Sample Flow Rate Scan in Electrospray Ionization Mass Spectrometry Reveals Alterations in Protein Charge State Distribution

Moderate Signal Enhancement in Electrospray Ionization Mass Spectrometry by Focusing Electrospray Plume with a Dielectric Layer around the Mass Spectrometer's Orifice

Electrospray ionization (ESI) is among the commonly used atmospheric pressure ionization techniques in mass spectrometry (MS). One of the drawbacks of ESI is the formation of divergent plumes composed of polydisperse microdroplets, which lead to low transmission efficiency. Here, we propose a new method to potentially improve the transmission efficiency of ESI, which does not require additional electrical components and complex interface modification. A dielectric plate-made of ceramic-was used in place of a regular metallic sampling cone. Due to the charge accumulation on the dielectric surface, the dielectric layer around the MS orifice distorts the electric field, focusing the charged electrospray cloud towards the MS inlet. The concept was first verified using charge measurement on the dielectric material surface and computational simulation; then, online experiments were carried out to demonstrate the potential of this method in MS applications. In the online experiment, signal enhancements were observed for dielectric plates with different geometries, distances of the electrospray needle axis from the MS inlet, and various compounds. For example, in the case of acetaminophen (15 μM), the signal enhancement was up to 1.82 times (plate B) using the default distance of the electrospray needle axis from the MS inlet (d = 1.5 mm) and 12.18 times (plate C) using a longer distance (d = 7 mm).

Uncovering Distinct Peptide Charging Behaviors in Electrospray Ionization Mass Spectrometry Using a Large-Scale Dataset

Electrospray ionization is a powerful and prevalent technique used to ionize analytes in mass spectrometry. The distribution of charges that an analyte receives (charge state distribution, CSD) is an important consideration for interpreting mass spectra. However, due to an incomplete understanding of the ionization mechanism, the analyte properties that influence CSDs are not fully understood. Here, we employ a machine learning-based approach and analyze CSDs of hundreds of thousands of peptides. Interestingly, half of the peptides exhibit charges that differ from what one would naively expect (the number of basic sites). We find that these peptides can be classified into two regimes (undercharging and overcharging) and that these two regimes display markedly different charging characteristics. Notably, peptides in the overcharging regime show minimal dependence on basic site count, and more generally, the two regimes exhibit distinct sequence determinants. These findings highlight the rich ionization behavior of peptides and the potential of CSDs for enhancing peptide identification.

Collision-Induced Unfolding, Tandem MS, Bottom-up Proteomics, and Interactomics for Identification of Protein Complexes in Native Surface Mass Spectrometry

Endogenously occurring salts and nonvolatile matrix components in untreated biological surfaces can suppress protein ionization and promote adduct formation, challenging protein identification. Characterization of labile proteins within biological specimens is particularly demanding because additional purification or sample treatment steps can be time-intensive and can disrupt noncovalent interactions. It is demonstrated that the combined use of collision-induced unfolding, tandem mass spectrometry, and bottom-up proteomics improves protein characterization in native surface mass spectrometry (NSMS). This multiprong analysis is achieved by acquiring NSMS, MS/MS, ion mobility (IM), and bottom-up proteomics data from a single surface extracted sample. The validity of this multiprong approach was confirmed by the successful characterization of nine surface-deposited proteins, with molecular weights ranging from 8 to 147 kDa, in two separate mixtures. Bottom-up proteomics provided a list of proteins to match against observed proteins in NSMS and their detected subunits in tandem MS. The method was applied to characterize endogenous proteins from untreated chicken liver samples. The subcapsular liver sampling for NSMS analysis allowed for the detection of endogenous proteins with molecular weights of up to ∼220 kDa. Moreover, using IM-MS, collision cross sections and collision-induced unfolding pathways of enzymatic proteins and protein complexes of up to 145 kDa were obtained.

