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Gozzo TA, Bush MF. Effects of charge on protein ion structure: Lessons from cation-to-anion, proton-transfer reactions. MASS SPECTROMETRY REVIEWS 2024; 43:500-525. [PMID: 37129026 DOI: 10.1002/mas.21847] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 04/10/2023] [Accepted: 04/11/2023] [Indexed: 05/03/2023]
Abstract
Collision cross-section values, which can be determined using ion mobility experiments, are sensitive to the structures of protein ions and useful for applications to structural biology and biophysics. Protein ions with different charge states can exhibit very different collision cross-section values, but a comprehensive understanding of this relationship remains elusive. Here, we review cation-to-anion, proton-transfer reactions (CAPTR), a method for generating a series of charge-reduced protein cations by reacting quadrupole-selected cations with even-electron monoanions. The resulting CAPTR products are analyzed using a combination of ion mobility, mass spectrometry, and collisional activation. We compare CAPTR to other charge-manipulation strategies and review the results of various CAPTR-based experiments, exploring their contribution to a deeper understanding of the relationship between protein ion structure and charge state.
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Affiliation(s)
- Theresa A Gozzo
- Department of Chemistry, University of Washington, Seattle, Washington, USA
| | - Matthew F Bush
- Department of Chemistry, University of Washington, Seattle, Washington, USA
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2
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Kinlein Z, Clowers BH. Altering Conformational States of Dynamic Ion Populations using Traveling Wave Structures for Lossless Ion Manipulations. Anal Chem 2024; 96:6450-6458. [PMID: 38603648 DOI: 10.1021/acs.analchem.4c00692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/13/2024]
Abstract
With its capacity to store and translate ions across considerable distances and times, traveling wave structures for lossless ion manipulations (TW-SLIM) provide the foundation to expand the scope of ion mobility spectrometry (IMS) experiments. While promising, the dynamic electric fields and consequential ion-neutral collisions used to realize extensive degrees of separation have a considerable impact on the empirical results and the fundamental interpretation of observed arrival time distributions. Using a custom-designed set of TW-SLIM boards (∼9 m) coupled with a time-of-flight mass spectrometer (SLIM-ToF), we detail the capacity to systematically alter the gas-phase distribution of select peptide conformers. In addition to discussing the role charge-transfer may play in TW-SLIM experiments that occur at extended time scales, the ability of the SLIM-ToF to perform tandem IMS was leveraged to confirm that both the compact and elongated conformers of bradykinin2+ undergo interconversion within the SLIM. Storage experiments in which ions are confined within SLIM using static potential wells suggest that factors aside from TW-induced ion motion contribute to interconversion. Further investigation into this matter suggests that the use of radio frequency (RF) fields to confine ions within SLIM may play a role in ion heating. Aside from interconversion, storage experiments also provide insight into charge transfer behavior over the course of extended periods. The results of the presented experiments suggest that considerations should be taken when analyzing labile species and inform strategies for the TW-SLIM design and method development.
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Affiliation(s)
- Zackary Kinlein
- Department of Chemistry, Washington State University, Pullman, Washington 99164, United States
| | - Brian H Clowers
- Department of Chemistry, Washington State University, Pullman, Washington 99164, United States
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3
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Zercher BP, Feng Y, Bush MF. Towards IM n with Electrostatic Drift Fields: Resetting the Potential of Trapped Ions Between Dimensions of Ion Mobility. INTERNATIONAL JOURNAL OF MASS SPECTROMETRY 2024; 495:117163. [PMID: 37928050 PMCID: PMC10621600 DOI: 10.1016/j.ijms.2023.117163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2023]
Abstract
Increasing the dimensionality of ion mobility (IM) presents an enticing opportunity to increase the information content and selectivity of many analyses. However, for implementations of IM that use constant electrostatic gradients to separate ions in a buffer gas, technical challenges have limited the adoption of the technique and number of dimensions within individual experiments. Here, we introduce a strategy to "reset" the potentials of ions between IM dimensions. To achieve this, mobility-selected ions are trapped between dimensions of IM, using a combination of RF and electrostatic fields, while the subsequent dimension of IM is devoid of any drift field. By applying an incremental voltage ramp, the potential of the trapping region is elevated, simultaneously establishing the drift field in the subsequent dimension of IM. The trapped ions are then released and separated. We measured similar arrival-time distributions of protein ions using this strategy and a method without potential resetting, suggesting that potential resetting can be performed without additional losses or activation of ions. The findings of those experiments were corroborated by ion trajectory simulations, which exhibited a very small changes in ion position and no significant changes in effective temperatures during potential resetting. Finally, we demonstrate that IM information can be preserved during potential resetting by selecting subpopulations of 9+ cytochrome c ions, resetting their potential, subjecting them to a second-dimension IM separation, and observing the retention of conformers within each subpopulation. We anticipate that this strategy will be useful for advancing flexible, multidimensional experiments on electrostatic IM instruments.
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Affiliation(s)
- Benjamin P. Zercher
- University of Washington Department of Chemistry, Box 351700, Seattle, WA 98195-1700
| | - Yuan Feng
- University of Washington Department of Chemistry, Box 351700, Seattle, WA 98195-1700
| | - Matthew F. Bush
- University of Washington Department of Chemistry, Box 351700, Seattle, WA 98195-1700
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4
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Zercher BP, Hong S, Roush AE, Feng Y, Bush MF. Are the Gas-Phase Structures of Molecular Elephants Enduring or Ephemeral? Results from Time-Dependent, Tandem Ion Mobility. Anal Chem 2023; 95:9589-9597. [PMID: 37294019 PMCID: PMC10549206 DOI: 10.1021/acs.analchem.3c01222] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The structural stability of biomolecules in the gas phase remains an important topic in mass spectrometry applications for structural biology. Here, we evaluate the kinetic stability of native-like protein ions using time-dependent, tandem ion mobility (IM). In these tandem IM experiments, ions of interest are mobility-selected after a first dimension of IM and trapped for up to ∼14 s. Time-dependent, collision cross section distributions are then determined from separations in a second dimension of IM. In these experiments, monomeric protein ions exhibited structural changes specific to both protein and charge state, whereas large protein complexes did not undergo resolvable structural changes on the timescales of these experiments. We also performed energy-dependent experiments, i.e., collision-induced unfolding, as a comparison for time-dependent experiments to understand the extent of unfolding. Collision cross section values observed in energy-dependent experiments using high collision energies were significantly larger than those observed in time-dependent experiments, indicating that the structures observed in time-dependent experiments remain kinetically trapped and retain some memory of their solution-phase structure. Although structural evolution should be considered for highly charged, monomeric protein ions, these experiments demonstrate that higher-mass protein ions can have remarkable kinetic stability in the gas phase.
