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

Evaluation of major historical ICR cell designs using electric field simulations

In Fourier-transform ion cyclotron resonance mass spectrometry, ions are detected by measuring image current induced in the detecting electrodes by trapped ions rotating in a magnetic field at their cyclotron frequencies. The ion trap used for this purpose is called the Penning trap. It can have various configurations of electrodes that are used to create a trapping electric field, to excite cyclotron motion, and to detect the induced signal. The evolution of this type of mass spectrometry is mainly driven by progress in the technology of superconducting magnets and in the constantly improved design of the ion cyclotron resonance (ICR) measuring cell. In this review, we focus on ICR cell designs. We consider that the driving forces of this evolution are the desire to increase resolution, mass accuracy and dynamic range, as well as to adapt new methods for creating and trapping ions.

Parallel Detection of Fundamental and Sixth Harmonic Signals Using an ICR Cell with Dipole and Sixth Harmonic Detectors

Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) is a powerful instrument for high-resolution analysis of biomolecules. However, relatively long signal acquisition periods are needed to achieve mass spectra with high resolution. The use of multiple detector electrodes for detection of harmonic frequencies has been introduced as one approach to increase scan rate for a given resolving power or to obtain increased resolving power for a given detection period. The achieved resolving power and scan rate increase linearly with the order of detected harmonic signals. In recent years, ICR cell geometries have been investigated to increase the order of the harmonic frequencies and enhance harmonic signal intensities. In this study, we demonstrated PCB-based ICR cell designs with dipole and sixth harmonic detectors for parallel detection of fundamental and harmonic (6f) signals. The sixth harmonic signals from the sixth harmonic detector showed an expected 6 times higher resolving power with (M + 3H)3+ charge state insulin ions as compared with that from fundamental signals from the dipole detector. Moreover, the insulin isotopic peaks with sixth harmonic frequency signals acquired with the sixth harmonic detector were resolved for a 40 ms data acquisition period but unresolved with the same duration dipole detector signals, corresponding to a 6-fold improvement in achievable spectral acquisition rates for a given resolving power.

NeuCode Proteomics Reveals Bap1 Regulation of Metabolism

We introduce neutron-encoded (NeuCode) amino acid labeling of mice as a strategy for multiplexed proteomic analysis in vivo. Using NeuCode, we characterize an inducible knockout mouse model of Bap1, a tumor suppressor and deubiquitinase whose in vivo roles outside of cancer are not well established. NeuCode proteomics revealed altered metabolic pathways following Bap1 deletion, including profound elevation of cholesterol biosynthetic machinery coincident with reduced expression of gluconeogenic and lipid homeostasis proteins in liver. Bap1 loss increased pancreatitis biomarkers and reduced expression of mitochondrial proteins. These alterations accompany a metabolic remodeling with hypoglycemia, hypercholesterolemia, hepatic lipid loss, and acinar cell degeneration. Liver-specific Bap1 null mice present with fully penetrant perinatal lethality, severe hypoglycemia, and hepatic lipid deficiency. This work reveals Bap1 as a metabolic regulator in liver and pancreas, and it establishes NeuCode as a reliable proteomic method for deciphering in vivo biology.

Developments in FTICR-MS and Its Potential for Body Fluid Signatures

Fourier transform mass spectrometry (FTMS) is the method of choice for measurements that require ultra-high resolution. The establishment of Fourier transform ion cyclotron resonance (FTICR) MS, the availability of biomolecular ionization techniques and the introduction of the Orbitrap™ mass spectrometer have widened the number of FTMS-applications enormously. One recent example involves clinical proteomics using FTICR-MS to discover and validate protein biomarker signatures in body fluids such as serum or plasma. These biological samples are highly complex in terms of the type and number of components, their concentration range, and the structural identity of each species, and thus require extensive sample cleanup and chromatographic separation procedures. Clearly, such an elaborate and multi-step sample preparation process hampers high-throughput analysis of large clinical cohorts. A final MS read-out at ultra-high resolution enables the analysis of a more complex sample and can thus simplify upfront fractionations. To this end, FTICR-MS offers superior ultra-high resolving power with accurate and precise mass-to-charge ratio (m/z) measurement of a high number of peptides and small proteins (up to 20 kDa) at isotopic resolution over a wide mass range, and furthermore includes a wide variety of fragmentation strategies to characterize protein sequence and structure, including post-translational modifications (PTMs). In our laboratory, we have successfully applied FTICR “next-generation” peptide profiles with the purpose of cancer disease classifications. Here we will review a number of developments and innovations in FTICR-MS that have resulted in robust and routine procedures aiming for ultra-high resolution signatures of clinical samples, exemplified with state-of-the-art examples for serum and saliva.

