A number of simple tests can be conducted to assess whether or not these factors are prevalent under the conditions used. In addition, the fidelity of the method can be scrutinized by performing measurements over a wide concentration range. Overall, this work supports the viability of the direct ESI-MS approach for determining binding affinities of protein-protein complexes in solution.

Real-time reaction monitoring by probe electrospray ionization mass spectrometry

Probe electrospray ionization (PESI) is a modified version of the electrospray ionization (ESI), where the capillary for sampling and spraying is replaced by a solid needle. High tolerance to salts and direct ambient sampling are major advantages of PESI compared with conventional ESI. In this study, PESI-MS was used to monitor some biological and chemical reactions in real-time, such as acid-induced protein denaturation, hydrogen/deuterium exchange (HDX) of peptides, and Schiff base formation. By using PESI-MS, time-resolved mass spectra and ion chromatograms can be obtained reproducibly. Real-time PESI-MS monitoring can give direct and detailed information on each chemical species taking part in reactions, and this is valuable for a better understanding of the whole reaction process and for the optimization of reaction parameters. PESI-MS can be considered as a potential tool for real-time reaction monitoring due to its simplicity in instrumental setup, direct sampling with minimum sample preparation and low sample consumption.

Minimizing analyte electrolysis in electrospray ionization mass spectrometry using a redox buffer coated emitter electrode

An emitter electrode with an electroactive poly(pyrrole) (PPy) polymer film coating was constructed for use in electrospray ionization mass spectrometry (ESI-MS). The PPy film acted as a surface-attached redox buffer limiting the interfacial potential of the emitter electrode. While extensive oxidation of selected analytes (reserpine and amodiaquine) was observed in positive ion mode ESI using a bare metal (gold) emitter electrode, the oxidation was suppressed for these same analytes when using the PPy-coated electrode. A semi-quantitative relationship between the rate of oxidation observed and the interfacial potential of the emitter electrode was shown. The redox buffer capacity, and therefore the lifetime of the redox buffering effect, correlated with the oxidation potential of the analyte and with the magnitude of the film charge capacity. Online reduction of the PPy polymer layer using negative ion mode ESI between analyte injections was shown to successfully restore the redox buffering capacity of the polymer film to its initial state.

Electrochemical aspects of electrospray and laser desorption/ionization for mass spectrometry

Soft-ionization methods, namely electrospray ionization and laser desorption/ionization, are widely used to transfer large molecules as intact gas-phase ions either from a solution or from a solid substrate. During both processes, in-source electrochemical and photoelectrochemical reactions occur. These electrode reactions, which take place at interfaces, play important roles in influencing the ionization products, but they have received little attention. We show that having good control over both types of electrochemical reactions can lead to new analytical applications. Examples include online tagging by grafting of mass tags and in-source photooxidation of peptides.

Nanoscale patterns of oligonucleotides formed by electrohydrodynamic jet printing with applications in biosensing and nanomaterials assembly

The widespread use of DNA in microarrays for applications in biotechnology, combined with its promise in programmed nanomaterials assembly, unusual electronic devices, and other areas has created interest in methods for patterning DNA with high spatial resolution. Techniques based on thermal or piezoelectric inkjet printing are attractive due to their noncontacting nature and their compatibility with diverse materials and substrate types; their modest resolution (i.e., 10-20 microm) represents a major limitation for certain systems. Here we demonstrate the use of an operationally similar printing approach that exploits electrohydrodynamic forces, rather than thermal or acoustic energy, to eject DNA inks through fine nozzles, in a controlled fashion. This DNA printer is capable of resolution approaching 100 nm. A range of experiments on patterns of DNA formed with this printer demonstrates its key features. Example applications in DNA-directed nanoparticle assembly and DNA aptamer-based biosensing illustrate two representative uses of the patterns that can be formed.

