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Rajkovic M, Benter S, Hammelrath M, Thinius M, Benter T, Wißdorf W. IDSimF: An Open-Source Framework for the Simulation of Molecular Ion Dynamics in Mass Spectrometry and Ion Mobility Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:1451-1460. [PMID: 38828667 DOI: 10.1021/jasms.4c00054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2024]
Abstract
The development of mass spectrometric and ion mobility devices heavily depends on a comprehensive understanding of the behavior of ions within such systems. Therefore, numerical modeling of ion paths helps to optimize and verify existing devices, and contributes to the development of innovative ion optical systems and multipole geometries. This Article introduces IDSimF (Ion Dynamics Simulation Framework), an open-source simulation tool tailored to the nonrelativistic dynamics of molecular ions in mass and ion mobility spectrometry applications. Addressing limitations in existing software packages, as for example SIMION, OpenFOAM, and COMSOL, IDSimF offers a specialized platform for simulating ion trajectories in electric fields. IDSimF efficiently accounts for space charge effects and considers various ion-neutral collision models while handling chemical kinetics. The framework is highly modular with reduced user input configuration complexity and aims to support simulation efforts in development and optimization of in mass spectrometers.
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Affiliation(s)
- Michelle Rajkovic
- Department of Physical and Theoretical Chemistry, University of Wuppertal, Gaussstraße 20, 42119 Wuppertal, Germany
| | - Sanna Benter
- Department of Physical and Theoretical Chemistry, University of Wuppertal, Gaussstraße 20, 42119 Wuppertal, Germany
| | - Maja Hammelrath
- Department of Physical and Theoretical Chemistry, University of Wuppertal, Gaussstraße 20, 42119 Wuppertal, Germany
| | - Marco Thinius
- Department of Physical and Theoretical Chemistry, University of Wuppertal, Gaussstraße 20, 42119 Wuppertal, Germany
| | - Thorsten Benter
- Department of Physical and Theoretical Chemistry, University of Wuppertal, Gaussstraße 20, 42119 Wuppertal, Germany
| | - Walter Wißdorf
- Department of Physical and Theoretical Chemistry, University of Wuppertal, Gaussstraße 20, 42119 Wuppertal, Germany
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Neugebauer TS, Memboeuf A. The Resonant Excitation Process in Commercial Quadrupole Ion Traps Revisited. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:2685-2697. [PMID: 34606712 DOI: 10.1021/jasms.1c00219] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The collision-induced resonant excitation process in real quadrupole ion traps is revisited theoretically and experimentally by explicitly including in the discussion the influence of higher order potential impurities. This includes mainly the dependence of the secular oscillation frequency fion on the ion's oscillation amplitude zmax. Due to frequency calibration, commercial ion traps use excitation frequencies fexc that are higher than the theoretical secular oscillation frequency fion. This may lead to switching in frequency order between fexc and fion that can allow ions to stay longer in on-resonance. It is also found that there is a most efficient but also a harshest excitation frequency, which are not identical. These phenomena are explained and described with a simple harmonic oscillator model and precise numerical calculations, using the trajectory simulation program ITSIM 5.0. Experimental MS2 have been performed with the thermometer ion leucine-enkephalin, which are then in line with expectations from the trajectory calculations. The important difference to the existing literature is that, here, overexcitation is characterized by the observed a4/b4 fragment-ion ratio, while the fragmentation efficiency was kept constant. By slightly increasing the excitation frequency one can obtain drastically different effective collisional temperatures. This knowledge gives even commercial ion traps, without instrument adjustments, the possibility of producing energetically versatile fragment ion spectra. It is also shown that the damped driven harmonic oscillator cannot be used as a simplified model of the motion during the resonant excitation process in real ion traps.