Ion trap with narrow aperture detection electrodes for Fourier transform ion cyclotron resonance mass spectrometry

The current paradigm in ion trap (cell) design for Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) is the ion detection with wide aperture detection electrodes. Specifically, excitation and detection electrodes are typically 90° wide and positioned radially at a similar distance from the ICR cell axis. Here, we demonstrate that ion detection with narrow aperture detection electrodes (NADEL) positioned radially inward of the cell's axis is feasible and advantageous for FT-ICR MS. We describe design details and performance characteristics of a 10 T FT-ICR MS equipped with a NADEL ICR cell having a pair of narrow aperture (flat) detection electrodes and a pair of standard 90° excitation electrodes. Despite a smaller surface area of the detection electrodes, the sensitivity of the NADEL ICR cell is not reduced attributable to improved excite field distribution, reduced capacitance of the detection electrodes, and their closer positioning to the orbits of excited ions. The performance characteristics of the NADEL ICR cell are comparable with the state-of-the-art FT-ICR MS implementations for small molecule, peptide, protein, and petroleomics analyses. In addition, the NADEL ICR cell's design improves the flexibility of ICR cells and facilitates implementation of advanced capabilities (e.g., quadrupolar ion detection for improved mainstream applications). It also creates an intriguing opportunity for addressing the major bottleneck in FTMS-increasing its throughput via simultaneous acquisition of multiple transients or via generation of periodic non-sinusoidal transient signals.

Neutron encoded labeling for peptide identification

Metabolic labeling of cells using heavy amino acids is most commonly used for relative quantitation; however, partner mass shifts also detail the number of heavy amino acids contained within the precursor species. Here, we use a recently developed metabolic labeling technique, NeuCode (neutron encoding) stable isotope labeling with amino acids in cell culture (SILAC), which produces precursor partners spaced ~40 mDa apart to enable amino acid counting. We implement large scale counting of amino acids through a program, "Amino Acid Counter", which determines the most likely combination of amino acids within a precursor based on NeuCode SILAC partner spacing and filters candidate peptide sequences during a database search using this information. Counting the number of lysine residues for precursors selected for MS/MS decreases the median number of candidate sequences from 44 to 14 as compared to an accurate mass search alone (20 ppm). Furthermore, the ability to co-isolate and fragment NeuCode SILAC partners enables counting of lysines in product ions, and when the information is used, the median number of candidates is reduced to 7. We then demonstrate counting leucine in addition to lysine results in a 6-fold decrease in search space, 43 to 7, when compared to an accurate mass search. We use this scheme to analyze a nanoLC-MS/MS experiment and demonstrate that accurate mass plus lysine and leucine counting reduces the number of candidate sequences to one for ~20% of all precursors selected, demonstrating an ability to identify precursors without MS/MS analysis.

Fourier transform mass spectrometry

This article provides an introduction to Fourier transform-based mass spectrometry. The key performance characteristics of Fourier transform-based mass spectrometry, mass accuracy and resolution, are presented in the view of how they impact the interpretation of measurements in proteomic applications. The theory and principles of operation of two types of mass analyzer, Fourier transform ion cyclotron resonance and Orbitrap, are described. Major benefits as well as limitations of Fourier transform-based mass spectrometry technology are discussed in the context of practical sample analysis, and illustrated with examples included as figures in this text and in the accompanying slide set. Comparisons highlighting the performance differences between the two mass analyzers are made where deemed useful in assisting the user with choosing the most appropriate technology for an application. Recent developments of these high-performing mass spectrometers are mentioned to provide a future outlook.

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.

Initial experimental characterization of a new ultra-high resolution FTICR cell with dynamic harmonization

A new Fourier transform ion cyclotron resonance (FTICR) cell based on completely new principles of formation of the effective electric potential distribution in Penning type traps, Boldin and Nikolaev (Proceedings of the 58th ASMS Conference, 2010), Boldin and Nikolaev (Rapid Commun Mass Spectrom 25:122-126, 2011) is constructed and tested experimentally. Its operation is based on the concept of electric potential space-averaging via charged particle cyclotron motion. Such an averaging process permits an effective electric force distribution in the entire volume of a cylindrical Penning trap to be equal to its distribution in the field created by hyperbolic electrodes in an ideal Penning trap. The excitation and detection electrodes of this new cell are shaped for generating a quadratic dependence on axial coordinates of an averaged (along cyclotron motion orbit) electric potential at any radius of the cyclotron motion. These electrodes together with the trapping segments form a cylindrical surface like in a conventional cylindrical cell. In excitation mode this cell being elongated behaves almost like an open cylindrical cell of the same length. It is more effective in ion motion harmonization at larger cyclotron radii than a Gabrielse et al.-type (Int J Mass Spectrom Ion Processes 88:319-332, 1989) cylindrical cell with four compensation sections. A mass resolving power of more than twenty millions of reserpine (m/z 609) and more than one million of highly charged BSA molecular ions (m/z 1357) has been obtained in a 7T magnetic field.

