1
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Griffiths D, Anderson M, Richardson K, Inaba-Inoue S, Allen WJ, Collinson I, Beis K, Morris M, Giles K, Politis A. Cyclic Ion Mobility for Hydrogen/Deuterium Exchange-Mass Spectrometry Applications. Anal Chem 2024; 96:5869-5877. [PMID: 38561318 PMCID: PMC11024883 DOI: 10.1021/acs.analchem.3c05753] [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] [Received: 12/18/2023] [Revised: 03/20/2024] [Accepted: 03/21/2024] [Indexed: 04/04/2024]
Abstract
Hydrogen/deuterium exchange-mass spectrometry (HDX-MS) has emerged as a powerful tool to probe protein dynamics. As a bottom-up technique, HDX-MS provides information at peptide-level resolution, allowing structural localization of dynamic changes. Consequently, the HDX-MS data quality is largely determined by the number of peptides that are identified and monitored after deuteration. Integration of ion mobility (IM) into HDX-MS workflows has been shown to increase the data quality by providing an orthogonal mode of peptide ion separation in the gas phase. This is of critical importance for challenging targets such as integral membrane proteins (IMPs), which often suffer from low sequence coverage or redundancy in HDX-MS analyses. The increasing complexity of samples being investigated by HDX-MS, such as membrane mimetic reconstituted and in vivo IMPs, has generated need for instrumentation with greater resolving power. Recently, Giles et al. developed cyclic ion mobility (cIM), an IM device with racetrack geometry that enables scalable, multipass IM separations. Using one-pass and multipass cIM routines, we use the recently commercialized SELECT SERIES Cyclic IM spectrometer for HDX-MS analyses of four detergent solubilized IMP samples and report its enhanced performance. Furthermore, we develop a novel processing strategy capable of better handling multipass cIM data. Interestingly, use of one-pass and multipass cIM routines produced unique peptide populations, with their combined peptide output being 31 to 222% higher than previous generation SYNAPT G2-Si instrumentation. Thus, we propose a novel HDX-MS workflow with integrated cIM that has the potential to enable the analysis of more complex systems with greater accuracy and speed.
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Affiliation(s)
- Damon Griffiths
- Faculty
of Biology, Medicine and Health, School of Biological Sciences, The University of Manchester, Manchester M13 9PT, United Kingdom
- Manchester
Institute of Biotechnology, University of
Manchester, Princess
Street, Manchester M1 7DN, United Kingdom
| | - Malcolm Anderson
- Waters
Corporation, Stamford Avenue, Altrincham Road, Wilmslow SK9 4AX, United
Kingdom
| | - Keith Richardson
- Waters
Corporation, Stamford Avenue, Altrincham Road, Wilmslow SK9 4AX, United
Kingdom
| | - Satomi Inaba-Inoue
- Department
of Life Sciences, Imperial College London, Exhibition Road, South Kensington, London SW7 2AZ, United Kingdom
- Rutherford
Appleton Laboratory, Research Complex at Harwell, Oxfordshire, Didcot OX11 0FA, United Kingdom
- Diffraction
and Scattering Division, Japan Synchrotron
Radiation Research Institute, SPring-8, 1-1-1, Kouto, Sayo, Hyogo 679-5198, Japan
| | - William J. Allen
- School
of Biochemistry, University of Bristol, Bristol BS8 1TD, United Kingdom
| | - Ian Collinson
- School
of Biochemistry, University of Bristol, Bristol BS8 1TD, United Kingdom
| | - Konstantinos Beis
- Department
of Life Sciences, Imperial College London, Exhibition Road, South Kensington, London SW7 2AZ, United Kingdom
- Rutherford
Appleton Laboratory, Research Complex at Harwell, Oxfordshire, Didcot OX11 0FA, United Kingdom
| | - Michael Morris
- Waters
Corporation, Stamford Avenue, Altrincham Road, Wilmslow SK9 4AX, United
Kingdom
| | - Kevin Giles
- Waters
Corporation, Stamford Avenue, Altrincham Road, Wilmslow SK9 4AX, United
Kingdom
| | - Argyris Politis
- Faculty
of Biology, Medicine and Health, School of Biological Sciences, The University of Manchester, Manchester M13 9PT, United Kingdom
- Manchester
Institute of Biotechnology, University of
Manchester, Princess
Street, Manchester M1 7DN, United Kingdom
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2
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Chen X, Latif M, Gandhi VD, Chen X, Hua L, Fukushima N, Larriba-Andaluz C. Enhancing Separation and Constriction of Ion Mobility Distributions in Drift Tubes at Atmospheric Pressure Using Varying Fields. Anal Chem 2022; 94:5690-5698. [PMID: 35357157 DOI: 10.1021/acs.analchem.2c00467] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
A linearly decreasing electric field has been previously proven to be effective for diffusional correction of ions in a varying field drift tube (VFDT) system, leading to higher resolving powers compared to a conventional drift tube due to its capacity to narrow distributions midflight. However, the theoretical predictions in resolving power of the VFDT were much higher than what was observed experimentally. The reason behind this discrepancy has been identified as the difference between the theoretically calculated resolving power (spatial) and the experimental one (time). To match the high spatial resolving power experimentally, a secondary high voltage pulse (HVP) at a properly adjusted time is used to provide the ions with enough momentum to increase their drift velocity and hence their time-resolving power. A series of systematic numerical simulations and experimental tests have been designed to corroborate our theoretical findings. The HVP-VFDT atmospheric pressure portable system improves the resolving power from the maximum expected of 60-80 for a regular drift tube to 250 in just 21 cm in length and 7kV, an unprecedent accomplishment.