Conformational and noncovalent complexation changes in proteins during electrospray ionization

Electrospray ion sources efficiently produce gas-phase ions from proteins and their noncovalent complexes. Charge-state distributions of these ions are increasingly used to gauge their conformations in the solution phase. Here we investigate how this correlation is affected by the spraying conditions at the early stage of droplet generation, prior to the ionization process. We followed the folding behavior of model proteins cytochrome c and ubiquitin and the dissociation of the noncovalent holomyoglobin complex. Spray current measurements, fast Taylor cone imaging, and mass analysis of the generated ions indicated that the protein structure experienced conformational or complexation changes upon variations in the spraying mode of the electrospray ionization source. These effects resulted in a departure from the original secondary, tertiary, and quaternary structure of proteins, possibly introducing artifacts in related studies. Therefore, if a particular gas-phase ion conformation is required or correlations with the liquid-phase conformations are studied, it is advantageous to maintain a particular spraying mode. Alternatively, spraying mode-induced changes can be utilized to alter the structure of proteins in, for example, time-resolved experiments for the study of protein folding dynamics.

Monitoring copopulated conformational states during protein folding events using electrospray ionization-ion mobility spectrometry-mass spectrometry

The precise mechanism of protein folding remains elusive and there is a deficiency of biophysical techniques that are capable of monitoring the individual behavior of copopulated protein conformers during the folding process. Herein, an ion mobility spectrometry (IMS) device integrated with electrospray ionization mass spectrometry (ESI-MS) has been used to successfully separate and analyze protein conformers differing in cross section and/or charge state. In an initial test, an ensemble of folded and partially folded conformers of the protein cytochrome c was separated. A detailed study undertaken on the amyloidogenic protein beta(2)-microglobulin (beta(2)m), which forms fibrils by protein unfolding followed by self-aggregation and is responsible for the disease dialysis-related amyloidosis, has generated important insights into its folding landscape. Initially, a systematic titration of beta(2)m over the pH range 2 to 7 using ESI-IMS-MS allowed individual conformers to be monitored and quantified throughout the acid denaturation process. Furthermore, a comparison of wild-type beta(2)m with single and double amino acid variants with a range of folding stabilities and propensities for amyloid fibril formation has provided illuminating evidence of the role of different conformers in protein stability and amyloidogenic aggregation. The ESI-IMS-MS data presented here not only demonstrate an important and informative further dimension to ESI-MS, but also illustrate the potential of the ESI-IMS-MS technique for unravelling protein folding enigmas in general and studying protein misfolding diseases in particular.

Spraying mode effect on droplet formation and ion chemistry in electrosprays

Depending on the spraying conditions and fluid properties, a variety of electrospray regimes exists. Here we explore the changes in ion production that accompany the transitions among the three axial spraying modes, the burst mode, the pulsating Taylor cone mode, and the cone-jet mode. Spray current oscillation and phase Doppler anemometry measurements, fast imaging of the electrified meniscus, and mass spectrometry are utilized to study the formation, size, velocity, and chemical composition of droplets produced in the three modes. High-speed images indicate that the primary droplets are produced by varicose waves and lateral kink instabilities on the liquid jet emerging from the Taylor cone, whereas secondary droplets are formed by fission. Dramatic changes in the droplet size distributions result from the various production and breakup mechanisms observed at different emitter voltages and liquid flow rates. We demonstrate that droplet fission can be facilitated by space charge effects along the liquid jet and in the plume. Compared to the other two regimes, a significantly enhanced signal-to-noise ratio, a lower degree of analyte oxidation, and milder fragmentation are observed for the cone-jet mode.

Oxidation artifacts in the electrospray mass spectrometry of Abeta Peptide

Gradual corrosion of stainless steel electrospray emitters under conditions of normal use generates surface irregularities that can promote electrical discharge. The increased emission current affects the electrochemical reactions associated with the spray process. When sampling the peptide Abeta(1-40), this is manifest by oxidation of methionine at position 35 to methionine sulfoxide. The resultant mass shift and reduced sensitivity can adversely affect H/D exchange experiments. These effects can be avoided by adding a redox buffer or (preferably) by repolishing the emitter, especially to a rounded geometry.