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Affiliation(s)
| | - Antony Memboeuf
- Université de Brest, CNRS, UMR 6521 CEMCA, F-29200 Brest, France
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Abstract
The ion trap is a unique type of device that is used for quantum studies in physics and mass analysis in chemistry. The space charge effect, which is due to trapping of an excessive number of ions, has long been recognized to be harmful for ion manipulation or mass spectrometry analysis. Here, we show an interesting phenomenon in which the energy exchange through collective interaction between the ion species could be effectively used for ion manipulation and high-quality mass measurement. This observation not only reveals a fundamentally interesting process in ion trap operation but also suggests a new alternative means for mass analysis.
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Affiliation(s)
- Xiaoyu Zhou
- State Key Laboratory of Precision Measurement Technology and Instruments, Department of Precision Instrument, Tsinghua University, Beijing 100084, China
| | - Zheng Ouyang
- State Key Laboratory of Precision Measurement Technology and Instruments, Department of Precision Instrument, Tsinghua University, Beijing 100084, China
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Park Y, Jung C, Seong M, Lee M, Cho DD, Kim T. A New Measurement Method for High Voltages Applied to an Ion Trap Generated by an RF Resonator. SENSORS 2021; 21:s21041143. [PMID: 33562053 PMCID: PMC7914741 DOI: 10.3390/s21041143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 01/18/2021] [Accepted: 02/04/2021] [Indexed: 11/25/2022]
Abstract
A new method is proposed to measure unknown amplitudes of radio frequency (RF) voltages applied to ion traps, using a pre-calibrated voltage divider with RF shielding. In contrast to previous approaches that estimate the applied voltage by comparing the measured secular frequencies with a numerical simulation, we propose using a pre-calibrated voltage divider to determine the absolute amplitude of large RF voltages amplified by a helical resonator. The proposed method does not require measurement of secular frequencies and completely removes uncertainty caused by limitations of numerical simulations. To experimentally demonstrate our method, we first obtained a functional relation between measured secular frequencies and large amplitudes of RF voltages using the calibrated voltage divider. A comparison of measured relations and simulation results without any fitting parameters confirmed the validity of the proposed method. Our method can be applied to most ion trap experiments. In particular, it will be an essential tool for surface ion traps which are extremely vulnerable to unknown large RF voltages and for improving the accuracy of numerical simulations for ion trap experiments.
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Affiliation(s)
- Yunjae Park
- Department of Electrical and Computer Engineering, Seoul National University, Seoul 08826, Korea; (Y.P.); (C.J.); (M.L.); (D.D.C.)
- Automation and Systems Research Institute, Seoul National University, Seoul 08826, Korea
- Inter-University Semiconductor Research Center, Seoul National University, Seoul 08826, Korea
| | - Changhyun Jung
- Department of Electrical and Computer Engineering, Seoul National University, Seoul 08826, Korea; (Y.P.); (C.J.); (M.L.); (D.D.C.)
- Automation and Systems Research Institute, Seoul National University, Seoul 08826, Korea
- Inter-University Semiconductor Research Center, Seoul National University, Seoul 08826, Korea
| | - Myeongseok Seong
- Department of Mechanical Engineering, Seoul National University, Seoul 08826, Korea;
| | - Minjae Lee
- Department of Electrical and Computer Engineering, Seoul National University, Seoul 08826, Korea; (Y.P.); (C.J.); (M.L.); (D.D.C.)
- Automation and Systems Research Institute, Seoul National University, Seoul 08826, Korea
- Inter-University Semiconductor Research Center, Seoul National University, Seoul 08826, Korea
| | - Dongil Dan Cho
- Department of Electrical and Computer Engineering, Seoul National University, Seoul 08826, Korea; (Y.P.); (C.J.); (M.L.); (D.D.C.)