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Affiliation(s)
- Benjamin P. Zercher
- University of Washington, Department of Chemistry, Box 351700, Seattle, WA 98195-1700
| | - Seoyeon Hong
- University of Washington, Department of Chemistry, Box 351700, Seattle, WA 98195-1700
| | - Addison E. Roush
- University of Washington, Department of Chemistry, Box 351700, Seattle, WA 98195-1700
| | - Yuan Feng
- University of Washington, Department of Chemistry, Box 351700, Seattle, WA 98195-1700
| | - Matthew F. Bush
- University of Washington, Department of Chemistry, Box 351700, Seattle, WA 98195-1700
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5
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Zercher BP, Gozzo TA, Wageman A, Bush MF. Enhancing the Depth of Analyses with Next-Generation Ion Mobility Experiments. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2023; 16:27-48. [PMID: 37000959 PMCID: PMC10545071 DOI: 10.1146/annurev-anchem-091522-031329] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Recent developments in ion mobility (IM) technology have expanded the capability to separate and characterize gas-phase ions of biomolecules, especially when paired with mass spectrometry. This next generation of IM technology has been ushered in by creative innovation focused on both instrument architectures and how electric fields are applied. In this review, we focus on the application of high-resolution and multidimensional IM to biomolecular analyses, encompassing the fields of glycomics, lipidomics, peptidomics, and proteomics. We highlight selected research that demonstrates the application of the new IM toolkit to challenging biomolecular systems. Through our review of recently published literature, we outline the current strengths of respective technologies and perspectives for future applications.
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Affiliation(s)
- Benjamin P Zercher
- Department of Chemistry, University of Washington, Seattle, Washington, USA;
| | - Theresa A Gozzo
- Department of Chemistry, University of Washington, Seattle, Washington, USA;
| | - AnneClaire Wageman
- Department of Chemistry, University of Washington, Seattle, Washington, USA;
| | - Matthew F Bush
- Department of Chemistry, University of Washington, Seattle, Washington, USA;
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6
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Fu D, Habtegabir SG, Wang H, Feng S, Han Y. Understanding of protomers/deprotomers by combining mass spectrometry and computation. Anal Bioanal Chem 2023:10.1007/s00216-023-04574-1. [PMID: 36737499 DOI: 10.1007/s00216-023-04574-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 01/19/2023] [Accepted: 01/27/2023] [Indexed: 02/05/2023]
Abstract
Multifunctional compounds may form different prototropic isomers under different conditions, which are known as protomers/deprotomers. In biological systems, these protomer/deprotomer isomers affect the interaction modes and conformational landscape between compounds and enzymes and thus present different biological activities. Study on protomers/deprotomers is essentially the study on the acidity/basicity of each intramolecular functional group and its effect on molecular structure. In recent years, the combination of mass spectrometry (MS) and computational chemistry has been proven to be a powerful and effective means to study prototropic isomers. MS-based technologies are developed to discriminate and characterize protomers/deprotomers to provide structural information and monitor transformations, showing great superiority than other experimental methods. Computational chemistry is used to predict the thermodynamic stability of protomers/deprotomers, provide the simulated MS/MS spectra, infrared spectra, and calculate collision cross-section values. By comparing the theoretical data with the corresponding experimental results, the researchers can not only determine the protomer/deprotomer structure, but also investigate the structure-activity relationship in a given system. This review covers various MS methods and theoretical calculations and their devotion to isomer discrimination, structure identification, conformational transformation, and phase transition investigation of protomers/deprotomers.
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Affiliation(s)
- Dali Fu
- State Key Laboratory of Heavy Oil Processing, College of Chemical Engineering and Environment, China University of Petroleum-Beijing, Beijing, 102249, People's Republic of China
| | - Sara Girmay Habtegabir
- State Key Laboratory of Heavy Oil Processing, College of Chemical Engineering and Environment, China University of Petroleum-Beijing, Beijing, 102249, People's Republic of China
| | - Haodong Wang
- State Key Laboratory of Heavy Oil Processing, College of Chemical Engineering and Environment, China University of Petroleum-Beijing, Beijing, 102249, People's Republic of China
| | - Shijie Feng
- State Key Laboratory of Heavy Oil Processing, College of Chemical Engineering and Environment, China University of Petroleum-Beijing, Beijing, 102249, People's Republic of China
| | - Yehua Han
- State Key Laboratory of Heavy Oil Processing, College of Chemical Engineering and Environment, China University of Petroleum-Beijing, Beijing, 102249, People's Republic of China.
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7
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Lee J, Chai M, Bleiholder C. Differentiation of Isomeric, Nonseparable Carbohydrates Using Tandem-Trapped Ion Mobility Spectrometry-Mass Spectrometry. Anal Chem 2023; 95:747-757. [PMID: 36547374 PMCID: PMC10126951 DOI: 10.1021/acs.analchem.2c02844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Carbohydrates play important roles in biological processes, but their identification remains a significant analytical problem. While mass spectrometry has increasingly enabled the elucidation of carbohydrates, current approaches are limited in their abilities to differentiate isomeric carbohydrates when these are not separated prior to tandem-mass spectrometry analysis. This analytical challenge takes on increased relevance because of the pervasive presence of isomeric carbohydrates in biological systems. Here, we demonstrate that TIMS2-MS2 workflows enabled by tandem-trapped ion mobility spectrometry-mass spectrometry (tTIMS/MS) provide a general approach to differentiate isomeric, nonseparated carbohydrates. Our analysis shows that (1) cross sections measured by TIMS are sufficiently precise and robust for ion identification; (2) fragment ion cross sections from TIMS2 analysis can be analytically exploited to identify carbohydrate precursors even if the precursor ions are not separated by TIMS; (3) low-abundant fragment ions can be exploited to identify carbohydrate precursors even if the precursor ions are not separated by IMS. (4) MS2 analysis of fragment ions produced by TIMS2 can be used to validate and/or further characterize carbohydrate structures. Taken together, our analysis underlines the opportunities that tandem-ion mobility spectrometry/MS methods offer for the characterization of mixtures of isomeric carbohydrates.