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Affiliation(s)
- Xi Chen
- Department of Mechanical Engineering, Indiana University-Purdue University Indianapolis (IUPUI), 723 West Michigan Street, Indianapolis, Indiana 46202, United States.,Purdue University, West Lafayette, Indiana 47907, United States
| | - Mohsen Latif
- Department of Mechanical Engineering, Indiana University-Purdue University Indianapolis (IUPUI), 723 West Michigan Street, Indianapolis, Indiana 46202, United States
| | - Viraj D Gandhi
- Department of Mechanical Engineering, Indiana University-Purdue University Indianapolis (IUPUI), 723 West Michigan Street, Indianapolis, Indiana 46202, United States.,Purdue University, West Lafayette, Indiana 47907, United States
| | - Xuemeng Chen
- Department of Mechanical Engineering, Indiana University-Purdue University Indianapolis (IUPUI), 723 West Michigan Street, Indianapolis, Indiana 46202, United States.,Institute of Physics, University of Tartu, W. Ostwaldi 1, EE-50411 Tartu, Estonia
| | - Leyan Hua
- Department of Mechanical Engineering, Indiana University-Purdue University Indianapolis (IUPUI), 723 West Michigan Street, Indianapolis, Indiana 46202, United States
| | | | - Carlos Larriba-Andaluz
- Department of Mechanical Engineering, Indiana University-Purdue University Indianapolis (IUPUI), 723 West Michigan Street, Indianapolis, Indiana 46202, United States
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3
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Shaw JB, Cooper-Shepherd DA, Hewitt D, Wildgoose JL, Beckman JS, Langridge JI, Voinov VG. Enhanced Top-Down Protein Characterization with Electron Capture Dissociation and Cyclic Ion Mobility Spectrometry. Anal Chem 2022; 94:3888-3896. [PMID: 35188751 PMCID: PMC8908312 DOI: 10.1021/acs.analchem.1c04870] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Tandem mass spectrometry of denatured, multiply charged high mass protein precursor ions yield extremely dense spectra with hundreds of broad and overlapping product ion isotopic distributions of differing charge states that yield an elevated baseline of unresolved "noise" centered about the precursor ion. Development of mass analyzers and signal processing methods to increase mass resolving power and manipulation of precursor and product ion charge through solution additives or ion-ion reactions have been thoroughly explored as solutions to spectral congestion. Here, we demonstrate the utility of electron capture dissociation (ECD) coupled with high-resolution cyclic ion mobility spectrometry (cIMS) to greatly increase top-down protein characterization capabilities. Congestion of protein ECD spectra was reduced using cIMS of the ECD product ions and "mobility fractions", that is, extracted mass spectra for segments of the 2D mobiligram (m/z versus drift time). For small proteins, such as ubiquitin (8.6 kDa), where mass resolving power was not the limiting factor for characterization, pre-IMS ECD and mobility fractions did not significantly increase protein sequence coverage, but an increase in the number of identified product ions was observed. However, a dramatic increase in performance, measured by protein sequence coverage, was observed for larger and more highly charged species, such as the +35 charge state of carbonic anhydrase (29 kDa). Pre-IMS ECD combined with mobility fractions yielded a 135% increase in the number of annotated isotope clusters and a 75% increase in unique product ions compared to processing without using the IMS dimension. These results yielded 89% sequence coverage for carbonic anhydrase.
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Affiliation(s)
- Jared B. Shaw
- e-MSion
Inc., 2121 NE Jack London Street, Corvallis, Oregon 97330, United States, (J.S.)
| | | | - Darren Hewitt
- Waters
Corporation, Wilmslow, Cheshire SK9 4AX, U.K.
| | | | - Joseph S. Beckman
- e-MSion
Inc., 2121 NE Jack London Street, Corvallis, Oregon 97330, United States,Linus
Pauling Institute and the Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331, United States
| | | | - Valery G. Voinov
- e-MSion
Inc., 2121 NE Jack London Street, Corvallis, Oregon 97330, United States
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4
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Hollerbach AL, Conant CR, Nagy G, Ibrahim YM. Implementation of Ion Mobility Spectrometry-Based Separations in Structures for Lossless Ion Manipulations (SLIM). Methods Mol Biol 2022; 2394:453-469. [PMID: 35094340 PMCID: PMC9526429 DOI: 10.1007/978-1-0716-1811-0_23] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Structures for Lossless Ion Manipulations (SLIM) is a powerful variant of traveling wave ion mobility spectrometry (TW-IMS) that uses a serpentine pattern of microelectrodes deposited onto printed circuit boards to achieve ultralong ion path lengths (13.5 m). Ions are propelled through SLIM platforms via arrays of TW electrodes while RF and DC electrodes provide radial confinement, establishing near lossless transmission. The recent ability to cycle ions multiple times through a SLIM has allowed ion path lengths to exceed 1000 m, providing unprecedented separation power and the ability to observe ion structural conformations unobtainable with other IMS technologies. The combination of high separation power, high signal intensity, and the ability to couple with mass spectrometry places SLIM in the unique position of being able to address longstanding proteomics and metabolomics challenges by allowing the characterization of isomeric mixtures containing low abundance analytes.
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Affiliation(s)
| | | | - Gabe Nagy
- Pacific Northwest National Laboratory, Richland, WA, USA
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5
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Moghadamchargari Z, Huddleston J, Shirzadeh M, Zheng X, Clemmer DE, M Raushel F, Russell DH, Laganowsky A. Intrinsic GTPase Activity of K-RAS Monitored by Native Mass Spectrometry. Biochemistry 2019; 58:3396-3405. [PMID: 31306575 DOI: 10.1021/acs.biochem.9b00532] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Mutations in RAS are associated with many different cancers and have been a therapeutic target for more than three decades. RAS cycles from an active to inactive state by both intrinsic and GTPase-activating protein (GAP)-stimulated hydrolysis. The activated enzyme interacts with downstream effectors, leading to tumor proliferation. Mutations in RAS associated with cancer are insensitive to GAP, and the rate of inactivation is limited to their intrinsic hydrolysis rate. Here, we use high-resolution native mass spectrometry (MS) to determine the kinetics and transition state thermodynamics of intrinsic hydrolysis for K-RAS and its oncogenic mutants. MS data reveal heterogeneity where both 2'-deoxy and 2'-hydroxy forms of GDP (guanosine diphosphate) and GTP (guanosine triphosphate) are bound to the recombinant enzyme. Intrinsic GTPase activity is directly monitored by the loss in mass of K-RAS bound to GTP, which corresponds to the release of phosphate. The rates determined from MS are in direct agreement with those measured using an established solution-based assay. Our results show that the transition state thermodynamics for the intrinsic GTPase activity of K-RAS is both enthalpically and entropically unfavorable. The oncogenic mutants G12C, Q61H, and G13D unexpectedly exhibit a 2'-deoxy GTP intrinsic hydrolysis rate higher than that for GTP.
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Affiliation(s)
- Zahra Moghadamchargari
- Department of Chemistry , Texas A&M University , College Station , Texas 77843 , United States
| | - Jamison Huddleston
- Department of Chemistry , Texas A&M University , College Station , Texas 77843 , United States
| | - Mehdi Shirzadeh
- Department of Chemistry , Texas A&M University , College Station , Texas 77843 , United States
| | - Xueyun Zheng
- Department of Chemistry , Texas A&M University , College Station , Texas 77843 , United States
| | - David E Clemmer
- Department of Chemistry , Indiana University , Bloomington , Indiana , 47405 , United States
| | - Frank M Raushel
- Department of Chemistry , Texas A&M University , College Station , Texas 77843 , United States
| | - David H Russell
- Department of Chemistry , Texas A&M University , College Station , Texas 77843 , United States
| | - Arthur Laganowsky
- Department of Chemistry , Texas A&M University , College Station , Texas 77843 , United States
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6
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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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7
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Chouinard CD, Nagy G, Smith RD, Baker ES. Ion Mobility-Mass Spectrometry in Metabolomic, Lipidomic, and Proteomic Analyses. ADVANCES IN ION MOBILITY-MASS SPECTROMETRY: FUNDAMENTALS, INSTRUMENTATION AND APPLICATIONS 2019. [DOI: 10.1016/bs.coac.2018.11.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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8
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Tose LV, Benigni P, Leyva D, Sundberg A, Ramírez CE, Ridgeway ME, Park MA, Romão W, Jaffé R, Fernandez-Lima F. Coupling trapped ion mobility spectrometry to mass spectrometry: trapped ion mobility spectrometry-time-of-flight mass spectrometry versus trapped ion mobility spectrometry-Fourier transform ion cyclotron resonance mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2018; 32:1287-1295. [PMID: 29756663 DOI: 10.1002/rcm.8165] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Revised: 03/28/2018] [Accepted: 05/03/2018] [Indexed: 05/05/2023]
Abstract
RATIONALE There is a need for fast, post-ionization separation during the analysis of complex mixtures. In this study, we evaluate the use of a high-resolution mobility analyzer with high-resolution and ultrahigh-resolution mass spectrometry for unsupervised molecular feature detection. Goals include the study of the reproducibility of trapped ion mobility spectrometry (TIMS) across platforms, applicability range, and potential challenges during routine analysis. METHODS A TIMS analyzer was coupled to time-of-flight mass spectrometry (TOF MS) and Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) instruments for the analysis of singly charged species in the m/z 150-800 range of a complex mixture (Suwannee River Fulvic Acid Standard). Molecular features were detected using an unsupervised algorithm based on chemical formula and IMS profiles. RESULTS TIMS-TOF MS and TIMS-FT-ICR MS analysis provided 4950 and 7760 m/z signals, 1430 and 3050 formulas using the general Cx Hy N0-3 O0-19 S0-1 composition, and 7600 and 22 350 [m/z; chemical formula; K; CCS] features, respectively. CONCLUSIONS TIMS coupled to TOF MS and FT-ICR MS showed similar performance and high reproducibility. For the analysis of complex mixtures, both platforms were able to capture the major trends and characteristics; however, as the chemical complexity at the level of nominal mass increases with m/z (m/z >300-350), only TIMS-FT-ICR MS was able to report the lower abundance compositional trends.
