1
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Kumar M, Attygalle AB. Manipulating Non-Dissociative Transformations of Gaseous Ion Ensembles Prior to Ion-Mobility Separation. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:1197-1207. [PMID: 38718179 DOI: 10.1021/jasms.4c00032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2024]
Abstract
Molecules with multiple sites capable of accepting protons form ensembles of protomers. The manifested protomer ratios in such ensembles are influenced by many experimental conditions. In a Synapt G2 ion mobility (IM)-enabled mass spectrometry system, there are several physical locations where ion population changes can be manifested. Using APCI-generated protomers of aminonaphthalenes, we investigated its intramolecular proton transfers from the N-protomer to the C-protomer. This lossless transformation of the N-protomer to the thermodynamically favored C-protomer can take place in the ion source itself. Initially, we learned that the cone gas slows down the transformation to the C-protomer. Gaseous ions are then accelerated in the first vacuum region, where ions undergo collisional activation (heating), which facilitates the transformation to the C-protomer. Afterward, the ions are mass selected and transferred to the pre-IM (Trap)-collision cell, where ions can also be transformed to the thermodynamically favored protomers. Trap accumulated ions are then released to the IM separator via a helium-filled entry cell. The role of helium is to minimize ion activation and scattering taking place upon entry to the high-pressure T-Wave IM separator (TWIMS). The helium cell is known to increase the IM peak resolution. However, we found that significant changes occur depending on the presence or absence of helium. Without helium, source-generated protomers rapidly changed to a predominantly thermodynamically favorable ensemble protomers. Apparently, the introduction of helium into the precell induced a dramatic decrease in collisional "heating" effect, which effectively slowed down the conversion rate of the amino-protomer into the more favorable ring-protomer. The final message is that mobilograms should not be considered as direct real-time, or intrinsic, representations of the protomer ratios in the ion source.
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Affiliation(s)
- Meenu Kumar
- Center for Mass Spectrometry, Department of Chemistry and Chemical Biology, Stevens Institute of Technology, Hoboken, New Jersey 07030, United States
| | - Athula B Attygalle
- Center for Mass Spectrometry, Department of Chemistry and Chemical Biology, Stevens Institute of Technology, Hoboken, New Jersey 07030, United States
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2
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Thurman HA, Wijegunawardena G, Berthias F, Williamson DL, Wu H, Nagy G, Jensen ON, Shvartsburg AA. Multiplatform High-Definition Ion Mobility Separations of the Largest Epimeric Peptides. Anal Chem 2024; 96:2318-2326. [PMID: 38301112 DOI: 10.1021/acs.analchem.3c03079] [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: 02/03/2024]
Abstract
Ion mobility spectrometry (IMS) coupled to mass spectrometry (MS) has become a versatile tool to fractionate complex mixtures, distinguish structural isomers, and elucidate molecular geometries. Along with the whole MS field, IMS/MS advances to ever larger species. A topical proteomic problem is the discovery and characterization of d-amino acid-containing peptides (DAACPs) that are critical to neurotransmission and toxicology. Both linear IMS and FAIMS previously disentangled d/l epimers with up to ∼30 residues. In the first study using all three most powerful IMS methodologies─trapped IMS, cyclic IMS, and FAIMS─we demonstrate baseline resolution of the largest known d/l peptides (CHH from Homarus americanus with 72 residues) with a dynamic range up to 100. This expands FAIMS analyses of isomeric modified peptides, especially using hydrogen-rich buffers, to the ∼50-100 residue range of small proteins. The spectra for d and l are unprecedentedly strikingly similar except for a uniform shift of the separation parameter, indicating the conserved epimer-specific structural elements across multiple charge states and conformers. As the interepimer resolution tracks the average for smaller DAACPs, the IMS approaches could help search for yet larger DAACPs. The a priori method to calibrate cyclic (including multipass) IMS developed here may be broadly useful.
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Affiliation(s)
- Hayden A Thurman
- Department of Chemistry, Wichita State University, 1845 Fairmount, Wichita, Kansas 67260, United States
| | - Gayani Wijegunawardena
- Department of Chemistry, Wichita State University, 1845 Fairmount, Wichita, Kansas 67260, United States
| | - Francis Berthias
- Department of Biochemistry & Molecular Biology and VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, DK-5230 Odense M, Denmark
| | - David L Williamson
- Department of Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
| | - Haifan Wu
- Department of Chemistry, Wichita State University, 1845 Fairmount, Wichita, Kansas 67260, United States
| | - Gabe Nagy
- Department of Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
| | - Ole N Jensen
- Department of Biochemistry & Molecular Biology and VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, DK-5230 Odense M, Denmark
| | - Alexandre A Shvartsburg
- Department of Chemistry, Wichita State University, 1845 Fairmount, Wichita, Kansas 67260, United States
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3
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Mubas-Sirah F, Gandhi VD, Latif M, Hua L, Tootchi A, Larriba-Andaluz C. Ion mobility calculations of flexible all-atom systems at arbitrary fields using two-temperature theory. Phys Chem Chem Phys 2024; 26:4118-4124. [PMID: 38226667 DOI: 10.1039/d3cp05415b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2024]
Abstract
Ion mobility spectrometry (IMS) separates and analyzes ions based on their mobility in a gas under an electric field. When the field is increased, the mobility varies in a complex way that depends on the relative velocity between gas and ion, their electrostatic potential interactions, and the effects from direct impingement. Recently, the two-temperature theory, primarily developed for monoatomic ions in monoatomic gases, has been extended to study mobilities at arbitrary fields using polyatomic ions in polyatomic gases, with some success. However, this extension poses challenges, such as inelastic collisions between gas and ion and structural modifications of ions as they heat up. These challenges become significant when working with diatomic gases and flexible molecules. In a previous study, experimental mobilities of tetraalkylammonium salts were obtained using a FAIMS instrument, showing satisfactory agreement with numerical two-temperature theory predictions. However, deviations occurred at fields greater than 100 Td. To address this issue, this paper introduces a modified high-field calculation method that accounts for the structural changes in ions due to field heating. The study focuses on tetraheptylammonium (THA+), tetradecylammonium (TDA+), and tetradodecylammonium (TDDA+) salts. Molecular structures were generated at various temperatures using MM2 forcefield. The mobility was calculated using IMoS 1.13 with two-temperature trajectory method calculations up to the fourth approximation. Multiple effective temperatures were considered, and a linear weighing system was used to create mobility vs. reduced field strength plots. The results suggest that the structural enlargement due to ion heating plays a significant role in mobility at high fields, aligning better with experimental data. FAIMS' dispersion plots also show improved agreement with experimental results. However, the contribution of inelastic collisions and energy transfer to rotational degrees of freedom in gas molecules remains a complex and challenging aspect.
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Affiliation(s)
- Farah Mubas-Sirah
- Department of Mechanical Engineering, Indiana University - Purdue University Indianapolis, Indianapolis, IN, USA.
| | - Viraj D Gandhi
- Department of Mechanical Engineering, Indiana University - Purdue University Indianapolis, Indianapolis, IN, USA.
- Department of Mechanical Engineering, Purdue University, West Lafayette, IN, USA
| | - Mohsen Latif
- Department of Mechanical Engineering, Indiana University - Purdue University Indianapolis, Indianapolis, IN, USA.
| | - Leyan Hua
- Department of Mechanical Engineering, Indiana University - Purdue University Indianapolis, Indianapolis, IN, USA.
| | - Amirreza Tootchi
- Department of Mechanical Engineering, Indiana University - Purdue University Indianapolis, Indianapolis, IN, USA.
| | - Carlos Larriba-Andaluz
- Department of Mechanical Engineering, Indiana University - Purdue University Indianapolis, Indianapolis, IN, USA.
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4
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Li J, Liu R, Gao W, Yu J, Tang K. Ion storage biases in the ion funnel trap of a Hybrid ion mobility spectrometer/time of flight mass spectrometer. Talanta 2023; 260:124621. [PMID: 37149942 DOI: 10.1016/j.talanta.2023.124621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Revised: 04/27/2023] [Accepted: 04/30/2023] [Indexed: 05/09/2023]
Abstract
A detailed experimental characterization on the ion storage biases in an ion funnel trap, related to ion structure, charge state and RF voltage applied to the ion funnel trap, is reported by using both cytochrome C and ubiquitin samples. It was first observed experimentally that an unavoidable ion overflow would occur when the incoming ions exceeded the capacity of ion funnel trap. The conformers with extended structures would lose preferentially in the ion overflow process. Accordingly, a significant structural bias in the ion mobility spectrometry/time of flight mass spectrometry (IMS-TOF MS) spectrum was created, as the peak intensities for conformers with compact structures and extended structures would continuously increase and decrease, respectively, when the ion overflow time of the ion funnel trap was increased. Furthermore, the experimental results also showed that the effect of this ion structural bias was more significant when the RF voltage applied to the ion funnel trap was increased. In addition, an ion charge state bias in the ion funnel trap was also observed. The effect of the ion structural bias depends significantly on the specific charge state of the ions. For a given analyte, its lower charge state ions show a greater sensitivity to the ion structural bias than the higher charge state ones under the same ion funnel trap operating conditions. Therefore, it is extremely important to set a reasonable operation condition for the ion funnel trap to avoid ion storage biases in IMS-TOF MS.
