A novel Fourier transform ion cyclotron resonance mass spectrometer with improved ion trapping and detection capabilities

A planar quadrupole device for transmitting and trapping ions in high vacuum

RATIONALE

Hybrid mass spectrometers combine multiple mass analyzers to achieve optimal performance in terms of tandem mass spectrometry, high mass resolving power, and mass measurement accuracy for studying highly complex samples. As a result, the need for transport, trapping, and control of ion kinetic energies is critical for the successful integration of multiple mass analyzers and hybrid instrument operation. In addition, transportation of ion populations between two physically distinct locations can result in time-of-flight (TOF) discrimination against ions with widely disparate m/z values, compromising full mass spectral performance. In this work, we demonstrated a new ion guide, referred to as a planar quadrupole (PQ) ion guide, composed of two parallel printed circuit boards (PCB) that allow radiofrequency (RF) and direct current (DC) voltages to be combined to enable both axial transport and trapping of ion populations in the ultrahigh vacuum region of the mass spectrometer. As compared with a conventional multipole ion guide, the PQ ion guide showed comparable performance in ion m/z values, signal-to-noise, and intensity and effectively reduced mass discrimination caused by TOF effects.

METHODS

A PQ device was developed with two PCBs and simulated with SIMION 8.1. Electrospray ionization and Fourier transform ion cyclotron resonance mass spectrometry instrumentation were used for the testing of PQ performance.

RESULTS

.In this work, we demonstrated a planar quadrupole (PQ) ion guide composed of two parallel PCB plates. The PQ enables both axial ion transport and trapping of ion populations throughout the ion transfer process from a LTQ to an ICR cell. As compared with a conventional multipole ion guide, the PQ showed comparable ion transmission efficiency and effectively reduced mass discrimination caused by TOF effects.

CONCLUSIONS

The PQ is a simple design that can be implemented for ion transmission and trapping on virtually any mass spectrometer.

Fourier transform ion cyclotron resonance mass spectrometry at the true cyclotron frequency

Ion cyclotron resonance (ICR) cells provide stability and coherence of ion oscillations in crossed electric and magnetic fields over extended periods of time. Using the Fourier transform enables precise measurements of ion oscillation frequencies. These precisely measured frequencies are converted into highly accurate mass-to-charge ratios of the analyte ions by calibration procedures. In terms of resolution and mass accuracy, Fourier transform ICR mass spectrometry (FT-ICR MS) offers the highest performance of any MS technology. This is reflected in its wide range of applications. However, in the most challenging MS application, for example, imaging, enhancements in the mass accuracy of fluctuating ion fluxes are required to continue advancing the field. One approach is to shift the ion signal power into the peak corresponding to the true cyclotron frequency instead of the reduced cyclotron frequency peak. The benefits of measuring the true cyclotron frequency include increased tolerance to electric fields within the ICR cell, which enhances frequency measurement precision. As a result, many attempts to implement this mode of FT-ICR MS operation have occurred. Examples of true cyclotron frequency measurements include detection of magnetron inter-harmonics of the reduced cyclotron frequency (i.e., the sidebands), trapping field-free (i.e., screened) ICR cells, and hyperbolic ICR cells with quadrupolar ion detection. More recently, ICR cells with spatially distributed ion clouds have demonstrated attractive performance characteristics for true cyclotron frequency ion detection. Here, we review the corresponding developments in FT-ICR MS over the past 40 years.

Towards Higher Sensitivity of Mass Spectrometry: A Perspective From the Mass Analyzers

Mass spectrometry (MS) is one of the most widely used analytical techniques in many fields. Recent developments in chemical and biological researches have drawn much attention to the measurement of substances with low abundances in samples. Continuous efforts have been made consequently to further improve the sensitivity of MS. Modifications on the mass analyzers of mass spectrometers offer a direct, universal and practical way to obtain higher sensitivity. This review provides a comprehensive overview of the latest developments in mass analyzers for the improvement of mass spectrometers' sensitivity, including quadrupole, ion trap, time-of-flight (TOF) and Fourier transform ion cyclotron (FT-ICR), as well as different combinations of these mass analyzers. The advantages and limitations of different mass analyzers and their combinations are compared and discussed. This review provides guidance to the selection of suitable mass spectrometers in chemical and biological analytical applications. It is also beneficial to the development of novel mass spectrometers.

