Formation of Gaseous Peptide Ions from Electrospray Droplets: Competition between the Ion Evaporation Mechanism and Charged Residue Mechanism

Characterizing Protein Solvent Accessible Surface Area in Solution by Dual Polarity Native Mass Spectrometry

Native mass spectrometry (nMS) is rapidly emerging as a pivotal technique for exploring protein conformations and protein-ligand interactions. Pioneering research has demonstrated that the charge state distribution (CSD) of proteins in native mass spectra can be indicative of their solvent accessible surface area (SASA). Moreover, beyond SASA, it is postulated that the abundance of acidic and basic amino acids on the protein surface may also impact the CSD. Specifically, basic amino acids tend to acquire positive charges during electrospray ionization (ESI), whereas acidic amino acids are prone to adopting negative charges. Consequently, this study investigates the CSDs of globular proteins in both positive and negative ion modes to provide a comprehensive characterization of protein SASA. Experiments were conducted under both native ESI and native nano-ESI conditions. By harnessing the average charges observed across dual polarity nMS data, we achieved significantly enhanced log linear correlations between protein SASA and its CSDs. The coefficient of determination (R2) improved from 0.9866 to 0.9888 under ESI conditions and from 0.9677 to 0.9902 under nano-ESI conditions when compared to models utilizing only positive ion mode data. These findings suggest that the SASA of globular proteins can be effectively characterized through the CSDs derived from dual polarity nMS analysis.

Thermometer Ions, Internal Energies, and In-Source Fragmentation in Ambient Ionization

Ionization and fragmentation are at the core of mass spectrometry. But they are not necessarily separated in space, as in-source fragmentation can also occur. Here, we survey the literature published since our 2005 review on the internal energy and fragmentation in electrospray ionization sources. We present new thermometer molecules to diagnose and quantify source heating, provide tables of recommended threshold (E0) and appearance energies (Eapp) for the survival yield method, and attempt to compare the softness of a variety of ambient pressure ionization sources. The droplet size distribution and desolvation dynamics play a major role: lower average internal energies are obtained when the ions remain protected by a solvation shell and spend less time nakedly exposed to activating conditions in the transfer interface. Methods based on small droplet formation without charging can thus be softer than electrospray. New dielectric barrier discharge sources can gas-phase ionize small molecules while conferring barely more internal energy than electrospray ionization. However, the tuning of the entire source interface often has an even greater influence on ion internal energies and fragmentation than on the ionization process itself. We hope that this review will facilitate further research to control and standardize in-source ion activation conditions, and to ensure the transferability of data and research results in mass spectrometry.

MD Simulations of Peptide-Containing Electrospray Droplets: Effects of Parameter Settings on the Predicted Mechanisms of Gas Phase Ion Formation

Electrospray ionization (ESI) mass spectrometry is widely used for interrogating peptides, proteins, and other biomolecular analytes. A growing number of laboratories use molecular dynamics (MD) simulations for uncovering ESI mechanisms by modeling the behavior of highly charged nanodroplets. The outcome of any MD simulation depends on certain assumptions and parameter settings, and it is desirable to optimize these factors by benchmarking computational data against experiments. Unfortunately, benchmarking of ESI simulations is difficult because experimentally generated gaseous ions do not generally retain any features that would reveal their formation pathway [e.g., the charged residue mechanism (CRM) or the ion evaporation mechanism (IEM)]. Here, we tackle this problem by examining the effects of various MD settings on the ESI behavior of the 9-residue peptide bradykinin in acidic aqueous droplets. Several parameters were found to significantly affect the kinetic competition between peptide IEM and CRM. By systematically probing the droplet behavior, we uncovered problems associated with certain settings, including peptide/solvent temperature imbalances, unexpected peptide deceleration during IEM, and a dependence of the ESI mechanism on the water model. We also noted different simulation outcomes for different force fields. On the basis of comprehensive tests, we propose a set of "best practice" parameter settings for MD simulations of ESI droplets. The strategies used here should be transferable to other types of droplet simulations, paving the way toward a more solid understanding of ESI mechanisms.

Spontaneous Recycling of Electrosprayed Sample by Retrograde Motion of Microdroplets

Here, we discuss an interesting phenomenon occurring spontaneously near the sample liquid meniscus at the tip of the electrospray emitter. While most ejected droplets move from the emitter tip toward the counter electrode, some of the droplets decelerate and move backward to the liquid meniscus. When they hit the surface of the liquid meniscus, they either merge with the bulk liquid or get recharged during intermittent contact with the liquid meniscus and immediately reaccelerate toward the counter electrode. In some cases, while in contact with the meniscus they spontaneously form a secondary Taylor cone and emit progeny droplets. This observation suggests that the amount of electric charge transferred to such a droplet is sufficient to surpass the Rayleigh limit. Similar effects were previously observed for water as well as for NaCl-water and ethanol-water mixtures. However, here we observed it for electrolyte solutions commonly used in electrospray ionization mass spectrometry: methanol-water solutions with the addition of ammonium acetate, formic acid, or ammonium hydroxide. The reported phenomenon reveals the ongoing recycling of sample liquid in electrosprays. Such recycling can contribute to enhancement of sample utilization efficiency in electrospray ionization.