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Affiliation(s)
- Lilian V Tose
- Federal University of Espírito Santo, Petroleomic and Forensic Chemistry Laboratory, Department of Chemistry, 29075-910, Vitória, ES, Brazil
| | - Paolo Benigni
- Florida International University, Department of Chemistry and Biochemistry, Miami, FL, 33199, USA
| | - Dennys Leyva
- Florida International University, Department of Chemistry and Biochemistry, Miami, FL, 33199, USA
| | - Abigail Sundberg
- Florida International University, Department of Chemistry and Biochemistry, Miami, FL, 33199, USA
| | - César E Ramírez
- Florida International University, Department of Chemistry and Biochemistry, Miami, FL, 33199, USA
| | | | | | - Wanderson Romão
- Federal University of Espírito Santo, Petroleomic and Forensic Chemistry Laboratory, Department of Chemistry, 29075-910, Vitória, ES, Brazil
- Federal Institute of Education, Science and Technology of Espírito Santo, 29106-010, Vila Velha, ES, Brazil
| | - Rudolf Jaffé
- Florida International University, Department of Chemistry and Biochemistry, Miami, FL, 33199, USA
- Florida International University, Southeast Environmental Research Center, Miami, FL, 33199, USA
| | - Francisco Fernandez-Lima
- Florida International University, Department of Chemistry and Biochemistry, Miami, FL, 33199, USA
- Florida International University, Southeast Environmental Research Center, Miami, FL, 33199, USA
- Biomolecular Sciences Institute, Florida International University, Miami, FL, 33199, USA
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9
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Adams KJ, Smith NF, Ramirez CE, Fernandez-Lima F. Discovery and targeted monitoring of polychlorinated biphenyl metabolites in blood plasma using LC-TIMS-TOF MS. INTERNATIONAL JOURNAL OF MASS SPECTROMETRY 2018; 427:133-140. [PMID: 29915519 PMCID: PMC6003708 DOI: 10.1016/j.ijms.2017.11.009] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
In the present work, the potential for rapid, targeted analysis of hydroxylated metabolites of polychlorinated biphenyls (OH-PCBs) in diluted human blood plasma using liquid chromatography coupled with trapped ion mobility spectrometry and TOF high resolution mass spectrometry (LC-TIMS-TOF MS) was evaluated. Experimental OH-PCB collisional cross section (CCSN2) and gas-phase candidate structures (<3% error) are reported for the first time and used, in addition to the LC retention time and accurate m/z, as OH-PCB identification features in order to increase the detection selectivity. The proposed LC-TIMS-TOF MS workflow combines a "dilute-and-shoot" sample preparation strategy, a robust liquid chromatography step, a high-resolving power mobility separation (R ~ 150-250) and high-resolution mass spectrometry (R ~ 30-40k) for the separation, identification and quantification of common OH-PCB isomers with limits of detection comparable to traditional workflows (e.g., LOD and LOQ of ~10 pg/mL and ~50 pg/mL, respectively). The higher selectivity and low detection limits provides multiple advantages compared to current methodologies that typically require long, labor-intensive preparation and/or derivatization steps prior to gas or liquid chromatography-mass spectrometry.
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Affiliation(s)
- Kendra J. Adams
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, United States
| | - Natalie F. Smith
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, United States
| | - Cesar E. Ramirez
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, United States
| | - Francisco Fernandez-Lima
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, United States
- Biomolecular Sciences Institute, Florida International University, Miami, FL 33199, United States
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10
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Eyers CE, Vonderach M, Ferries S, Jeacock K, Eyers PA. Understanding protein–drug interactions using ion mobility–mass spectrometry. Curr Opin Chem Biol 2018; 42:167-176. [DOI: 10.1016/j.cbpa.2017.12.013] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Revised: 12/08/2017] [Accepted: 12/22/2017] [Indexed: 01/23/2023]
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11
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Dodds JN, May JC, McLean JA. Correlating Resolving Power, Resolution, and Collision Cross Section: Unifying Cross-Platform Assessment of Separation Efficiency in Ion Mobility Spectrometry. Anal Chem 2017; 89:12176-12184. [PMID: 29039942 PMCID: PMC5744666 DOI: 10.1021/acs.analchem.7b02827] [Citation(s) in RCA: 112] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Here we examine the relationship among resolving power (Rp), resolution (Rpp), and collision cross section (CCS) for compounds analyzed in previous ion mobility (IM) experiments representing a wide variety of instrument platforms and IM techniques. Our previous work indicated these three variables effectively describe and predict separation efficiency for drift tube ion mobility spectrometry experiments. In this work, we seek to determine if our previous findings are a general reflection of IM behavior that can be applied to various instrument platforms and mobility techniques. Results suggest IM distributions are well characterized by a Gaussian model and separation efficiency can be predicted on the basis of the empirical difference in the gas-phase CCS and a CCS-based resolving power definition (CCS/ΔCCS). Notably traveling wave (TWIMS) was found to operate at resolutions substantially higher than a single-peak resolving power suggested. When a CCS-based Rp definition was utilized, TWIMS was found to operate at a resolving power between 40 and 50, confirming the previous observations by Giles and co-workers. After the separation axis (and corresponding resolving power) is converted to cross section space, it is possible to effectively predict separation behavior for all mobility techniques evaluated (i.e., uniform field, trapped ion mobility, traveling wave, cyclic, and overtone instruments) using the equations described in this work. Finally, we are able to establish for the first time that the current state-of-the-art ion mobility separations benchmark at a CCS-based resolving power of >300 that is sufficient to differentiate analyte ions with CCS differences as small as 0.5%.