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Affiliation(s)
- Junhui Li
- Institute of Mass Spectrometry, Zhejiang Engineering Research Center of Advanced Mass Spectrometry and Clinical Application, Ningbo University, Ningbo, 315211, PR China; Zhenhai Institute of Mass Spectrometry, Ningbo, 315211, PR China; Faculty of Electrical Engineering and Computer Science, Ningbo University, Ningbo, 315211, PR China
| | - Rong Liu
- Institute of Mass Spectrometry, Zhejiang Engineering Research Center of Advanced Mass Spectrometry and Clinical Application, Ningbo University, Ningbo, 315211, PR China; Zhenhai Institute of Mass Spectrometry, Ningbo, 315211, PR China; School of Material Science and Chemical Engineering, Ningbo University, Ningbo, 315211, PR China
| | - Wenqing Gao
- Institute of Mass Spectrometry, Zhejiang Engineering Research Center of Advanced Mass Spectrometry and Clinical Application, Ningbo University, Ningbo, 315211, PR China; Zhenhai Institute of Mass Spectrometry, Ningbo, 315211, PR China; School of Material Science and Chemical Engineering, Ningbo University, Ningbo, 315211, PR China
| | - Jiancheng Yu
- Institute of Mass Spectrometry, Zhejiang Engineering Research Center of Advanced Mass Spectrometry and Clinical Application, Ningbo University, Ningbo, 315211, PR China; Zhenhai Institute of Mass Spectrometry, Ningbo, 315211, PR China; Faculty of Electrical Engineering and Computer Science, Ningbo University, Ningbo, 315211, PR China
| | - Keqi Tang
- Institute of Mass Spectrometry, Zhejiang Engineering Research Center of Advanced Mass Spectrometry and Clinical Application, Ningbo University, Ningbo, 315211, PR China; Zhenhai Institute of Mass Spectrometry, Ningbo, 315211, PR China; School of Material Science and Chemical Engineering, Ningbo University, Ningbo, 315211, PR China.
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5
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Díaz-Galiano FJ, Murcia-Morales M, Monteau F, Le Bizec B, Dervilly G. Collision cross-section as a universal molecular descriptor in the analysis of PFAS and use of ion mobility spectrum filtering for improved analytical sensitivities. Anal Chim Acta 2023; 1251:341026. [PMID: 36925298 DOI: 10.1016/j.aca.2023.341026] [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: 11/29/2022] [Revised: 02/15/2023] [Accepted: 02/26/2023] [Indexed: 03/06/2023]
Abstract
The massive usage of per- and polyfluoroalkyl substances (PFAS), as well as their high chemical stability, have led to their ubiquitous presence in environmental matrices and direct human exposure through contaminated food, particularly fish. In the analysis of this large group of substances, the use of ion mobility coupled to mass spectrometry is of particular relevance because it uses an additional descriptor, the collision cross-section (CCS), which results in increased selectivity. In the present work, the TWCCSN2 of 24 priority PFAS were experimentally obtained, and the reproducibility of these measurements was evaluated over seven weeks. The average values were employed to critically assess previously reported data and theoretical calculations. This gain in selectivity made it possible to increase the sensitivity of the detection on complex matrices (biota, food and human serum) by using the drift time associated to each analyte as a filter, thus reducing the interferences and background noise and allowing their detection at trace levels.
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Affiliation(s)
- Francisco José Díaz-Galiano
- ONIRIS, INRAE, LABERCA, Nantes, 44000, France; University of Almería, Department of Chemistry and Physics, Agrifood Campus of International Excellence (ceiA3), Ctra. Sacramento s/n, La Cañada de San Urbano, 04120, Almería, Spain
| | - María Murcia-Morales
- ONIRIS, INRAE, LABERCA, Nantes, 44000, France; University of Almería, Department of Chemistry and Physics, Agrifood Campus of International Excellence (ceiA3), Ctra. Sacramento s/n, La Cañada de San Urbano, 04120, Almería, Spain
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6
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Pathak P, Shvartsburg AA. Assessing the Dipole Moments and Directional Cross Sections of Proteins and Complexes by Differential Ion Mobility Spectrometry. Anal Chem 2022; 94:7041-7049. [PMID: 35500292 DOI: 10.1021/acs.analchem.2c00343] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Ion mobility spectrometry (IMS) has become a mainstream approach to fractionate complex mixtures, separate isomers, and assign the molecular geometries. All modalities were grouped into linear IMS (based on the absolute ion mobility, K) and field asymmetric waveform IMS (FAIMS) relying on the evolution of K at a high normalized electric field (E/N) that induces strong ion heating. In the recently demonstrated low-field differential (LOD) IMS, the field is too weak for significant heating but locks the macromolecular dipoles to produce novel separations controlled by the relevant directional collision cross sections (CCSs). Here, we show LODIMS for mass-selected species, exploring the dipole alignment across charge states for the monomers and dimers of an exemplary protein, the alcohol dehydrogenase. Distinct conformational families for aligned species are revealed with directional CCS estimated from the field-dependent trend lines. We set up a model to extract the fractions of pendular conformers as a function of field intensity and translate them into dipole moment distributions. These developments make a critical step toward establishing LODIMS as a new tool for top-down proteomics and integrative structural biology.
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Affiliation(s)
- Pratima Pathak
- Department of Chemistry, Wichita State University, 1845 Fairmount, Wichita, Kansas 67260, United States
| | - Alexandre A Shvartsburg
- Department of Chemistry, Wichita State University, 1845 Fairmount, Wichita, Kansas 67260, United States
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7
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Li J, Li L, Gao W, Shi S, Yu J, Tang K. Two-Dimensional FAIMS-IMS Characterization of Peptide Conformers with Resolution Exceeding 1000. Anal Chem 2022; 94:6363-6370. [PMID: 35412805 DOI: 10.1021/acs.analchem.2c00805] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A high-performance field asymmetric waveform ion mobility spectrometry (FAIMS)-IMS-MS platform was developed and applied to explore the conformational diversity of the singly and doubly charged bradykinin (BK + H+)+ and (BK + 2H+)2+ ions. With pure N2 as the FAIMS carrier gas, more than ten conformers of (BK + H+)+ can be resolved using FAIMS-IMS, as compared to only four conformers resolved using either FAIMS or IMS alone. Interestingly, multiple conformers of (BK + H+)+ were found to have completely different values of FAIMS compensation voltage (CV), while their IMS drift times were essentially the same, which were also proven experimentally to not result from the structural annealing by the collisional heating in the ion funnel. The separations in the FAIMS and IMS dimensions are substantially orthogonal, and the overall resolving power of two-dimensional FAIMS-IMS separation is largely proportional to the product of the separation resolving powers of FAIMS and IMS. Using a gas mixture of N2/He to further improve the resolving power of the FAIMS separation, the total resolving powers of the combined FAIMS and IMS separation were estimated to be about 1020 and 1400 for (BK + H+)+ and (BK + 2H+)2+ ions, respectively, which are significantly higher than the resolving power of any ion mobility-based separation techniques demonstrated so far. The combined FAIMS-IMS can thus be a much more powerful technique to explore the structural diversity of biomolecules.
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Affiliation(s)
- Junhui Li
- Institute of Mass Spectrometry, Zhejiang Engineering Research Center of Advanced Mass spectrometry and Clinical Application, Ningbo University, Ningbo 315211, P. R. China.,Faculty of Electrical Engineering and Computer Science, Ningbo University, Ningbo 315211, P. R. China
| | - Lei Li
- Institute of Mass Spectrometry, Zhejiang Engineering Research Center of Advanced Mass spectrometry and Clinical Application, Ningbo University, Ningbo 315211, P. R. China.,School of Material Science and Chemical Engineering, Ningbo University, Ningbo 315211, P. R. China
| | - Wenqing Gao
- Institute of Mass Spectrometry, Zhejiang Engineering Research Center of Advanced Mass spectrometry and Clinical Application, Ningbo University, Ningbo 315211, P. R. China.,School of Material Science and Chemical Engineering, Ningbo University, Ningbo 315211, P. R. China
| | - Shoudong Shi
- Faculty of Electrical Engineering and Computer Science, Ningbo University, Ningbo 315211, P. R. China
| | - Jiancheng Yu
- Institute of Mass Spectrometry, Zhejiang Engineering Research Center of Advanced Mass spectrometry and Clinical Application, Ningbo University, Ningbo 315211, P. R. China.,Faculty of Electrical Engineering and Computer Science, Ningbo University, Ningbo 315211, P. R. China
| | - Keqi Tang
- Institute of Mass Spectrometry, Zhejiang Engineering Research Center of Advanced Mass spectrometry and Clinical Application, Ningbo University, Ningbo 315211, P. R. China.,School of Material Science and Chemical Engineering, Ningbo University, Ningbo 315211, P. R. China
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8
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Pham KN, Fernandez-Lima F. Structural Characterization of Human Histone H4.1 by Tandem Nonlinear and Linear Ion Mobility Spectrometry Complemented with Molecular Dynamics Simulations. ACS OMEGA 2021; 6:29567-29576. [PMID: 34778628 PMCID: PMC8582071 DOI: 10.1021/acsomega.1c03744] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 10/15/2021] [Indexed: 06/13/2023]
Abstract
Extracellular histone H4 is an attractive drug target owing to its roles in organ failure in sepsis and other diseases. To identify inhibitors using in silico methods, information on histone H4 structural dynamics and three-dimensional (3D) structural coordinates is required. Here, DNA-free histone H4 type 1 (H4.1) was characterized by utilizing tandem nonlinear and linear ion mobility spectrometry (FAIMS-TIMS) coupled to mass spectrometry (MS) complemented with molecular dynamics (MD) simulations. The gas-phase structures of H4.1 are dependent on the starting solution conditions, evidenced by differences in charge state distributions, mobility distributions, and collision-induced unfolding (CIU) pathways. The experimental results show that H4.1 adopts diverse conformational types from compact (C) to partially folded (P) and subsequently elongated (E) structures. Molecular dynamics simulations provided candidate structures for the histone H4.1 monomer in solution and for the gas-phase structures observed using FAIMS-IMS-TOF MS as a function of the charge state and mobility distribution. A combination of the FAIMS-TIMS experimental results with theoretical dipole calculations reveals the important role of charge distribution in the dipole alignment of H4.1 elongated structures at high electric fields. A comparison of the secondary and primary structures of DNA-free H2A.1 and H4.1 is made based on the experimental IMS-MS and MD findings.
