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James VK, Sanders JD, Aizikov K, Fort KL, Grinfeld D, Makarov A, Brodbelt JS. Expanding Orbitrap Collision Cross-Section Measurements to Native Protein Applications Through Kinetic Energy and Signal Decay Analysis. Anal Chem 2023; 95:7656-7664. [PMID: 37133913 DOI: 10.1021/acs.analchem.3c00594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The measurement of collision cross sections (CCS, σ) offers supplemental information about sizes and conformations of ions beyond mass analysis alone. We have previously shown that CCSs can be determined directly from the time-domain transient decay of ions in an Orbitrap mass analyzer as ions oscillate around the central electrode and collide with neutral gas, thus removing them from the ion packet. Herein, we develop the modified hard collision model, thus deviating from the prior FT-MS hard sphere model, to determine CCSs as a function of center-of-mass collision energy in the Orbitrap analyzer. With this model, we aim to increase the upper mass limit of CCS measurement for native-like proteins, characterized by low charge states and presumed to be in more compact conformations. We also combine CCS measurements with collision induced unfolding and tandem mass spectrometry experiments to monitor protein unfolding and disassembly of protein complexes and measure CCSs of ejected monomers from protein complexes.
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Affiliation(s)
- Virginia K James
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
| | - James D Sanders
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
| | | | - Kyle L Fort
- Thermo Fisher Scientific, Bremen 28199, Germany
| | | | - Alexander Makarov
- Thermo Fisher Scientific, Bremen 28199, Germany
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Utrecht 3584, The Netherlands
| | - Jennifer S Brodbelt
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
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James VK, Sanders JD, Aizikov K, Fort KL, Grinfeld D, Makarov A, Brodbelt JS. Advancing Orbitrap Measurements of Collision Cross Sections to Multiple Species for Broad Applications. Anal Chem 2022; 94:15613-15620. [DOI: 10.1021/acs.analchem.2c02146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Virginia K. James
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
| | - James D. Sanders
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
| | | | | | | | - Alexander Makarov
- Thermo Fisher Scientific, Bremen 28199, Germany
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Utrecht 3584, The Netherlands
| | - Jennifer S. Brodbelt
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
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Pope BL, Joaquin D, Hickey JT, Mismash N, Heravi T, Shrestha J, Arslanian AJ, Mortensen DN, Dearden DV. Multi-CRAFTI: Relative Collision Cross Sections from Fourier Transform Ion Cyclotron Resonance Mass Spectrometric Line Width Measurements. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:131-140. [PMID: 34928604 DOI: 10.1021/jasms.1c00297] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Determination of collision cross sections (CCS) using the cross-sectional areas by the Fourier transform ion cyclotron resonance (CRAFTI) technique is limited by the requirement that accurate pressures in the trapping cell of the mass spectrometer must be known. Experiments must also be performed in the energetic hard-sphere regime such that ions decohere after single collisions with neutrals; this limits application to ions that are not much more massive than the neutrals. To mitigate these problems, we have resonantly excited two (or more) ions of different m/z to the same center-of-mass kinetic energy in a single experiment, subjecting them to identical neutral pressures. We term this approach "multi-CRAFTI". This facilitates measurement of relative CCS without requiring knowledge of the pressure and enables determination of absolute CCS using internal standards. Experiments with tetraalkylammonium ions yield CCS in reasonable agreement with the one-ion-at-a-time CRAFTI approach and with ion mobility spectrometry (IMS) when differences in collision energetics are taken into account (multi-CRAFTI generally yields smaller CCS than does IMS due to the higher collision energies employed in multi-CRAFTI). Comparison of multi-CRAFTI and IMS results with CCS calculated from structures computed at the M06-2X/6-31+G* level of theory using projection approximation or trajectory method values, respectively, indicates that the computed structures have CCS increasingly smaller than the experimental CCS as m/z increases, implying the computational model overestimates interactions between the alkyl arms. For ions that undergo similar collisional decoherence processes, relative CCS reach constant values at lower collision energies than do absolute CCS values, suggesting a means of increasing the accessible upper m/z limit by employing multi-CRAFTI.
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Affiliation(s)
- Brigham L Pope
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602-1030, United States
| | - Daniel Joaquin
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602-1030, United States
| | - Jacob T Hickey
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602-1030, United States
| | - Noah Mismash
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602-1030, United States
| | - Tina Heravi
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602-1030, United States
| | - Jamir Shrestha
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602-1030, United States
| | - Andrew J Arslanian
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602-1030, United States
| | - Daniel N Mortensen
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602-1030, United States
| | - David V Dearden
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602-1030, United States
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Xiong C, Liu H, Liu C, Xue J, Zhan L, Nie Z. Mass, Size, and Density Measurements of Microparticles in a Quadrupole Ion Trap. Anal Chem 2019; 91:13508-13513. [PMID: 31608618 DOI: 10.1021/acs.analchem.9b02574] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The physical properties of microparticles, such as mass, size, and density, are critical for their functions. The comprehensive characterization of these physical parameters, however, remains a fundamental challenge. Here, we developed a particle mass spectrometry (PMS) methodology for determining the mass, size, and density of microparticles simultaneously. The collisional cross-section (CCS) and mass spectrometry (MS) measurements were performed in a single quadrupole ion trap (QIT), and the two modes can be switched easily by tuning the electric and gas hydrodynamic fields of the QIT. The feasibility of the method was demonstrated through a series of monodispersed polystyrene (PS) and silica (SiO2) particle standards. The SiO2/polypyrrole core-shell particles were also successfully characterized, and the measured results were verified by using conventional methods.