- Automation and Systems Research Institute, Seoul National University, Seoul 08826, Korea
- Inter-University Semiconductor Research Center, Seoul National University, Seoul 08826, Korea
| | - Taehyun Kim
- Automation and Systems Research Institute, Seoul National University, Seoul 08826, Korea
- Inter-University Semiconductor Research Center, Seoul National University, Seoul 08826, Korea
- Department of Computer Science and Engineering, Seoul National University, Seoul 08826, Korea
- Institute of Computer Technology, Seoul National University, Seoul 08826, Korea
- Correspondence: ; Tel.: +82-2-880-1725
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Hong J, Hou C, Xu Z, He M, Xu W. Liquid-Phase Ion Trap for Ion Trapping, Transfer, and Sequential Ejection in Solutions. Anal Chem 2020; 92:9065-9071. [PMID: 32441513 DOI: 10.1021/acs.analchem.0c01261] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In this study, a new method/mechanism to manipulate ions in solution was developed, based on which liquid-phase ion trap was built. In this liquid-phase ion trap, ion manipulations conventionally performed in a quadrupole ion trap or in a trapped ion mobility spectrometer placed in a vacuum were achieved in solutions. Through theoretical derivation and numerical simulation, it is found that ions have different motional characteristics than those in vacuum. Instead of a radio frequency quadrupole electric field, tunable DC electric fields together with a constant liquid flow were applied to control ion motions in solution. Different ions could be trapped and focused in a potential well, and ion densities could be increased by over 100-fold. By adjusting the DC electric field of the potential well, trapped ions could be transferred into another trapping region or sequentially released for detection. Ions released from the liquid-phase ion trap were then detected by a mass spectrometer interfaced with an electrospray ionization source. Since the ion manipulation mechanism in solution is different and complementary to that in vacuum, the use of a liquid-phase ion trap could also boost detection sensitivity and the mixture analysis capability of a mass spectrometer.
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Affiliation(s)
- Jie Hong
- School of Life Science, Beijing Institute of Technology, Beijing 100081, China
| | - Chenyue Hou
- School of Life Science, Beijing Institute of Technology, Beijing 100081, China
| | - Zuqiang Xu
- School of Life Science, Beijing Institute of Technology, Beijing 100081, China
| | - Muyi He
- Institute of Food Safety, Chinese Academy of Inspection & Quarantine, Beijing 100176, China
| | - Wei Xu
- School of Life Science, Beijing Institute of Technology, Beijing 100081, China
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Zhou X, Liu X, Ouyang Z. Statistical Algorithm Enables Rapid Computation of Space Charge Effect and Spectral Correction in a Miniature Ion Trap Mass Spectrometer. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:429-433. [PMID: 31940196 DOI: 10.1021/jasms.9b00115] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Computation of the space charge effect within an ion trap may cost a few days to even years in clusters. Here, we report a statistical algorithm that can compute the space charge effect within a few minutes via a personal computer, without scarifying the accuracy. The key technology developed here was an effective electric field extracted from the statistics of N ions to replace the time-consuming computation of ion-ion Coulombic interactions, therefore reducing the computational burden from ∼N2 to ∼N; then, the burden was further reduced by shrinking the sampling size to Nsim = 500. For a linear ion trap (LIT) with an ion capacity N = 1 × 10 5∼1 × 106, this indicated an improved efficiency of N2/Nsim , i.e., 20 million∼2 billion-fold. Using the algorithm, space charge effects under different trapping conditions were explored, and the acquired knowledge enabled the spectral correction of the mass shift and peak broadening due to the effect in a miniature dual-LIT mass spectrometer.
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Affiliation(s)
- Xiaoyu Zhou
- State Key Laboratory of Precision Measurement Technology and Instruments, Department of Precision Instrument , Tsinghua University , Beijing 100084 , China
| | - Xinwei Liu
- State Key Laboratory of Precision Measurement Technology and Instruments, Department of Precision Instrument , Tsinghua University , Beijing 100084 , China
| | - Zheng Ouyang
- State Key Laboratory of Precision Measurement Technology and Instruments, Department of Precision Instrument , Tsinghua University , Beijing 100084 , China
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