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Affiliation(s)
- Khoa N. Pham
- Department
of Chemistry and Biochemistry, Florida International
University, Miami, Florida 33199, United States
| | - Francisco Fernandez-Lima
- Department
of Chemistry and Biochemistry, Florida International
University, Miami, Florida 33199, United States
- Biomolecular
Science Institute, Florida International
University, Miami, Florida 33199, United
States
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9
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Andrzejewski R, Entwistle A, Giles R, Shvartsburg AA. Ion Mobility Spectrometry of Superheated Macromolecules at Electric Fields up to 500 Td. Anal Chem 2021; 93:12049-12058. [PMID: 34423987 DOI: 10.1021/acs.analchem.1c02299] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Since its inception in 1980s, differential or field asymmetric waveform ion mobility spectrometry (FAIMS) has been implemented at or near ambient gas pressure. We recently developed FAIMS at 15-30 Torr with mass spectrometry and utilized it to analyze amino acids, isomeric peptides, and protein conformers. The separations broadly mirrored those at atmospheric pressure, save for larger proteins that (as predicted) exhibited dipole alignment at ambient but not low pressure. Here we reduce the pressure down to 4.7 Torr, allowing normalized electric fields up to 543 Td-double the maximum in prior FAIMS or IMS studies of polyatomic ions. Despite the collisional heating to ∼1000 °C at the waveform peaks, the proteins of size from ubiquitin to albumin survived intact. The dissociation of macromolecules in FAIMS appears governed by the average ion temperature over the waveform cycle, unlike the isomerization controlled by the peak temperature. The global separation trends in this "superhot" regime extend those at moderately low pressures, with distinct conformers and no alignment as theorized. Although the scaling of the compensation voltage with the field fell below cubic at lower fields, the resolving power increased and the resolution of different proteins or charge states substantially improved.
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Affiliation(s)
- Roch Andrzejewski
- Shimadzu Research Laboratory, Wharfside, Trafford Wharf Road, Manchester M17 1GP, U.K
| | - Andrew Entwistle
- Shimadzu Research Laboratory, Wharfside, Trafford Wharf Road, Manchester M17 1GP, U.K
| | - Roger Giles
- Shimadzu Research Laboratory, Wharfside, Trafford Wharf Road, Manchester M17 1GP, U.K
| | - Alexandre A Shvartsburg
- Department of Chemistry, Wichita State University, 1845 Fairmount, Wichita, Kansas 67260, United States
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10
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Skeene K, Khatri K, Soloviev Z, Lapthorn C. Current status and future prospects for ion-mobility mass spectrometry in the biopharmaceutical industry. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2021; 1869:140697. [PMID: 34246790 DOI: 10.1016/j.bbapap.2021.140697] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 06/11/2021] [Accepted: 07/06/2021] [Indexed: 12/12/2022]
Abstract
Detailed characterization of protein reagents and biopharmaceuticals is key in defining successful drug discovery campaigns, aimed at bringing molecules through different discovery stages up to development and commercialization. There are many challenges in this process, with complex and detailed analyses playing paramount roles in modern industry. Mass spectrometry (MS) has become an essential tool for characterization of proteins ever since the onset of soft ionization techniques and has taken the lead in quality assessment of biopharmaceutical molecules, and protein reagents, used in the drug discovery pipeline. MS use spans from identification of correct sequences, to intact molecule analyses, protein complexes and more recently epitope and paratope identification. MS toolkits could be incredibly diverse and with ever evolving instrumentation, increasingly novel MS-based techniques are becoming indispensable tools in the biopharmaceutical industry. Here we discuss application of Ion Mobility MS (IMMS) in an industrial setting, and what the current applications and outlook are for making IMMS more mainstream.
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Affiliation(s)
- Kirsty Skeene
- Biopharm Process Research, Medicinal Science and Technology, GlaxoSmithKline, Stevenage SG1 2NY, UK.
| | - Kshitij Khatri
- Structure and Function Characterization, CMC-Analytical, GlaxoSmithKline, Collegeville, PA 19406, USA.
| | - Zoja Soloviev
- Protein, Cellular and Structural Sciences, Medicinal Science and Technology, GlaxoSmithKline, Stevenage SG1 2NY, UK.
| | - Cris Lapthorn
- Structure and Function Characterization, CMC-Analytical, GlaxoSmithKline, Stevenage SG1 2NY, UK.
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11
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Pham KN, Mamun Y, Fernandez-Lima F. Structural Heterogeneity of Human Histone H2A.1. J Phys Chem B 2021; 125:4977-4986. [PMID: 33974801 PMCID: PMC8568062 DOI: 10.1021/acs.jpcb.1c00335] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Histones are highly basic chromatin proteins that tightly package and order eukaryotic DNA into nucleosomes. While the atomic structure of the nucleosomes has been determined, the three-dimensional structure of DNA-free histones remains unresolved. Here, we combine tandem nonlinear and linear ion mobility spectrometry (FAIMS-TIMS) coupled to mass spectrometry in parallel with molecular modeling to study the conformational space of a DNA-free histone H2A type 1 (H2A.1). Experimental results showed the dependence of the gas-phase structures on the starting solution conditions, characterized by charge state distributions, mobility distributions, and collision-induced-unfolding pathways. The measured H2A.1 gas-phase structures showed a high diversity of structural features ranging from compact (C) to partially folded (P) and then highly elongated (E) conformations. Molecular dynamics simulations provided candidate structures for the solution H2A.1 native conformation with folded N- and C-terminal tails, as well as gas-phase candidate structures associated with the mobility trends. Complementary collision cross section and dipole calculations showed that the charge distribution in the case of elongated gas-phase structures, where basic and acidic residues are mostly exposed (e.g., z > 15+), is sufficient to induce differences in the dipole alignment at high electric fields, in good agreement with the trends observed during the FAIMS-TIMS experiments.
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Affiliation(s)
- Khoa N Pham
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida 33199, United States
| | - Yasir Mamun
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida 33199, United States
| | - Francisco Fernandez-Lima
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida 33199, United States.,Biomolecular Science Institute, Florida International University, Miami, Florida 33199, United States
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12
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Conant CR, Attah IK, Garimella SVB, Nagy G, Bilbao A, Smith RD, Ibrahim YM. Evaluation of Waveform Profiles for Traveling Wave Ion Mobility Separations in Structures for Lossless Ion Manipulations. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:225-236. [PMID: 33126794 PMCID: PMC8170696 DOI: 10.1021/jasms.0c00282] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Structures for lossless ion manipulations (SLIM) have recently enabled a powerful implementation of traveling wave ion mobility spectrometry (TWIMS) for ultrahigh resolution separations; however, experimental parameters have not been optimized, and potential significant gains may be feasible. Most TWIMS separations have utilized square-shaped waveforms applied by time-dependent voltage stepping across repeating sets of electrodes, but alternative waveforms may provide further improvements to resolution. Here, we characterize five waveforms (including square and sine) in terms of their transmission efficiency, IMS resolution, and resolving power, and explore the effects of TW amplitude and speed on the performance of each. We found, consistent with previous work, separations were generally improved with higher TW amplitudes, moderately improved by lower speeds (limited by ion "surfing" with the waves), and found decreases in signal intensity at the extremes of operating conditions. The triangle and asymmetric "ramp forward" shaped profiles were found to provide modestly greater resolution and resolving power, an observation we tentatively attribute to their relatively uniform fields and minimal low-field regions.
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Affiliation(s)
- Christopher R Conant
- 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
| | - Sandilya V B Garimella
- 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
| | - Aivett Bilbao
- 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
| | - Yehia M Ibrahim
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
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13
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Inutan ED, Jarois DR, Lietz CB, El-Baba TJ, Elia EA, Karki S, Sampat AAS, Foley CD, Clemmer DE, Trimpin S. Comparison of gaseous ubiquitin ion structures obtained from a solid and solution matrix using ion mobility spectrometry/mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2021; 35 Suppl 1:e8793. [PMID: 32220130 DOI: 10.1002/rcm.8793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2019] [Revised: 03/24/2020] [Accepted: 03/24/2020] [Indexed: 06/10/2023]
Abstract
RATIONALE Examining surface protein conformations, and especially achieving this with spatial resolution, is an important goal. The recently discovered ionization processes offer spatial-resolution measurements similar to matrix-assisted laser desorption/ionization (MALDI) and produce charge states similar to electrospray ionization (ESI) extending higher-mass protein applications directly from surfaces on high-performance mass spectrometers. Studying a well-interrogated protein by ion mobility spectrometry-mass spectrometry (IMS-MS) to access effects on structures using a solid vs. solvent matrix may provide insights. METHODS Ubiquitin was studied by IMS-MS using new ionization processes with commercial and homebuilt ion sources and instruments (Waters SYNAPT G2(S)) and homebuilt 2 m drift-tube instrument; MS™ sources). Mass-to-charge and drift-time (td )-measurements are compared for ubiquitin ions obtained by inlet and vacuum ionization using laserspray ionization (LSI), matrix- (MAI) and solvent-assisted ionization (SAI), respectively, and compared with those from ESI under conditions that are most comparable. RESULTS Using the same solution conditions with SYNAPT G2(S) instruments, td -distributions of various ubiquitin charge states from MAI, LSI, and SAI are similar to those from ESI using a variety of solvents, matrices, extraction voltages, a laser, and temperature only, showing subtle differences in more compact features within the elongated distribution of structures. However, on a homebuilt drift-tube instrument, within the elongated distribution of structures, both similar and different td -distributions are observed for ubiquitin ions obtained by MAI and ESI. MAI-generated ions are frequently narrower in their td -distributions. CONCLUSIONS Direct comparisons between ESI and the new ionization methods operational directly from surfaces suggest that the protein in its solution structure prior to exposure to the ionization event is either captured (frozen out) at the time of crystallization, or that the protein in the solid matrix is associated with sufficient solvent to maintain the solution structure, or, alternatively, that the observed structures are those related to what occurs in the gas phase with ESI- or MAI-generated ions and not with the solution structures.
