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.
KeywordsFourier transform FT Fourier transform mass spectrometry FTMS Ion cyclotron resonance ICR Transient signal Ion trap Proteomics
Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) provides the highest resolving power and mass accuracy for molecular structural analysis [1, 2, 3, 4, 5, 6]. Top-down proteomics and petroleomics, because of their extreme requirements for analytical performance, are the primary application areas of FT-ICR MS nowadays [3, 7]. Over the past decade, other application areas of interest were primarily addressed using Orbitrap FTMS and high-resolution time-of-flight (TOF) MS [4, 8, 9, 10, 11]. Nevertheless, the extreme analytical challenges in molecular structural analysis require further increase of FTMS performance. Owing to its fundamental power, further development of FT-ICR MS is feasible and may allow bridging the gap between the analytical requirements and MS capabilities. For that, a corresponding increase in high-performance analysis throughput is required. For example, even at the current data acquisition rate, the exceptional FT-ICR MS capabilities trigger development of novel approaches of molecular structural analysis . Among those, the uses of isotopic fine structure information in qualitative bottom-up proteomics and mass defect information in quantitative bottom-up proteomics appear particularly attractive [13, 14, 15]. Increased, for example, by a factor of 2–10, data acquisition rate should allow interrogation of more peptides at the required structural level and provide improved qualitative and quantitative protein analyses. Development of novel concepts for ion conditioning and manipulation in ICR cells based on improved understanding of ion motion fundamentals has thus become a target of recent innovations in the field [6, 16].
Since the inception of FT-ICR MS by Marshall and Comisarow, the design of ICR cells has been primarily based on the use of wide aperture detection electrodes and sinusoidal ion signals (that is, generation of transient signals whose spectral energy is concentrated primarily at the fundamental ion frequency) [12, 17]. Since the last decade or so, the most common ICR cell configuration has been a cylindrical cell with a pair of 90°-wide excitation electrodes and a pair of similar 90°-wide detection electrodes [4, 18]. The detected image charge ion signal is averaged during ion motion along the detection electrode surface, requiring low frequency (as determined from Nyquist criteria) sampling. The drawbacks of this configuration include a certain limitation on the acquisition rate, substantial perturbation of excitation radio frequency RF field by detection electrodes, and a low degree of design flexibility.
Marshall and co-workers have recently demonstrated by simulations that 120°-wide excitation electrodes are optimal for coherent ion dipolar excitation and elimination of the third harmonic . However, implementation of such electrodes for ion excitation would reduce the efficiency of ion detection using the currently employed ICR cell design concept. A feasible, although technically challenging, solution to this problem is the use of external switching electronic circuitry allowing for ion excitation and detection using the same pair of 120°-wide electrodes.
Quadrupolar modes of ion excitation, including the quadrature excitation, are other attractive approaches for improving the coherence of excited ion motion [20, 21, 22, 23]. ICR cell operation in these modes also suffers from the same low flexibility of the current ICR cell design, when wide aperture detection electrodes compete with the excitation electrodes for space. Improved coherence of ion motion in ICR cells has been efficiently addressed via harmonization of the trapping electric fields by a number of approaches, including those of Tolmachev et al. [24, 25], Gross et al. , Bruce et al. [27, 28], and Nikolaev and co-workers [29, 30]. The obtained improvements in FT-ICR MS performance are quite dramatic. Specifically, the transient lifetime has been substantially, about 10- to 100-fold, increased. The dynamically harmonized ICR cell, following the original idea of Boldin and Nikolaev , is particularly impressive, with demonstrated resolution of up to 40 million on a peptide (single peak) and a routinely achieved isotopic fine structure resolution on peptide ions even in moderate, 7 T, magnetic fields . The main drawback of the harmonized cells is that they do not improve the throughput (or the acquisition rate) of FT-ICR MS.
