Large Molecule Characterization Based upon Individual Ion Detection with Electrospray Ionization-FTICR Mass Spectrometry

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.

Dynamic Energy Measurements in Charge Detection Mass Spectrometry Eliminate Adverse Effects of Ion-Ion Interactions

Ion-ion interactions in charge detection mass spectrometers that use electrostatic traps to measure masses of individual ions have not been reported previously, although ion trajectory simulations have shown that these types of interactions affect ion energies and thereby degrade measurement performance. Here, examples of interactions between simultaneously trapped ions that have masses ranging from ca. 2 to 350 MDa and ca. 100 to 1000 charges are studied in detail using a dynamic measurement method that makes it possible to track the evolution of the mass, charge, and energy of individual ions over their trapping lifetimes. Signals from ions that have similar oscillation frequencies can have overlapping spectral leakage artifacts that result in slightly increased uncertainties in the mass determination, but these effects can be mitigated by the careful choice of parameters used in the short-time Fourier transform analysis. Energy transfers between physically interacting ions are also observed and quantified with individual ion energy measurement resolution as high as ∼950. The mass and charge of interacting ions do not change, and their corresponding measurement uncertainties are equivalent to ions that do not undergo physical interactions. Simultaneous trapping of multiple ions in CDMS can greatly decrease the acquisition time necessary to accumulate a statistically meaningful number of individual ion measurements. These results demonstrate that while ion-ion interactions can occur when multiple ions are trapped, they have negligible effects on mass accuracy when using the dynamic measurement method.

Large Individual Ion FTICR Measurements from the Mid-1990s Using Reactions for Charge Determination Mass Spectrometry

This article discusses from a personal and present-day perspective the first studies of large highly charged individual molecular ions that were conducted using electrospray ionization with Fourier transform ion cyclotron resonance MS in the mid-1990s. These studies are distinguished from Current Charge Detection Mass Spectrometry (CDMS) primarily by their use of individual ion charge state changes due to reactions for accurate charge determination. This work describes the key differences in technologies and methods with present CDMS and the likely implications of these differences. I comment on surprising individual ion behavior observed in some measurements involving increases in charge state, as well as their possible basis, and also briefly discuss the potential utility of the reaction-based mass measurement approach used in the context of what might more globally be referred to as "Charge Determination Mass Spectrometry".

Applications of Charge Detection Mass Spectrometry in Molecular Biology and Biotechnology

Charge detection mass spectrometry (CDMS) is a single-particle technique where the masses of individual ions are determined from simultaneous measurement of their mass-to-charge ratio (m/z) and charge. Masses are determined for thousands of individual ions, and then the results are binned to give a mass spectrum. Using this approach, accurate mass distributions can be measured for heterogeneous and high-molecular-weight samples that are usually not amenable to analysis by conventional mass spectrometry. Recent applications include heavily glycosylated proteins, protein complexes, protein aggregates such as amyloid fibers, infectious viruses, gene therapies, vaccines, and vesicles such as exosomes.

Ion Imaging of Native Protein Complexes Using Orthogonal Time-of-Flight Mass Spectrometry and a Timepix Detector

Native mass spectrometry (native MS) has emerged as a powerful technique to study the structure and stoichiometry of large protein complexes. Traditionally, native MS has been performed on modified time-of-flight (TOF) systems combined with detectors that do not provide information on the arrival coordinates of each ion at the detector. In this study, we describe the implementation of a Timepix (TPX) pixelated detector on a modified orthogonal TOF (O-TOF) mass spectrometer for the analysis and imaging of native protein complexes. In this unique experimental setup, we have used the impact positions of the ions at the detector to visualize the effects of various ion optical parameters on the flight path of ions. We also demonstrate the ability to unambiguously detect and image individual ion events, providing the first report of single-ion imaging of protein complexes in native MS. Furthermore, the simultaneous space- and time-sensitive nature of the TPX detector was critical in the identification of the origin of an unexpected TOF signal. A signal that could easily be mistaken as a fragment of the protein complex was explicitly identified as a secondary electron signal arising from ion-surface collisions inside the TOF housing. This work significantly extends the mass range previously detected with the TPX and exemplifies the value of simultaneous space- and time-resolved detection in the study of ion optical processes and ion trajectories in TOF mass spectrometers.