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Affiliation(s)
- Ellen D Inutan
- MSTM, LLC, Newark, DE, USA
- Department of Chemistry, Wayne State University, Detroit, MI, USA
- Mindanao State University-Iligan Institute of Technology, Iligan City, Philippines
| | - Dean R Jarois
- Department of Chemistry, Wayne State University, Detroit, MI, USA
| | | | - Tarick J El-Baba
- Department of Chemistry, Indiana University, Bloomington, IN, USA
| | | | - Santosh Karki
- Department of Chemistry, Wayne State University, Detroit, MI, USA
| | | | - Casey D Foley
- Department of Chemistry, Wayne State University, Detroit, MI, USA
| | - David E Clemmer
- Department of Chemistry, Indiana University, Bloomington, IN, USA
| | - Sarah Trimpin
- MSTM, LLC, Newark, DE, USA
- Department of Chemistry, Wayne State University, Detroit, MI, USA
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14
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Pathak P, Shvartsburg AA. Low-Field Differential Ion Mobility Spectrometry of Dipole-Aligned Macromolecules. Anal Chem 2020; 92:13855-13863. [DOI: 10.1021/acs.analchem.0c02551] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Pratima Pathak
- Department of Chemistry, Wichita State University, 1845 Fairmount, Wichita, Kansas 67260, United States
| | - Alexandre A. Shvartsburg
- Department of Chemistry, Wichita State University, 1845 Fairmount, Wichita, Kansas 67260, United States
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15
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Hale OJ, Illes-Toth E, Mize TH, Cooper HJ. High-Field Asymmetric Waveform Ion Mobility Spectrometry and Native Mass Spectrometry: Analysis of Intact Protein Assemblies and Protein Complexes. Anal Chem 2020; 92:6811-6816. [PMID: 32343119 PMCID: PMC7304667 DOI: 10.1021/acs.analchem.0c00649] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
![]()
High-field asymmetric
waveform ion mobility spectrometry (FAIMS)
enables the separation of ions on the basis of their differential
mobility in an asymmetric oscillating electric field. We, and others,
have previously demonstrated the benefits of FAIMS for the analysis
of peptides and denatured proteins. To date, FAIMS has not been integrated
with native mass spectrometry of folded proteins and protein complexes,
largely due to concerns over the heating effects associated with the
high electric fields employed. Here, we demonstrate the newly introduced
cylindrical FAIMS Pro device coupled with an Orbitrap Eclipse enables
analysis of intact protein assemblies up to 147 kDa. No evidence for
dissociation was detected suggesting that any field heating is insufficient
to disrupt the noncovalent interactions governing these assemblies.
Moreover, the FAIMS device was integrated into native liquid extraction
surface analysis (LESA) MS of protein assemblies directly from thin
tissue sections. Intact tetrameric hemoglobin (64 kDa) and trimeric
reactive intermediate deiminase A (RidA, 43 kDa) were detected. Improvements
in signal-to-noise of between 1.5× and 12× were observed
for these protein assemblies on integration of FAIMS.
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Affiliation(s)
- Oliver J Hale
- School of Biosciences, University of Birmingham, Edgbaston B15 2TT, U.K
| | - Eva Illes-Toth
- School of Biosciences, University of Birmingham, Edgbaston B15 2TT, U.K
| | - Todd H Mize
- School of Biosciences, University of Birmingham, Edgbaston B15 2TT, U.K
| | - Helen J Cooper
- School of Biosciences, University of Birmingham, Edgbaston B15 2TT, U.K
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16
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Ieritano C, Featherstone J, Haack A, Guna M, Campbell JL, Hopkins WS. How Hot Are Your Ions in Differential Mobility Spectrometry? JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:582-593. [PMID: 31967812 DOI: 10.1021/jasms.9b00043] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Ions can experience significant field-induced heating in a differential mobility cell. To investigate this phenomenon, the fragmentation of several para-substituted benzylpyridinium "thermometer" ions (R = OMe, Me, F, Cl, H, CN) was monitored in a commercial differential mobility spectrometer (DMS). The internal energy of each benzylpyridinium derivative was characterized by monitoring the degree of fragmentation to obtain an effective temperature, Teff, which corresponds to a temperature consistent with treating the observed fragmentation ratio using a unimolecular dissociation rate weighted by a Boltzmann distribution at a temperature T. It was found that ions are sufficiently thermalized after initial activation from the ESI process to the temperature of the bath gas, Tbath. Once a critical field strength was surpassed, significant fragmentation of the benzylpyridinium ions was detected. At the maximum bath gas temperature (450 K) and separation voltage (SV; 4400 V) for our instrument, Teff for the benzylpyridinium derivatives ranged from 664 ± 9 K (p-OMe) to 759 ± 17 K (p-H). The extent of activation at a given SV depends on the ion's mass, degrees of freedom, (NDoF), and collision frequency as represented by the ion's collision cross section. Plots of Teff vs the product of ion mass and NDoF and the inverse of collision cross section produce strong linear relationships. This provides an attractive avenue to estimate ion temperatures at a given SV using only intrinsic properties. Moreover, experimentally determined Teff correlate with theoretically predicted Teff using with a self-consistent method based on two-temperature theory. The various instrumental and external parameters that influence Teff are additionally discussed.
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Affiliation(s)
- Christian Ieritano
- Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo, Ontario N2L 3G1, Canada
| | - Joshua Featherstone
- Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo, Ontario N2L 3G1, Canada
| | - Alexander Haack
- Department of Physical and Theoretical Chemistry, University of Wuppertal, Gauss Strasse 20, Wuppertal 42119, Germany
| | - Mircea Guna
- SCIEX, 71 Four Valley Drive, Concord, Ontario L4K 4 V8, Canada
| | - J Larry Campbell
- Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo, Ontario N2L 3G1, Canada
- SCIEX, 71 Four Valley Drive, Concord, Ontario L4K 4 V8, Canada
| | - W Scott Hopkins
- Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo, Ontario N2L 3G1, Canada
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17
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Shliaha PV, Gorshkov V, Kovalchuk SI, Schwämmle V, Baird MA, Shvartsburg AA, Jensen ON. Middle-Down Proteomic Analyses with Ion Mobility Separations of Endogenous Isomeric Proteoforms. Anal Chem 2020; 92:2364-2368. [DOI: 10.1021/acs.analchem.9b05011] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Pavel V. Shliaha
- Department of Biochemistry & Molecular Biology and VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, DK-5230 Odense M, Denmark
| | - Vladimir Gorshkov
- Department of Biochemistry & Molecular Biology and VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, DK-5230 Odense M, Denmark
| | - Sergey I. Kovalchuk
- Department of Biochemistry & Molecular Biology and VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, DK-5230 Odense M, Denmark
| | - Veit Schwämmle
- Department of Biochemistry & Molecular Biology and VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, DK-5230 Odense M, Denmark
| | - Matthew A. Baird
- Department of Chemistry, Wichita State University, 1845 Fairmount, Wichita, Kansas 67260, United States
| | - Alexandre A. Shvartsburg
- Department of Chemistry, Wichita State University, 1845 Fairmount, Wichita, Kansas 67260, United States
| | - Ole N. Jensen
- Department of Biochemistry & Molecular Biology and VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, DK-5230 Odense M, Denmark
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18
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Pathak P, Baird MA, Shvartsburg AA. Structurally Informative Isotopic Shifts in Ion Mobility Spectra for Heavier Species. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:137-145. [PMID: 32881519 DOI: 10.1021/jasms.9b00018] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The isotopic molecular envelopes due to stable isotopes for most elements were a staple of mass spectrometry since its origins, often leveraged to identify and quantify compounds. However, all isomers share one MS envelope. As the molecular motion in media also depends on the isotopic composition, separations such as liquid chromatography (LC) and ion mobility spectrometry (IMS) must also feature isotopic envelopes. These were largely not observed because of limited resolution, except for the (structurally uninformative) shifts in LC upon H/D exchange. We recently found the isotopic shifts in FAIMS for small haloanilines (∼130-170 Da) to hinge on the halogen position, opening a novel route to isomer characterization. Here, we extend the capability to heavier species: dibromoanilines (DBAs, ∼250 Da) and tribromoanilines (TBAs, ∼330 Da). The 13C shifts for DBAs and TBAs vary across isomers, some changing sign. While 81Br shifts are less specific, the 2-D 13C/81Br shifts unequivocally differentiate all isomers. The trends for DBAs track those for dichloroanilines, with the 13C shift order preserved for most isomers. The peak broadening due to merged isotopomers is also isomer-specific. The absolute shifts for TBAs are smaller than those for lighter haloanilines, but differentiate isomers as well because of compressed uncertainties. These results showcase the feasibility of broadly distinguishing isomers in the more topical ∼200-300 Da range using the isotopic shifts in IMS spectra.