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Affiliation(s)
- Jusung Lee
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306-4390, USA
| | - Mengqi Chai
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306-4390, USA
| | - Christian Bleiholder
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306-4390, USA
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306-4390, USA
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8
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McCabe JW, Hebert MJ, Shirzadeh M, Mallis CS, Denton JK, Walker TE, Russell DH. THE IMS PARADOX: A PERSPECTIVE ON STRUCTURAL ION MOBILITY-MASS SPECTROMETRY. MASS SPECTROMETRY REVIEWS 2021; 40:280-305. [PMID: 32608033 PMCID: PMC7989064 DOI: 10.1002/mas.21642] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 06/03/2020] [Indexed: 05/06/2023]
Abstract
Studies of large proteins, protein complexes, and membrane protein complexes pose new challenges, most notably the need for increased ion mobility (IM) and mass spectrometry (MS) resolution. This review covers evolutionary developments in IM-MS in the authors' and key collaborators' laboratories with specific focus on developments that enhance the utility of IM-MS for structural analysis. IM-MS measurements are performed on gas phase ions, thus "structural IM-MS" appears paradoxical-do gas phase ions retain their solution phase structure? There is growing evidence to support the notion that solution phase structure(s) can be retained by the gas phase ions. It should not go unnoticed that we use "structures" in this statement because an important feature of IM-MS is the ability to deal with conformationally heterogeneous systems, thus providing a direct measure of conformational entropy. The extension of this work to large proteins and protein complexes has motivated our development of Fourier-transform IM-MS instruments, a strategy first described by Hill and coworkers in 1985 (Anal Chem, 1985, 57, pp. 402-406) that has proved to be a game-changer in our quest to merge drift tube (DT) and ion mobility and the high mass resolution orbitrap MS instruments. DT-IMS is the only method that allows first-principles determinations of rotationally averaged collision cross sections (CSS), which is essential for studies of biomolecules where the conformational diversities of the molecule precludes the use of CCS calibration approaches. The Fourier transform-IM-orbitrap instrument described here also incorporates the full suite of native MS/IM-MS capabilities that are currently employed in the most advanced native MS/IM-MS instruments. © 2020 John Wiley & Sons Ltd. Mass Spec Rev.
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Affiliation(s)
- Jacob W McCabe
- Department of Chemistry, Texas A&M University, College Station, TX, 77843
| | - Michael J Hebert
- Department of Chemistry, Texas A&M University, College Station, TX, 77843
| | - Mehdi Shirzadeh
- Department of Chemistry, Texas A&M University, College Station, TX, 77843
| | | | - Joanna K Denton
- Department of Chemistry, Texas A&M University, College Station, TX, 77843
| | - Thomas E Walker
- Department of Chemistry, Texas A&M University, College Station, TX, 77843
| | - David H Russell
- Department of Chemistry, Texas A&M University, College Station, TX, 77843
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9
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Naylor CN, Ridgeway ME, Park MA, Clowers BH. Evaluation of Trapped Ion Mobility Spectrometry Source Conditions Using Benzylammonium Thermometer Ions. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:1593-1602. [PMID: 32510214 DOI: 10.1021/jasms.0c00151] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
A key aspect of reduced pressure ion mobility spectrometry (IMS) experiments is to identify experimental conditions that minimize the role of collisional energy transfer that allows for assessing effective ion-neutral collision cross sections of metabolites, peptides, and proteins in "native-like" or compact states. Across two separate experimental campaigns using a prototype trapped ion mobility spectrometer (TIMS) coupled to a time-of-flight mass spectrometer, we present independent findings that support the results recently published by Morsa et al. using a different set of thermometer ions (Morsa et al. Anal. Chem. 2020, 92 (6), 4573-4582). First, using five para-substituted benzylammonium ions, we conducted survival yield experiments to assess ion internal energy across different experimental settings. Results from the present set of experiments illustrate that greater ion heating occurs at lower pressures and higher voltage settings applied to the TIMS. At the "softest" settings where the benzylammonium thermometer ions have an effective average energy of 1.73 eV, we observe the majority of bradykinin in the compact state. Under more extreme operating conditions where the energy of the benzylammonium ions varies from 1.83 to 1.86 eV, the bradykinin transitions from the compact to the elongated state. In addition to independently confirming the findings of Morsa et al., we also report the mobilities for the benzylammonium parent and fragment ions using the tandem drift-tube-TIMS calibration procedure described by Naylor et al. ( J. Am. Soc. Mass Spectrom. 2019, 30 (10), 2152-2162).
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Affiliation(s)
- Cameron N Naylor
- Department of Chemistry, Washington State University, Pullman, Washington 99163, United States
| | - Mark E Ridgeway
- Bruker Daltonics Inc., Billerica, Massachusetts 01821, United States
| | - Melvin A Park
- Bruker Daltonics Inc., Billerica, Massachusetts 01821, United States
| | - Brian H Clowers
- Department of Chemistry, Washington State University, Pullman, Washington 99163, United States
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10
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France AP, Migas LG, Sinclair E, Bellina B, Barran PE. Using Collision Cross Section Distributions to Assess the Distribution of Collision Cross Section Values. Anal Chem 2020; 92:4340-4348. [DOI: 10.1021/acs.analchem.9b05130] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Aidan P. France
- Michael Barber Centre for Collaborative Mass Spectrometry, Manchester Institute of Biotechnology and Photon Science Institute, University of Manchester, 131 Princess Street, Manchester, M1 7DN, U.K
| | - Lukasz G. Migas
- Michael Barber Centre for Collaborative Mass Spectrometry, Manchester Institute of Biotechnology and Photon Science Institute, University of Manchester, 131 Princess Street, Manchester, M1 7DN, U.K
| | - Eleanor Sinclair
- Michael Barber Centre for Collaborative Mass Spectrometry, Manchester Institute of Biotechnology and Photon Science Institute, University of Manchester, 131 Princess Street, Manchester, M1 7DN, U.K
| | - Bruno Bellina
- Michael Barber Centre for Collaborative Mass Spectrometry, Manchester Institute of Biotechnology and Photon Science Institute, University of Manchester, 131 Princess Street, Manchester, M1 7DN, U.K
| | - Perdita E. Barran
- Michael Barber Centre for Collaborative Mass Spectrometry, Manchester Institute of Biotechnology and Photon Science Institute, University of Manchester, 131 Princess Street, Manchester, M1 7DN, U.K
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11
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Dodds JN, Baker ES. Ion Mobility Spectrometry: Fundamental Concepts, Instrumentation, Applications, and the Road Ahead. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2019; 30:2185-2195. [PMID: 31493234 PMCID: PMC6832852 DOI: 10.1007/s13361-019-02288-2] [Citation(s) in RCA: 220] [Impact Index Per Article: 44.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 07/08/2019] [Accepted: 07/15/2019] [Indexed: 05/07/2023]
Abstract
Ion mobility spectrometry (IMS) is a rapid separation technique that has experienced exponential growth as a field of study. Interfacing IMS with mass spectrometry (IMS-MS) provides additional analytical power as complementary separations from each technique enable multidimensional characterization of detected analytes. IMS separations occur on a millisecond timescale, and therefore can be readily nested into traditional GC and LC/MS workflows. However, the continual development of novel IMS methods has generated some level of confusion regarding the advantages and disadvantages of each. In this critical insight, we aim to clarify some common misconceptions for new users in the community pertaining to the fundamental concepts of the various IMS instrumental platforms (i.e., DTIMS, TWIMS, TIMS, FAIMS, and DMA), while addressing the strengths and shortcomings associated with each. Common IMS-MS applications are also discussed in this review, such as separating isomeric species, performing signal filtering for MS, and incorporating collision cross-section (CCS) values into both targeted and untargeted omics-based workflows as additional ion descriptors for chemical annotation. Although many challenges must be addressed by the IMS community before mobility information is collected in a routine fashion, the future is bright with possibilities.