Measurement of Individual Ions Sharply Increases the Resolution of Orbitrap Mass Spectra of Proteins

It is well-known that with Orbitrap-based Fourier-transform-mass-spectrometry (FT-MS) analysis, longer-time-domain signals are needed to better resolve species of interest. Unfortunately, increasing the signal-acquisition period comes at the expense of increasing ion decay, which lowers signal-to-noise ratios and ultimately limits resolution. This is especially problematic for intact proteins, including antibodies, which demonstrate rapid decay because of their larger collisional cross-sections, and result in more frequent collisions with background gas molecules. Provided here is a method that utilizes numerous low-ion-count spectra and single-ion processing to reconstruct a conventional m/ z spectrum. This technique has been applied to proteins varying in molecular weight from 8 to 150 kDa, with a resolving power of 677 000 achieved for transients of carbonic anhydrase (29 kDa) with a duration of only ∼250 ms. A resolution improvement ranging from 10- to 20-fold was observed for all proteins, providing isotopic resolution where none was previously present.

Expanding the data depth for the analysis of complex crude oil samples by Fourier transform ion cyclotron resonance mass spectrometry using the spectral stitching method

RATIONALE

Crude oil samples are very complex mixtures of compounds and only Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) provides the ultra-high mass resolution necessary to resolve them. However, FT-ICR MS operates best when only a small amount of ions is present during each transient. This cannot be accomplished with crude oil samples without chromatography because more than 50,000 compounds can be present, with the result that species with low intensity may be suppressed and are detected either with low intensity or not at all.

METHODS

Spectral stitching was used to overcome the problems associated with suppression effects, where only short mass windows of 30 amu were scanned to reduce the amount of ions present in each individual scan. Afterwards, all the scans were co-added and the subsequent spectrum was used to calculate individual class distributions.

RESULTS

A heavy crude oil sample was analyzed using spectral stitching and this approach was compared with analysis using a broadband-method in order to illustrate the enhancement in depth of information. Although both methods took the same analysis time a seven-times increase in the number of detected species was observed when the spectral stitching method was used compared with the commonly applied broadband method in a 900 amu mass window.

CONCLUSIONS

Spectral stitching using smaller selected ion monitoring (SIM) windows for complex crude oil samples allows better class distribution to be obtained because less ion suppression is observed.

Unit mass baseline resolution for an intact 148 kDa therapeutic monoclonal antibody by Fourier transform ion cyclotron resonance mass spectrometry

Fourier transform ion cyclotron resonance mass spectrometry (FTICR MS) provides the highest mass resolving power and mass measurement accuracy for unambiguous identification of biomolecules. Previously, the highest-mass protein for which FTICR unit mass resolution had been obtained was 115 kDa at 7 T. Here, we present baseline resolution for an intact 147.7 kDa monoclonal antibody (mAb), by prior dissociation of noncovalent adducts, optimization of detected total ion number, and optimization of ICR cell parameters to minimize space charge shifts, peak coalescence, and destructive ion cloud Coulombic interactions. The resultant long ICR transient lifetime (as high as 20 s) results in magnitude-mode mass resolving power of ~420,000 at m/z 2,593 for the 57+ charge state (the highest mass for which baseline unit mass resolution has been achieved), auguring for future characterization of even larger intact proteins and protein complexes by FTICR MS. We also demonstrate up to 80% higher resolving power by phase correction to yield an absorption-mode mass spectrum.

Electrically compensated Fourier transform ion cyclotron resonance cell for complex mixture mass analysis