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Affiliation(s)
- Pratima Pathak
- Department of Chemistry, Wichita State University, 1845 Fairmount, Wichita, Kansas 67260, United States
| | - Matthew A Baird
- Department of Chemistry, Wichita State University, 1845 Fairmount, Wichita, Kansas 67260, United States
| | - Alexandre A Shvartsburg
- Department of Chemistry, Wichita State University, 1845 Fairmount, Wichita, Kansas 67260, United States
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19
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Shvartsburg AA, Andrzejewski R, Entwistle A, Giles R. Ion Mobility Spectrometry of Macromolecules with Dipole Alignment Switchable by Varying the Gas Pressure. Anal Chem 2019; 91:8176-8183. [DOI: 10.1021/acs.analchem.9b00525] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Alexandre A. Shvartsburg
- Department of Chemistry, Wichita State University, 1845 Fairmount, Wichita, Kansas 67260, United States
| | - Roch Andrzejewski
- Shimadzu Research Laboratory, Wharfside, Trafford Wharf Road, Manchester M17 1GP, United Kingdom
| | - Andrew Entwistle
- Shimadzu Research Laboratory, Wharfside, Trafford Wharf Road, Manchester M17 1GP, United Kingdom
| | - Roger Giles
- Shimadzu Research Laboratory, Wharfside, Trafford Wharf Road, Manchester M17 1GP, United Kingdom
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20
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Baird MA, Shliaha PV, Anderson GA, Moskovets E, Laiko V, Makarov AA, Jensen ON, Shvartsburg AA. High-Resolution Differential Ion Mobility Separations/Orbitrap Mass Spectrometry without Buffer Gas Limitations. Anal Chem 2019; 91:6918-6925. [DOI: 10.1021/acs.analchem.9b01309] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Matthew A. Baird
- Department of Chemistry, Wichita State University, 1845 Fairmount, Wichita, Kansas 67260, United States
| | - Pavel V. Shliaha
- Department of Biochemistry and Molecular Biology, VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, DK-5230 Odense M, Denmark
| | - Gordon A. Anderson
- GAACE, 101904 Wiser Parkway Suite 105, Kennewick, Washington 99338, United States
| | - Eugene Moskovets
- MassTech Inc., 6992 Columbia Gateway Drive, Columbia, Maryland 21046, United States
| | - Victor Laiko
- MassTech Inc., 6992 Columbia Gateway Drive, Columbia, Maryland 21046, United States
| | - Alexander A. Makarov
- Thermo Fisher Scientific, Hanna-Kunath Strasse 11, Bremen 28199, Germany
- Department of Chemistry, University of Utrecht, 3508 TC Utrecht, Netherlands
| | - Ole N. Jensen
- Department of Biochemistry and Molecular Biology, VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, DK-5230 Odense M, Denmark
| | - Alexandre A. Shvartsburg
- Department of Chemistry, Wichita State University, 1845 Fairmount, Wichita, Kansas 67260, United States
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21
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Kirk AT, Bohnhorst A, Raddatz CR, Allers M, Zimmermann S. Ultra-high-resolution ion mobility spectrometry-current instrumentation, limitations, and future developments. Anal Bioanal Chem 2019; 411:6229-6246. [PMID: 30957205 DOI: 10.1007/s00216-019-01807-0] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2018] [Revised: 03/15/2019] [Accepted: 03/25/2019] [Indexed: 12/29/2022]
Abstract
With recent advances in ionization sources and instrumentation, ion mobility spectrometers (IMS) have transformed from a detector for chemical warfare agents and explosives to a widely used tool in analytical and bioanalytical applications. This increasing measurement task complexity requires higher and higher analytical performance and especially ultra-high resolution. In this review, we will discuss the currently used ion mobility spectrometers able to reach such ultra-high resolution, defined here as a resolving power greater than 200. These instruments are drift tube IMS, traveling wave IMS, trapped IMS, and field asymmetric or differential IMS. The basic operating principles and the resulting effects of experimental parameters on resolving power are explained and compared between the different instruments. This allows understanding the current limitations of resolving power and how ion mobility spectrometers may progress in the future. Graphical abstract.
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Affiliation(s)
- Ansgar T Kirk
- Institute of Electrical Engineering and Measurement Technology, Department of Sensors and Measurement Technology, Leibniz Universität Hannover, Appelstr. 9A, 30167, Hannover, Germany.
| | - Alexander Bohnhorst
- Institute of Electrical Engineering and Measurement Technology, Department of Sensors and Measurement Technology, Leibniz Universität Hannover, Appelstr. 9A, 30167, Hannover, Germany
| | - Christian-Robert Raddatz
- Institute of Electrical Engineering and Measurement Technology, Department of Sensors and Measurement Technology, Leibniz Universität Hannover, Appelstr. 9A, 30167, Hannover, Germany
| | - Maria Allers
- Institute of Electrical Engineering and Measurement Technology, Department of Sensors and Measurement Technology, Leibniz Universität Hannover, Appelstr. 9A, 30167, Hannover, Germany
| | - Stefan Zimmermann
- Institute of Electrical Engineering and Measurement Technology, Department of Sensors and Measurement Technology, Leibniz Universität Hannover, Appelstr. 9A, 30167, Hannover, Germany
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22
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Baird MA, Anderson GA, Shliaha PV, Jensen ON, Shvartsburg AA. Differential Ion Mobility Separations/Mass Spectrometry with High Resolution in Both Dimensions. Anal Chem 2018; 91:1479-1485. [DOI: 10.1021/acs.analchem.8b04518] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Matthew A. Baird
- Department of Chemistry, Wichita State University, 1845 Fairmount, Wichita, Kansas 67260, United States
| | - Gordon A. Anderson
- GAACE, 101904 Wiser Parkway Ste 105, Kennewick, Washington 99338, United States
| | - Pavel V. Shliaha
- Department of Biochemistry and Molecular Biology, VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, DK-5230 Odense M, Denmark
| | - Ole N. Jensen
- Department of Biochemistry and Molecular Biology, VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, DK-5230 Odense M, Denmark
| | - Alexandre A. Shvartsburg
- Department of Chemistry, Wichita State University, 1845 Fairmount, Wichita, Kansas 67260, United States
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23
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Haler JRN, Massonnet P, Chirot F, Kune C, Comby-Zerbino C, Jordens J, Honing M, Mengerink Y, Far J, Dugourd P, De Pauw E. Comparison of Different Ion Mobility Setups Using Poly (Ethylene Oxide) PEO Polymers: Drift Tube, TIMS, and T-Wave. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2018; 29:114-120. [PMID: 29027151 DOI: 10.1007/s13361-017-1822-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Revised: 09/20/2017] [Accepted: 09/25/2017] [Indexed: 06/07/2023]
Abstract
Over the years, polymer analyses using ion mobility-mass spectrometry (IM-MS) measurements have been performed on different ion mobility spectrometry (IMS) setups. In order to be able to compare literature data taken on different IM(-MS) instruments, ion heating and ion temperature evaluations have already been explored. Nevertheless, extrapolations to other analytes are difficult and thus straightforward same-sample instrument comparisons seem to be the only reliable way to make sure that the different IM(-MS) setups do not greatly change the gas-phase behavior. We used a large range of degrees of polymerization (DP) of poly(ethylene oxide) PEO homopolymers to measure IMS drift times on three different IM-MS setups: a homemade drift tube (DT), a trapped (TIMS), and a traveling wave (T-Wave) IMS setup. The drift time evolutions were followed for increasing polymer DPs (masses) and charge states, and they are found to be comparable and reproducible on the three instruments. ᅟ.
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Affiliation(s)
- Jean R N Haler
- Mass Spectrometry Laboratory, University of Liège, Quartier Agora, Allée du Six Aout 11, B-4000, Liège, Belgium.
| | - Philippe Massonnet
- Mass Spectrometry Laboratory, University of Liège, Quartier Agora, Allée du Six Aout 11, B-4000, Liège, Belgium
| | - Fabien Chirot
- Institut des Sciences Analytiques, Université de Lyon, Université Lyon1, Ens de Lyon, CNRS, 69100, Villeurbanne, France
| | - Christopher Kune
- Mass Spectrometry Laboratory, University of Liège, Quartier Agora, Allée du Six Aout 11, B-4000, Liège, Belgium
| | - Clothilde Comby-Zerbino
- Institut Lumière Matière, Université de Lyon, Université Lyon 1, CNRS, 69100, Villeurbanne, France
| | | | | | | | - Johann Far
- Mass Spectrometry Laboratory, University of Liège, Quartier Agora, Allée du Six Aout 11, B-4000, Liège, Belgium
| | - Philippe Dugourd
- Institut Lumière Matière, Université de Lyon, Université Lyon 1, CNRS, 69100, Villeurbanne, France
| | - Edwin De Pauw
- Mass Spectrometry Laboratory, University of Liège, Quartier Agora, Allée du Six Aout 11, B-4000, Liège, Belgium
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24
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Shvartsburg AA, Haris A, Andrzejewski R, Entwistle A, Giles R. Differential Ion Mobility Separations in the Low-Pressure Regime. Anal Chem 2017; 90:936-943. [DOI: 10.1021/acs.analchem.7b03925] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Alexandre A. Shvartsburg
- Department of Chemistry, Wichita State University, 1845 Fairmount, Wichita, Kansas 67260, United States
| | - Anisha Haris
- Shimadzu Research Laboratory, Wharfside, Trafford Wharf Road, Manchester M17 1GP, United Kingdom
| | - Roch Andrzejewski
- Shimadzu Research Laboratory, Wharfside, Trafford Wharf Road, Manchester M17 1GP, United Kingdom
| | - Andrew Entwistle
- Shimadzu Research Laboratory, Wharfside, Trafford Wharf Road, Manchester M17 1GP, United Kingdom
| | - Roger Giles
- Shimadzu Research Laboratory, Wharfside, Trafford Wharf Road, Manchester M17 1GP, United Kingdom
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25
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Santiago BG, Campbell MT, Glish GL. Variables Affecting the Internal Energy of Peptide Ions During Separation by Differential Ion Mobility Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:2160-2169. [PMID: 28653242 DOI: 10.1007/s13361-017-1726-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Revised: 05/07/2017] [Accepted: 05/22/2017] [Indexed: 06/07/2023]
Abstract
Differential ion mobility spectrometry (DIMS) devices separate ions on the basis of differences in ion mobility in low and high electric fields, and can be used as a stand-alone analytical method or as a separation step before further analysis. As with other ion mobility separation techniques, the ability of DIMS separations to retain the structural characteristics of analytes has been of concern. For DIMS separations, this potential loss of ion structure originates from the fact that the separations occur at atmospheric pressure and the ions, during their transit through the device, undergo repeated collisions with the DIMS carrier gas while being accelerated by the electric field. These collisions have the ability to increase the internal energy distribution of the ions, which can cause isomerization or fragmentation. The increase in internal energy of the ions is based on a number of variables, including the dispersion field and characteristics of the carrier gas such as temperature and composition. The effects of these parameters on the intra-DIMS fragmentation of multiply charged ions of the peptides bradykinin (RPPGFSPFR) and GLISH are discussed herein. Furthermore, similarities and differences in the internal energy deposition that occur during collisional activation in tandem mass spectrometry experiments are discussed, as the fragmentation pathways accessed by both are similar. Graphical Abstract ᅟ.