Signal detection at multiples of ion (reduced) cyclotron frequency, which is a feasible approach for increasing the throughput [32, 33, 34, 35, 36], is also limited by the design of those cells: they also comprise relatively wide aperture excitation and detection electrodes, resulting in a restricted factor of the generated multiples (e.g., ~22° electrodes and the fourth multiple for a 16-electrode ICR cell). A number of attempts have been made to reduce the aperture of detection electrodes. For example, Nikolaev and co-workers suggested an ICR cell with four detection electrodes made of conducting wires . However, the experimental implementation of the suggested ICR cell was deferred. One of the possible reasons for the failure was the positioning of these electrodes directly below the excitation electrodes in the areas with strong excite RF field, leading to excitation field distortion and pre-amplifier saturation prior to ion detection.
Here, we describe a concept, design, and implementation of an ICR cell with narrow aperture (flat) detection electrodes (NADEL) addressing the limitations of FT-ICR MS design and capabilities specified above. The analytical characteristics of thus introduced NADEL ICR cells are presented and their particular advantages are outlined.
Substance P, MRFA, Ultramark, and ubiquitin were purchased from Sigma-Aldrich (Buchs, Switzerland). ESI calibration mixture pre-formulated at low concentration was purchased from Agilent (Basel, Switzerland). Serum albumin (bovine) was purchased from Fisher Scientific (Schwerte, Germany). Polyphosphoric acid was obtained from Fluka (Buchs, Switzerland). C-terminally amidated peptides P1, P2, and P3: P1 – EESTR (monoisotopic mass 619.29255 Da), P2 – PMMSR (619.29342 Da), and P3 – HDGHR (619.29389 Da) were synthesized in-house with solid state peptide synthesis. All peptide and protein samples were used without further purification. LC-MS grade acetonitrile and water were obtained from Fluka (Buchs, Switzerland). Formic acid was obtained from Merck (Zug, Switzerland). Peptide and protein solutions were prepared in 1:1 (v/v) water/acetonitrile solvent mixtures containing 0.1% (v/v) of formic acid. The final sample concentration for all samples was ~1 μM, except ~10 μM for albumin. The polyphosphoric calibration mixture was prepared by adding 1% (v/v) of polyphosphoric acid to 1 mL of water. Maltene fraction of Venezuelan crude oil was dissolved in dichloromethane, followed by 1:23 dilution in acetonitrile with the addition of 2% of formic acid (by volume), as described previously .
NADEL ICR Cell Design and Mass Spectrometry
The NADEL as well as a standard Ultra (90° detection electrodes) ICR cells were mounted, one at a time, onto a hybrid linear ion trap Fourier transform ion cyclotron resonance mass spectrometer (LTQ FT-ICR MS; Thermo Scientific, Bremen, Germany) equipped with a 10 T actively shielded superconducting magnet (Oxford Nanoscience, Oxon, UK), described elsewhere. Instrument control was performed by the standard electronics and software (Xcalibur, Thermo Scientific). The ions were formed with robotic chip-based nano-electrospray ionization source (Triversa Nanomate; Advion Biosciences, Ithaca, NY, USA) and transported to the linear ion trap (LTQ) through an inlet set of multipole ion guides. A predetermined number of charges to be transferred into the ICR cell using another set of multipole ion guides were controlled by the automatic gain control (AGC) function of the LTQ. For petroleomics measurements the AGC function was disabled and accumulation time in the LTQ was set to 50 ms, while the potentials of the inlet transfer system were further optimized manually. For petroleomics analysis, these experimental parameters provided the best correlation of ion distribution envelope (the total width and position of the maximum of ion distribution) between ion detection in LTQ and in the ICR cell. Vacuum conditions in FT-ICR MS with NADEL or Ultra ICR cells were identical (2E-10 Torr).
where z is an axial coordinate and R is the electrode’s radius of curvature. For the NADEL ICR cell reported here, with 70 mm long detection electrodes, we selected a compromise value of R, 125 mm, as it provides a reasonable ratio of radial and axial trapping electric fields along the z-axis (as stated above, trapping potential distribution should be close to quadratic). SIMION calculations confirmed that the selected shape of the detection electrodes provides improved trapping field compared to rectangular narrow aperture detection electrodes, Figures S1 and S2 (Supporting Information). The parameters r0 and R can be optimized both numerically (e.g., using SIMION, and experimentally in further studies.