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Affiliation(s)
| | | | - John A. McLean
- Department of Chemistry, Center for Innovative Technology, Vanderbilt Institute of Chemical Biology, Vanderbilt Institute for Integrative Biosystems Research and Education, Vanderbilt University, Nashville Tennessee 37235, United States
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12
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Deng L, Webb IK, Garimella SVB, Hamid AM, Zheng X, Norheim RV, Prost SA, Anderson GA, Sandoval JA, Baker ES, Ibrahim YM, Smith RD. Serpentine Ultralong Path with Extended Routing (SUPER) High Resolution Traveling Wave Ion Mobility-MS using Structures for Lossless Ion Manipulations. Anal Chem 2017; 89:4628-4634. [PMID: 28332832 PMCID: PMC5627996 DOI: 10.1021/acs.analchem.7b00185] [Citation(s) in RCA: 155] [Impact Index Per Article: 22.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Ion mobility (IM) separations have a broad range of analytical applications, but insufficient resolution often limits their utility. Here, we report on ion mobility separations in a structures for lossless ion manipulations (SLIM) serpentine ultralong path with extended routing (SUPER) traveling wave (TW) ion mobility (IM) module in conjunction with mass spectrometry (MS). Ions were confined in the SLIM by rf fields in conjunction with a DC guard bias, enabling essentially lossless TW transmission over greatly extended paths. The extended routing utilized multiple passes (e.g., ∼1094 m over 81 passes through the 13.5 m serpentine path) and was facilitated by the introduction of a lossless ion switch that allowed ions to be directed to either the MS detector or for another pass through the serpentine separation region, allowing theoretically unlimited IM path lengths. The multipass SUPER IM-MS provided resolution approximately proportional to the square root of the number of passes (or total path length). More than 30-fold higher IM resolution (∼340 vs ∼10) for Agilent tuning mix m/z 622 and 922 ions was achieved for 40 passes compared to commercially available drift tube IM and other TWIM-based platforms. An initial evaluation of the isomeric sugars lacto-N-hexaose and lacto-N-neohexaose showed the isomeric structures to be baseline resolved, and a new conformational feature for lacto-N-neohexaose was revealed after 9 passes. The new SLIM SUPER high resolution TWIM platform has broad utility in conjunction with MS and is expected to enable a broad range of previously challenging or intractable separations.
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Affiliation(s)
| | | | - Sandilya V. B. Garimella
- Biological Sciences Division, Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, 902 Battelle Boulevard, P.O. Box 999, MSIN K8-98, Richland, Washington 99352, United States
| | - Ahmed M. Hamid
- Biological Sciences Division, Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, 902 Battelle Boulevard, P.O. Box 999, MSIN K8-98, Richland, Washington 99352, United States
| | - Xueyun Zheng
- Biological Sciences Division, Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, 902 Battelle Boulevard, P.O. Box 999, MSIN K8-98, Richland, Washington 99352, United States
| | - Randolph V. Norheim
- Biological Sciences Division, Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, 902 Battelle Boulevard, P.O. Box 999, MSIN K8-98, Richland, Washington 99352, United States
| | - Spencer A. Prost
- Biological Sciences Division, Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, 902 Battelle Boulevard, P.O. Box 999, MSIN K8-98, Richland, Washington 99352, United States
| | - Gordon A. Anderson
- Biological Sciences Division, Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, 902 Battelle Boulevard, P.O. Box 999, MSIN K8-98, Richland, Washington 99352, United States
| | - Jeremy A. Sandoval
- Biological Sciences Division, Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, 902 Battelle Boulevard, P.O. Box 999, MSIN K8-98, Richland, Washington 99352, United States
| | - Erin S. Baker
- Biological Sciences Division, Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, 902 Battelle Boulevard, P.O. Box 999, MSIN K8-98, Richland, Washington 99352, United States
| | - Yehia M. Ibrahim
- Biological Sciences Division, Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, 902 Battelle Boulevard, P.O. Box 999, MSIN K8-98, Richland, Washington 99352, United States
| | - Richard D. Smith
- Biological Sciences Division, Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, 902 Battelle Boulevard, P.O. Box 999, MSIN K8-98, Richland, Washington 99352, United States
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13
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Garabedian A, Butcher D, Lippens JL, Miksovska J, Chapagain PP, Fabris D, Ridgeway ME, Park MA, Fernandez-Lima F. Structures of the kinetically trapped i-motif DNA intermediates. Phys Chem Chem Phys 2016; 18:26691-26702. [PMID: 27711445 PMCID: PMC5652045 DOI: 10.1039/c6cp04418b] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
In the present work, the conformational dynamics and folding pathways of i-motif DNA were studied in solution and in the gas-phase as a function of the solution pH conditions using circular dichroism (CD), photoacoustic calorimetry analysis (PAC), trapped ion mobility spectrometry-mass spectrometry (TIMS-MS), and molecular dynamics (MD). Solution studies showed at thermodynamic equilibrium the existence of a two-state folding mechanism, whereas during the pH = 7.0 → 4.5 transition a fast and slow phase (ΔHfast + ΔHslow = 43 ± 7 kcal mol-1) with a volume change associated with the formation of hemiprotonated cytosine base pairs and concomitant collapse of the i-motif oligonucleotide into a compact conformation were observed. TIMS-MS experiments showed that gas-phase, kinetically trapped i-motif DNA intermediates produced by nanoESI are preserved, with relative abundances depending on the solution pH conditions. In particular, a folded i-motif DNA structure was observed in nanoESI-TIMS-MS for low charge states in both positive and negative ion mode (e.g., z = ±3 to ±5) at low pH conditions. As solution pH increases, the cytosine neutralization leads to the loss of cytosine-cytosine+ (C·CH+) base pairing in the CCC strands and in those conditions we observe partially unfolded i-motif DNA conformations in nanoESI-TIMS-MS for higher charge states (e.g., z = -6 to -9). Collisional induced activation prior to TIMS-MS showed the existence of multiple local free energy minima, associated with the i-motif DNA unfolding at z = -6 charge state. For the first time, candidate gas-phase structures are proposed based on mobility measurements of the i-motif DNA unfolding pathway. Moreover, the inspection of partially unfolded i-motif DNA structures (z = -7 and z = -8 charge states) showed that the presence of inner cations may or may not induce conformational changes in the gas-phase. For example, incorporation of ammonium adducts does not lead to major conformational changes while sodium adducts may lead to the formation of sodium mediated bonds between two negatively charged sides inducing the stabilization towards more compact structures in new local, free energy minima in the gas-phase.