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Affiliation(s)
- Brandon G Santiago
- Department of Chemistry, Caudill Laboratories, The University of North Carolina at Chapel Hill, Campus Box 3290, Chapel Hill, NC, 27599-3290, USA
| | - Matthew T Campbell
- Department of Chemistry, Caudill Laboratories, The University of North Carolina at Chapel Hill, Campus Box 3290, Chapel Hill, NC, 27599-3290, USA
| | - Gary L Glish
- Department of Chemistry, Caudill Laboratories, The University of North Carolina at Chapel Hill, Campus Box 3290, Chapel Hill, NC, 27599-3290, USA.
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26
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Schneider BB, Londry F, Nazarov EG, Kang Y, Covey TR. Maximizing Ion Transmission in Differential Mobility Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:2151-2159. [PMID: 28664477 DOI: 10.1007/s13361-017-1727-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Revised: 05/10/2017] [Accepted: 05/22/2017] [Indexed: 06/07/2023]
Abstract
We provide modeling and experimental data describing the dominant ion-loss mechanisms for differential mobility spectrometry (DMS). Ion motion is considered from the inlet region of the mobility analyzer to the DMS exit, and losses resulting from diffusion to electrode surfaces, insufficient effective gap, ion fragmentation, and fringing field effects are considered for a commercial DMS system with 1-mm gap height. It is shown that losses due to diffusion and radial oscillations can be minimized with careful consideration of residence time, electrode spacing, gas flow rate, and waveform frequency. Fragmentation effects can be minimized by limitation of the separation field. When these parameters were optimized, fringing field effects at the DMS inlet contributed the most to signal reduction. We also describe a new DMS cell configuration that improves the gas dynamics at the mobility cell inlet. The new cell provides a gas jet that decreases the residence time for ions within the fringing field region, resulting in at least twofold increase in ion signal as determined by experimental data and simulations. Graphical Abstract ᅟ.
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Affiliation(s)
| | - Frank Londry
- SCIEX, 71 Four Valley Drive, Concord, ON, L4K 4V8, Canada
| | | | - Yang Kang
- SCIEX, 71 Four Valley Drive, Concord, ON, L4K 4V8, Canada
| | - Thomas R Covey
- SCIEX, 71 Four Valley Drive, Concord, ON, L4K 4V8, Canada
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27
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Bowman AP, Abzalimov RR, Shvartsburg AA. Broad Separation of Isomeric Lipids by High-Resolution Differential Ion Mobility Spectrometry with Tandem Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:1552-1561. [PMID: 28462493 DOI: 10.1007/s13361-017-1675-2] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Revised: 03/13/2017] [Accepted: 03/27/2017] [Indexed: 05/18/2023]
Abstract
Maturation of metabolomics has brought a deeper appreciation for the importance of isomeric identity of lipids to their biological role, mirroring that for proteoforms in proteomics. However, full characterization of the lipid isomerism has been thwarted by paucity of rapid and effective analytical tools. A novel approach is ion mobility spectrometry (IMS) and particularly differential or field asymmetric waveform IMS (FAIMS) at high electric fields, which is more orthogonal to mass spectrometry. Here we broadly explore the power of FAIMS to separate lipid isomers, and find a ~75% success rate across the four major types of glycero- and phospho- lipids (sn, chain length, double bond position, and cis/trans). The resolved isomers were identified using standards, and (for the first two types) tandem mass spectrometry. These results demonstrate the general merit of incorporating high-resolution FAIMS into lipidomic analyses. Graphical Abstract ᅟ.
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Affiliation(s)
- Andrew P Bowman
- Department of Chemistry, Wichita State University, 1845 Fairmount, Wichita, KS, 67260, USA
| | - Rinat R Abzalimov
- Department of Chemistry, Wichita State University, 1845 Fairmount, Wichita, KS, 67260, USA
- City University of New York, 85 Saint Nicholas Terrace, New York, NY, 10031, USA
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Creese AJ, Cooper HJ. Separation of cis and trans Isomers of Polyproline by FAIMS Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2016; 27:2071-2074. [PMID: 27704474 PMCID: PMC5088216 DOI: 10.1007/s13361-016-1482-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Revised: 07/12/2016] [Accepted: 08/12/2016] [Indexed: 06/06/2023]
Abstract
High field asymmetric waveform ion mobility spectrometry (FAIMS) is well-established as a tool for separating peptide isomers (sequence inversions and post-translationally modified localization variants). Here, we demonstrate the FAIMS is able to differentiate cis and trans isomers of polyproline. Polyproline assumes an all-cis conformation-the PPI helix-in 1-propanol, and an all-trans conformation-the PPII helix-in aqueous solutions. Differentiation of these conformers may be achieved both through use of a cylindrical FAIMS device and a miniaturized ultrahigh field planar FAIMS device. Graphical Abstract ᅟ.
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Affiliation(s)
- Andrew J Creese
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Helen J Cooper
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK.
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29
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Baird MA, Shvartsburg AA. Localization of Post-Translational Modifications in Peptide Mixtures via High-Resolution Differential Ion Mobility Separations Followed by Electron Transfer Dissociation. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2016; 27:2064-2070. [PMID: 27644938 PMCID: PMC7063994 DOI: 10.1007/s13361-016-1498-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Revised: 08/28/2016] [Accepted: 08/31/2016] [Indexed: 05/02/2023]
Abstract
Precise localization of post-translational modifications (PTMs) on proteins and peptides is an outstanding challenge in proteomics. While electron transfer dissociation (ETD) has dramatically advanced PTM analyses, mixtures of localization variants that commonly coexist in cells often require prior separation. Although differential or field asymmetric waveform ion mobility spectrometry (FAIMS) achieves broad variant resolution, the need for standards to identify the features has limited the utility of approach. Here we demonstrate full a priori characterization of variant mixtures by high-resolution FAIMS coupled to ETD and the procedures to systematically extract the FAIMS spectra for all variants from such data. Graphical Abstract ᅟ.
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Affiliation(s)
- Matthew A Baird
- Department of Chemistry, Wichita State University, 1845 Fairmount, Wichita, KS, 67260-0051, USA
| | - Alexandre A Shvartsburg
- Department of Chemistry, Wichita State University, 1845 Fairmount, Wichita, KS, 67260-0051, USA.
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30
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Schneider BB, Nazarov EG, Londry F, Vouros P, Covey TR. Differential mobility spectrometry/mass spectrometry history, theory, design optimization, simulations, and applications. MASS SPECTROMETRY REVIEWS 2016; 35:687-737. [PMID: 25962527 DOI: 10.1002/mas.21453] [Citation(s) in RCA: 124] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2014] [Accepted: 11/26/2014] [Indexed: 05/28/2023]
Abstract
This review of differential mobility spectrometry focuses primarily on mass spectrometry coupling, starting with the history of the development of this technique in the Soviet Union. Fundamental principles of the separation process are covered, in addition to efforts related to design optimization and advancements in computer simulations. The flexibility of differential mobility spectrometry design features is explored in detail, particularly with regards to separation capability, speed, and ion transmission. 2015 Wiley Periodicals, Inc. Mass Spec Rev 35:687-737, 2016.
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Affiliation(s)
| | | | | | - Paul Vouros
- Department of Chemistry and Chemical Biology, Barnett Institute, Northeastern University, Boston, MA 02115
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31
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Cooper HJ. To What Extent is FAIMS Beneficial in the Analysis of Proteins? JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2016; 27:566-77. [PMID: 26843211 PMCID: PMC4792363 DOI: 10.1007/s13361-015-1326-4] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Revised: 12/08/2015] [Accepted: 12/10/2015] [Indexed: 05/11/2023]
Abstract
High field asymmetric waveform ion mobility spectrometry (FAIMS), also known as differential ion mobility spectrometry, is emerging as a tool for biomolecular analysis. In this article, the benefits and limitations of FAIMS for protein analysis are discussed. The principles and mechanisms of FAIMS separation of ions are described, and the differences between FAIMS and conventional ion mobility spectrometry are detailed. Protein analysis is considered from both the top-down (intact proteins) and the bottom-up (proteolytic peptides) perspective. The roles of FAIMS in the analysis of complex mixtures of multiple intact proteins and in the analysis of multiple conformers of a single protein are assessed. Similarly, the application of FAIMS in proteomics and targeted analysis of peptides are considered.
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Affiliation(s)
- Helen J Cooper
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK.
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32
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Liu FC, Kirk SR, Bleiholder C. On the structural denaturation of biological analytes in trapped ion mobility spectrometry – mass spectrometry. Analyst 2016; 141:3722-30. [DOI: 10.1039/c5an02399h] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Trapped ion mobility spectra recorded for ubiquitin are consistent with structures reported for the native state by NMR.
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Affiliation(s)
- Fanny C. Liu
- Department of Chemistry and Biochemistry
- Florida State University
- Tallahassee
- USA
| | - Samuel R. Kirk
- Department of Chemistry and Biochemistry
- Florida State University
- Tallahassee
- USA
| | - Christian Bleiholder
- Department of Chemistry and Biochemistry
- Florida State University
- Tallahassee
- USA
- Institute of Molecular Biophysics
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33
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Shvartsburg AA. Ultrahigh-Resolution Differential Ion Mobility Separations of Conformers for Proteins above 10 kDa: Onset of Dipole Alignment? Anal Chem 2014; 86:10608-15. [DOI: 10.1021/ac502389a] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Alexandre A. Shvartsburg
- Biological Sciences Division, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99352, United States
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34
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Menlyadiev MR, Eiceman GA. Tandem differential mobility spectrometry in purified air for high-speed selective vapor detection. Anal Chem 2014; 86:2395-402. [PMID: 24484354 DOI: 10.1021/ac4031169] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A tandem ion mobility instrument based on differential mobility spectrometry (DMS) was used to demonstrate selectivity in response through differences in field dependence of mobility for ions in purified air at ambient pressure. The concept of chemical selectivity solely from characteristic dispersion curves or from field dependence of ion mobility was experimentally demonstrated in three steps with mixtures of increasing complexity. In a mixture of four alcohols with carbon numbers four and below, distinct pairs of separation voltage and compensation voltage, applied to the first and second DMS stages, permitted isolation of ions from individual substances without detectable levels of other substances. In a three-component mixture of a ketone, alcohol, and organophosphorus compound, the same level of ion isolation was observed using specific and characteristic separation and compensation voltages on each DMS stage. In the last experiment, the isolation of product ions of individual substances from a mixture of 23 volatile organic compounds from four chemical groups was incomplete though the improvement in the ratio of analyte signal to chemical noise was calculated as 31 for DMMP and 106 for 1-hexanol. These findings demonstrate that chemical information available in dispersion curves can be accessed in response times below 100 ms through a tandem DMS measurement.
