High-Pressure Electrospray Ionization Yields Supercharged Protein Complexes from Native Solutions While Preserving Noncovalent Interactions

Mass spectrometry-based methods to characterize highly heterogeneous biopharmaceuticals, vaccines, and nonbiological complex drugs at the intact-mass level

The intact-mass MS measurements are becoming increasingly popular in characterization of a range of biopolymers, especially those of interest to biopharmaceutical industry. However, as the complexity of protein therapeutics and other macromolecular medicines increases, the new challenges arise, one of which is the high levels of structural heterogeneity that are frequently exhibited by such products. The very notion of the molecular mass measurement loses its clear and intuitive meaning when applied to an extremely heterogenous system that cannot be characterized by a unique mass, but instead requires that a mass distribution be considered. Furthermore, convoluted mass distributions frequently give rise to unresolved ionic signal in mass spectra, from which little-to-none meaningful information can be extracted using standard approaches that work well for homogeneous systems. However, a range of technological advances made in the last decade, such as the hyphenation of intact-mass MS measurements with front-end separations, better integration of ion mobility in MS workflows, development of an impressive arsenal of gas-phase ion chemistry tools to supplement MS methods, as well as the revival of the charge detection MS and its triumphant entry into the field of bioanalysis already made impressive contributions towards addressing the structural heterogeneity challenge. An overview of these techniques is accompanied by critical analysis of the strengths and weaknesses of different approaches, and a brief overview of their applications to specific classes of biopharmaceutical products, vaccines, and nonbiological complex drugs.

A 3D-printed sub-atmospheric pressure electrospray ionization source for robust, facile, and flexible mass spectrometry analysis

The operation and performance of electrospray ionization (ESI) is affected by the surrounding environment. In this study, a compact sub-atmospheric pressure ESI (SAP-ESI) source was designed and fabricated using the 3D printing method. This source has a simple structure and is easy to operate, as the sample solution and auxiliary gas are continuously sucked into the source through the pressure difference. The compact and enclosed ionization chamber can reduce the fluctuation of the surrounding gas flow to ensure a remarkably stable (< 3%) electrospray. Moreover, the source can offer variable SAP conditions for ESI analysis. The yield of analyte ions increases with decreasing pressure, while the production of background ions is suppressed under these conditions. In the analysis of protein samples, SAP-ESI can increase the yield and charge state of ions, which may be due to the reduction of proton transfer between charged proteins and surrounding gas. The SAP-ESI source was then used to continuously monitor the extract aqueous solution of tea leaves, and to detect the carbendazim residues on the apple surface by coupling with the liquid extraction surface analysis technique. Experimental results demonstrate that the developed SAP-ESI is a stable, practical, and versatile ionization technique.

Development and application of a miniature mass spectrometer with continuous sub-atmospheric pressure interface and integrated ionization source

For the miniature mass spectrometer (MS) with a continuous atmospheric pressure interface (CAPI), the gas in the multi-stage chambers directly affects the performance of the instrument. In this study, a sealed ionization chamber is designed to couple with a conventional mini CAPI-MS. In this configuration, the gas environment in the first ionization chamber can be flexibly changed to regulate the gas conditions throughout the entire instrument. By studying the effect of gas pressure on the performance of the instrument, we found that the instrument shows some unique advantages when the first ionization chamber is under sub-atmospheric pressure (SAP) conditions, such as reducing the load of the vacuum pump by 40%, achieving pump-free injection for gas and liquid samples, and improving the resolution by a factor of 2 without loss of detection sensitivity. Therefore, we propose a new integrated interface called continuous sub-atmospheric pressure interface (CSAPI) for building a miniature ion trap mass spectrometer. The CSAPI specially integrates sample introduction, gas/ions interface, and ionizations, including electrospray ionization (ESI) and secondary electrospray ionization (SESI), making this system more convenient for non-professional handlers to rapidly identify or monitor target analytes in gaseous- and solution-phase samples. We also use this system to study gas composition to further improve performance, being able to achieve a 5-fold sensitivity and 2-fold resolution improvement. At last, some custom applications of the current CSAPI-MS platform are explored and demonstrated, including real-time monitoring of chemical reactions in solution and long-distance sampling and analysis of dried Chinese herbs. In conclusion, this study provides a new approach to constructing a complete, versatile and practical miniature MS instrument.