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Affiliation(s)
- Alyssa Garabedian
- Department of Chemistry and Biochemistry, Florida International University, Miami, USA.
| | - David Butcher
- Department of Chemistry and Biochemistry, Florida International University, Miami, USA.
| | | | - Jaroslava Miksovska
- Department of Chemistry and Biochemistry, Florida International University, Miami, USA. and Biomolecular Science Institute, Florida International University, Miami, USA
| | - Prem P Chapagain
- Biomolecular Science Institute, Florida International University, Miami, USA and Department of Physics, Florida International University, Miami, USA
| | | | | | - Melvin A Park
- Bruker Daltonics Inc., Billerica, Massachusetts, USA
| | - Francisco Fernandez-Lima
- Department of Chemistry and Biochemistry, Florida International University, Miami, USA. and Biomolecular Science Institute, Florida International University, Miami, USA
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14
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Benigni P, Marin R, Molano-Arevalo JC, Garabedian A, Wolff JJ, Ridgeway ME, Park MA, Fernandez-Lima F. Towards the Analysis of High Molecular Weight Proteins and Protein complexes using TIMS-MS. INTERNATIONAL JOURNAL FOR ION MOBILITY SPECTROMETRY : OFFICIAL PUBLICATION OF THE INTERNATIONAL SOCIETY FOR ION MOBILITY SPECTROMETRY 2016; 19:95-104. [PMID: 27818614 PMCID: PMC5091298 DOI: 10.1007/s12127-016-0201-8] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Revised: 05/26/2016] [Accepted: 05/29/2016] [Indexed: 01/02/2023]
Abstract
In the present work, we demonstrate the potential and versatility of TIMS for the analysis of proteins, DNA-protein complexes and protein-protein complexes in their native and denatured states. In addition, we show that accurate CCS measurement are possible and in good agreement with previously reported CCS values using other IMS analyzers (<5% difference). The main challenges for the analysis of high mass proteins and protein complexes in the mobility and m/z domain are described. That is, the analysis of high molecular weight systems in their native state may require the use of higher electric fields or a compromise in the TIMS mobility resolution by reducing the bath gas velocity in order to effectively trap at lower electric fields. This is the first report of CCS measurements of high molecular weight biomolecules and biomolecular complexes (~ 150 kDa) using TIMS-MS.
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Affiliation(s)
- Paolo Benigni
- Department of Chemistry & Biochemistry, Florida International University, Miami, FL 33199, USA
| | - Rebecca Marin
- Department of Chemistry & Biochemistry, Florida International University, Miami, FL 33199, USA
| | | | - Alyssa Garabedian
- Department of Chemistry & Biochemistry, Florida International University, Miami, FL 33199, USA
| | | | | | - Melvin A. Park
- Bruker Daltonics, Inc., Billerica, Massachusetts 01821, USA
| | - Francisco Fernandez-Lima
- Department of Chemistry & Biochemistry, Florida International University, Miami, FL 33199, USA
- Biomolecular Science Institute, Florida International University, Miami, FL 33199, USA
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15
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Garimella SVB, Ibrahim YM, Tang K, Webb IK, Baker ES, Tolmachev AV, Chen TC, Anderson GA, Smith RD. Spatial Ion Peak Compression and its Utility in Ion Mobility Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2016; 27:1128-35. [PMID: 27052738 PMCID: PMC4955798 DOI: 10.1007/s13361-016-1371-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Revised: 02/17/2016] [Accepted: 02/19/2016] [Indexed: 05/13/2023]
Abstract
A novel concept for ion spatial peak compression is described, and discussed primarily in the context of ion mobility spectrometry (IMS). Using theoretical and numerical methods, the effects of using non-constant (e.g., linearly varying) electric fields on ion distributions (e.g., an ion mobility peak) is evaluated both in the physical and temporal domains. The application of a linearly decreasing electric field in conjunction with conventional drift field arrangements is shown to lead to a reduction in IMS physical peak width. When multiple ion packets (i.e., peaks) in a selected mobility window are simultaneously subjected to such fields, there is ion packet compression (i.e., a reduction in peak widths for all species). This peak compression occurs with only a modest reduction of resolution, which can be quickly recovered as ions drift in a constant field after the compression event. Compression also yields a significant increase in peak intensities. Ion mobility peak compression can be particularly useful for mitigating diffusion-driven peak broadening over very long path length separations (e.g., in cyclic multi-pass arrangements), and for achieving higher S/N and IMS resolution over a selected mobility range. Graphical Abstract ᅟ.
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Affiliation(s)
- Sandilya V B Garimella
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Yehia M Ibrahim
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Keqi Tang
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Ian K Webb
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Erin S Baker
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Aleksey V Tolmachev
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Tsung-Chi Chen
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Gordon A Anderson
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Richard D Smith
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA.
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16
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Isomer Separation of Polybrominated Diphenyl Ether Metabolites using nanoESI-TIMS-MS. ACTA ACUST UNITED AC 2016; 19:69-76. [PMID: 27642261 DOI: 10.1007/s12127-016-0198-z] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
In this paper, high-resolution nano-electrospray ionization-trapped ion mobility spectrometry coupled to mass spectrometry (nESI-TIMS-MS) is used for the study of hydroxylated polybrominated diphenyl ether (OH-PBDE) metabolites. In particular, experimental ion-neutral collision cross sections (CCS) were measured for five structural OH-PBDE isomers using TIMS-MS. Candidate structures were proposed for each IMS band observed in good agreement with the experimental CCS measurements (5% error). The analytical power of TIMS-MS to baseline and partially separate structural isomers of OH-BDE in binary and ternary mixtures is shown for single charge species with a mobility resolving power of RIMS ~ 400. This work provides the proof of concept for the analysis of low concentration OH-PBDE in environmental samples based on accurate collision cross section and mass measurements without the need for derivatization and pre-fractionation protocols, thus significantly reducing the cost and analysis time.
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17
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Garimella SVB, Ibrahim YM, Webb IK, Ipsen AB, Chen TC, Tolmachev AV, Baker ES, Anderson GA, Smith RD. Ion manipulations in structures for lossless ion manipulations (SLIM): computational evaluation of a 90° turn and a switch. Analyst 2016; 140:6845-52. [PMID: 26289106 DOI: 10.1039/c5an00844a] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The process of redirecting ions through 90° turns and 'tee' switches utilizing Structures for Lossless Ion Manipulations (SLIM) was evaluated at 4 Torr pressure using SIMION simulations and theoretical methods. The nature of pseudo-potential in SLIM-tee structures has also been explored. Simulations show that 100% transmission efficiency in SLIM devices can be achieved with guard electrode voltages lower than ∼10 V. The ion plume width in these conditions is ∼1.6 mm while at lower guard voltages lead to greater plume widths. Theoretical calculations show marginal loss of ion mobility resolving power (<5%) during ion turn due to the finite plume widths (i.e. race track effect). More robust SLIM designs that reduce the race track effect while maximizing ion transmission are also reported. In addition to static turns, the dynamic switching of ions into orthogonal channels was also evaluated both using SIMION ion trajectory simulations and experimentally. Simulations and theoretical calculations were in close agreement with experimental results and were used to develop more refined SLIM designs.
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Affiliation(s)
- Sandilya V B Garimella
- Biological Sciences Division, Pacific Northwest National Laboratory, P.O. Box 999, Richland, WA 99352, USA.