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Affiliation(s)
- Marlen R Menlyadiev
- Department of Chemistry and Biochemistry, New Mexico State University , Las Cruces, New Mexico, 88003, United States
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35
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Shvartsburg AA, Smith RD. Separation of protein conformers by differential ion mobility in hydrogen-rich gases. Anal Chem 2013; 85:6967-73. [PMID: 23855890 PMCID: PMC3749073 DOI: 10.1021/ac4015963] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Proteins in solution or the gas phase tend to exhibit multiple conformational families, each comprising distinct structures. Separation methods have generally failed to resolve these, with their convolution producing wide peaks. Here, we report full separation of >10 conformers for most ubiquitin charge states by the new approach of differential ion mobility spectrometry (field asymmetric waveform ion mobility spectrometry, FAIMS) employing H2/N2 gas mixtures with up to 85% H2. The resolving power (up to 400) is five times the highest previously achieved (using He/N2 buffers), greatly increasing the separation specificity. The peak widths match the narrowest obtained by FAIMS for any species under the same conditions and scale with the protein charge state (z) and ion residence time (t) as z(-1/2) and t(-1/2), as prescribed for instrumental (diffusional) broadening. This suggests resolution of specific geometries rather than broader ensembles.
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Affiliation(s)
- Alexandre A Shvartsburg
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States.
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36
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An X, Eiceman GA, Räsänen RM, Rodriguez JE, Stone JA. Dissociation of Proton Bound Ketone Dimers in Asymmetric Electric Fields with Differential Mobility Spectrometry and in Uniform Electric Fields with Linear Ion Mobility Spectrometry. J Phys Chem A 2013; 117:6389-401. [DOI: 10.1021/jp401640t] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Xinxia An
- Department of Chemistry and
Biochemistry, New Mexico State University, Las Cruces, New Mexico 88003, United States
| | - Gary A. Eiceman
- Department of Chemistry and
Biochemistry, New Mexico State University, Las Cruces, New Mexico 88003, United States
| | - Riikka-Marjaana Räsänen
- Department of Chemistry and
Biochemistry, New Mexico State University, Las Cruces, New Mexico 88003, United States
| | - Jaime E. Rodriguez
- Department of Chemistry and
Biochemistry, New Mexico State University, Las Cruces, New Mexico 88003, United States
| | - John A. Stone
- Department of Chemistry, Queens University, Kingston, Ontario Canada
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37
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Abstract
Use of elevated electric fields and helium-rich gases has recently enabled differential ion mobility spectrometry (IMS) with a resolving power up to R ∼ 300. Here we applied that technique to a protein (ubiquitin), achieving R up to ∼80 and separating previously unresolved conformers. While still limited by conformational multiplicity, this resolution is some 4 times greater than that previously reported using either conventional (drift-tube or traveling-wave) or differential IMS. The capability for fine resolution of protein conformers may open new avenues for proteoform separations in top-down and intact-protein proteomics.
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38
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Han L, Hyung SJ, Ruotolo BT. Dramatically stabilizing multiprotein complex structure in the absence of bulk water using tuned Hofmeister salts. Faraday Discuss 2013; 160:371-88; discussion 389-403. [PMID: 23795511 PMCID: PMC3695445 DOI: 10.1039/c2fd20099f] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
The role that water plays in the salt-based stabilization of proteins is central to our understanding of protein biophysics. Ion hydration and the ability of ions to alter water surface tension are typically invoked, along with direct ion-protein binding, to describe Hofmeister stabilization phenomena observed for proteins experimentally, but the relative influence of these forces has been extraordinarily difficult to measure directly. Recently, we have used gas-phase measurements of proteins and large multiprotein complexes, using a combination of innovative ion mobility (IM) and mass spectrometry (MS) techniques, to assess the ability of bound cations and anions to stabilize protein ions in the absence of the solvation forces described above. Our previous work has studied a broad set of 12 anions bound to a range of proteins and protein complexes, and while primarily motivated by the analytical challenges surrounding the gas-phase measurement of solution-phase relevant protein structures, our work has also lead to a detailed physical mechanism of anion-protein complex stabilization in the absence of bulk solvent. Our more-recent work has screened a similarly-broad set of cations for their ability to stabilize gas-phase protein structure, and we have discovered surprising differences between the operative mechanisms for cations and anions in gas-phase protein stabilization. In both cases, cations and anions affect protein stabilization in the absence of solvent in a manner that is generally reversed relative to their ability to stabilize the same proteins in solution. In addition, our evidence suggests that the relative solution-phase binding affinity of the anions and cations studied here is preserved in our gas-phase measurements, allowing us to study the influence of such interactions in detail. In this report, we collect and summarize such gas-phase measurements to distill a generalized picture of salt-based protein stabilization in the absence of bulk water. Further, we communicate our most recent efforts to study the combined effects of stabilizing cations and anions on gas-phase proteins, and identify those salts that bear anion/cation pairs having the strongest stabilizing influence on protein structures
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Affiliation(s)
- Linjie Han
- Department of Chemistry, University of Michigan, 930 N. University Ave., Ann Arbor, MI 48109
| | - Suk-Joon Hyung
- Department of Chemistry, University of Michigan, 930 N. University Ave., Ann Arbor, MI 48109
| | - Brandon T. Ruotolo
- Department of Chemistry, University of Michigan, 930 N. University Ave., Ann Arbor, MI 48109
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39
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Shvartsburg AA, Smith RD. Protein analyses using differential ion mobility microchips with mass spectrometry. Anal Chem 2012; 84:7297-300. [PMID: 22889348 PMCID: PMC3462738 DOI: 10.1021/ac3018636] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Differential ion mobility spectrometry (FAIMS) integrated with mass spectrometry (MS) is a powerful new tool for biological and environmental analyses. Large proteins occupy regions of FAIMS spectra distinct from peptides, lipids, or other medium-size biomolecules, likely because strong electric fields align huge dipoles common to macroions. Here we confirm this phenomenon in separations of proteins at extreme fields using FAIMS chips coupled to MS and demonstrate their use to detect even minor amounts of large proteins in complex matrixes of smaller proteins and peptides.
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40
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Shvartsburg AA, Zheng Y, Smith RD, Kelleher NL. Separation of variant methylated histone tails by differential ion mobility. Anal Chem 2012; 84:6317-20. [PMID: 22812477 PMCID: PMC3418378 DOI: 10.1021/ac301541r] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Differential ion mobility spectrometry (field asymmetric waveform ion mobility spectrometry (FAIMS)) is emerging as a broadly useful tool for separation of isomeric modified peptides with post-translational modifications (PTMs) attached to alternative residues. Such separations were anticipated to become more challenging for smaller PTMs and longer peptides. Here, we show that FAIMS can fully resolve localization variants involving a PTM as minuscule as methylation, even for larger peptides in the middle-down range.
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41
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Papadopoulos G, Svendsen A, Boyarkin OV, Rizzo TR. Conformational distribution of bradykinin [bk + 2 H]2+ revealed by cold ion spectroscopy coupled with FAIMS. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2012; 23:1173-81. [PMID: 22528205 DOI: 10.1007/s13361-012-0384-0] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2012] [Revised: 03/22/2012] [Accepted: 03/23/2012] [Indexed: 05/25/2023]
Abstract
We employ cold ion spectroscopy (CIS) in conjunction with high-field asymmetric waveform ion mobility spectrometry (FAIMS) to study the peptide bradykinin in its doubly protonated charge state ([bk + 2 H](2+)). Using FAIMS, we partially separate the electrosprayed [bk + 2 H](2+) ions into two conformational families and selectively introduce one of them at a time into a cold ion trap mass spectrometer, where we probe them by UV photofragment spectroscopy. Although the two conformational families have distinct electronic spectra, some cross-conformer contamination can be observed under certain conditions. We demonstrate that this contamination comes from isomerization of ions energized during and/or after their separation and not from incomplete separation of the initially electrosprayed conformations in the FAIMS stage. By varying the injection voltage of the ions into our mass spectrometer, we can intentionally induce isomerization to produce what seems to be a gas phase equilibrium distribution of conformers. This distribution is different from the one produced initially by electrospray, indicating that some of the conformers are kinetically trapped and may be related to conformers that are more favored in solution.
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Affiliation(s)
- Georgios Papadopoulos
- Laboratoire de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne, CH-1015, Lausanne, Switzerland
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42
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Shvartsburg AA, Zheng Y, Smith RD, Kelleher NL. Ion mobility separation of variant histone tails extending to the "middle-down" range. Anal Chem 2012; 84:4271-6. [PMID: 22559289 PMCID: PMC3353003 DOI: 10.1021/ac300612y] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Differential ion mobility spectrometry (FAIMS) can baseline-resolve multiple variants of post-translationally modified peptides extending to the 3-4 kDa range, which differ in the localization of a PTM as small as acetylation. Essentially orthogonal separations for different charge states expand the total peak capacity with the number of observed states that increases for longer polypeptides. This potentially enables resolving localization variants for yet larger peptides and even intact proteins.
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Affiliation(s)
- Alexandre A Shvartsburg
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States.
