Electrostatic Linear Ion Trap Optimization Strategy for High Resolution Charge Detection Mass Spectrometry

Single particle charge detection mass spectrometry enables molecular characterization of lipid nanoparticles and mRNA packaging

Lipid nanoparticles (LNPs) are effective delivery systems for RNA therapeutics, yet their intrinsic heterogeneity in size and composition make them challenging to characterize. Charge detection mass spectrometry (CDMS) was used to rapidly weigh thousands of individual LNPs. Diameter distributions of empty LNPs from CDMS and cryo-TEM measurements are in excellent agreement demonstrating that these particles are sufficiently stable in the high vacuum environment of the mass spectrometer for accurate mass analysis. A similarly prepared mRNA-packaged LNP sample has a peak mass at ∼70 MDa, 31 MDa higher than that of the empty LNP sample. Four freeze-thaw (FT) cycles of the mRNA-LNPs results in a peak mass at ∼26.5 MDa, indicating significantly degraded LNPs. The degraded LNPs are about 28 % of the population of the mRNA-LNP sample after the first FT cycle. A non-linear least squares fitting routine was developed to convolve the mass distribution of the LNP core with a function that describes the packaging distribution to fit the mRNA-LNP data. Two models of the lipid core mass distribution were used to obtain the distribution of mRNA in the packaged LNPs. These two models provide a lower and upper limit to the average mRNA packaging of 43 and 107 mRNA copies, consistent with a rough estimate of an average of 62 mRNA copies obtained from cryo-TEM images. These results demonstrate the potential for label-free, rapid characterization of mass, diameter, packaging, and stability of LNPs with CDMS.

Dual Apodization Maximizes Charge Resolution and Frequency Precision in Charge Detection Mass Spectrometry

Charge detection mass spectrometry (CD-MS) is a single-particle technique in which the masses of individual ions are determined from simultaneous measurements of their m/z ratio and charge. Ions are trapped in an electrostatic linear ion trap and oscillate back and forth through a detection cylinder coupled to a low noise charge sensitive amplifier. The resulting signal is analyzed using short-time Fourier transforms (STFTs) to determine the m/z ratio and charge. The m/z ratio is determined from the oscillation frequency, and the charge is obtained from the magnitude of the fundamental. Here we compare the methods used to analyze time domain data for single ion measurements including STORI plots. We conclude that the original STFT approach remains the best method for the analysis of CD-MS data. However, there are many ways of implementing the STFT approach. We compare the options with the goal of maximizing precision of the charge and m/z determinations while simultaneously maximizing the number of ions that are detected. A variety of apodization methods are compared, and the effects of scalloping loss, equivalent noise bandwidth, computation time, window length, and step size are evaluated. Maximizing the precision of the charge and m/z determinations places conflicting constraints on the window length, and we conclude that a dual apodization strategy, with different window lengths, provides the most robust approach to analyzing results for the broad range of different samples that can be measured by CD-MS.

High performance charge detection mass spectrometry without ultra-high vacuum

Charge detection mass spectrometry (CDMS) measurements of individual ions using either Orbitrap or electrostatic ion trap-based instruments have heretofore been performed under ultra-high vacuum conditions (10-9 Torr or lower). The rationale for this expensive and often cumbersome requirement is that these measurements need to be performed in an environment where collisions with background gas do not adversely affect the measurements. Here, the use of an electrostatic trap that accepts a broad range of ion energies and a dynamic ion signal analysis method enables accurate CDMS mass measurements at pressures as high as 1 × 10-6 Torr, multiple orders of magnitude higher than previously demonstrated. Consistent, accurate masses were obtained for pentameric antibody complexes (∼800 kDa), adeno-associated viruses (∼4.8 MDa), and both ∼50 and ∼100 nm diameter polystyrene nanoparticles (∼35 MDa and ∼330 MDa, respectively) at pressures ranging from 1 × 10-8 Torr to 1 × 10-6 Torr. The relationships between ion mass, trap pressure, ion lifetimes, individual ion energies and survival rates were investigated over a 1 s trapping period. Larger ions are more robust to higher pressures. While the trapping lifetimes of smaller ions decrease with increasing pressure, enough survive long enough for accurate mass measurements to be made. Some ions are lost because collisional dampening decreases their energies below the minimum stability threshold of the trap, but others with sufficient energy are still lost due to collision-induced scattering that moves the ions too far from the central trapping axis.