Complex natural organic mixtures such as petroleum require ultrahigh mass spectral resolution to separate and identify thousands of elemental compositions. Here, we incorporate a custom-built, voltage-compensated ICR cell for Fourier transform ion cyclotron resonance mass spectrometry (FTICR MS), based on a prior design by Tolmachev to produce optimal mass resolution. The compensated ICR cell installed in a custom-built 9.4 T FTICR mass spectrometer consists of seven cylindrical segments with axial proportions designed to generate a dc trapping potential that approaches an ideal three-dimensional axial quadrupolar potential. However, the empirically optimized compensation voltages do not correspond to the most quadrupolar trapping field. The compensation electrodes minimize variation in the reduced cyclotron frequency by balancing imperfections in the magnetic and electric field. The optimized voltages applied to compensation electrodes preserve ion cloud coherence for longer transient duration by approximately a factor of 2, enabling separation and identification of isobaric species (compounds with the same nominal mass but different exact mass) common in petroleum, such as C(3) vs SH(4) (separated by 3.4 mDa) and SH(3)(13)C vs (12)C(4) (separated by 1.1 mDa). The improved performance of the ICR cell provides more symmetric peak shape and better mass measurement accuracy. A positive ion atmospheric pressure photoionization (APPI) petroleum spectrum yields more than 26,000 assigned peaks, Fourier-limited resolving power of 800,000 at m/z 500 (6.6 s transient duration), and 124 part per billion root mean square (rms) error. The tunability of the compensation electrodes is critical for optimal performance.

Ultrahigh-mass mass spectrometry of single biomolecules and bioparticles

Since the advent of soft ionization methods, mass spectrometry (MS) has found widespread application in the life sciences. Mass is now known to be a critical parameter for characterization of biomolecules and their complexes; it is also a useful parameter to characterize bioparticles such as viruses and cells. However, because of the genetic diversity of these entities, it is necessary to measure their masses individually and to obtain the corresponding mean masses and mass distributions. Here, I review recent technological developments that enable mass measurement of ultrahigh-mass biomolecules and bioparticles at the single-ion level. Some representative examples include cryodetection time-of-flight MS of single-megadalton protein ions, Millikan-type mass measurements of single viruses in a cylindrical ion trap, and charge-detection quadrupole ion trap MS of single whole cells. I also discuss the promises and challenges of these new technologies in real-world applications.

Observation of Increased Ion Cyclotron Resonance Signal Duration through Electric Field Perturbations

Ion motion in Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) is complex and the subject of ongoing theoretical and experimental studies. Two predominant pathways for the loss of ICR signals are thought to include damping of cyclotron motion, in which ions lose kinetic energy and radially damp toward the center of the ICR cell, and dephasing of ion coherence, in which ions of like cyclotron frequency become distributed out of phase at similar cyclotron radii. Both mechanisms result in the loss of induced ion image current in FTICR-MS measurements and are normally inseparable during time-domain signal analysis. For conventional ICR measurements which take advantage of ion ensembles, maximization of the ion population size and density can produce the desired effect of increasing phase coherence of ions during cyclotron motion. However, this approach also presents the risk of coalescence of ion packets of similar frequencies. In general, ICR researchers in the past have lacked the tools necessary to distinguish or independently control dephasing and damping mechanisms for ICR signal loss. Nonetheless, the ability to impart greater phase coherence of ions in ICR measurements will allow significant advances in FTICR-MS research by improving the current understanding of ICR signal loss contributions of dephasing and damping of ion ensembles, increasing overall time-domain signal length, and possibly, resulting in more routine ultrahigh resolution measurements. The results presented here demonstrate the ability to employ a high density electron beam to perturb electric fields within the ICR cell during detection of cyclotron motion, in an approach we call electron-promoted ion coherence (EPIC). As such, EPIC reduces ICR signal degradation through loss of phase coherence, and much longer time-domain signals can be obtained. Our results demonstrate that time-domain signals can be extended by more than a factor of 4 with the implementation of EPIC, as compared to conventional experiments with otherwise identical conditions. The application of EPIC has also been observed to reduce the appearance of peak coalescence. These capabilities are not yet fully optimized nor fully understood in terms of the complex physics that underlies the enhancement. However, the enhanced time-domain signals can result in improved resolution in frequency-domain signals, and as such, this result is important for more efficient utilization of FTICR-MS. High resolution and accurate mass analysis are prime motivating factors in the application of advanced FTICR technology. We believe the approach presented here and derivatives from it may have significant benefit in future applications of advanced FTICR technology.