Observation of Protein Unfolding during pH Ramp Evoked by Lipase-Catalyzed Ester Hydrolysis

Studies of protein folding often involve offline experimental methods such as titrating protein samples with denaturants or equilibrating them in the presence of denaturants. Here, we demonstrate an online analytical approach in which the protein structure is perturbed by a pH ramp evoked by immobilized lipase-catalyzed ester hydrolysis. Changes in the tertiary structure of the protein in response to a pH ramp (from approximately 6.3 to 2.8) are monitored using electrospray ionization mass spectrometry and spectrofluorometry. Interestingly, we discovered a side reaction of ammonium and formate leading to the production of cyanide that occurred during the ionization process. We also found that only certain protein analytes were bound to the formed cyanide species. Nevertheless, this problem was readily overcome by carefully selecting a specific ester substrate. Overall, the alterations in the charge-state distribution and fluorescence intensity─caused by the lipase-induced pH ramp─reveal conformational transitions in different proteins. In line with previous reports, the acid-induced denaturation of holo-myoglobin occurs through a two-step mechanism, which is supported by identification of protein-unfolding intermediates and the loss of noncovalent protein ligand (heme). The results─obtained using the developed catalytic method─are also consistent with the results of equilibrium-based experiments, while sample preparation steps are substantially reduced. The proposed approach simplifies the identification of the pH range that has the greatest impact on the protein structure. Thus, it has the potential to be a useful tool for studying protein conformational transitions in the course of pH changes.

Are Most Micrometer Droplets (>10 μm) Wasted in Electrospray Ionization? An Insight from Real-Time High-Speed Imaging

Electrospray ionization (ESI) is one of the main techniques used in mass spectrometry (MS) of nonvolatile compounds. ESI is a disordered process, in which a large number of polydisperse droplets are projected from a fluctuating Taylor cone and jet protruding ESI emitter. Here, we disclose a system for sectioning electrospray plumes to discrete packets with millisecond and submillisecond lifetime, which are introduced to the MS orifice, one at a time. A high-speed camera was triggered at 10,000 frames per second to capture consecutive images of the electrospray packets transmitted to the mass spectrometer. We further correlated the high-speed images of electrospray packets with MS signals of a test analyte (acetaminophen). Following computational treatment of the images, we determined the number of droplet observations (<300), average diameter of droplets (∼10-20 μm), and average volume of droplets (few tens of picoliters) in the individual electrospray packets. The result shows that most micrometer droplets (>10 μm) do not have any significant contribution to the MS signals. This finding is in agreement with the prior conjecture that most of the MS signals are mainly attributed to nanodroplets. Based on this finding, one can deduce that only a small number of the initial microdroplets effectively carry analyte molecules that undergo ionization. We discuss that, in future, one may propose a way to "recharge" the emitted initial micrometer droplets to increase the efficiency of conventional ESI setups.

A native multi-dimensional monitoring workflow for at-line characterization of mAb titer, size, charge, and glycoform heterogeneities in cell culture supernatant

With growing maturity of the biopharmaceutical industry, new modalities entering the therapeutic design space and increasing complexity of formulations such as combination therapy, the demands and requirements on analytical workflows have also increased. A recent evolution in newer analytical workflows is that of multi-attribute monitoring workflows designed on chromatography-mass spectrometry (LC-MS) platform. In comparison to traditional one attribute per workflow paradigm, multi-attribute workflows are designed to monitor multiple critical quality attributes through a single workflow, thus reducing the overall time to information and increasing efficiency and throughput. While the 1^st generation multi-attribute workflows focused on bottom-up characterization following peptide digestion, the more recent workflows have been focussing on characterization of intact biologics, preferably in native state. So far intact multi-attribute monitoring workflows suitable for comparability, utilizing single dimension chromatography coupled with MS have been published. In this study, we describe a native multi-dimensional multi-attribute monitoring workflow for at-line characterization of monoclonal antibody (mAb) titer, size, charge, and glycoform heterogeneities directly in cell culture supernatant. This has been achieved through coupling ProA in series with size exclusion chromatography in 1^st dimension followed by cation exchange chromatography in the 2^nd dimension. Intact paired glycoform characterization has been achieved through coupling 2D-LC with q-ToF-MS. The workflow with a single heart cut can be completed in 25 mins and utilizes 2D-liquid chromatography (2D-LC) to maximize separation and monitoring of titer, size as well as charge variants.