Ion excitation with NADEL ICR cell was technically performed in the same way as with Ultra ICR cell . Coherent motion of ions was excited by standard dipolar frequency-sweep excitation in the range of 72–2150 kHz applied during 10 ms to the excitation grids. The peak-to-peak amplitude of the excitation RF voltage was varied from 0 to 100 V. The particular advantage of the NADEL ICR cell compared with other ICR cell designs, including the Ultra cell, is in the improved excitation field distribution, Figure S3, top left (Supporting Information). Due to the positioning of the detection electrodes in the central plane, symmetrically between the top and bottom excitation electrodes, narrow aperture detection electrodes disturb the RF excite field significantly less than the standard 90° detection electrodes, as employed in Ultra cell. Therefore, ion excitation in the NADEL cell is more efficient than for a regular ICR cell, especially when exciting to a larger radius. Overall, the maximum excitation radius is limited by the location of the detection electrodes. However, to the best of our knowledge, ion excitation to large, >0.7 radius, orbits is not employed in modern FT-ICR MS [22, 24, 37]. Moreover, according to the estimation by the authors, most of the ICR cells function with ion excitation to 0.3–0.4 cell radius because of the increasing of the inhomogeneity of magnetic field at higher radii, although the exact data could not be found in publications. Therefore, the detection electrodes were placed at the corresponding positions, allowing ion excitation to 0.6 cell radius, and thus not reducing the effective ion volume. Note, a finite initial magnetron radius would correspondingly reduce the maximum achievable excitation radius. Figure S3, bottom (Supporting Information) demonstrates the difference in the ion detection conditions between NADEL and Ultra cells. Compared with the standard 90° detection electrodes, the narrow aperture detection electrodes increase the non-linear character of ion detection as a function of a post-excitation radius. Importantly, for NADEL cell sensitivity level, detection electrode capacitance of the installed NADEL cell (measured together with the connecting wires and feedthrough) was reduced four-fold compared with the Ultra ICR cell, as expected.
Ion detection was performed using the commercial ion detection configuration of the Ultra ICR cell. Briefly, standard dipolar differential detection was employed to acquire time domain signals (transients). The transients of variable length in the range of 96 ms–25 s were recorded in MIDAS format at 1–5 MHz sampling frequency (a regime with sinusoidal signals) using the advanced software interface of the built-in data acquisition system (Thermo Scientific). A given number (e.g., 10–100) of transients were averaged to obtain the final transients, which were Hann-apodized and zero-filled once before fast Fourier transformation (FFT) to yield Fourier spectra, which were further transformed to mass spectra using standard data analysis software (Xcalibur; Thermo Scientific) and the pyFTMS framework developed in-house.
Finally, the offset DC potentials in the range from –100 to +100 mV were applied to the NADEL and Ultra ICR cell detection and excitation electrodes independently relative to each other to vary the position of the ion cloud prior to ion excitation and during ion detection events. The influence of offset potentials on ion motion was monitored with diverse quality attributes of mass spectra (e.g., peak shape and magnetron sidebands ). Overall, it was possible to optimize the offset potentials to effectively decrease the magnetron sideband intensities below 1% relative to the corresponding reduced cyclotron frequency peak for each experiment at the optimal post-excitation ion cyclotron radius.