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Affiliation(s)
- James N Dodds
- Department of Chemistry, North Carolina State University, Raleigh, NC, 27695, USA
| | - Erin S Baker
- Department of Chemistry, North Carolina State University, Raleigh, NC, 27695, USA.
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12
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Wojcik R, Nagy G, Attah IK, Webb IK, Garimella SVB, Weitz KK, Hollerbach A, Monroe ME, Ligare MR, Nielson FF, Norheim RV, Renslow RS, Metz TO, Ibrahim YM, Smith RD. SLIM Ultrahigh Resolution Ion Mobility Spectrometry Separations of Isotopologues and Isotopomers Reveal Mobility Shifts due to Mass Distribution Changes. Anal Chem 2019; 91:11952-11962. [PMID: 31450886 PMCID: PMC7188075 DOI: 10.1021/acs.analchem.9b02808] [Citation(s) in RCA: 72] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
We report on separations of ion isotopologues and isotopomers using ultrahigh-resolution traveling wave-based Structures for Lossless Ion Manipulations with serpentine ultralong path and extended routing ion mobility spectrometry coupled to mass spectrometry (SLIM SUPER IMS-MS). Mobility separations of ions from the naturally occurring ion isotopic envelopes (e.g., [M], [M+1], [M+2], ... ions) showed the first and second isotopic peaks (i.e., [M+1] and [M+2]) for various tetraalkylammonium ions could be resolved from their respective monoisotopic ion peak ([M]) after SLIM SUPER IMS with resolving powers of ∼400-600. Similar separations were obtained for other compounds (e.g., tetrapeptide ions). Greater separation was obtained using argon versus helium drift gas, as expected from the greater reduced mass contribution to ion mobility described by the Mason-Schamp relationship. To more directly explore the role of isotopic substitutions, we studied a mixture of specific isotopically substituted (15N, 13C, and 2H) protonated arginine isotopologues. While the separations in nitrogen were primarily due to their reduced mass differences, similar to the naturally occurring isotopologues, their separations in helium, where higher resolving powers could also be achieved, revealed distinct additional relative mobility shifts. These shifts appeared correlated, after correction for the reduced mass contribution, with changes in the ion center of mass due to the different locations of heavy atom substitutions. The origin of these apparent mass distribution-induced mobility shifts was then further explored using a mixture of Iodoacetyl Tandem Mass Tag (iodoTMT) isotopomers (i.e., each having the same exact mass, but with different isotopic substitution sites). Again, the observed mobility shifts appeared correlated with changes in the ion center of mass leading to multiple monoisotopic mobilities being observed for some isotopomers (up to a ∼0.04% difference in mobility). These mobility shifts thus appear to reflect details of the ion structure, derived from the changes due to ion rotation impacting collision frequency or momentum transfer, and highlight the potential for new approaches for ion structural characterization.
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Affiliation(s)
- Roza Wojcik
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Gabe Nagy
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Isaac. K. Attah
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Ian K. Webb
- Department of Chemistry, Indiana University Purdue University Indianapolis, Indianapolis, Indiana 46202, United States
| | - Sandilya V. B. Garimella
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Karl K. Weitz
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Adam Hollerbach
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Matthew E. Monroe
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Marshall R. Ligare
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Felicity F. Nielson
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Randolph V. Norheim
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Ryan S. Renslow
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Thomas O. Metz
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Yehia M. Ibrahim
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Richard D. Smith
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
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13
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Gerth F, Jäpel M, Sticht J, Kuropka B, Schmitt XJ, Driller JH, Loll B, Wahl MC, Pagel K, Haucke V, Freund C. Exon Inclusion Modulates Conformational Plasticity and Autoinhibition of the Intersectin 1 SH3A Domain. Structure 2019; 27:977-987.e5. [DOI: 10.1016/j.str.2019.03.020] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Revised: 01/21/2019] [Accepted: 03/25/2019] [Indexed: 11/16/2022]
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14
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Eaton RM, Allen SJ, Bush MF. Principles of Ion Selection, Alignment, and Focusing in Tandem Ion Mobility Implemented Using Structures for Lossless Ion Manipulations (SLIM). JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2019; 30:1115-1125. [PMID: 30963456 DOI: 10.1007/s13361-019-02170-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Revised: 02/20/2019] [Accepted: 02/20/2019] [Indexed: 06/09/2023]
Abstract
Tandem ion mobility (IM) enables the characterization of subpopulations of ions from larger ensembles, including differences that cannot be resolved in a single dimension of IM. Tandem IM consists of at least two IM regions that are each separated by an ion selection region. In many implementations of tandem IM, ions eluting from a dimension of separation are filtered and immediately transferred to the subsequent dimension of separation (selection-only experiments). We recently reported a mode of operation in which ions eluting from a dimension are trapped prior to the subsequent dimension (selection-trapping experiments), which was implemented on an instrument constructed using the structures for lossless ion manipulations (SLIM) architecture. Here, we use a combination of experiments and trajectory simulations to characterize aspects of the selection, trapping, and separation processes underlying these modes of operation. For example, the actual temporal profile of filtered ions can be very similar to the width of the waveforms used for selection, but depending on experimental parameters, can differ by up to ± 500 μs. Experiments and simulations indicate that ions in selection-trapping experiments can be spatially focused between dimensions, which removes the broadening that occurred during the preceding dimension. During focusing, individual ions are thermalized, which aligns and establishes common initial conditions for the subsequent dimension. Therefore, selection-trapping experiments appear to offer significant advantages relative to selection-only experiments, which we anticipate will become more pronounced in future experiments that make use of longer IM separations, additional dimensions of analysis, and the outcomes of this study. Graphical Abstract.