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Affiliation(s)
- Caiqiao Xiong
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry , Chinese Academy of Sciences , Beijing 100190 China.,University of Chinese Academy of Sciences , Beijing 100049 , China
| | - Huihui Liu
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry , Chinese Academy of Sciences , Beijing 100190 China.,University of Chinese Academy of Sciences , Beijing 100049 , China
| | - Chaozi Liu
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry , Chinese Academy of Sciences , Beijing 100190 China.,University of Chinese Academy of Sciences , Beijing 100049 , China
| | - Jinjuan Xue
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry , Chinese Academy of Sciences , Beijing 100190 China.,University of Chinese Academy of Sciences , Beijing 100049 , China
| | - Lingpeng Zhan
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry , Chinese Academy of Sciences , Beijing 100190 China.,University of Chinese Academy of Sciences , Beijing 100049 , China
| | - Zongxiu Nie
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry , Chinese Academy of Sciences , Beijing 100190 China.,University of Chinese Academy of Sciences , Beijing 100049 , China
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Hu M, Zhang L, He S, Xu C, Shi Q. Collision cross section (CCS) measurement by ion cyclotron resonance mass spectrometry with short-time Fourier transform. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2018; 32:751-761. [PMID: 29486526 DOI: 10.1002/rcm.8096] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2017] [Revised: 02/17/2018] [Accepted: 02/18/2018] [Indexed: 05/26/2023]
Abstract
RATIONALE The collision cross section (CCS) is an important shape parameter which is often used in molecular structure investigation. In Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS), the CCS affects the ion signal damping shape due to the effect of ion-neutral collisions. It is potential to obtain ion CCS values from FTICR-MS with the help of a proper ion-collision model. METHODS We have developed a rapid method to obtain the ion damping profile and CCS for mixtures by only one FTICR-MS measurement. The method utilizes short-time Fourier transform (STFT) to process FTICR-MS time domain signals. The STFT-processed result is a three-dimensional (3D) spectrum which has an additional time axis in addition to the conventional mass-to-charge ratio and intensity domains. The damping profile of each ion can be recognized from the 3D spectrum. RESULTS After extracting the decay profile of a specified ion, all the three ion-neutral collision models were tested in curve fitting. The hard-sphere model was proven to be suitable for our experimental setup. A linear relationship was observed between the CCS value and hard-sphere model parameters. Therefore, the CCS values of all the peaks were obtained through the addition of internal model compounds and linear calibration. CONCLUSIONS The proposed method was successfully applied to determine the CCSs of fatty acids and polyalanines in a petroleum gas oil matrix. This technique can be used for simultaneous measurement of cross sections for many ions in congested spectra.
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Affiliation(s)
- Miao Hu
- State Key Laboratory of Heavy Oil Processing, China University of Petroleum, Beijing, 102249, China
- CNOOC Research Institute of Refining and Petrochemicals, Beijing, 102200, China
| | - Linzhou Zhang
- State Key Laboratory of Heavy Oil Processing, China University of Petroleum, Beijing, 102249, China
| | - Shan He
- State Key Laboratory of Heavy Oil Processing, China University of Petroleum, Beijing, 102249, China
| | - Chunming Xu
- State Key Laboratory of Heavy Oil Processing, China University of Petroleum, Beijing, 102249, China
| | - Quan Shi
- State Key Laboratory of Heavy Oil Processing, China University of Petroleum, Beijing, 102249, China
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Sanders JD, Grinfeld D, Aizikov K, Makarov A, Holden DD, Brodbelt JS. Determination of Collision Cross-Sections of Protein Ions in an Orbitrap Mass Analyzer. Anal Chem 2018; 90:5896-5902. [DOI: 10.1021/acs.analchem.8b00724] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- James D. Sanders
- Department of Chemistry University of Texas at Austin Austin, Texas 78712, United States
| | | | | | | | - Dustin D. Holden
- Department of Chemistry University of Texas at Austin Austin, Texas 78712, United States
| | - Jennifer S. Brodbelt
- Department of Chemistry University of Texas at Austin Austin, Texas 78712, United States
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Jiang T, He M, Guo D, Zhai Y, Xu W. Ion collision cross section analyses in quadrupole ion traps using the filter diagonalization method: a theoretical study. Phys Chem Chem Phys 2017; 18:12058-64. [PMID: 27066889 DOI: 10.1039/c6cp00613b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Previously, we have demonstrated the feasibility of measuring ion collision cross sections (CCSs) within a quadrupole ion trap by performing time-frequency analyses of simulated ion trajectories. In this study, an improved time-frequency analysis method, the filter diagonalization method (FDM), was applied for data analyses. Using the FDM, high resolution could be achieved in both time- and frequency-domains when calculating ion time-frequency curves. Owing to this high-resolution nature, ion-neutral collision induced ion motion frequency shifts were observed, which further cause the intermodulation of ion trajectories and thus accelerate image current attenuation. Therefore, ion trap operation parameters, such as the ion number, high-order field percentage and buffer gas pressure, were optimized for ion CCS measurements. Under optimized conditions, simulation results show that a resolving power from 30 to more than 200 could be achieved for ion CCS measurements.
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Affiliation(s)
- Ting Jiang
- School of Life Science, Beijing Institute of Technology Haidian, Beijing 100081, China.
| | | | - Dan Guo
- School of Life Science, Beijing Institute of Technology Haidian, Beijing 100081, China.
| | - Yanbing Zhai
- School of Life Science, Beijing Institute of Technology Haidian, Beijing 100081, China.
| | - Wei Xu
- School of Life Science, Beijing Institute of Technology Haidian, Beijing 100081, China. and Key Laboratory of Convergence Medical Engineering System and Healthcare Technology, The Ministry of Industry and Information Technology, Beijing Institute of Technology, Beijing 100081, China
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