Results and Discussion
NADEL ICR Cell Initial Performance Tests: MS and MS/MS Data Acquisition
In-cell tandem mass spectrometry (MS/MS) experiments with NADEL ICR cell demonstrate efficiency comparable to Ultra cell. Typical electron capture dissociation (ECD) , infrared multiphoton dissociation (IRMPD) , and electron induced dissociation (EID) [42, 43] FT-ICR mass spectra are shown in Figure S5 (Supporting Information). MS/MS broadband mass spectra contain analyte peaks with a magnitude spreading over 3–4 decimal orders. Particularly, the spectral dynamic range (ion abundance ratio of the highest to the lowest peaks within a single mass spectrum)  of 4.4 orders was achieved for EID MS/MS measurements. Thus, NADEL ICR cell provides dipolar excitation and detection of ions, either injected from an external ion source or produced inside of the cell, in the wide mass range without the discrimination of different m/z ions and at a dynamic range comparable to the state-of-the-art FT-ICR MS performance. Note, the employed ion excitation for this mode of operation (generation of sinusoidal ion signals) aims to excite ions to moderate radii, when ions do not yet approach the detection electrodes. The resulting transient components for these regimes are primarily sinusoidal, with a very low (<5%) high-order harmonic content.
NADEL ICR Cell Performance: Sensitivity
The sensitivity levels of the NADEL ICR cell and the standard Ultra cell with 90° detection electrodes were compared for an isolated singly protonated MRFA peptide (m/z 524.3) under identical optimal instrumental parameters for both cells. As expected, a signal-to-noise ratio (SNR) of peak corresponding to the reduced cyclotron frequency ω+ linearly increased with the number of charges (ion abundance) for both NADEL and Ultra ICR cells, Figure 3 top right. The SNR values reached a plateau at around 1E5–2E5 number of charges in the isolation mode for both cells as well. This is likely due to the limitations of accumulation in LTQ and ion transport from LTQ to ICR cell for ions with the same nominal mass-to-charge ratio. Importantly, Figure 3 top right shows the increase of the peak SNR almost two times for the NADEL cell compared with the standard Ultra cell. Therefore, the experimental results demonstrate higher signal voltage developed across the detection circuit of the NADEL ICR cell compared with the corresponding signal in the standard 90° electrode Ultra ICR cell, despite the significantly reduced surface area of detection electrodes of the NADEL cell. This result can be explained by the substantially lower capacitance of the flat detect electrodes and shorter distance between the orbit of excited ions and detection electrodes. It is thus not surprising that only a few charges, approximately 10 ions (AGC = 30) per cell load, of triply protonated substance P (m/z 449.9) ions were detected with acquisition period of 384 ms and five transients averaging, Figure S6 (Supporting Information). This result correlates well with the known sensitivity performance level of 50 charges of the state-of-the-art FT-ICR MS with standard ICR cells.
NADEL ICR Cell Performance: Mass Accuracy
For low trapping potentials (<1 V) , the reduced cyclotron frequency ω+ peak remained within the frequency range of 1 ppm over the entire range of excitation amplitudes where ion signal can be detected, except the region of low excitation amplitudes, Figure 3, bottom right. However, frequency reduced with an increase in the trapping potential for high excitation amplitudes due to reduced harmonicity of the trapping electric potential. Thus, the electric field distribution of the NADEL ICR cell is uniform in the wide range of excitation amplitudes (post-excitation radii) at low trapping potentials. Note, the DC offset potentials were adjusted for each trapping potential independently when constructing these dependencies. Furthermore, at low excitation amplitudes (small post-excitation radii) for all trapping potentials a space charge of significant ion abundance (AGC = 5E4) is the reason for the observed frequency shift, as reported earlier . A scaling factor of the magnetron frequency was experimentally determined to be 2.7 Hz/V, Figure 3, bottom right. Experimental results allowed us to define optimal trapping potentials 0.8–1.0 V and excitation amplitude of 30–40 V with a duration of 10 ms. Additionally, the stability of the reduced cyclotron frequency measured for isolated singly protonated ions of MRFA 524.3 m/z with trapping potential of 1.0 V and excitation amplitude of 30 V indicates the absence of space charge effect in the wide range of number of charges, AGC = 1E2–1E5, for the NADEL ICR cell, Figure 3, bottom left.