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18
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Ewing MA, Glover MS, Clemmer DE. Hybrid ion mobility and mass spectrometry as a separation tool. J Chromatogr A 2016; 1439:3-25. [DOI: 10.1016/j.chroma.2015.10.080] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Revised: 10/05/2015] [Accepted: 10/21/2015] [Indexed: 11/29/2022]
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19
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Benigni P, Marin R, Fernandez-Lima F. Towards unsupervised polyaromatic hydrocarbons structural assignment from SA-TIMS-FTMS data. ACTA ACUST UNITED AC 2015; 18:151-157. [PMID: 26525904 DOI: 10.1007/s12127-015-0175-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
With the advent of high resolution ion mobility analyzers and their coupling to ultrahigh resolution mass spectrometers, there is a need to further develop a theoretical workflow capable of correlating experimental accurate mass and mobility measurements with tridimensional candidate structures. In the present work, a general workflow is described for unsupervised tridimensional structural assignment based on accurate mass measurements, mobility measurements, in silico 2D-3D structure generation, and theoretical mobility calculations. In particular, the potential of this workflow will be shown for the analysis of polyaromatic hydrocarbons from Coal Tar SRM 1597a using selected accumulation - trapped ion mobility spectrometry (SA-TIMS) coupled to Fourier transform-ion cyclotron resonance mass spectrometry (FT-ICR MS). The proposed workflow can be adapted to different IMS scenarios, can utilize different collisional cross-section calculators and has the potential to include MSn and IMSn measurements for faster and more accurate tridimensional structural assignment.
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Affiliation(s)
- Paolo Benigni
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL, USA
| | - Rebecca Marin
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL, USA
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20
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Schenk ER, Nau F, Fernandez-Lima F. Theoretical predictor for candidate structure assignment from IMS data of biomolecule-related conformational space. INTERNATIONAL JOURNAL FOR ION MOBILITY SPECTROMETRY : OFFICIAL PUBLICATION OF THE INTERNATIONAL SOCIETY FOR ION MOBILITY SPECTROMETRY 2015; 18:23-29. [PMID: 27330407 PMCID: PMC4909055 DOI: 10.1007/s12127-015-0165-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The ability to correlate experimental ion mobility data with candidate structures from theoretical modeling provides a powerful analytical and structural tool for the characterization of biomolecules. In the present paper, a theoretical workflow is described to generate and assign candidate structures for experimental trapped ion mobility and H/D exchange (HDX-TIMS-MS) data following molecular dynamics simulations and statistical filtering. The applicability of the theoretical predictor is illustrated for a peptide and protein example with multiple conformations and kinetic intermediates. The described methodology yields a low computational cost and a simple workflow by incorporating statistical filtering and molecular dynamics simulations. The workflow can be adapted to different IMS scenarios and CCS calculators for a more accurate description of the IMS experimental conditions. For the case of the HDX-TIMS-MS experiments, molecular dynamics in the "TIMS box" accounts for a better sampling of the molecular intermediates and local energy minima.
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Affiliation(s)
- Emily R Schenk
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA
| | - Frederic Nau
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA
| | - Francisco Fernandez-Lima
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA; Biomolecular Sciences Institute, Florida International University, Miami, FL 33199, USA
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21
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Benigni P, Thompson CJ, Ridgeway ME, Park MA, Fernandez-Lima F. Targeted high-resolution ion mobility separation coupled to ultrahigh-resolution mass spectrometry of endocrine disruptors in complex mixtures. Anal Chem 2015; 87:4321-5. [PMID: 25818070 PMCID: PMC4867114 DOI: 10.1021/ac504866v] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Traditional separation and detection of targeted compounds from complex mixtures from environmental matrices requires the use of lengthy prefractionation steps and high-resolution mass analyzers due to the large number of chemical components and their large structural diversity (highly isomeric). In the present work, selected accumulation trapped ion mobility spectrometry (SA-TIMS) is coupled to Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) for direct separation and characterization of targeted endocrine-disrupting compounds (EDC) from a complex environmental matrix in a single analysis. In particular, targeted identification based on high-resolution mobility (R ∼ 70-120) and ultrahigh-resolution mass measurements (R > 400 000) of seven commonly targeted EDC and their isobars (e.g., bisphenol A, (Z)- and (E)-diethylstilbestrol, hexestrol, estrone, α-estradiol, and 17-ethynylestradiol) is shown from a complex mixture of water-soluble organic matter (e.g., Suwannee River Fulvic Acid Standard II) complemented with reference standard measurements and theoretical calculations (<3% error).
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Affiliation(s)
- Paolo Benigni
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida 33199, United States
| | | | - Mark E. Ridgeway
- Bruker Daltonics Inc., Billerica, Massachusetts 01821, United States
| | - Melvin A. Park
- Bruker Daltonics Inc., Billerica, Massachusetts 01821, United States
| | - Francisco Fernandez-Lima
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida 33199, United States
- Biomolecular Sciences Institute, Florida International University, Miami, Florida 33199, United States
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22
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Donohoe GC, Khakinejad M, Valentine SJ. Ion mobility spectrometry-hydrogen deuterium exchange mass spectrometry of anions: part 1. Peptides to proteins. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2015; 26:564-576. [PMID: 25510931 DOI: 10.1007/s13361-014-1045-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2014] [Revised: 10/28/2014] [Accepted: 10/28/2014] [Indexed: 06/04/2023]
Abstract
Ion mobility spectrometry (IMS) coupled with hydrogen deuterium exchange (HDX)-mass spectrometry (MS) has been used to study the conformations of negatively-charged peptide and protein ions. Results are presented for ion conformers of angiotensin 1, a synthetic peptide (SP), bovine insulin, ubiquitin, and equine cytochrome c. In general, the SP ion conformers demonstrate a greater level of HDX efficiency as a greater proportion of the sites undergo HDX. Additionally, these ions exhibit the fastest rates of exchange. Comparatively, the angiotensin 1 ions exhibit a lower rate of exchange and HDX level presumably because of decreased accessibility of exchange sites by charge sites. The latter are likely confined to the peptide termini. Insulin ions show dramatically reduced HDX levels and exchange rates, which can be attributed to decreased conformational flexibility resulting from the disulfide bonds. For the larger ubiquitin and protein ions, increased HDX is observed for larger ions of higher charge state. For ubiquitin, a conformational transition from compact to more elongated species (from lower to higher charge states) is reflected by an increase in HDX levels. These results can be explained by a combination of interior site protection by compact conformers as well as decreased access by charge sites. The elongated cytochrome c ions provide the largest HDX levels where higher values correlate with charge state. These results are consistent with increased exchange site accessibility by additional charge sites. The data from these enhanced IMS-HDX experiments are described in terms of charge site location, conformer rigidity, and interior site protection.
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Affiliation(s)
- Gregory C Donohoe
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV, 26506, USA
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23
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Webb IK, Garimella SVB, Tolmachev AV, Chen TC, Zhang X, Cox JT, Norheim R, Prost S, LaMarche B, Anderson GA, Ibrahim YM, Smith RD. Mobility-resolved ion selection in uniform drift field ion mobility spectrometry/mass spectrometry: dynamic switching in structures for lossless ion manipulations. Anal Chem 2014; 86:9632-7. [PMID: 25222548 PMCID: PMC4188271 DOI: 10.1021/ac502139e] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2014] [Accepted: 09/15/2014] [Indexed: 11/29/2022]
Abstract
A Structures for Lossless Ion Manipulations (SLIM) module that allows ion mobility separations and the switching of ions between alternative drift paths is described. The SLIM switch component has a "Tee" configuration and allows the efficient switching of ions between a linear path and a 90-degree bend. By controlling switching times, ions can be efficiently directed to an alternative channel as a function of their mobilities. In the initial evaluation the switch is used in a static mode and shown compatible with high performance ion mobility separations at 4 Torr. In the dynamic mode, we show that mobility-selected ions can be switched into the alternative channel, and that various ion species can be independently selected based on their mobilities for time-of-flight mass spectrometer (TOF MS) IMS detection and mass analysis. This development also provides the basis of, for example, the selection of specific mobilities for storage and accumulation, and the key component of modules for the assembly of SLIM devices enabling much more complex sequences of ion manipulations.
