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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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Yan H, Li D, Xu W. A high resolution Fourier transform ion trap enabled by image current splicing: a theoretical study. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2023; 15:1345-1354. [PMID: 36815265 DOI: 10.1039/d2ay02034c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
The relatively high work pressure within an ion trap has limited the implementation of the Fourier transform technique for high resolution mass analysis. The main reason is that high buffer gas pressure will cause the rapid decay of ion oscillations. In this study, an image current splicing method based on the filter diagonalization method (FDM) and the Hilbert transform was developed to increase the resolving power of nondestructive mass analysis in a linear ion trap. First, multiple repeated experiments (or ion trajectory simulations) were performed to collect multiple sets of data. Using the FDM, the frequency component distribution was extracted from short image current transients collected from each experiment. The Hilbert transform was then applied to calculate and normalize the decay envelope of each transient. The relative abundance was calculated by counting the envelopes. Finally, image current transients collected from these multiple experiments were spliced and merged into a whole signal with much longer duration and continuous phase. This splicing method could effectively increase the duration of the image current, and thus improve the mass resolution of the ion trap mass analyzer. The mass resolution (m/Δm) was improved from 183.5 to 5.8 × 103, and the average relative difference was 2.8%. The proposed method resolved 3 adjacent peaks which originally could not be resolved from the raw signal by the fast Fourier transform (FFT). Besides simulated data, this method was also applied to the experimental data collected from a Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometer. The influence of electronic noise on the proposed method was also discussed in this study.
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Affiliation(s)
- Haoqiang Yan
- College of Computer Science and Engineering, Northeastern University, Shenyang, 110819, China.
| | - Dayu Li
- College of Computer Science and Engineering, Northeastern University, Shenyang, 110819, China.
| | - Wei Xu
- State Key Laboratory of Explosion Science and Technology, School of Life Science, Beijing Institute of Technology, Haidian, Beijing 100081, China.
- Key Laboratory of Convergence Medical Engineering System and Healthcare Technology, Beijing Institute of Technology, Beijing, 100081, China
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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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