RMS Mass Accuracy of Agilent ESI-L Low Concentration Tuning Mixture (Internal Calibration) and Polyphosphoric Acid (External Calibration, Based on the ESI-L Mixture) Obtained with Two Values of a Number of Charges (AGC Equal to 5E5 or 2E6)
RMS mass error, ppm
Mass range: 300–1400 m/z;
Tacq = 568 ms; Vtrap = 1 V (2 V)
Mass range: 300–3000 m/z;
Tacq = 1336 ms; Vtrap = 1 V
Mass calibration was evaluated by considering the mass measurement accuracies achieved in the same mass ranges for analyte peaks of polyphosphoric acid Hn+2PnO3n+1, n = 3–30, (monoisotopic peaks of protonated and ammonium adducts, as well as the 18O isotopologue of the protonated species), Table 1. Only analyte peaks with SNR higher than 3 were taken into account. The mass error did not exceed 750 ppb level with the root-mean-square (RMS) value of 330 ppb in the mass range 300–1400 m/z for both AGC settings and both trapping potentials. These results are comparable to those obtained using conventional ICR cells with external mass calibration [24, 46, 47]. Mass error increased for wider mass range, especially for higher AGC value; the corresponding dependencies are given in Figure S7 (Supporting information).
RMS Mass Accuracy of Polyphosphoric Acid (Internal Calibration) as a Function of Number of Charges
Mass range, m/z
RMS mass error, ppm
AGC = 3E5
AGC = 7E5
AGC = 2E6
AGC = 4E6
AGC = 6E6
300–1000 (8 peaks)
300–2000 (19 peaks)
300–3100 (29 peaks)
Thus, mass accuracy performance with NADEL ICR cell is comparable to those obtained with conventional and harmonized ICR cells. This conclusion also follows from the analysis of a crude oil fraction using NADEL ICR cell, vide infra. Application of absorption mode FT signal processing allows improving RMS mass accuracy values two times, as expected [50, 51, 52]. However, the observed increase in mass inaccuracy when a very wide m/z range is analyzed, Figure S7 (Supporting Information) and Table 1, needs further investigation. Particularly, influence of the modified trapping field should be considered. Indeed, Figure S1 (Supporting Information) shows that the detection electrode configuration described here introduces an azimuthal component of a trapping electric field, previously avoided in FT-ICR MS cell designs. On the other hand, it is known that the offset DC potentials typically employed to reduce harmonic content in FT-ICR mass spectra and improve peak shapes may introduce a similar azimuthal component to the trapping field distribution. Therefore, the exact character, destructive or constructive, of the modified trapping field is to be evaluated. Finally, further optimization of narrow aperture detection electrodes may reduce the introduced modulation of the trapping electric field.
NADEL ICR Cell Performance: Resolving Power
The resolving power performance of the NADEL ICR cell was evaluated in the analysis of peptide and protein samples with maximum detection period of 24.576 s for the employed hardware configuration. Acquisition of longer transients was not possible because of the technical limitations imposed by the on-board LTQ FT computer memory, whereas the lifetime of excited and coherent ion motion apparently surpasses this temporal limitation; for example see Figure S8 (Supporting Information). Notably, the achieved ion detection period of ~25 s is the record for LTQ FTMS instruments reports.
To evaluate NADEL ICR cell performance for heavy protein analysis, protein mass measurements were performed for a bovine serum albumin (BSA) with direct infusion ESI. Broadband mass spectrum of BSA obtained by averaging of 50 single scans of 1.536 s shows the charge state distribution in the range from 35+ up to 72+, Figure S9 (Supporting Information). Furthermore, the resolving power of 320′000 was achieved for an isolated BSA48+ charge state with a single scan and acquisition period of 6.144 s, Figure S10 (Supporting Information).