Insights into Phosphorylation-Induced Protein Allostery and Conformational Dynamics of Glycogen Phosphorylase via Integrative Structural Mass Spectrometry and In Silico Modeling

Allosteric regulation plays a fundamental role in innumerable biological processes. Understanding its dynamic mechanism and impact at the molecular level is of great importance in disease diagnosis and drug discovery. Glycogen phosphorylase (GP) is a phosphoprotein responding to allosteric regulation and has significant biological importance to glycogen metabolism. Although the atomic structures of GP have been previously solved, the conformational dynamics of GP related to allostery regulation remain largely elusive due to its macromolecular size (∼196 kDa). Here, we integrated native top-down mass spectrometry (nTD-MS), hydrogen-deuterium exchange MS (HDX-MS), protection factor (PF) analysis, molecular dynamics (MD) simulations, and allostery signaling analysis to examine the structural basis and dynamics for the allosteric regulation of GP by phosphorylation. nTD-MS reveals differences in structural stability as well as oligomeric state between the unphosphorylated (GPb) and phosphorylated (GPa) forms. HDX-MS, PF analysis, and MD simulations further pinpoint the structural differences between GPb and GPa involving the binding interfaces (the N-terminal and tower-tower helices), catalytic site, and PLP-binding region. More importantly, it also allowed us to complete the missing link of the long-range communication process from the N-terminal tail to the catalytic site caused by phosphorylation. This integrative MS and in silico-based platform is highly complementary to biophysical approaches and yields valuable insights into protein structures and dynamic regulation.

Approaches to Heterogeneity in Native Mass Spectrometry

Native mass spectrometry (MS) is aimed at preserving and determining the native structure, composition, and stoichiometry of biomolecules and their complexes from solution after they are transferred into the gas phase. Major improvements in native MS instrumentation and experimental methods over the past few decades have led to a concomitant increase in the complexity and heterogeneity of samples that can be analyzed, including protein-ligand complexes, protein complexes with multiple coexisting stoichiometries, and membrane protein-lipid assemblies. Heterogeneous features of these biomolecular samples can be important for understanding structure and function. However, sample heterogeneity can make assignment of ion mass, charge, composition, and structure very challenging due to the overlap of tens or even hundreds of peaks in the mass spectrum. In this review, we cover data analysis, experimental, and instrumental advances and strategies aimed at solving this problem, with an in-depth discussion of theoretical and practical aspects of the use of available deconvolution algorithms and tools. We also reflect upon current challenges and provide a view of the future of this exciting field.

Generation of Ions from Aqueous Taylor Cones near the Minimum Flow Rate: "True Nanoelectrospray" without Narrow Capillary

Generating ultrafine charged droplets using electrospray is crucial for attaining high ionization efficiency for mass spectrometry. The size of the precursor charged droplets depends on the spray flow rate, and conventional wisdom holds that an electrospray of a nL/min flow rate (nanoelectrospray) is only possible using narrow capillaries with an inner diameter of ∼1 μm or smaller. Here, the electrospray of aqueous solutions with high electric conductivities generated from a large off-line capillary of 0.4 mm i.d. has been performed using a high-pressure ion source. The electric discharge is avoided by operating the ion source at 2.5 bar gauge pressure. The highly stable Taylor cone can be tuned to a near-hydrostatic state that exhibits the "true nanoelectrospray" properties, i.e., high salt tolerance and minimal ion suppression. The Q^1/2 scaling law describing the electrospray current I and flow rate Q is found to be valid down to the nanoflow regime under a condition that is free of electric discharge. For a given solution, the flow rate and the size of the initial droplets and ionization species can be controlled with the spray current as the indicator for the instantaneous flow rate without changing the emitter capillary of different sizes. In regard to the application, the nanoelectrospray with a large micropipette tip is easy to use, free of clogging when dealing with viscous and high-salt buffer solutions, and with reduced surface interaction with the emitter inner surface. An acquisition of very clean mass spectra of proteins from concentrated solutions of nonvolatile salts such as phosphate-buffered saline is demonstrated.

Charge Manipulation Using Solution and Gas-Phase Chemistry to Facilitate Analysis of Highly Heterogeneous Protein Complexes in Native Mass Spectrometry

Structural heterogeneity is a significant challenge complicating (and in some cases making impossible) electrospray ionization mass spectrometry (ESI MS) analysis of noncovalent complexes comprising structurally heterogeneous biopolymers. The broad mass distribution exhibited by such species inevitably gives rise to overlapping ionic signals representing different charge states, resulting in a continuum spectrum with no discernible features that can be used to assign ionic charges and calculate their masses. This problem can be circumvented by using limited charge reduction, which utilizes gas-phase chemistry to induce charge-transfer reactions within ionic populations selected within narrow m/z windows, thereby producing well-defined and readily interpretable charge ladders. However, the ionic signal in native MS typically populates high m/z regions of mass spectra, which frequently extend beyond the precursor ion isolation limits of most commercial mass spectrometers. While the ionic signal of single-chain proteins can be shifted to lower m/z regions simply by switching to a denaturing solvent, this approach cannot be applied to noncovalent assemblies due to their inherent instability under denaturing conditions. An alternative approach explored in this work relies on adding supercharging reagents to protein solutions as a means of increasing the extent of multiple charging of noncovalent complexes in ESI MS without compromising their integrity. This shifts the ionic signal down the m/z scale to the region where ion selection and isolation can be readily accomplished with a front-end quadrupole, followed by limited charge reduction of the isolated ionic population. The feasibility of the new approach is demonstrated using noncovalent complexes formed by hemoglobin with structurally heterogeneous haptoglobin.