Optimization of the Entropy-Based Wavelet Method for Removing Strong RF and AC Interferences in a Charge Detection Linear Ion Trap Mass Spectrometer

We developed an entropy-based wavelet method to effectively remove interference from strong radio frequency (RF) and auxiliary alternating current (AC) fields in a linear ion trap (LIT) mass spectrometer coupled to a charge sensing particle detector (CSPD). By optimizing the energy-to-Shannon entropy, we identified the optimal mother wavelet family and decomposition level and determined suitable threshold values based on the median of sub-band coefficients at each decomposition level. These thresholds were applied as rigid criteria across all decomposition levels to eliminate noise interferences and avoid the arbitrary choice of the threshold. This entropy wavelet-based method successfully denoised high-mass protein mass spectra, achieving significant improvements in signal-to-noise ratio (S/N) for immunoglobulin G (IgG) and alpha-2-macroglobulin (A2M) ions, with increases of 68.03% and 81.73%, respectively. Our method surpasses previously reported baseline correction techniques, such as orthogonal wavelet packet decomposition (OWPD) filtering, and enhances the sensitivity of LIT mass spectrometry (LIT-MS) in analyzing high-mass protein ions.

Combining Fourier Transform Ion Mobility with Charge Detection Mass Spectrometry for the Analysis of Multimeric Protein Complexes

Charge detection mass spectrometry (CDMS) allows direct mass measurement of heterogeneous samples by simultaneously determining the charge state and the mass-to-charge ratio (m/z) of individual ions, unlike conventional MS methods that use large ensembles of ions. CDMS typically requires long acquisition times and the collection of thousands of spectra, each containing tens to hundreds of ions, to generate sufficient ion statistics, making it difficult to interface with the time scales of online separation techniques such as ion mobility. Here, we demonstrate the application of Fourier transform multiplexing and drift tube ion mobility joined with Orbitrap-based CDMS for the analysis of multimeric protein complexes. Stepped frequency modulation was utilized to enable unambiguous frequency assignment during mobility sweeps and allow spectral averaging, which improves the accuracy and signal-to-noise of ion mobility spectra and CDMS measurements. Fourier transformation of the signal reveals the arrival times and collision cross sections of ions while simultaneously collecting charge information for thousands of individual ions. Combining Fourier transform multiplexing ion mobility and CDMS provides insight into each ion's size and mass while showcasing a potential solution to the duty cycle mismatch of online separation techniques in the single ion regime.

Advances in Single Particle Mass Analysis

Single particle mass analysis methods allow the measurement and characterization of individual nanoparticles, viral particles, as well as biomolecules like protein aggregates and complexes. Several key benefits are associated with the ability to analyze individual particles rather than bulk samples, such as high sensitivity and low detection limits, and virtually unlimited dynamic range, as this figure of merit strictly depends on analysis time. However, data processing and interpretation of single particle data can be complex, often requiring advanced algorithms and machine learning approaches. In addition, particle ionization, transfer, and detection efficiency can be limiting factors for certain types of analytes. Ongoing developments in the field aim to address these challenges and expand the capabilities of single particle mass analysis techniques. Charge detection mass spectrometry is a single particle version of mass spectrometry in which the charge (z) is determine independently from m/z. Nano-electromechanical resonator mass analysis relies on changes in a nanoscale device's resonance frequency upon deposition of a particle to directly derive its inertial mass. Mass photometry uses interferometric video-microscopy to derive particle mass from the intensity of the scattered light. A common feature of these approaches is the acquisition of single particle data, which can be filtered and concatenated in the form of a particle mass distribution. In the present article, dedicated to our honored colleague Richard Cole, we cover the latest technological advances and applications of these single particle mass analysis approaches.

Charge Detection Mass Spectrometry Enables Molecular Characterization of Nucleic Acid Nanoparticles

Nucleic acid nanoparticles (NANPs) are increasingly used in preclinical investigations as delivery vectors. Tools that can characterize assembly and assess quality will accelerate their development and clinical translation. Standard techniques used to characterize NANPs, like gel electrophoresis, lack the resolution for precise characterization. Here, we introduce the use of charge detection mass spectrometry (CD-MS) to characterize these materials. Using this technique, we determined the mass of NANPs varying in size, shape, and molecular mass, NANPs varying in production quality due to formulations lacking component oligonucleotides, and NANPs functionalized with protein and nucleic acid-based secondary molecules. Based on these demonstrations, CD-MS is a promising tool to precisely characterize NANPs, enabling more precise assessments of the manufacturing and processing of these materials.