A high-throughput approach reveals distinct peptide charging behaviors in electrospray ionization mass spectrometry

Electrospray ionization is a powerful and prevalent technique used to ionize analytes in mass spectrometry. The distribution of charges that an analyte receives (charge state distribution, CSD) is an important consideration for interpreting mass spectra. However, due to an incomplete understanding of the ionization mechanism, the analyte properties that influence CSDs are not fully understood. Here, we employ a machine learning-based high-throughput approach and analyze CSDs of hundreds of thousands of peptides. Interestingly, half of the peptides exhibit charges that differ from what one would naively expect (number of basic sites). We find that these peptides can be classified into two regimes-undercharging and overcharging-and that these two regimes display markedly different charging characteristics. Strikingly, peptides in the overcharging regime show minimal dependence on basic site count, and more generally, the two regimes exhibit distinct sequence determinants. These findings highlight the rich ionization behavior of peptides and the potential of CSDs for enhancing peptide identification.

Native Mass Spectrometry and Collision-Induced Unfolding of Laser-Ablated Proteins

Infrared laser ablation sample transfer (LAST) was used to collect samples from solid surfaces for mass spectrometry under native spray conditions. Native mass spectrometry was utilized to probe the charge states and collision-induced unfolding (CIU) characteristics of bovine serum albumin (BSA), bovine hemoglobin (BHb), and jack-bean concanavalin A (ConA) via direct injection electrospray, after liquid extraction surface sampling, and after LAST. Each protein was deposited from solution on solid surfaces and laser-ablated for off-line analysis or sampled for online analysis. It was found that the protein ion gas-phase charge-state distributions were comparable for direct infusion, liquid extraction, and laser ablation experiments. Moreover, calculated average collision cross section (CCS) values from direct injection, liquid extraction, and laser ablation experiments were consistent with previously reported literature values. Additionally, an equivalent number of mobility features and conformational turnovers were identified from unfolding pathways from all three methods for all charge states of each protein analyzed in this work. The presented work suggests that laser ablation yields intact proteins (BSA, BHb, and ConA), is compatible with native mass spectrometry, and could be suitable for spatially resolved interrogation of unfolding pathways of proteins.

Tuning Electrospray Ionization with Low-Frequency Sound

Electrospray ionization (ESI) mass spectrometry (MS) is one of the key techniques used in biomolecular analysis nowadays. It relies on formation of polydisperse microdroplets, which undergo desolvation and liberate ions to the gas phase. Here we demonstrate low-frequency-sound-modulated ESI for analysis of biomolecules. By using a low-frequency (50-350 Hz) sound, it is possible to deflect electrospray microdroplets toward the mass spectrometer's orifice. Microdroplets of different sizes are deflected to a different extent leading to a partial size segregation. This effect leads to either an increase or decrease of MS signal intensity as well as signal-to-noise ratio. It also affects the selectivity of the ESI-MS analysis. The observations are rationalized by taking into account different pathways of ion formation and the likelihood of deflecting microdroplets of certain size. The online ESI-MS observations are supported with offline shadowgraphs obtained at varied sound frequencies, signal amplitudes, and phase shifts.

Investigation on the binary ionization choices for large conjugated amines during electrospray ionization

RATIONALE

Generally, amines form protonated cations ([M + H]⁺ ) in positive polarity during electrospray ionization (ESI). However, it was found that large conjugated amines (LCAs) had binary ionization choices of generating either radical cations (M^•+ ) or [M + H]⁺ during ESI. Investigation on the mechanism would further our understanding of ESI.

METHODS

In this work, the binary ionization behavior of LCAs was reported and studied. Internal factors (functional groups and sizes of conjugated systems) and external factors (solvent type, flow rate, and electrode position) were systematically investigated and discussed.