Proteomics by FTICR mass spectrometry: top down and bottom up

This review provides a broad overview of recent Fourier transform ion cyclotron resonance (FTICR) applications and technological developments relevant to the field of proteomics. Both the "bottom up" (peptide level) and "top down" (intact protein level) approaches are discussed and illustrated with examples. "Bottom up" topics include peptide fragmentation, the accurate mass and time (AMT) tag approach and dynamic range extension technology, aspects of quantitative proteomics measurements, post-translational modifications, and developments in FTICR operation software focused on peptide and protein identification. Topics related to the "top down" approach include various aspects of high mass measurements, protein tandem mass spectrometry, methods for the study of protein conformations, and protein complexes as well as advanced technologies that may become of practical utility in the coming years. Finally, early examples of the integration of both FTICR approaches to biomedical proteomics applications are presented, along with an outlook for future directions.

Ultrasensitive and quantitative analyses from combined separations-mass spectrometry for the characterization of proteomes

This article describes developments in fundamental and applied aspects of separations, electrospray ionization phenomena, and mass spectrometric instrumentation that are interrelated and important for making more effective and quantitative measurements, particularly for proteomics applications. The basis for better quantitation and ultrahigh sensitivity is highlighted for high-resolution capillary liquid chromatography separations that provide low nanoliter per minute flow rates to an electrospray ionization interface. The increased dynamic range of measurements and low zeptomole regime detection limits obtainable open new avenues for biological research.

New Trends in Food Processing

In this work some of the newest trends in food processing are reviewed. This revision intends to provide an updated overview (including works published until February 2001) on the newest food processes, including food manufacturing, preservation, and control. Modern processes for food and food ingredients manufacturing based on membrane technology, super-critical fluid technology, and some applications of biotechnology are presented, mainly applied to obtain functional foods, "all-natural" enriched foods, probiotics and prebiotics. Also included is a critical assessment concerning non-thermal preservation techniques used for food preservation, such as high hydrostatic pressure, pulsed electric fields, ultrasound, pulsed light, hurdle systems, etc. Finally, a group of new analytical techniques (i.e., molecular techniques such as Polymerase Chain Reaction (PCR), food image analysis, and biosensors) and their use for food and process control is reviewed.

Acid-induced cloud point extraction and preconcentration of polycyclic aromatic hydrocarbons from environmental solid samples

The effectiveness of the acid-induced phase separation of anionic surfactants (acid-induced cloud point extraction, ACPE) to extract polycyclic aromatic hydrocarbons (PAHs) from different environmental samples (soils, sediments and sludges), prior to chromatographic analysis, was evaluated. Variables affecting the ACPE efficiency were optimised using a natural matrix (a harbour sediment, CRM 535). Temperature, surfactant concentration and stirring were of primary importance to maximise recovery, whereas temperature and surfactant/hydrochloric acid concentration influenced the volume of the surfactant-rich phase and therefore the preconcentration factor achieved. The optimal conditions (2% sodium dodecanesulphonate (SDoS), 4.2 M HCl, 60 degrees C, 1 h) were applied to the extraction of PAHs from various matrices and the ACPE recoveries compared to certified results from Soxhlet extractions. Recoveries obtained for four to five aromatic ring PAHs ranged from 71 to 98%. Uncertainties obtained using ACPE were similar to or lower than those provided for the certified values. The volume of the extracts ranged from 1 to 2 ml. The method did not require additional clean-up or preconcentration steps.

Mass analysis at the advent of the 21st century

There have been many new and exciting developments in mass spectrometer systems in recent years. Many of these developments are being driven by challenges presented by molecular biology. The activity is fueled by resources being devoted to drug development, for example, and other medically and biologically related activities. Progress in these applications will be accelerated by improved sensitivity, specificity, and speed. In mass spectrometry, this translates to greater mass resolving power, mass accuracy, mass-to-charge range, efficiency, and speed. It is safe to say that the demands resulting from current analytical needs are likely to be met to varying degrees but probably not by a single analyzer technology or hybrid instrument. On-line and/or off-line separations and manipulations combined with mass spectrometry will also play increasingly important roles. For any analyzer, or combination of analyzers, to become widely used it must have an important application for which its figures of merit are best suited, relative to competing approaches. The relative cost of competing technologies is also an important factor. The mass filter has seen so much use in the past 30 years because its characteristics best fit a wide range of applications. As an example, biological applications, which are currently driving many instrument development activities in mass spectrometry, demand more information, of higher quality, from less material, faster, and at lower cost. Which technologies will dominate biological applications in the coming years is open to speculation. However, in considering the relative merits of today's dominant mass analyzers, areas of opportunity for improvement are apparent. Furthermore, new and more demanding measurement needs are constantly being recognized that will continue to exercise the creativity of the mass spectrometry community.