Realization of Higher Resolution Charge Detection Mass Spectrometry

Charge detection mass spectrometry (CD-MS) allows mass distributions to be measured for heterogeneous samples that cannot be analyzed by conventional MS. With CD-MS, the m/z and charge are measured for individual ions using a detection cylinder embedded in an electrostatic linear ion trap (ELIT). Imprecision in both the m/z and charge measurements contribute to the mass resolution. However, if the charge can be measured with a precision of <0.2 e the charge state can be assigned with a low error rate and the mass resolving power only depends on the m/z resolution. Prior to this work, the best resolving power demonstrated experimentally for CD-MS was 700. Here we demonstrate a resolving power of >14,600, 20-times higher than the previous best. Trajectory simulations were used to optimize the geometry and electrostatic potentials of the ELIT. We found conditions where the energy dependence of the oscillation frequency becomes parabolic, and then operated with a nominal ion energy at the minimum of the parabola. The 14,600 resolving power was obtained with a beam collimator before the ELIT. With the collimator removed, the resolving power of the optimized ELIT is 7300, which is still an order of magnitude higher than the previous best. The resolving power was demonstrated by resolving the isotope distributions for peptides and proteins. High resolution CD-MS measurements were then used to resolve the glycans on a monoclonal antibody and applied to the analysis of hepatitis B virus capsids. The results indicate that procedures for adduct removal need to be improved for the full benefit of the higher resolving power to be realized for higher mass species. However, these results represent a key step toward using CD-MS to analyze very complex protein mixtures where charge states are not well resolved in the m/z spectrum because of congestion from numerous overlapping peaks.

Single-Ion Mass Spectrometry for Heterogeneous and High Molecular Weight Samples

In charge detection mass spectrometry (CD-MS) the mass of each individual ion is determined from the measurement of its mass to charge ratio (m/z) and charge. Performing this measurement for thousands of ions allows mass distributions to be measured for heterogeneous and high mass samples that cannot be analyzed by conventional mass spectrometry (MS). CD-MS opens the door to accurate mass measurements for samples into the giga-Dalton regime, vastly expanding the reach of MS and allowing mass distributions to be determined for viruses, gene therapies, and vaccines. Following the success of CD-MS, single-ion mass measurements have recently been performed on an Orbitrap. CD-MS and Orbitrap individual ion mass spectrometry (I2MS) are described. Illustrative examples are provided, and the prospects for higher resolution measurements discussed. In the case of CD-MS, computer simulations indicate that much higher resolving powers are within reach. The ability to perform high-resolution CD-MS analysis of heterogeneous samples will be enabling and disruptive in top-down MS as high-resolution m/z and accurate charge measurements will allow very complex m/z spectra to be unraveled.

Multiple Ion Charge Extraction (MICE) for High-Throughput Charge Detection Mass Spectrometry

Charge detection mass spectrometry (CD-MS) is a single-particle technique, where the masses of individual ions are determined from simultaneous measurements of their mass-to-charge ratio (m/z) and charge. The ions are trapped in an electrostatic linear ion trap (ELIT) and oscillate back and forth through a conducting cylinder connected to a charge-sensitive amplifier. The oscillating ions generate a periodic signal that is processed with fast Fourier transforms (FFTs) to obtain the oscillation frequency (which is related to m/z) and magnitude (which is proportional to the charge). The simultaneous trapping of two or more ions is a way to increase throughput. However, when multiple ions are trapped, it is possible that some of them have overlapping oscillation frequencies, which can lead to an error in the charge determination. To avoid this error, results from overlapping ions are usually discarded. When measurements are performed with many trapped ions, the most abundant m/z species are discarded at a higher rate, which affects the relative abundances in the mass distribution. Here, we report the development of a post-processing method called multiple ion charge extraction (MICE) that uses a statistical approach to assign charges to ions with overlapping frequencies. MICE recovers single-ion information from high signal measurements and makes the relative abundances more resilient to the signal intensity. This approach corrects for high signal m/z biasing, allowing analysis to be faster and more reliable. Using MICE, CD-MS measurements were made at rates of 120 ions/s with little m/z biasing.

Combined Multiharmonic Frequency Analysis for Improved Dynamic Energy Measurements and Accuracy in Charge Detection Mass Spectrometry

The ability to determine ion energies in electrostatic ion-trap-based charge detection mass spectrometry (CDMS) experiments is important for the accurate measurement of individual ion m/z, charge, and mass. Dynamic energy measurements throughout the time an ion is trapped take advantage of the relationship between ion energy and the harmonic amplitude ratio (HAR) composed from the fundamental and second harmonic amplitudes in the Fourier transform of the ion signal. This method eliminates the need for energy-filtering optics in CDMS and makes it possible to measure energy lost in collisions and changes in ion masses due to dissociation. However, the accuracy of the energy measurement depends on the signal-to-noise ratio (S/N) of the amplitudes used to determine the HAR. Here, a major improvement to this HAR-based dynamic energy measurement method is achieved using HARs composed of higher-order harmonics in addition to the fundamental and second harmonic to determine ion energies. This combined harmonic amplitude ratios for precision energy refinement (CHARPER) method is applied to the analysis of a 103 nm polystyrene nanoparticle ion (359.7 MDa, m/z = 308,300) and the energy resolution (3140) and effective mass resolution (730) achieved are the best yet demonstrated in electrostatic ion-trap-based CDMS. The CHARPER method applied to an ensemble of several thousand adeno-associated virus ion signals also results in higher mass resolution compared to the basic HAR method, making it possible to resolve additional features in the composite mass histogram.