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Affiliation(s)
- Ian K. Webb
- Biological
Sciences Division
and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, 3335 Innovation Avenue (K8-98), P.O. Box 999, Richland, Washington 99352, United States
| | - Sandilya V. B. Garimella
- Biological
Sciences Division
and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, 3335 Innovation Avenue (K8-98), P.O. Box 999, Richland, Washington 99352, United States
| | - Aleksey V. Tolmachev
- Biological
Sciences Division
and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, 3335 Innovation Avenue (K8-98), P.O. Box 999, Richland, Washington 99352, United States
| | - Tsung-Chi Chen
- Biological
Sciences Division
and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, 3335 Innovation Avenue (K8-98), P.O. Box 999, Richland, Washington 99352, United States
| | - Xinyu Zhang
- Biological
Sciences Division
and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, 3335 Innovation Avenue (K8-98), P.O. Box 999, Richland, Washington 99352, United States
| | - Jonathan T. Cox
- Biological
Sciences Division
and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, 3335 Innovation Avenue (K8-98), P.O. Box 999, Richland, Washington 99352, United States
| | - Randolph
V. Norheim
- Biological
Sciences Division
and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, 3335 Innovation Avenue (K8-98), P.O. Box 999, Richland, Washington 99352, United States
| | - Spencer
A. Prost
- Biological
Sciences Division
and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, 3335 Innovation Avenue (K8-98), P.O. Box 999, Richland, Washington 99352, United States
| | - Brian LaMarche
- Biological
Sciences Division
and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, 3335 Innovation Avenue (K8-98), P.O. Box 999, Richland, Washington 99352, United States
| | - Gordon A. Anderson
- Biological
Sciences Division
and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, 3335 Innovation Avenue (K8-98), P.O. Box 999, Richland, Washington 99352, United States
| | - Yehia M. Ibrahim
- Biological
Sciences Division
and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, 3335 Innovation Avenue (K8-98), P.O. Box 999, Richland, Washington 99352, United States
| | - Richard D. Smith
- Biological
Sciences Division
and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, 3335 Innovation Avenue (K8-98), P.O. Box 999, Richland, Washington 99352, United States
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24
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Lanucara F, Holman SW, Gray CJ, Eyers CE. The power of ion mobility-mass spectrometry for structural characterization and the study of conformational dynamics. Nat Chem 2014; 6:281-94. [DOI: 10.1038/nchem.1889] [Citation(s) in RCA: 655] [Impact Index Per Article: 65.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2013] [Accepted: 02/11/2014] [Indexed: 02/07/2023]
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25
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Zhang Z, Wu S, Stenoien DL, Paša-Tolić L. High-throughput proteomics. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2014; 7:427-454. [PMID: 25014346 DOI: 10.1146/annurev-anchem-071213-020216] [Citation(s) in RCA: 168] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Mass spectrometry (MS)-based high-throughput proteomics is the core technique for large-scale protein characterization. Due to the extreme complexity of proteomes, sophisticated separation techniques and advanced MS instrumentation have been developed to extend coverage and enhance dynamic range and sensitivity. In this review, we discuss the separation and prefractionation techniques applied for large-scale analysis in both bottom-up (i.e., peptide-level) and top-down (i.e., protein-level) proteomics. Different approaches for quantifying peptides or intact proteins, including label-free and stable-isotope-labeling strategies, are also discussed. In addition, we present a brief overview of different types of mass analyzers and fragmentation techniques as well as selected emerging techniques.
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26
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Glaskin RS, Ewing MA, Clemmer DE. Ion Trapping for Ion Mobility Spectrometry Measurements in a Cyclical Drift Tube. Anal Chem 2013; 85:7003-8. [DOI: 10.1021/ac4015066] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Rebecca S. Glaskin
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Michael A. Ewing
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - David E. Clemmer
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
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27
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Ewing MA, Zucker SM, Valentine SJ, Clemmer DE. Overtone mobility spectrometry: part 5. Simulations and analytical expressions describing overtone limits. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2013; 24:615-21. [PMID: 23468094 PMCID: PMC4521626 DOI: 10.1007/s13361-012-0559-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2012] [Revised: 12/04/2012] [Accepted: 12/05/2012] [Indexed: 05/26/2023]
Abstract
Mathematical expressions for the analytical duty cycle associated with different overtones in overtone mobility spectrometry are derived from the widths of the transmitted packets of ions under different instrumental operating conditions. Support for these derivations is provided through ion trajectory simulations. The outcome of the theory and simulations indicates that under all operating conditions there exists a limit or maximum observable overtone that will result in ion transmission. Implications of these findings on experimental design are discussed.
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Affiliation(s)
- Michael A. Ewing
- Department of Chemistry, Indiana University, Bloomington, IN 47405
| | - Steven M. Zucker
- Department of Chemistry, Indiana University, Bloomington, IN 47405
| | | | - David E. Clemmer
- Department of Chemistry, Indiana University, Bloomington, IN 47405
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28
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Shvartsburg AA, Seim TA, Danielson WF, Norheim R, Moore RJ, Anderson GA, Smith RD. High-definition differential ion mobility spectrometry with resolving power up to 500. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2013; 24:109-14. [PMID: 23345059 PMCID: PMC3581339 DOI: 10.1007/s13361-012-0517-5] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2012] [Revised: 10/05/2012] [Accepted: 10/08/2012] [Indexed: 05/18/2023]
Abstract
As the resolution of analytical methods improves, further progress tends to be increasingly limited by instrumental parameter instabilities that were previously inconsequential. This is now the case with differential ion mobility spectrometry (FAIMS), where fluctuations of the voltages and gas pressure have become critical. A new high-definition generator for FAIMS compensation voltage reported here provides a stable and accurate output than can be scanned with negligible steps. This reduces the spectral drift and peak width, thus improving the resolving power (R) and resolution. The gain for multiply-charged peptides that have narrowest peaks is up to ~40%, and R ~400-500 is achievable using He/N(2) or H(2)/N(2) gas mixtures.
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Affiliation(s)
- Alexandre A Shvartsburg
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA.
