Digital ion trap mass analysis of high mass protein complexes using IR activation coupled with ion/ion reactions

Digital Ion Trap Isolation and Mass Analysis of Macromolecular Analytes with Multiply Charged Ion Attachment

Multiply charged ions produced by electrospray ionization (ESI) of heterogeneous mixtures of macromolecular analytes under native conditions are typically confined to relatively narrow ranges of mass-to-charge (m/z) ratio, often with extensive overlap. This scenario makes charge and mass assignments extremely challenging, particularly when individual charge states are unresolved. An ion/ion reaction strategy involving multiply charged ion attachment (MIA) to the mixture components in a narrow range of m/z can facilitate charge and mass assignment. In MIA operation, multiply charged reagent ions are attached to the analyte ions of opposite polarity to provide large m/z displacements resulting from both large changes in mass and charge. However, charge reduction of the high m/z ions initially generated under native ESI conditions requires the ability to isolate high m/z ions and to analyze even higher m/z product ions. Digital ion trap (DIT) operation offers means for both high m/z ion isolation and high m/z mass analysis, in addition to providing conditions for the reaction of oppositely charged ions. The feasibility of conducting MIA experiments in a DIT that takes advantage of high m/z ion operation is demonstrated here using a tandem 2D-3D DIT instrument. Proof-of-concept MIA experiments with cations derived from β-galactosidase using the 20- charge state of human serum immunoglobulin G (IgG, ∼149 kDa) as the reagent anion are described. MIA experiments involving mixtures of ions derived from the E. coli. ribosome are also described. For example, three components in a mixture of 70S particles (>2.2 MDa) were resolved and assigned with masses and charges following an MIA experiment involving the 20- charge state of human serum IgG.

Single-Frequency Ion Parking in a Digital 3D Quadrupole Ion Trap

Single-frequency ion parking, a useful technique in electrospray mass spectrometry (ESI-MS), involves gas-phase charge-reduction ion/ion reactions in an electrodynamic ion trap in conjunction with the application of a supplementary oscillatory voltage to selectively inhibit the reaction rate of an ion of interest. The ion parking process provides a means for limiting the extent of charge reduction in a controlled fashion and allows for ions distributed over a range of charge states to be concentrated into fewer charge states (a single charge state under optimal conditions). As charge reduction inherently leads to an increase in the mass-to-charge (m/z) ratio of the ions, it is important that the means for storing and analyzing ions be able to accommodate ions of high m/z ratios. The so-called 'digital ion trap' (DIT), which uses a digital waveform as the trapping RF, has been demonstrated to be well-suited for the analysis of high m/z ions by taking advantage of its ability to manipulate the waveform frequency. In this study, the feasibility of ion parking in a 3D quadrupole ion trap operated as a DIT using a slow-amplitude single-frequency sine-wave for selective inhibition of an ion/ion reaction is demonstrated. A recently described model that describes ion parking has been adjusted for the DIT case and is used to interpret experimental data for proteins ranging in mass from 8600 Da to 467,000 Da.

Simulation study of digital waveform-driven quadrupole mass filter operated in higher stability regions for high-resolution inductively coupled plasma mass spectrometry

RATIONALE

The use of a frequency-scanned digital quadrupole mass filter (QMF) with varying duty cycles shows promise for application as a high-resolution mass analyzer design for inductively coupled plasma mass spectrometry (ICP-MS). High resolution in ICP-MS is important to overcome isobaric polyatomic interferences. Here, we explore the possibility and the characteristics of using a digital quadrupole operating in higher stability regions for ICP-MS.

METHODS

We perform computational simulations in SIMION of a digital QMF that is operated by scanning the frequency of the digital waveform at a fixed driving voltage and various duty cycles. For ions in the atomic mass range (7-238 m/z), we investigate the expected resolution, transmission, fringe field effects, and ion trajectories. We compare different characteristics between sine and digital waveform QMF.