Peak Assignments and Mass Errors in the Segments Around 451 m/z of the Positive ESI Broadband Mass Spectrum of a Crude Oil fraction. Corresponding Inset is Shown in Figure 6
To conclude, the combined benefits of trapping and excitation field configuration in the NADEL cell provide comparable performance to standard ICR cells in routine analysis in regard to resolving power performance. The obtained characteristics approach those of the most sophisticated ICR cells with complex approaches to electric field harmonization, either statically or dynamically, for the investigated 10 T magnetic field [24, 29, 46]. The described NADEL ICR cell has been employed to perform routine mass analysis in our laboratory and demonstrated an ability to achieve the required analytical objectives of molecular structural analysis in a number of applications, for example in the analysis of supramolecular complexes .
NADEL ICR Cell Concept Advantages
The particular benefits of the NADEL ICR cell concept for current and envisioned FT-ICR MS configurations include: (1) enhanced dipolar ion excitation conditions because of improved configuration of excite electric field. The latter is achieved by reduced excitation field disturbance by radially inserted detection electrodes compared with the standard 90° degrees wide detection electrodes, Figure S3 (Supporting Information). Further improvement of excite electric field distribution can be presumably obtained by utilization of wide aperture excitation electrodes with an optimized angle, which can be now varied up to 180°. Interestingly, flat (wide aperture) excitation electrodes (capacitor configuration) may be considered to provide an optimum excitation field configuration; (2) simultaneous detection of a number of transients or detection at frequency multiples when several NADEL pairs are employed, for instance leading to an optimized design of the recently implemented quadruple frequency multiple detection ICR cell ; (3) enabling implementation of efficient quadrature ion excitation and quadrupolar ion detection schemes when two pairs of 90° wide excite electrodes and two NADEL pairs are employed without the need for a high-frequency switch between excitation and detection modes. Quadrupolar ion detection should further benefit high mass accuracy and high dynamic range demanding applications by providing measurements of trapping potential-insensitive unperturbed ion cyclotron frequency [23, 55]; (4) creation of special ion motion conditions in ICR cell even with dipolar ion excitation leading to ion detection at unperturbed cyclotron frequency ; (5) facilitating and improving the efficiency of fluorescence-based ion spectroscopy due to substantially increased optical access to and from the cell [57, 58, 59]; and, last but not least, (6) enabling high throughput high-resolution mass spectrometry by accelerating ions to high post-excitation radii when, significantly, an order of magnitude higher resolving power can be obtained in the same ion detection period. The latter regime requires the development of the matching signal processing methods, capable of efficient analysis of periodic non-sinusoidal transients with high order harmonics .
We designed and implemented an ICR cell with a pair of narrow aperture detection electrodes (NADEL) for improving the analytical capabilities and increasing the mass analyzer design flexibility of FT-ICR MS. The obtained results demonstrate that the narrow aperture (flat) detection electrodes provide comparable or superior performance relative to the standard (commercial) ICR cells in modern FT-ICR MS. As proven here, the ability to replace the currently employed wide aperture (azimuthally large) detection electrodes in all ICR cell designs with the narrow aperture ones opens new avenues for ICR cell development and FT-ICR MS capabilities. A number of advantages and envisioned benefits validate the importance of the described ICR cell development. Rationalizing the underlying ion physics phenomena leading to these capabilities (e.g., unperturbed ion cyclotron frequency detection with dipolar ion detection) requires in-depth theoretical analysis of the described NADEL ICR cell and its further modifications.
The authors are grateful to Konstantin O. Zhurov for technical assistance and discussions. The authors also express their gratitude to Thermo Fisher Scientific Inc. for providing access under license to LTQ FT transient signals and advanced user interface. They acknowledge financial support through the Swiss National Science Foundation (SNF project 200021-125147/1) and the European Research Council (ERC Starting Grant 280271).
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