Ion Behavior in an Electrically Compensated Ion Cyclotron Resonance Trap

We recently described a new electrically compensated trap in FT ion cyclotron resonance mass spectrometry and developed a means of tuning traps of this general design. Here, we describe a continuation of that research by comparing the ion transient lifetimes and the resulting mass resolving powers and signal-to-noise (S/N) ratios that are achievable in the compensated vs. uncompensated modes of this trap. Transient lifetimes are ten times longer under the same conditions of pressure, providing improved mass resolving power and S/N ratios. The mass resolving power as a function of m/z is linear (log-log plot) and nearly equal to the theoretical maximum. Importantly, the ion cyclotron frequency as a function of ion number decreases linearly in accord with theory, unlike its behavior in the uncompensated mode. This linearity should lead to better control in mass calibration and increased mass accuracy than achievable in the uncompensated mode.

Fourier transform ion cyclotron resonance cell with dynamic harmonization of the electric field in the whole volume by shaping of the excitation and detection electrode assembly

A new principle of formation of the effective electric field distribution in a Penning trap is presented. It is based on the concept of electric potential space averaging via charged particle cyclotron motion. The method of making hyperbolic-type field distribution in the whole volume of a cylindrical Penning trap is developed on the basis of this new principal. The method is based on subdividing the cell cylindrical surface into segments with shapes producing quadratic dependence on axial coordinate of an averaged (along cyclotron motion orbit) electric potential at any radius of cyclotron motion. The cell performance is compared in digital experiments with the performance of a Gabrielse-type cylindrical cell with four compensation electrodes and is shown to be more effective in ion motion harmonization at higher cyclotron radii and axial oscillation amplitude.

Excite-coupled trapping ring electrode cell (eTREC): radial trapping field control, linearized excitation, and improved detection

A novel excite-coupled Trapping Ring Electrode Cell (eTREC) was designed and developed. eTREC technology provides greater linearity in the excitation electric field along with minimized variation in radial trapping field during detection. The variation in the radial trapping electric field is reduced through postexcitation modulation of the trapping potentials applied to the Trapping Ring Electrode Cell (TREC). Linearization of the electric field generated during radio frequency (RF) excitation is accomplished by coupling the RF excitation to a novel electrode arrangement superimposed onto the trapping rings of a TREC. The coupling of RF excitation to the trap plates effectively reduces z-axis ejection and allows for a more uniform postexcitation radius for the entire ion population. Using this technology, sensitivity was increased by >50%, resolution of (13)C(2) and (34)S fine structure peaks was achieved with the peptide MMMMG (approximately 330,000 RP) on a 3 T system, and the limit of detection was significantly reduced.

A tuning method for electrically compensated ion cyclotron resonance mass spectrometer traps

We describe a method for tuning electrically compensated ion cyclotron resonance (ICR) traps by tracking the observed cyclotron frequency of an ion cloud at different oscillation mode amplitudes. Although we have used this method to tune the compensation voltages of a custom-built electrically compensated trap, the approach is applicable to other designs that incorporate electrical compensation. To evaluate the effectiveness of tuning, we examined the frequency shift as a function of cyclotron orbit size at different z-mode oscillation amplitudes. The cyclotron frequencies varied initially by approximately 12 ppm for ions with low z-mode oscillation amplitudes compared with those with high z-mode amplitudes. This frequency difference decreased to approximately 1 ppm by one iteration of trap tuning.

The spontaneous loss of coherence catastrophe in Fourier transform ion cyclotron resonance mass spectrometry

The spontaneous loss of coherence catastrophe (SLCC) is a frequently observed, yet poorly studied, space-charge related effect in Fourier-transform ion cyclotron resonance mass spectrometry (FTICR-MS). This manuscript presents an application of the filter diagonalization method (FDM) in the analysis of this phenomenon. The temporal frequency behavior reproduced by frequency shift analysis using the FDM shows the complex nature of the SLCC, which can be explained by a combination of factors occurring concurrently, governed by electrostatics and ion packet trajectories inside the ICR cell.