RESULTS

Within the capability of current digital waveform generation technology, a digital QMF can produce variable mass resolution, from several hundred to more than 10 000. This mass resolution covers the low, medium, and high resolutions that are typical for sector-field ICP-MS. Additionally, simulations suggest that transmission of the QMF remains high at high resolution. For example, with 87.50/12.50 duty cycle (zone 4,1), resolution at 10% peak width is 10 420 for m/z 80. The transmission through the quadrupole, which is constant for all isoenergetic ions, is ~2.5%, and most ion loss is due to the defocusing effects of the fringe field. Compared to sinusoidal QMFs, ions need many fewer cycles in the digital QMF to obtain high resolution.

CONCLUSION

The results demonstrate that the use of a frequency-scanned, duty-cycle-modulated digital QMF as the mass analyzer for ICP-MS has the potential to produce high resolution while maintaining considerable transmission, thus overcoming most spectral interferences in elemental MS.

Increasing Isolation Efficiency Using a Segmented Quadrupole Mass Filter Operated with Rectangular Waveforms

The performance of a segmented quadrupole mass filter operated with rectangular waveforms and capacitively coupled rectangular waveforms applied to the prefilters was examined on a home-built quadrupole-Orbitrap platform. For peak widths of 50 m/z, 100% isolation efficiency was achieved, which fell to approximately 20% for 5 m/z peak width for a rectangular waveform of 150 V0-p. Due to a small exit aperture following the mass filter, peak structure was observed in both experimental peak shapes and those simulated using SIMION. A larger radius quadrupole was examined and achieved similar performance. While the segmented quadrupole does remove the defocusing effects of the fringing fields, the ion beam is only slightly refocused due to the low RF voltage which limits achievable gains in isolation efficiency.

Infrared Photoactivation Enables Improved Native Top-Down Mass Spectrometry of Transmembrane Proteins

Membrane proteins are often challenging targets for native top-down mass spectrometry experimentation. The requisite use of membrane mimetics to solubilize such proteins necessitates the application of supplementary activation methods to liberate protein ions prior to sequencing, which typically limits the sequence coverage achieved. Recently, infrared photoactivation has emerged as an alternative to collisional activation for the liberation of membrane proteins from surfactant micelles. However, much remains unknown regarding the mechanism by which IR activation liberates membrane protein ions from such micelles, the extent to which such methods can improve membrane protein sequence coverage, and the degree to which such approaches can be extended to support native proteomics. Here, we describe experiments designed to evaluate and probe infrared photoactivation for membrane protein sequencing, proteoform identification, and native proteomics applications. Our data reveal that infrared photoactivation can dissociate micelles composed of a variety of detergent classes, without the need for a strong IR chromophore by leveraging the relatively weak association energies of such detergent clusters in the gas phase. Additionally, our data illustrate how IR photoactivation can be extended to include membrane mimetics beyond micelles and liberate proteins from nanodiscs, liposomes, and bicelles. Finally, our data quantify the improvements in membrane protein sequence coverage produced through the use of IR photoactivation, which typically leads to membrane protein sequence coverage values ranging from 40 to 60%.

Optimization of a Digital Mass Filter for the Isolation of Intact Protein Complexes in Stability Zone 1,1

Digital mass filters are advantageous for the analysis of large molecules due to the ability to perform ion isolation of high-m/z ions without the generation of very high radio frequency (RF) and DC voltages. Experimentally determined Mathieu stability diagrams of stability zone 1,1 for capacitively coupled digital waveforms show a voltage offset between the quadrupole rod pairs is introduced by the capacitors which is dependent on the voltage magnitude of the waveform and the duty cycle. This changes the ion's a value from a = 0 to a < 0. These effects are illustrated for isolation for single-charge states for various protein complexes up to 800 kDa (GroEL) for stability zone 1,1. Isolation resolving power (m/Δm) of approximately 280 was achieved for an ion of m/z 12,315 (z = 65+ for 800.5 kDa GroEL D398A), which corresponds to an m/z window of 44.