A new optimization strategy for MALDI FTICR MS tissue analysis for untargeted metabolomics using experimental design and data modeling

Ultra-high-resolution imaging mass spectrometry using matrix-assisted laser desorption ionization (MALDI) MS coupled to a Fourier transform ion cyclotron resonance (FTICR) mass analyzer is a powerful technique for the visualization of small molecule distribution within biological tissues. The FTICR MS provides ultra-high resolving power and mass accuracy that allows large molecular coverage and molecular formula assignments, both essential for untargeted metabolomics analysis. These performances require fine optimizations of the MALDI FTICR parameters. In this context, this study proposes a new strategy, using experimental design, for the optimization of ion transmission voltages and MALDI parameters, for tissue untargeted metabolomics analysis, in both positive and negative ionization modes. These experiments were conducted by assessing the effects of nine factors for ion transmission voltages and four factors for MALDI on the number of peaks, the weighted resolution, and the mean error within m/z 150-1000 mass range. For this purpose, fractional factorial designs were used with multiple linear regression (MLR) to evaluate factor effects and to optimize parameter values. The optimized values of ion transmission voltages (RF amplitude TOF, RF amplitude octopole, frequency transfer optic, RF frequency octopole, deflector plate, funnel 1, skimmer, funnel RF amplitude, time-of-flight, capillary exit), MALDI parameters (laser fluence, number of laser shots), and detection parameters (data size, number of scans) led to an increase of 32% and 18% of the number of peaks, an increase of 8% and 39% of the resolution, and a decrease of 56% and 34% of the mean error in positive and negative ionization modes, respectively. Graphical abstract.

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.

A pulsed pinhole atmospheric pressure interface for simplified mass spectrometry instrumentation with enhanced sensitivity

RATIONALE

A proof-of-concept pulsed pinhole atmospheric pressure interface, namely PP-API, was developed and characterized for mass spectrometry instrumentation.

METHODS

The PP-API was analyzed and optimized theoretically with respect to gas flow rate, opening force and dimensions. A PP-API interfaced mass spectrometry system was then constructed and tested.

RESULTS

As a discontinuous pressure interface, the PP-API allows efficient ion transfer from atmosphere pressure ionization sources to ion traps directly. Both nano-ESI and APCI ionization sources have been successfully integrated with the PP-API interface for the detection of volatile, organic, peptide and polymer samples. The use of multiple ionization sources has also been demonstrated to enhance signal intensity, as well as avoid charge competitions in ionization sources.

CONCLUSIONS

With simplified geometry and high ion transfer efficiency, this PP-API would enable miniaturized mass spectrometry systems with high sensitivity.

Improved ion optics for introduction of ions into a 9.4-T Fourier transform ion cyclotron resonance mass spectrometer

Enhancements to the ion source and transfer optics of our 9.4 T Fourier transform ion cyclotron resonance (ICR) mass spectrometer have resulted in improved ion transmission efficiency for more sensitive mass measurement of complex mixtures at the MS and MS/MS levels. The tube lens/skimmer has been replaced by a dual ion funnel and the following octopole by a quadrupole for reduced ion cloud radial expansion before transmission into a mass-selective quadrupole. The number of ions that reach the ICR cell is increased by an order of magnitude for the funnel/quadrupole relative to the tube lens/skimmer/octopole.

Absorption-mode: the next generation of Fourier transform mass spectra

The Fourier transform spectrum can be presented in the absorption-mode (commonly used in FT-NMR), magnitude-mode (FT-ICR), and power-mode (engineering applications). As is routinely used in FT-NMR, it is well-known that the absorption-mode display gives a much narrower peak shape which greatly improves the spectrum; recently, the successful solution of the phase equation allowed broadband phase correction which makes it possible to apply the absorption-mode routinely in FT-ICR. With the empirical evidence provided herein, it has been confirmed that in addition to the improvement on resolving power, compared to the conventional magnitude-mode, the new absorption-mode improves the signal-to-noise ratio (S/N) of a spectrum by 1.4-fold and can improve the mass accuracy up to 2-fold with no extra cost in instrumentation. Therefore, it is worthwhile to apply and promote absorption-mode in routine FT-ICR experiments.

A novel 9.4 tesla FTICR mass spectrometer with improved sensitivity, mass resolution, and mass range

Fourier transform ion cyclotron resonance (FTICR) mass spectrometry provides unparalleled mass measurement accuracy and resolving power. However, propagation of the technique into new analytical fields requires continued advances in instrument speed and sensitivity. Here, we describe a substantial redesign of our custom-built 9.4 tesla FTICR mass spectrometer that improves sensitivity, acquisition speed, and provides an optimized platform for future instrumentation development. The instrument was designed around custom vacuum chambers for improved ion optical alignment, minimized distance from the external ion trap to magnetic field center, and high conductance for effective differential pumping. The length of the transfer optics is 30% shorter than the prior system, for reduced time-of-flight mass discrimination and increased ion transmission and trapping efficiency at the ICR cell. The ICR cell, electrical vacuum feedthroughs, and cabling have been improved to reduce the detection circuit capacitance (and improve detection sensitivity) 2-fold. The design simplifies access to the ICR cell, and the modular vacuum flange accommodates new ICR cell technology, including linearized excitation, high surface area detection, and tunable electrostatic trapping potential.

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.

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.

Ion trajectory simulations in a high-pressure cylindrical ion trap

We present the simulation of a cylindrical ion trap (CIT) at high pressure (5-25 Torr range). SIMION 7.0 software was used for the simulations. The effect of pressure, RF frequency and trap dimensions has been investigated. The shape of stability diagrams at non-zero pressure is drastically different from the one observed in vacuum. Preliminary experimental results are shown, using a r = z = 3 mm-long CIT at 12 Torr for trapping peptide and protein ions.