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43
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Merenbloom SI, Flick TG, Williams ER. How hot are your ions in TWAVE ion mobility spectrometry? JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2012; 23:553-62. [PMID: 22203576 PMCID: PMC3296450 DOI: 10.1007/s13361-011-0313-7] [Citation(s) in RCA: 109] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2011] [Revised: 11/30/2011] [Accepted: 12/02/2011] [Indexed: 05/04/2023]
Abstract
Effective temperatures of ions during traveling wave ion mobility spectrometry (TWIMS) analysis were measured using singly protonated leucine enkephalin dimer as a chemical thermometer by monitoring dissociation of the dimer into monomer, as well as the subsequent dissociation of monomer into a-, b-, and y-ions, as a function of instrumental parameters. At fixed helium cell and TWIMS cell gas flow rates, the extent of dissociation does not vary significantly with either the wave velocity or wave height, except at low (<500 m/s) wave velocities that are not commonly used. Increasing the flow rate of nitrogen gas into the TWIMS cell and decreasing the flow rate of helium gas into the helium cell resulted in greater dissociation. However, the mobility distributions of the fragment ions formed by dissociation of the dimer upon injection into the TWIMS cell are nearly indistinguishable from those of fragment ions formed in the collision cell prior to TWIMS analysis for all TWIMS experiments. These results indicate that heating and dissociation occur when ions are injected into the TWIMS cell, and that the effective temperature subsequently decreases to a point at which no further dissociation is observed during the TWIMS analysis. An upper limit to the effective ion temperature of 449 K during TWIMS analysis is obtained at a helium flow rate of 180 mL/min, TWIMS flow rate of 80 mL/min, and traveling wave height of 40 V, which is well below previously reported values. Effects of ion heating in TWIMS on gas-phase protein conformation are presented.
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Affiliation(s)
- Samuel I Merenbloom
- Department of Chemistry, University of California, Berkeley, CA 94720-1460, USA
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44
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Shvartsburg AA, Creese AJ, Smith RD, Cooper HJ. Separation of a set of peptide sequence isomers using differential ion mobility spectrometry. Anal Chem 2011; 83:6918-23. [PMID: 21863819 PMCID: PMC3173593 DOI: 10.1021/ac201640d] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Protein identification in bottom-up proteomics requires disentangling isomers of proteolytic peptides, a major class of which are sequence inversions. Their separation using ion mobility spectrometry (IMS) has been limited to isomeric pairs. Here we demonstrate baseline separation of all seven 8-mer tryptic peptide isomers using differential IMS. Evaluation of peak capacity implies that even larger libraries should be resolved for heavier peptides with higher charge states.
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45
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Barnett DA, Ouellette RJ. Elimination of the helium requirement in high-field asymmetric waveform ion mobility spectrometry (FAIMS): beneficial effects of decreasing the analyzer gap width on peptide analysis. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2011; 25:1959-1971. [PMID: 21698679 DOI: 10.1002/rcm.5078] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Cylindrical geometry high-field asymmetric waveform ion mobility spectrometry (FAIMS) focuses and separates gas-phase ions at atmospheric pressure and room (or elevated) temperature. Addition of helium to a nitrogen-based separation medium offers significant advantages for FAIMS including improved resolution, selectivity and sensitivity. Aside from gas composition, ion transmission through FAIMS is governed by electric field strength (E/N) that is determined by the applied voltage, the analyzer gap width, atmospheric pressure and electrode temperature. In this study, the analyzer width of a cylindrical FAIMS device is varied from 2.5 to 1.25 mm to achieve average electric field strengths as high as 187.5 Townsend (Td). At these electric fields, the performance of FAIMS in an N(2) environment is dramatically improved over a commercial system that uses an analyzer width of 2.5 mm in 1:1 N(2) /He. At fields of 162 Td using electrodes at room temperature, the average effective temperature for the [M+2H](2+) ion of angiotensin II reaches 365 K. This has a dramatic impact on the curtain gas flow rate, resulting in lower optimum flows and reduced turbulence in the ion inlet. The use of narrow analyzer widths in a N(2) carrier gas offers previously unattainable baseline resolution of the [M+2H](2+) and [M+3H](3+) ions of angiotensin II. Comparisons of absolute ion current with FAIMS to conventional electrospray ionization (ESI) are as high as 77% with FAIMS versus standard ESI-MS.
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Affiliation(s)
- David A Barnett
- Atlantic Cancer Research Institute, Hotel-Dieu Pavilion, 35 Providence Street, Moncton, New Brunswick, Canada, E1C 8X3.
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46
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Chan YT, Li X, Yu J, Carri GA, Moorefield CN, Newkome GR, Wesdemiotis C. Design, synthesis, and traveling wave ion mobility mass spectrometry characterization of iron(II)- and ruthenium(II)-terpyridine metallomacrocycles. J Am Chem Soc 2011; 133:11967-76. [PMID: 21718066 DOI: 10.1021/ja107307u] [Citation(s) in RCA: 139] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
New metallomacrocycles composed of 2,2':6',2″-terpyridine (tpy) ligands and Ru(II) or Fe(II) transition metal ions were prepared by stepwise directed assembly and characterized by 2D diffusion NMR spectroscopy (DOSY), electrospray ionization traveling wave ion mobility mass spectrometry (ESI TWIM MS), and molecular modeling. The supramolecular polymers synthesized include a homonuclear all-Ru hexamer as well as heteronuclear hexamer and nonamer with alternating Ru/Ru/Fe metal centers. ESI MS yields several charge states from each supramacromolecule. If ESI is interfaced with TWIM MS, overlapping charge states and the isomeric components of an individual charge state are separated based on their unique drift times through the TWIM region. From experimentally measured drift times, collision cross-sections can be deduced. The collision cross-sections obtained for the synthesized supramacromolecules are in good agreement with those predicted by molecular modeling for macrocyclic structures. Similarly, the hydrodynamic radii of the synthesized complexes derived from 2D DOSY NMR experiments agree excellently with the radii calculated for macrocyclic architectures, confirming the ESI TWIM MS finding. ESI TWIM MS and 2D DOSY NMR spectroscopy provide an alternative approach for the structural analysis of supramolecules that are difficult or impossible to crystallize, such as the large macrocyclic assemblies investigated. ESI TWIM MS will be particularly valuable for the characterization of supramolecular assemblies not available in the quantity or purity required for NMR studies.
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Affiliation(s)
- Yi-Tsu Chan
- Departments of Polymer Science, The University of Akron, Akron, Ohio, 44325, USA
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47
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Shvartsburg AA, Smith RD. Ultrahigh-resolution differential ion mobility spectrometry using extended separation times. Anal Chem 2011; 83:23-9. [PMID: 21117630 PMCID: PMC3012152 DOI: 10.1021/ac102689p] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Ion mobility spectrometry (IMS), and particularly differential IMS or field asymmetric waveform IMS (FAIMS), is emerging as a versatile tool for separation and identification of gas-phase ions, especially in conjunction with mass spectrometry. For over two decades since its inception, the utility of FAIMS was constrained by resolving power (R) of less than ∼20. Stronger electric fields and optimized gas mixtures have recently raised achievable R to ∼200, but further progress with such approaches is impeded by electrical breakdown. However, the resolving power of planar FAIMS devices using any gas and field intensity scales as the square root of separation time (t). Here, we extended t from the previous maximum of 0.2 s up to 4-fold by reducing the carrier gas flow and increased the resolving power by up to 2-fold as predicted, to >300 for multiply charged peptides. The resulting resolution gain has enabled separation of previously "co-eluting" peptide isomers, including folding conformers and localization variants of modified peptides. More broadly, a peak capacity of ∼200 has been reached in tryptic digest separations.
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Affiliation(s)
- Alexandre A Shvartsburg
- Biological Sciences Division, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99352, United States
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Papadopoulos G, Svendsen A, Boyarkin OV, Rizzo TR. Spectroscopy of mobility-selected biomolecular ions. Faraday Discuss 2011; 150:243-55; discussion 257-92. [DOI: 10.1039/c0fd00004c] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
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Fernandez-Lima FA, Blase RC, Russell DH. A Study of Ion-Neutral Collision Cross Section Values for Low Charge States of Peptides, Proteins, and Peptide/Protein Complexes. INTERNATIONAL JOURNAL OF MASS SPECTROMETRY 2010; 298:111-118. [PMID: 21503273 PMCID: PMC3077763 DOI: 10.1016/j.ijms.2009.10.009] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Here, we report ion-helium collision cross sections (CCS) for a number of peptide, small protein, and peptide/protein ionic complexes. The CCS values reported here are compared to previously reported results.[1, 2] We also compare values for low charge state species, i.e., [M + H](+) and [M + 2H](2+), formed by MALDI with values for high charge state species formed by ESI, and the measured CCSs are compared with predicted CCS for solid-state and solution phase structures and calculated structures obtained by using a protein-protein structure algorithm generator, based on a combined Biomolecular complex Generation with Global Evaluation and Ranking[3] and Multi Dimensional Scaling[4].
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Shvartsburg AA, Creese AJ, Smith RD, Cooper HJ. Separation of peptide isomers with variant modified sites by high-resolution differential ion mobility spectrometry. Anal Chem 2010; 82:8327-34. [PMID: 20843012 PMCID: PMC2973842 DOI: 10.1021/ac101878a] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Many proteins and proteolytic peptides incorporate the same post-translational modification (PTM) at different sites, creating multiple localization variants with different functions or activities that may coexist in cells. Current analytical methods based on liquid chromatography (LC) followed by tandem mass spectrometry (MS/MS) are challenged by such isomers that often coelute in LC and/or produce nonunique fragment ions. The application of ion mobility spectrometry (IMS) was explored, but success has been limited by insufficient resolution. We show that high-resolution differential ion mobility spectrometry (FAIMS) employing helium-rich gases can readily separate phosphopeptides with variant modification sites. Use of He/N(2) mixtures containing up to 74% He has allowed separating to >95% three monophosphorylated peptides of identical sequence. Similar separation was achieved at 50% He, using an elevated electric field. Bisphosphorylated isomers that differ in only one modification site were separated to the same extent. We anticipate FAIMS capabilities for such separations to extend to other PTMs.
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Affiliation(s)
- Alexandre A Shvartsburg
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99352, USA
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