Synchronized Reverse Scan Collision Induced Dissociation in Digital Ion Trap Mass Spectrometer for Improving Fragment Ion Detection

Development of fragment ion detection methods is of great importance for mass spectrometer advancement or substance identification. To date, collision induced dissociation (CID) remains the most commonly used ion activation method in MS/MS experiments, and the effectiveness of CID in an ion trap mass spectrometer is limited by low mass cutoff and weak fragmentation yields. Theoretically, controlling the q value is the key to maintain the fragment efficiency and trapping efficiency of MS/MS, thus improving the detection of fragment ion, while currently reported techniques usually require complex circuitry and often produce different CID patterns. In this paper, with the developed synchronized reversed scanning-collision induced dissociation (SRS-CID) technique, we demonstrate its effective improvement in fragment ion detection. The SRS-CID is implemented on a digital ion trap mass spectrometer (DITMS) by reverse scanning the q values during CID process, or specifically, the frequency is increased during the CID process. With the SRS-CID technique, the fragmentation efficiency of precursor ions can be slightly improved. For reserpine analyte, the trapping efficiency for low-mass fragment ions is improved at least 3 times, and for YGGFL, the trapping efficiency for low-mass fragment ions is improved at least 9 times. These experimental results can also be validated by simulations, and the kinetic energy variation plot suggests consecutive fragmentation occurs. In any case, the SRS-CID provides a solution to the low efficiency of fragment ion detection during tandem MS analysis, which will certainly be useful in the future.

Influence of Pseudopotential Well Depth on the Performance of Hybrid Linear Ion Trap/Time-of-Flight Mass Spectrometry Driven by Square and Sinusoidal Waveform

Quadrupole devices are widely used as ion analyzers and ion guides, which are usually driven by a sinusoidal waveform. Recently, these devices driven by a digital waveform have attracted much attention. Driven by different rf waveforms, the pseudopotential well depth of quadrupole devices is significantly different, which will affect their performance. However, there is a lack of comprehensive view on the performance differences of quadrupole devices or hybrid instrument driven by different rf waveforms. In this paper, the differences in mass range, resolution, sensitivity, and ion fragmentation of LIT/TOFMS driven by square and sinusoidal waveforms were investigated. Compared with the sinusoidal mode, the square mode had a wider mass range and better mass resolution. Toluene was used to study the difference in sensitivity and ion fragmentation between the two modes. The results showed that the sensitivity of the square mode was 1.7-2.5 times that of the sinusoidal mode at different ion densities. According to the sensitivity differences, it was inferred that the ion-trapping efficiency and ion capacity of LIT in the square mode were 2.0 times and 1.7 times those in sinusoidal mode. It was found that the square mode behaved "softer" and presented less fragmentation, and the proportion of fragment ions in the sinusoidal mode can reach 3.2 times that in the square mode at high ion density. Therefore, LIT/TOFMS driven by a square waveform shows greater potential in the application of the complex matrix system with a wide mass range.

Measurement of the effective electric field radius on digital ion trap spectrometer

The effective electric field radius is a fundamental parameter of ion traps, and it has a significant influence on ion-trapping capability, signal intensity, mass range and some other properties of the ion trap. For a quadrupole ion trap built with ideal hyperbolic electrodes, its effective electric field radius can be obtained by its geometrical size, while it is very difficult to obtain the effective electric field radius for a non-hyperbolic ion trap. In this study, the effective electric field radius of a linear ion trap and some ceramic rectilinear ion traps (cRITs) were investigated via the digital ion trap technology. The dipole frequency of supplementary AC for excitation was locked at a certain value of the main RF trapping wave, and the characteristic q values for excitation could be determined accordingly. The q values could be further used to calculate the effective electric field radius through theoretical calculations. A linear equation had been fitted between the q values for excitation and the square of period T2 through experiments subsequently. The relative deviation between the measured electric field radius and the simulative electric field radius is less than 2%. The simulation results and experimental validation show that the approach has predictive power for modeling and measuring the effective field radius of non-hyperbolic ion traps. It is certainly significant for further understanding the performances of non-hyperbolic quadrupole systems.