A novel high-performance fourier transform ion cyclotron resonance cell for improved biopolymer characterization

A new trapped ion cell design for use with Fourier transform ion cyclotron resonance mass spectrometry is described. The design employs 15 cylindrical ring electrodes to generate trapping potential wells and 32 separately assignable rod electrodes for excitation and detection. The rod electrodes are positioned internal to the ring electrodes and provide excitation fields that are thereby linearized along the magnetic field over the entire trapped ion volume. The new design also affords flexibility in the shaping of the trapping field using the 15 ring electrodes. Many different trapping well shapes can be generated by applying different voltages to the individual ring electrodes, ranging from quadratic to linearly ramped along the magnetic field axis, to a shape that is nearly flat over the entire trap volume, but rises very steeply near the ends of the trap. This feature should be useful for trapping larger ion populations and extension of the useful range of ion manipulation and dissociation experiments since the number of stages of ion manipulation or dissociation is limited in practice by the initial trapped ion population size. Predicted trapping well shapes for two different ring electrode configurations are presented, and these and several other possible configurations are discussed, as are the predicted excitation fields based on the use of rod electrodes internal to the trapping ring electrodes. Initial results are presented from an implementation of the design using a 3.5 T superconducting magnet. It was found that ions can be successfully trapped and detected with this cell design and that selected ion accumulation can be performed with the utilization of four rods for quadrupolar excitation. The initial results presented here illustrate the feasibility of this cell design and demonstrate differences in observed performance based upon different trapping well shapes.

High-mass-measurement accuracy and 100% sequence coverage of enzymatically digested bovine serum albumin from an ESI-FTICR mass spectrum

The application of Fourier transform ion cyclotron resonance (FTICR) mass spectrometry to the analysis of polypeptide mixtures resulting from proteolytic digestion is described. A new 11.5-T FTICR mass spectrometer has been applied for the analysis of tryptic digestion mixtures of the protein bovine serum albumin (BSA). The improved cyclotron frequency stability and reduced frequency shifts observed over a wide range of trapped ion population sizes provide the ability to signal average spectra without degrading mass measurement accuracy, requiring internal calibration or advanced data processing schemes to compensate for variations in ion cyclotron signals brought about by different population sizes. A total of 100 spectra were signal-averaged leading to the observation of a total of 123 isotope distributions with a signal-to-noise ratio greater than 3:1. From those distributions, 86 can be ascribed to tryptic fragments of BSA on the basis of mass measurement errors of 10 ppm or less. Of these, 71 were within 2 ppm error limits corresponding to complete amino acid sequence coverage and an average error of 0.77 ppm. These results indicate that high-accuracy measurements are feasible for a large number of species detected simultaneously without the necessity for internal calibration and indicate the potential of such measurements, when combined with chromatographic separations, for facilitating more rapid identification of large numbers of proteins.

Electrospray ionization-Fourier transform ion cyclotron resonance mass spectrometry at 11.5 tesla: instrument design and initial results

Initial results obtained using a new electrospray ionization (ESI) Fourier transform ion cyclotron resonance (FTICR) mass spectrometer operated at a magnetic field 11.5 tesla are presented. The new instrument utilized an electrostatic ion guide between the ESI source and FTICR trap that provided up to 5% overall transmission efficiency for light ions and up to 30% efficiency for heavier biomolecules. The higher magnetic field in combination with an enlarged FTICR ion trap made it possible to substantially improve resolving power and operate in a more robust fashion for large biopolymers compared to lower field instruments. Mass resolution up to 10(6) has been achieved for intermediate size biopolymers such as bovine ubiquitin (8.6 kDa) and bovine cytochrome c (12.4 kDa) without the use of frequency drift correction methods. A mass resolution of 370,000 has been demonstrated for isotopically resolved molecular ions of bovine serum albumin (66.5 kDa). Comparative measurements were made with the same spectrometer using a lower field 3.5-tesla magnet allowing the performance gains to be more readily quantified. Further improvements in pumping capacity of the vacuum system and efficiency of ion transmission from the source are expected to lead to further substantial sensitivity gains.