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29
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Kirk AT, Allers M, Cochems P, Langejuergen J, Zimmermann S. A compact high resolution ion mobility spectrometer for fast trace gas analysis. Analyst 2013; 138:5200-7. [DOI: 10.1039/c3an00231d] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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30
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Vidal-de-Miguel G, Macía M, Cuevas J. Transversal Modulation Ion Mobility Spectrometry (TM-IMS), a new mobility filter overcoming turbulence related limitations. Anal Chem 2012; 84:7831-7. [PMID: 22924856 DOI: 10.1021/ac301127u] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The analysis of ions according to their mobility is a technique that is attracting increasing interest. The new technology presented here, which we have termed Transversal Modulation Ion Mobility Spectrometry (TM-IMS), utilizes only electric fields, operates at atmospheric pressure, produces a continuous output of mobility selected ions (according to their true mobility and not to nonlinear effects), and has a very accessible inlet and outlet. These features would make it an ideal choice for tandem IMS-MS analysis in combination with most commercial Atmospheric Pressure Interface MS (API-MS) systems. We modeled and evaluated two different TM-IMS configurations (TM-IMS, and multistage TM-IMS), and we concluded that the most promising configuration would be a two-stage TM-IMS. We developed and tested a TM-IMS, and the measured resolving power is R = 55. The TM-IMS behaves similarly to the planar Differential Mobility Analyzer, but the TM-IMS utilizes only electric fields, and no fragile flow with high Reynolds numbers is required. We tested the robustness of the TM-IMS, which proves to be a very robust and reliable analyzer: the required voltage accuracy is 5 V in 10 kV, and the mechanical precision is 1 mm in 5 cm.
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Kurulugama RT, Nachtigall FM, Valentine SJ, Clemmer DE. Overtone mobility spectrometry: part 4. OMS-OMS analyses of complex mixtures. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2011; 22:2049-60. [PMID: 21952760 PMCID: PMC3659428 DOI: 10.1007/s13361-011-0217-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2011] [Revised: 07/13/2011] [Accepted: 07/15/2011] [Indexed: 05/31/2023]
Abstract
A new, two-dimensional overtone mobility spectrometry (OMS-OMS) instrument is described for the analysis of complex peptide mixtures. OMS separations are based on the differences in mobilities of ions in the gas phase. The method utilizes multiple drift regions with modulated drift fields such that only ions with appropriate mobilities are transmitted to the detector. Here we describe a hybrid OMS-OMS combination that utilizes two independently operated OMS regions that are separated by an ion activation region. Mobility-selected ions from the first OMS region are exposed to energizing collisions and may undergo structural transitions before entering the second OMS region. This method generates additional peak capacity and allows for higher selectivity compared with the one-dimensional OMS method. We demonstrate the approach using a three-protein tryptic digest spiked with the peptide Substance P. The [M + 3H](3+) ion from Substance P can be completely isolated from other components in this complex mixture prior to introduction into the mass spectrometer.
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Affiliation(s)
- Ruwan T. Kurulugama
- Department of Chemistry, Indiana University, Bloomington, IN 47405, USA
- Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Fabiane M. Nachtigall
- Department of Chemistry, Indiana University, Bloomington, IN 47405, USA
- Max-Planck Inst. für Kohlenforschung, Mülheim/Ruhr, Germany
| | | | - David E. Clemmer
- Department of Chemistry, Indiana University, Bloomington, IN 47405, USA
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Valentine SJ, Kurulugama RT, Clemmer DE. Overtone mobility spectrometry: part 3. On the origin of peaks. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2011; 22:804-16. [PMID: 21472515 PMCID: PMC3253535 DOI: 10.1007/s13361-011-0087-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2010] [Revised: 01/15/2011] [Accepted: 01/18/2011] [Indexed: 05/12/2023]
Abstract
The origin of non-integer overtone peaks in overtone mobility spectrometry (OMS) spectra is investigated by ion trajectory simulations. Simulations indicate that these OMS features arise from higher-order overtone series. An empirically-derived formula is presented as a means of describing the positions of peaks. The new equation makes it possible to determine collision cross sections from any OMS peak. Additionally, it is extended as a means of predicting the resolving power for any peak in an OMS distribution.
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Affiliation(s)
| | | | - David E. Clemmer
- Department of Chemistry, Indiana University, Bloomington, IN, 47405, USA
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Li Z, Valentine SJ, Clemmer DE. Complexation of amino compounds by 18C6 improves selectivity by IMS-IMS-MS: application to petroleum characterization. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2011; 22:817-27. [PMID: 21472516 PMCID: PMC4140651 DOI: 10.1007/s13361-011-0105-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2010] [Revised: 02/02/2011] [Accepted: 02/09/2011] [Indexed: 05/28/2023]
Abstract
Complexation of a series of related amino compounds by 18-crown-6 ether (18C6) is studied as a means of improving the resolution of mixtures by combinations of ion mobility spectrometry (IMS) and mass spectrometry (MS) techniques. Mixtures of the isomeric amines n-octylamine (NOA), dibutylamine (DBA), and diisopropylethylamine (DIPEA) were electrosprayed to produce gaseous [M + H](+) ions. These species have overlapping mobilities and are not resolved by IMS. Addition of 18C6 yields [M + 18C6 + H](+) ion complexes that are resolved by IMS. In subsequent experiments, [M + 18C6 + H](+) ion complexes are separated according to their mobilities and specific species are selected and exposed to collisional activation. This analysis yields dissociation voltages that are inversely correlated with the number of separate substitutions on the nitrogen atom of the amino compounds; dissociation voltages of ~40, ~90, and ~150 V are obtained for the tri-, di-, and mono-substituted amino compounds DIPEA, DBA, and NOA, respectively. For these complexes, an inverse correlation is also observed with respect to the gas-phase basicities (GB) of the amino compounds (964, 935, and 895 kJ mol(-1), respectively). Studies of 18C6 complexes with a series of n-alkylamines (C( n )H(2n+3)N where n=3 to 18, respectively) show that dissociation voltages increase systematically (from ~140 to ~190 V) under the conditions employed. The sensitivity to collision energy provides an additional means of distinguishing between classes of compounds. The approach is extended as a means of separating nitrogen-containing compounds from petroleum.
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Affiliation(s)
- Zhiyu Li
- Department of Chemistry, Indiana University, 800 E. Kirkwood Ave., Bloomington, IN 47405, USA
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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: 59] [Impact Index Per Article: 4.5] [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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Lee S, Ewing MA, Nachtigall FM, Kurulugama RT, Valentine SJ, Clemmer DE. Determination of cross sections by overtone mobility spectrometry: evidence for loss of unstable structures at higher overtones. J Phys Chem B 2010; 114:12406-15. [PMID: 20822127 PMCID: PMC2989665 DOI: 10.1021/jp1060123] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Overtone mobility spectrometry (OMS) is examined as a means of determining the collision cross sections for multiply charged ubiquitin and substance P ions, as well as for singly charged rafinose and melezitose ions. Overall, values of collision cross section measured by OMS for stable ion conformations are found to be in agreement with values determined by conventional ion mobility spectrometry (IMS) measurements to within ∼1% relative uncertainty. The OMS spectra for ubiquitin ions appear to favor different conformations at higher overtones. We propose that the changes in the distributions as a function of the overtone region in which they are measured arise from the elimination of ions that undergo structural transitions in the drift regions. Kinetics simulations suggest that structural transitions occurring on the order of a few ms and resulting in an ∼4% change in ion collision cross sections are detected by OMS measurements. The unique method of distinguishing ion mobilities with OMS reveals these structural transitions which are not readily apparent from traditional IMS measurements.
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Affiliation(s)
- Sunyoung Lee
- Department of Chemistry, Indiana University, Bloomington, IN 47405
| | - Michael A. Ewing
- Department of Chemistry, Indiana University, Bloomington, IN 47405
| | | | | | | | - David E. Clemmer
- Department of Chemistry, Indiana University, Bloomington, IN 47405
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