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Affiliation(s)
- Rachel M Eaton
- Department of Chemistry, University of Washington, Box 351700, Seattle, WA, 98195-1700, USA
| | - Samuel J Allen
- Department of Chemistry, University of Washington, Box 351700, Seattle, WA, 98195-1700, USA
| | - Matthew F Bush
- Department of Chemistry, University of Washington, Box 351700, Seattle, WA, 98195-1700, USA.
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15
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Gabelica V, Shvartsburg AA, Afonso C, Barran P, Benesch JL, Bleiholder C, Bowers MT, Bilbao A, Bush MF, Campbell JL, Campuzano ID, Causon T, Clowers BH, Creaser CS, De Pauw E, Far J, Fernandez‐Lima F, Fjeldsted JC, Giles K, Groessl M, Hogan CJ, Hann S, Kim HI, Kurulugama RT, May JC, McLean JA, Pagel K, Richardson K, Ridgeway ME, Rosu F, Sobott F, Thalassinos K, Valentine SJ, Wyttenbach T. Recommendations for reporting ion mobility Mass Spectrometry measurements. MASS SPECTROMETRY REVIEWS 2019; 38:291-320. [PMID: 30707468 PMCID: PMC6618043 DOI: 10.1002/mas.21585] [Citation(s) in RCA: 288] [Impact Index Per Article: 57.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Revised: 11/01/2018] [Accepted: 11/02/2018] [Indexed: 05/02/2023]
Abstract
Here we present a guide to ion mobility mass spectrometry experiments, which covers both linear and nonlinear methods: what is measured, how the measurements are done, and how to report the results, including the uncertainties of mobility and collision cross section values. The guide aims to clarify some possibly confusing concepts, and the reporting recommendations should help researchers, authors and reviewers to contribute comprehensive reports, so that the ion mobility data can be reused more confidently. Starting from the concept of the definition of the measurand, we emphasize that (i) mobility values (K0 ) depend intrinsically on ion structure, the nature of the bath gas, temperature, and E/N; (ii) ion mobility does not measure molecular surfaces directly, but collision cross section (CCS) values are derived from mobility values using a physical model; (iii) methods relying on calibration are empirical (and thus may provide method-dependent results) only if the gas nature, temperature or E/N cannot match those of the primary method. Our analysis highlights the urgency of a community effort toward establishing primary standards and reference materials for ion mobility, and provides recommendations to do so. © 2019 The Authors. Mass Spectrometry Reviews Published by Wiley Periodicals, Inc.
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Affiliation(s)
- Valérie Gabelica
- University of Bordeaux, INSERM and CNRS, ARNA Laboratory, IECB site2 rue Robert Escarpit, 33600PessacFrance
| | | | | | - Perdita Barran
- Michael Barber Centre for Collaborative Mass SpectrometryManchester Institute for Biotechnology, University of ManchesterManchesterUK
| | - Justin L.P. Benesch
- Department of Chemistry, Chemistry Research LaboratoryUniversity of Oxford, Mansfield Road, OX1 3TAOxfordUK
| | - Christian Bleiholder
- Department of Chemistry and BiochemistryFlorida State UniversityTallahasseeFlorida32311
| | | | - Aivett Bilbao
- Biological Sciences DivisionPacific Northwest National LaboratoryRichlandWashington
| | - Matthew F. Bush
- Department of ChemistryUniversity of WashingtonSeattleWashington
| | | | | | - Tim Causon
- University of Natural Resources and Life Sciences (BOKU)Department of Chemistry, Division of Analytical ChemistryViennaAustria
| | - Brian H. Clowers
- Department of ChemistryWashington State UniversityPullmanWashington
| | - Colin S. Creaser
- Centre for Analytical ScienceDepartment of Chemistry, Loughborough UniversityLoughboroughUK
| | - Edwin De Pauw
- Laboratoire de spectrométrie de masse (L.S.M.) − Molecular SystemsUniversité de LiègeLiègeBelgium
| | - Johann Far
- Laboratoire de spectrométrie de masse (L.S.M.) − Molecular SystemsUniversité de LiègeLiègeBelgium
| | | | | | | | - Michael Groessl
- Department of Nephrology and Hypertension and Department of BioMedical ResearchInselspital, Bern University Hospital, University of Bern, Switzerland and TofwerkThunSwitzerland
| | | | - Stephan Hann
- University of Natural Resources and Life Sciences (BOKU)Department of Chemistry, Division of Analytical ChemistryViennaAustria
| | - Hugh I. Kim
- Department of ChemistryKorea UniversitySeoulKorea
| | | | - Jody C. May
- Department of ChemistryCenter for Innovative Technology, Vanderbilt UniversityNashvilleTennessee
| | - John A. McLean
- Department of ChemistryCenter for Innovative Technology, Vanderbilt UniversityNashvilleTennessee
| | - Kevin Pagel
- Freie Universitaet BerlinInstitute for Chemistry and BiochemistryBerlinGermany
| | | | | | - Frédéric Rosu
- CNRS, INSERM and University of BordeauxInstitut Européen de Chimie et BiologiePessacFrance
| | - Frank Sobott
- Antwerp UniversityBiomolecular & Analytical Mass SpectrometryAntwerpBelgium
- Astbury Centre for Structural Molecular BiologyUniversity of LeedsLeedsUK
- School of Molecular and Cellular BiologyUniversity of LeedsLeedsUK
| | - Konstantinos Thalassinos
- Institute of Structural and Molecular Biology, Division of BiosciencesUniversity College LondonLondonWC1E 6BTUK
- United Kingdom and Institute of Structural and Molecular BiologyDepartment of Biological Sciences, Birkbeck College, University of LondonLondonWC1E 7HXUK
| | - Stephen J. Valentine
- C. Eugene Bennett Department of ChemistryWest Virginia UniversityMorgantownWest Virginia
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16
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Lim D, Davidson KL, Son S, Ahmed A, Bush MF, Kim S. Determining Collision Cross‐Sections of Aromatic Compounds in Crude Oil by Using Aromatic Compound Mixture as Calibration Standard. B KOREAN CHEM SOC 2018. [DOI: 10.1002/bkcs.11653] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Dongwan Lim
- Department of ChemistryKyungpook National University Daegu 41566 Republic of Korea
| | | | - Seungwoo Son
- Department of ChemistryKyungpook National University Daegu 41566 Republic of Korea
| | - Arif Ahmed
- Department of ChemistryKyungpook National University Daegu 41566 Republic of Korea
| | - Matthew F. Bush
- Department of ChemistryUniversity of Washington Seattle WA, 98195‐1700 USA
| | - Sunghwan Kim
- Department of ChemistryKyungpook National University Daegu 41566 Republic of Korea
- Green‐Nano Materials Research Center Daegu 41566 Republic of Korea
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17
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Larriba-Andaluz C, Chen X, Nahin M, Wu T, Fukushima N. Analysis of Ion Motion and Diffusion Confinement in Inverted Drift Tubes and Trapped Ion Mobility Spectrometry Devices. Anal Chem 2018; 91:919-927. [DOI: 10.1021/acs.analchem.8b03930] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Carlos Larriba-Andaluz