High-Speed Schlieren Imaging of Vapor Formation in Electrospray Plume

Previous mechanistic descriptions of electrosprays mostly focused on the dynamics of Taylor cones, initial droplets, and progeny droplets. However, vapor formation during droplet desolvation in an electrospray plume has not been discussed to a great extent. Here, we implement a double-pass on-axis schlieren high-speed imaging system to observe generation and propagation of vapors in an offline electrospray source under different conditions. Switching between turbulent and laminar vapor flow was observed for all of the scanned conditions, which may be attributed to randomly occurring disturbances in the sample flow inside the electrospray emitter. Calculation of mean vapor flow velocity and analysis of vapor flow patterns were performed using in-house developed image processing programs. Experiments performed at different electrospray voltages (0-6 kV), solvent flow rates (100-600 μL min-1), and methanol concentrations (50-100%), indicate only a weak dependency between electrospray voltage and mean vapor velocity, implying that the vapor is mostly neutral; thus, the vapor is not accelerated by electric field. On the other hand, electrospraying solutions of analytes (with mass 151 Da or 12 kDa) did not remarkably increase the overall vapor flow velocity. The source of vapor's velocity is attributed to the inertia of the electrospray droplets. Although there are some differences between a modern electrospray ionization (ESI) setup and the setup used in our experiment (e.g., using a higher flow rate and larger emitter), we believe the findings of our study can be projected to a modern ESI setup.

Dynamics of Rayleigh Fission Processes in ∼100 nm Charged Aqueous Nanodrops

Fission of micron-size charged droplets has been observed using optical methods, but little is known about fission dynamics and breakup of smaller nanosize droplets that are important in a variety of natural and industrial processes. Here, spontaneous fission of individual aqueous nanodrops formed by electrospray is investigated using charge detection mass spectrometry. Fission processes ranging from formation of just two progeny droplets in 2 ms to production of dozens of progeny droplets over 100+ ms are observed for nanodrops that are charged above the Rayleigh limit. These results indicate that Rayleigh fission is a continuum of processes that produce progeny droplets that vary widely in charge, mass, and number.

Supercritical Fluid Nanospray Mass Spectrometry: II. Effects on Ionization

Nanospraying supercritical fluids coupled to a mass spectrometer (nSF-MS) using a 90% supercritical fluid CO₂ carrier (sCO₂) has shown an enhanced desolvation compared to traditional liquid eluents. Capillaries of 25, 50, and 75 μm internal diameter (i.d.) with pulled emitter tips provided high MS detection sensitivity. Presented here is an evaluation of the effect of proton affinity, hydrophobicity, and nanoemitter tip size on the nSF-MS signal. This was done using a set of primary, secondary, tertiary, and quaternary amines with butyl, hexyl, octyl, and decyl chains as analytes. Each amine class was analyzed individually to evaluate hydrophobicity and proton affinity effects on signal intensity. The system has shown a mass sensitive detection on a linear dynamic range of 0.1-100 μM. Results indicate that hydrophobicity has a larger effect on the signal response than proton affinity. Nanospraying a mixture of all amine classes using the 75 μm emitter has shown a quaternary amine signal not suppressed by competing analytes. Competing ionization was observed for primary, secondary, and tertiary amines. The 75 and 50 μm emitters demonstrated increased signal with increasing hydrophobicity. Surprisingly, the 25 μm i.d. emitter yielded a signal decrease as the alkyl chain length increased, contrary to conventional understanding. Nanospraying the evaporative fluid in a sub-500 nm emitter likely resulted in differences in the ionization mechanism. Results suggest that 90% sCO₂ with 9.99% methanol and 0.01% formic acid yielded fast desolvation, high ionization efficiency, and low matrix effect, which could benefit complex biological matrix analysis.

Atomistic Details of Peptide Reversed-Phase Liquid Chromatography from Molecular Dynamics Simulations

Peptide separations by reversed-phase liquid chromatography (RPLC) are an integral part of bottom-up proteomics. These separations typically employ C18 columns with water/acetonitrile gradient elution in the presence of formic acid. Despite the widespread use of such workflows, the exact nature of peptide interactions with the stationary and mobile phases is poorly understood. Here, we employ microsecond molecular dynamics (MD) simulations to uncover details of peptide RPLC. We examined two tryptic peptides, a hydrophobic and a hydrophilic species, in a slit pore lined with C18 chains that were grafted onto SiO₂ support. Our simulations explored peptide trapping, followed by desorption and elution. Trapping in an aqueous mobile phase was initiated by C18 contacts with Lys butyl moieties. This was followed by extensive anchoring of nonpolar side chains (Leu/Ile/Val) in the C18 layer. Exposure to water/acetonitrile triggered peptide desorption in a stepwise fashion; charged sites close to the termini were the first to lift off, followed by the other residues. During water/acetonitrile elution, both peptides preferentially resided close to the pore center. The hydrophilic peptide exhibited no contacts with the stationary phase under these conditions. In contrast, the hydrophobic species underwent multiple transient Leu/Ile/Val binding interactions with C18 chains. These nonpolar interactions represent the foundation of differential peptide retention, in agreement with the experimental elution behavior of the two peptides. Extensive peptide/formate ion pairing was observed in water/acetonitrile, particularly at N-terminal sites. Overall, this work uncovers an unprecedented level of RPLC molecular details, paving the way for MD simulations as a future tool for improving retention prediction algorithms and for the design of novel column materials.