RESULTS

For the internal factors, electron-donating groups and large conjugated structures of LCAs were conducive to the generation of M^•+ . For the external factors, aprotic solvent, higher flow rate, and shorter distance from the electrode to the spray cone facilitated the formation of M^•+ but hampered the generation of [M + H]⁺ .

CONCLUSION

The present study illustrated that the formations of M^•+ and [M + H]⁺ for LCAs were two independent processes. The M^•+ cations of LCAs were formed on the surface of the electrode through electrochemical oxidation, whereas the [M + H]⁺ cations were generated following the typical ESI evolution process. By regulating the external factors, the ionization results of LCAs could be well modulated.

Ammonium Bicarbonate Significantly Accelerates the Microdroplet Reactions of Amines with Carbon Dioxide

The reactions between amines and carbon dioxide (CO₂) are among the most commonly used and important carbon fixation reactions at present. Microdroplets generated by electrospray ionization (ESI) have been proved to increase the conversion ratio (R_C) of amines. In this work, we confirmed that the presence of ammonium bicarbonate (NH₄HCO₃) in ESI microdroplets significantly increased the R_C of amines. The R_C went up remarkably with the increase in the concentration of NH₄HCO₃ from 0.5 to 20 mM. The R_C of N,N-dibutyl-1,3-propanediamine (DBPA) reached 93.7% under 20 mM NH₄HCO₃, which was significantly higher than previous reports. The rise in R_C became insignificant when the concentration of NH₄HCO₃ was increased beyond 20 mM. Further investigations were made on the mechanism of the phenomenon. According to the results, it was suggested that NH₄HCO₃ decomposed into CO₂ and formed microbubbles within the microdroplets of ESI. The microbubbles acted as direct internal CO₂ sources. The conversion reactions occurred at the liquid-gas interface. The formation of CO₂ microbubbles remarkably increased the total area of the interface, thus promoting the conversion reactions. ¹³C-labeled experiments confirmed that NH₄HCO₃ acted as an internal CO₂ source. Factors that influenced the R_C of the reaction were optimized. Pure water was proved to be the optimal solvent. Lower temperature of the mass spectrometer's entrance capillary was beneficial to the stabilization of the product carbamic acids. The sample flow rate of ESI was crucial to the R_C. It determined the initial sizes of the microdroplet. Lower flow rates ensured higher R_C of amines. The present work implied that NH₄HCO₃ could be a superior medium for CO₂ capture and utilization. It might offer an alternative choice for future CO₂ conversion research studies. In addition, our study also provided evidence that NH₄HCO₃ decomposed and generated microbubbles in the droplets during ESI. Attention should be paid to this when using NH₄HCO₃ as an additive in mass spectrometry-based analysis.

Nested-channel for on-demand alternation between electrospray ionization regimes

On-demand electrospray ionization from different liquid channels in the same emitter was realized using filamented capillary and gas phase charge supply. The solution sub-channel was formed when back-filling solution to the emitter tip by capillary action along the filament. Gas phase charge carriers were used to trigger electrospray ionization from the solution meniscus at the tip. The meniscus at the tip opening may be fully filled or partially empty to generate electrospray ionization in main-channel regime and sub-channel regime, respectively. For emitters with 4 μm tip opening, the two nested electrospray (nested-ESI) channels accommodated ESI flow rates ranging from 50 pL min⁻¹ to 150 nL min⁻¹. The platform enabled on-demand regime alternations within one sample run, in which the sub-channel regime generated smaller charged droplets. Ionization efficiencies for saccharides, glycopeptide, and proteins were enhanced in the sub-channel regime. Non-specific salt adducts were reduced and identified by regime alternation. Surprisingly, the sub-channel regime produced more uniform responses for a peptide mixture whose relative ionization efficiencies were insensitive to ESI conditions in previous picoelectrospray study. The nested channels also allowed effective washing of emitter tip for multiple sampling and analysis operations.

Nested electrospray ionization alternates on-demand between microscale main-channel and nanscale sub-channels.