- Department of Mechanical Engineering, Indiana University−Purdue University Indianapolis (IUPUI), 723 W. Michigan St., Indianapolis, Indiana 46202, United States
| | - Xi Chen
- Department of Mechanical Engineering, Indiana University−Purdue University Indianapolis (IUPUI), 723 W. Michigan St., Indianapolis, Indiana 46202, United States
- Purdue University, West Lafayette, Indiana 47907, United States
| | - Minal Nahin
- Department of Mechanical Engineering, Indiana University−Purdue University Indianapolis (IUPUI), 723 W. Michigan St., Indianapolis, Indiana 46202, United States
| | - Tianyang Wu
- Department of Mechanical Engineering, Indiana University−Purdue University Indianapolis (IUPUI), 723 W. Michigan St., Indianapolis, Indiana 46202, United States
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18
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Iwamoto K, Fujimoto Y, Nakanishi T. Development of an ion mobility spectrometer using radio-frequency electric field. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2018; 89:115101. [PMID: 30501352 DOI: 10.1063/1.5050440] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 10/13/2018] [Indexed: 06/09/2023]
Abstract
This paper describes the development of a new ion mobility spectrometer (IMS) using the radio-frequency (RF) electric field. The proposed IMS has high ion transmission efficiency. Seven connected IMS devices, in which the RF and DC electric fields are created by separate electrodes, are constructed. The ions are confined by the RF electric field and drifted by the DC electric field. The electrodes in each IMS device include short quadrupole electrodes and segmented vane electrodes. The uniform electric field in the IMS is verified by simulated results obtained using SIMION. To measure the exact value of reduced mobility K 0 at low Td (1 Td = 10-17 V cm2), two ion gates are installed in the IMS. By installing the ion gates at suitable positions for eliminating the effect of gas flow, the exact ion velocity through the IMS can be measured. The K 0 values of O2 + and C6H6 + ions are measured as a function of Td. In addition, the K 0 of CH3OCH2 + fragment ions is measured. These K 0 measurement results are consistent with previous results obtained using electrostatic drift tube apparatus. In summary, as our IMS can measure K 0 under low Td conditions, it can be used to better understand the structure of small molecular or fragment ions.
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Affiliation(s)
- Kenichi Iwamoto
- Department of Chemistry, Graduate School of Science, Osaka Prefecture University, 1-1 Gakuencho Nakaku, Sakai, Osaka 599-8531, Japan
| | - Yusuke Fujimoto
- Department of Chemistry, Graduate School of Science, Osaka Prefecture University, 1-1 Gakuencho Nakaku, Sakai, Osaka 599-8531, Japan
| | - Toshiki Nakanishi
- Department of Chemistry, Graduate School of Science, Osaka Prefecture University, 1-1 Gakuencho Nakaku, Sakai, Osaka 599-8531, Japan
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19
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Canzani D, Laszlo KJ, Bush MF. Ion Mobility of Proteins in Nitrogen Gas: Effects of Charge State, Charge Distribution, and Structure. J Phys Chem A 2018; 122:5625-5634. [DOI: 10.1021/acs.jpca.8b04474] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Daniele Canzani
- Department of Chemistry, University of Washington, Box 351700, Seattle, Washington 98195-1700, United States
| | - Kenneth J. Laszlo
- Department of Chemistry, University of Washington, Box 351700, Seattle, Washington 98195-1700, United States
| | - Matthew F. Bush
- Department of Chemistry, University of Washington, Box 351700, Seattle, Washington 98195-1700, United States
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20
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Lee JW, Lee HHL, Davidson KL, Bush MF, Kim HI. Structural characterization of small molecular ions by ion mobility mass spectrometry in nitrogen drift gas: improving the accuracy of trajectory method calculations. Analyst 2018; 143:1786-1796. [DOI: 10.1039/c8an00270c] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
An accurate theoretical collision cross section calculation method in nitrogen was developed for reliable structural ion mobility mass spectrometry.
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Affiliation(s)
- Jong Wha Lee
- Center for Analytical Chemistry
- Division of Chemical and Medical Metrology
- Korea Research Institute of Standards and Science (KRISS)
- Daejeon 34113
- Republic of Korea
| | - Hyun Hee L. Lee
- Department of Chemistry
- Korea University
- Seoul 02841
- Republic of Korea
| | | | | | - Hugh I. Kim
- Department of Chemistry
- Korea University
- Seoul 02841
- Republic of Korea
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21
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Laszlo KJ, Bush MF. Effects of Charge State, Charge Distribution, and Structure on the Ion Mobility of Protein Ions in Helium Gas: Results from Trajectory Method Calculations. J Phys Chem A 2017; 121:7768-7777. [PMID: 28910102 DOI: 10.1021/acs.jpca.7b08154] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Collision cross section (Ω) values of gas-phase ions of proteins and protein complexes are used to probe the structures of the corresponding species in solution. Ions of many proteins exhibit increasing Ω-values with increasing charge state but most Ω-values calculated for protein ions have used simple collision models that do not explicitly account for charge. Here we use a combination of ion mobility mass spectrometry experiments with helium gas and trajectory method calculations to characterize the extents to which increases in experimental Ω-values with increasing charge state may be attributed to increased momentum transfer concomitant with enhanced long-range interactions between the protein ion and helium atoms. Ubiquitin and C-to-N terminally linked diubiquitin ions generated from different solution conditions exhibit more than a 2-fold increase in Ω with increasing charge state. For native and energy-relaxed models of the proteins and most methods for distributing charge, Ω-values calculated using the trajectory method increase by less than 1% over the range of charge states observed from typical solution conditions used for native mass spectrometry. However, the calculated Ω-values increase by 10% to 15% over the full range of charge states observed from all solution conditions. Therefore, contributions from enhanced ion-induced dipole interactions with increasing charge state are significant but without additional structural changes can account for only a fraction of the increase in Ω observed experimentally. On the basis of these results, we suggest guidelines for calculating Ω-values in the context of applications in biophysics and structural biology.