Trapping ring electrode cell: a FTICR mass spectrometer cell for improved signal-to-noise and resolving power

A novel FTICR cell called the trapping ring electrode cell (TREC) has been conceived, simulated, developed, and tested. The performance of the TREC is compared to a closed cylindrical cell at different excited cyclotron radii. The TREC permits the ability to maintain coherent ion motion at larger initial excited cyclotron radii by decreasing the change in radial electric field with respect to z-axis position in the cell. This is accomplished through postexcitation modulation of the trapping potentials applied to segmented trap plates. Resolving power approaching the theoretical limit was achieved using the novel TREC technology; over 420,000 resolving power was observed on melittin [M + 4H] (4+) species when employed under modest magnetic field strength (3T) and a data acquisition duration of 13 s. A 10-fold gain in signal-to-noise ratio is demonstrated over the closed cylindrical cell optimized with common potentials on all ring electrodes. The observed frequency drift during signal acquisition over long time periods was also significantly reduced, resulting in improved resolving power.

An electrically compensated trap designed to eighth order for FT-ICR mass spectrometry

We present the design, guided by theory to eighth order, and the first evaluation of a Fourier transform ion cyclotron resonance (FT-ICR) compensated trap. The purpose of the new trap is to reduce effects of the nonlinear components of the trapping electric field; those nonliner components introduce variations in the cyclotron frequency of an ion depending on its spatial position (its cyclotron and trapping mode amplitudes). This frequency spread leads to decreased mass resolving power and signal-to-noise. The reduction of the spread of cyclotron frequencies, as explicitly modeled in theory, serves as the basis for our design. The compensated trap shows improved signal-to-noise and at least a threefold increase in mass resolving power compared to the uncompensated trap at the same trapping voltage. Resolving powers (FWHH) as high as 1.7 x 10(7) for the [M + H](+) of vasopressin at m/z 1084.5 in a 7.0-tesla induction can be obtained when using trap compensation.

Trapped-ion cell with improved DC potential harmonicity for FT-ICR MS

The trapped-ion cell is a key component critical for optimal performance in Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometry (MS). To extend the performance of FT-ICR MS, we have developed a new cell design that is capable of generating a DC trapping potential which closely approaches that of an ideal Penning trap, i.e., a 3D axial quadrupolar potential distribution. The new cell design was built upon an open cylindrical geometry, supplemented with two pairs of cylindrical compensation segments. Electric potential calculations for trial cell geometries were aimed at minimizing spatial variations of the radial electric field divided by radius. The resulting cell proportions and compensation voltages delivered practically constant effective ion cyclotron frequency that was independent of ion radial and axial positions. Our customized 12 tesla FT-ICR instrument was upgraded with the new cell, and the performance was characterized for a range of ion excitation power and ion populations. Operating the compensated cell at increased postexcitation radii, approximately 0.7 of the cell inner radius, resulted in improved mass measurement accuracy together with increased signal intensity. Under these same operating conditions the noncompensated open cell configuration exhibited peak splitting and reduced signal life time. Mass accuracy tests using 11 calibrants covering a wide m/z range reproducibly produced under 0.05 ppm RMS precision of the internal calibration for reduced ion populations and the optimal excitation radius. Conditions of increased ion population resulted in a twofold improvement in mass accuracy compared with the noncompensated cell, due to the larger achievable excitation radii and correspondingly lower space charge related perturbations of the calibration law.

Reduction of axial kinetic energy induced perturbations on observed cyclotron frequency

With Fourier transform ion cyclotron resonance (FTICR) mass spectrometry one determines the mass-to-charge ratio of an ion by measuring its cyclotron frequency. However, the need to confine ions to the trapping region of the ion cyclotron resonance (ICR) cell with electric fields induces deviations from the unperturbed cyclotron frequency. Additional perturbations to the observed cyclotron frequency are often attributed to changes in space charge conditions. This study presents a detailed investigation of the observed ion cyclotron frequency as a function of ion z-axis kinetic energy. In a perfect three-dimensional quadrupolar field, cyclotron frequency is independent of position within the trap. However, in most ICR cell designs, this ideality is approximated only near the trap center and deviations arise from this ideal quadrupolar field as the ion moves both radially and axially from the center of the trap. To allow differentiation between deviations in observed cyclotron frequency caused from changes in space charge conditions or differences in oscillation amplitude, ions with identical molecular weights but different axial kinetic energy, and thus amplitude of z-axis motion, were simultaneously trapped within the ICR cell. This allows one to attribute deviations in observed cyclotron frequency to differences in the average force from the radial electric field experienced by ions of different axial amplitude. Experimentally derived magnetron frequency is compared with the magnetron frequency calculated using SIMION 7.0 for ions of different axial amplitude. Electron promoted ion coherence, or EPIC, is used to reduce the differences in radial electric fields at different axial positions. Thus with the application of EPIC, the differences in observed cyclotron frequencies are minimized for ions of different axial oscillation amplitudes.

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.