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Affiliation(s)
- Kenneth J Laszlo
- University of Washington , Department of Chemistry, Box 351700, Seattle, Washington 98195-1700, United States
| | - Matthew F Bush
- University of Washington , Department of Chemistry, Box 351700, Seattle, Washington 98195-1700, United States
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22
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Hines KM, Ross DH, Davidson KL, Bush MF, Xu L. Large-Scale Structural Characterization of Drug and Drug-Like Compounds by High-Throughput Ion Mobility-Mass Spectrometry. Anal Chem 2017; 89:9023-9030. [PMID: 28764324 PMCID: PMC5616088 DOI: 10.1021/acs.analchem.7b01709] [Citation(s) in RCA: 83] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
![]()
Ion mobility-mass spectrometry (IM-MS)
can provide orthogonal information,
i.e., m/z and collision cross section
(CCS), for the identification of drugs and drug metabolites. However,
only a small number of CCS values are available for drugs, which limits
the use of CCS as an identification parameter and the assessment of
structure–function relationships of drugs using IM-MS. Here,
we report the development of a rapid workflow for the measurement
of CCS values of a large number of drug or drug-like molecules in
nitrogen on the widely available traveling wave IM-MS (TWIM-MS) platform.
Using a combination of small molecule and polypeptide CCS calibrants,
we successfully determined the nitrogen CCS values of 1425 drug or
drug-like molecules in the MicroSource Discovery Systems’ Spectrum
Collection using flow injection analysis of 384-well plates. Software
was developed to streamline data extraction, processing, and calibration.
We found that the overall drug collection covers a wide CCS range
for the same mass, suggesting a large structural diversity of these
drugs. However, individual drug classes appear to occupy a narrow
and unique space in the CCS–mass 2D spectrum, suggesting a
tight structure–function relationship for each class of drugs
with a specific target. We observed bimodal distributions for several
antibiotic species due to multiple protomers, including the known
fluoroquinolone protomers and the new finding of cephalosporin protomers.
Lastly, we demonstrated the utility of the high-throughput method
and drug CCS database by quickly and confidently confirming the active
component in a pharmaceutical product.
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Affiliation(s)
- Kelly M Hines
- Department of Medicinal Chemistry, ‡Department of Chemistry, University of Washington , Seattle, Washington 98195, United States
| | - Dylan H Ross
- Department of Medicinal Chemistry, ‡Department of Chemistry, University of Washington , Seattle, Washington 98195, United States
| | - Kimberly L Davidson
- Department of Medicinal Chemistry, ‡Department of Chemistry, University of Washington , Seattle, Washington 98195, United States
| | - Matthew F Bush
- Department of Medicinal Chemistry, ‡Department of Chemistry, University of Washington , Seattle, Washington 98195, United States
| | - Libin Xu
- Department of Medicinal Chemistry, ‡Department of Chemistry, University of Washington , Seattle, Washington 98195, United States
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23
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Laszlo KJ, Bush MF. Interpreting the Collision Cross Sections of Native-like Protein Ions: Insights from Cation-to-Anion Proton-Transfer Reactions. Anal Chem 2017. [PMID: 28636334 DOI: 10.1021/acs.analchem.7b01474] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The effects of charge state on structures of native-like cations of serum albumin, streptavidin, avidin, and alcohol dehydrogenase were probed using cation-to-anion proton-transfer reactions (CAPTR), ion mobility, mass spectrometry, and complementary energy-dependent experiments. The CAPTR products all have collision cross-section (Ω) values that are within 5.5% of the original precursor cations. The first CAPTR event for each precursor yields products that have smaller Ω values and frequently exhibit the greatest magnitude of change in Ω resulting from a single CAPTR event. To investigate how the structures of the precursors affect the structures of the products, ions were activated as a function of energy prior to CAPTR. In each case, the Ω values of the activated precursors increase with increasing energy, but the Ω values of the CAPTR products are smaller than the activated precursors. To investigate the stabilities of the CAPTR products, the products were activated immediately prior to ion mobility. These results show that additional structures with smaller or larger Ω values can be populated and that the structures and stabilities of these ions depend most strongly on the identity of the protein and the charge state of the product, rather than the charge state of the precursor or the number of CAPTR events. Together, these results indicate that the excess charges initially present on native-like ions have a modest, but sometimes statistically significant, effect on their Ω values. Therefore, potential contributions from charge state should be considered when using experimental Ω values to elucidate structures in solution.
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Affiliation(s)
- Kenneth J Laszlo
- Department of Chemistry, University of Washington , Box 351700, Seattle, Washington 98195-1700, United States
| | - Matthew F Bush
- Department of Chemistry, University of Washington , Box 351700, Seattle, Washington 98195-1700, United States
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24
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Allen SJ, Eaton RM, Bush MF. Structural Dynamics of Native-Like Ions in the Gas Phase: Results from Tandem Ion Mobility of Cytochrome c. Anal Chem 2017. [PMID: 28636328 DOI: 10.1021/acs.analchem.7b01234] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Ion mobility (IM) is a gas-phase separation technique that is used to determine the collision cross sections of native-like ions of proteins and protein complexes, which are in turn used as restraints for modeling the structures of those analytes in solution. Here, we evaluate the stability of native-like ions using tandem IM experiments implemented using structures for lossless ion manipulations (SLIM). In this implementation of tandem IM, ions undergo a first dimension of IM up to a switch that is used to selectively transmit ions of a desired mobility. Selected ions are accumulated in a trap and then released after a delay to initiate the second dimension of IM. For delays ranging from 16 to 33 231 ms, the collision cross sections of native-like, 7+ cytochrome c ions increase monotonically from 15.1 to 17.1 nm2. The largest products formed in these experiments at near-ambient temperature are still far smaller than those formed in energy-dependent experiments (∼21 nm2). However, the collision cross section increases by ∼2% between delay times of 16 and 211 ms, which may have implications for other IM experiments on these time scales. Finally, two subpopulations from the full population were each mobility selected and analyzed as a function of delay time, showing that the three populations can be differentiated for at least 1 s. Together, these results suggest that elements of native-like structure can have long lifetimes at near-ambient temperature in the gas phase but that gas-phase dynamics should be considered when interpreting results from IM.
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Affiliation(s)
- Samuel J Allen
- University of Washington , Department of Chemistry, Box 351700, Seattle, Washington 98195-1700, United States
| | - Rachel M Eaton
- University of Washington , Department of Chemistry, Box 351700, Seattle, Washington 98195-1700, United States
| | - Matthew F Bush
- University of Washington , Department of Chemistry, Box 351700, Seattle, Washington 98195-1700, United States
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25
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Hollerbach A, Baird Z, Cooks RG. Ion Separation in Air Using a Three-Dimensional Printed Ion Mobility Spectrometer. Anal Chem 2017; 89:5058-5065. [PMID: 28383249 DOI: 10.1021/acs.analchem.7b00469] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Adam Hollerbach
- Chemistry
Department, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907, United States
| | | | - R. Graham Cooks
- Chemistry
Department, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907, United States
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26
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Ewing SA, Donor MT, Wilson JW, Prell JS. Collidoscope: An Improved Tool for Computing Collisional Cross-Sections with the Trajectory Method. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:587-596. [PMID: 28194738 PMCID: PMC5634518 DOI: 10.1007/s13361-017-1594-2] [Citation(s) in RCA: 100] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Revised: 12/09/2016] [Accepted: 12/29/2016] [Indexed: 05/19/2023]
Abstract
Ion mobility-mass spectrometry (IM-MS) can be a powerful tool for determining structural information about ions in the gas phase, from small covalent analytes to large, native-like or denatured proteins and complexes. For large biomolecular ions, which may have a wide variety of possible gas-phase conformations and multiple charge sites, quantitative, physically explicit modeling of collisional cross sections (CCSs) for comparison to IMS data can be challenging and time-consuming. We present a "trajectory method" (TM) based CCS calculator, named "Collidoscope," which utilizes parallel processing and optimized trajectory sampling, and implements both He and N2 as collision gas options. Also included is a charge-placement algorithm for determining probable charge site configurations for protonated protein ions given an input geometry in pdb file format. Results from Collidoscope are compared with those from the current state-of-the-art CCS simulation suite, IMoS. Collidoscope CCSs are within 4% of IMoS values for ions with masses from ~18 Da to ~800 kDa. Collidoscope CCSs using X-ray crystal geometries are typically within a few percent of IM-MS experimental values for ions with mass up to ~3.5 kDa (melittin), and discrepancies for larger ions up to ~800 kDa (GroEL) are attributed in large part to changes in ion structure during and after the electrospray process. Due to its physically explicit modeling of scattering, computational efficiency, and accuracy, Collidoscope can be a valuable tool for IM-MS research, especially for large biomolecular ions. Graphical Abstract ᅟ.
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Affiliation(s)
- Simon A Ewing
- Department of Chemistry and Biochemistry, University of Oregon, 1253 University of Oregon, Eugene, OR, 97403-1253, USA
| | - Micah T Donor
- Department of Chemistry and Biochemistry, University of Oregon, 1253 University of Oregon, Eugene, OR, 97403-1253, USA
| | - Jesse W Wilson
- Department of Chemistry and Biochemistry, University of Oregon, 1253 University of Oregon, Eugene, OR, 97403-1253, USA
| | - James S Prell
- Department of Chemistry and Biochemistry, University of Oregon, 1253 University of Oregon, Eugene, OR, 97403-1253, USA.
- Materials Science Institute, University of Oregon, 1252 University of Oregon, Eugene, OR, 97403-1252, USA.
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27
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Poyer S, Comby-Zerbino C, Choi CM, MacAleese L, Deo C, Bogliotti N, Xie J, Salpin JY, Dugourd P, Chirot F. Conformational Dynamics in Ion Mobility Data. Anal Chem 2017; 89:4230-4237. [DOI: 10.1021/acs.analchem.7b00281] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Salomé Poyer
- LAMBE,
Université Evry Val d’Essonne, CEA, CNRS, Université Paris-Saclay, F-91025, Evry, France
| | - Clothilde Comby-Zerbino
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, Institut Lumière Matière UMR 5306, F-69100, Villeurbanne, France
| | - Chang Min Choi
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, Institut Lumière Matière UMR 5306, F-69100, Villeurbanne, France
| | - Luke MacAleese
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, Institut Lumière Matière UMR 5306, F-69100, Villeurbanne, France
| | - Claire Deo
- PPSM,
ENS Paris-Saclay, CNRS, Université Paris-Saclay, F-94235 Cachan, France
| | - Nicolas Bogliotti
- PPSM,
ENS Paris-Saclay, CNRS, Université Paris-Saclay, F-94235 Cachan, France
| | - Juan Xie
- PPSM,
ENS Paris-Saclay, CNRS, Université Paris-Saclay, F-94235 Cachan, France
| | - Jean-Yves Salpin
- LAMBE,
Université Evry Val d’Essonne, CEA, CNRS, Université Paris-Saclay, F-91025, Evry, France
| | - Philippe Dugourd
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, Institut Lumière Matière UMR 5306, F-69100, Villeurbanne, France
| | - Fabien Chirot
- Univ Lyon, Université Claude Bernard Lyon 1, Ens de Lyon, CNRS, Institut des Sciences Analytiques UMR 5280, 5 rue de la Doua, F-69100, Villeurbanne, France
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28
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Davidson KL, Bush MF. Effects of Drift Gas Selection on the Ambient-Temperature, Ion Mobility Mass Spectrometry Analysis of Amino Acids. Anal Chem 2017; 89:2017-2023. [DOI: 10.1021/acs.analchem.6b04605] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Kimberly L. Davidson
- University of Washington, Department of Chemistry, Box 351700, Seattle, Washington 98195-1700, United States
| | - Matthew F. Bush
- University of Washington, Department of Chemistry, Box 351700, Seattle, Washington 98195-1700, United States
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29
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Lermyte F, Sobott F. A broader view on ion heating in traveling-wave devices using fragmentation of CsI clusters and extent of H˙ migration as molecular thermometers. Analyst 2017; 142:3388-3399. [DOI: 10.1039/c7an00161d] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Traveling-wave-dependent ion ‘heating’ is observed during mass spectrometry experiments under both ion mobility and electron transfer dissociation conditions and investigated using novel molecular ‘thermometers’.
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Affiliation(s)
- Frederik Lermyte
- Biomolecular & Analytical Mass Spectrometry Group
- Department of Chemistry
- University of Antwerp
- Antwerp
- Belgium
| | - Frank Sobott
- Biomolecular & Analytical Mass Spectrometry Group
- Department of Chemistry
- University of Antwerp
- Antwerp
- Belgium
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30
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Allen SJ, Eaton RM, Bush MF. Analysis of Native-Like Ions Using Structures for Lossless Ion Manipulations. Anal Chem 2016; 88:9118-26. [DOI: 10.1021/acs.analchem.6b02089] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Samuel J. Allen
- University of Washington, Department of Chemistry, Box 351700, Seattle, Washington 98195-1700, United States
| | - Rachel M. Eaton
- University of Washington, Department of Chemistry, Box 351700, Seattle, Washington 98195-1700, United States
| | - Matthew F. Bush
- University of Washington, Department of Chemistry, Box 351700, Seattle, Washington 98195-1700, United States
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