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Khalikova M, Jireš J, Horáček O, Douša M, Kučera R, Nováková L. What is the role of current mass spectrometry in pharmaceutical analysis? MASS SPECTROMETRY REVIEWS 2024; 43:560-609. [PMID: 37503656 DOI: 10.1002/mas.21858] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 06/02/2023] [Accepted: 06/25/2023] [Indexed: 07/29/2023]
Abstract
The role of mass spectrometry (MS) has become more important in most application domains in recent years. Pharmaceutical analysis is specific due to its stringent regulation procedures, the need for good laboratory/manufacturing practices, and a large number of routine quality control analyses to be carried out. The role of MS is, therefore, very different throughout the whole drug development cycle. While it dominates within the drug discovery and development phase, in routine quality control, the role of MS is minor and indispensable only for selected applications. Moreover, its role is very different in the case of analysis of small molecule pharmaceuticals and biopharmaceuticals. Our review explains the role of current MS in the analysis of both small-molecule chemical drugs and biopharmaceuticals. Important features of MS-based technologies being implemented, method requirements, and related challenges are discussed. The differences in analytical procedures for small molecule pharmaceuticals and biopharmaceuticals are pointed out. While a single method or a small set of methods is usually sufficient for quality control in the case of small molecule pharmaceuticals and MS is often not indispensable, a large panel of methods including extensive use of MS must be used for quality control of biopharmaceuticals. Finally, expected development and future trends are outlined.
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Affiliation(s)
- Maria Khalikova
- Department of Analytical Chemistry, Faculty of Pharmacy in Hradec Králové, Charles University, Hradec Králové, Czech Republic
- Department of Chemistry, Faculty of Science, University of Hradec Králové, Hradec Králové, Czech Republic
| | - Jakub Jireš
- Department of Analytical Chemistry, Faculty of Chemical Engineering, UCT Prague, Prague, Czech Republic
- Department of Development, Zentiva, k. s., Praha, Praha, Czech Republic
| | - Ondřej Horáček
- Department of Pharmaceutical Chemistry and Pharmaceutical Analysis, Faculty of Pharmacy in Hradec Králové, Charles University, Hradec Králové, Czech Republic
| | - Michal Douša
- Department of Development, Zentiva, k. s., Praha, Praha, Czech Republic
| | - Radim Kučera
- Department of Pharmaceutical Chemistry and Pharmaceutical Analysis, Faculty of Pharmacy in Hradec Králové, Charles University, Hradec Králové, Czech Republic
| | - Lucie Nováková
- Department of Analytical Chemistry, Faculty of Pharmacy in Hradec Králové, Charles University, Hradec Králové, Czech Republic
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2
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Kwantwi-Barima P, Garimella SVB, Attah IK, Zheng X, Ibrahim YM, Smith RD. Accumulation of Large Ion Populations with High Ion Densities and Effects Due to Space Charge in Traveling Wave-Based Structures for Lossless Ion Manipulations (SLIM) IMS-MS. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:365-377. [PMID: 38175933 PMCID: PMC10853970 DOI: 10.1021/jasms.3c00389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 11/19/2023] [Accepted: 12/13/2023] [Indexed: 01/06/2024]
Abstract
The accumulation of very large ion populations in traveling wave (TW)-based Structures for Lossless ion Manipulations (SLIM) has been studied to better understand aspects of "in-SLIM" ion accumulation, and particularly its use in conjunction with ion mobility spectrometry (IMS). A linear SLIM ion path was implemented that had a "gate" for blocking and accumulating ions for arbitrary time periods. Removing the gate potential caused ions to exit, and the spatial distributions of accumulated ions examined. The ion populations for a set of peptides increased approximately linearly with increased accumulation times until space change effects became significant, after which the peptide precursor ion populations decreased due to growing space charge-related ion activation, reactions, and losses. Ion activation increased with added storage times and the TW amplitude. Lower amplitude TWs in the accumulation/storage region prevented or minimized ion losses or ion heating effects that can also lead to fragmentation. Our results supported the use of an accumulation region close to the SLIM entrance for speeding accumulation, minimizing ion heating, and avoiding ion population profiles that result in IMS peak tailing. Importantly, space charge-driven separations were observed for large populations of accumulated species and attributed to the opposing effects of space charge and the TW. In these separations, ion species form distributions or peaks, sometimes moving against the TW, and are ordered in the SLIM based on their mobilities. Only the highest mobility ions located closest to the gate in the trapped ion population (and where the highest ion densities were achieved) were significantly activated. The observed separations may offer utility for ion prefractionation of ions and increasing the dynamic range measurements, increasing the resolving power of IMS separations by decreasing peak widths for accumulated ion populations, and other purposes benefiting from separations of extremely large ion populations.
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Affiliation(s)
- Pearl Kwantwi-Barima
- Biological Sciences Division, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99354, United States
| | - Sandilya V. B. Garimella
- Biological Sciences Division, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99354, United States
| | - Isaac K. Attah
- Biological Sciences Division, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99354, United States
| | - Xueyun Zheng
- Biological Sciences Division, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99354, United States
| | - Yehia M. Ibrahim
- Biological Sciences Division, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99354, United States
| | - Richard D. Smith
- Biological Sciences Division, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99354, United States
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3
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King AM, Wilson ID, Plumb RS, Gethings LA, Trengove R, Maker G. The rapid separation and characterization of sulfates of tyrosine and its metabolites in reaction mixtures and human urine using a cyclic ion mobility device and mass spectrometry. J Chromatogr A 2024; 1715:464597. [PMID: 38183784 DOI: 10.1016/j.chroma.2023.464597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 12/13/2023] [Accepted: 12/19/2023] [Indexed: 01/08/2024]
Abstract
Ion mobility (IM) separations, especially when combined with mass spectrometry, offer the opportunity for the rapid analysis and characterization of mixtures. However, the limited resolution afforded by many IM systems means that in practice applications may be limited. Here we have employed an IM separation on a high-resolution cyclic IM device with MS/MS to separate and characterize mixtures of sulfated isomers of tyrosine and associated metabolites containing multiple sulfated isoforms present in reaction mixtures. The cIMS device allowed ions, not resolved using a single pass, to be subjected to multiple passes, enabling the resolution of those with similar collision cross sections (CCS). Predicted single pass CCS values calculated for the isomers likely to be present in these mixtures showed only small differences between them, ranging between of between 0.1 - 0.7 % depending on structure. These small differences highlight the high degree of mobility resolution required for separating the isomers. Experimentally different isoforms of tyrosine sulfate and sulfated tyrosine metabolites could be sufficiently resolved via multipass separations (3-35 passes). This degree of separation provided resolving powers of up to 384 CCS/ΔCCS for sulfated dopamine which enabled good MS/MS spectra to be generated. In human urine the presence of a single sulfated form of tyrosine was detected and identified as the O-sulfate after 3 passes based on the synthetic standard. Of the other tyrosine-related sulfates for which synthetic standards had been prepared only dopamine sulfate was detected in this sample.
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Affiliation(s)
- Adam M King
- Waters Corporation, Wilmslow, Cheshire, SK9 4AX, UK; Medical and Molecular and Forensic Sciences, Murdoch University, South Street, Murdoch, WA 6150, Australia.
| | - Ian D Wilson
- Computational and Systems Medicine, Department of Metabolism, Digestion and Reproduction, Imperial College, Burlington Danes Building, Du Cane Road, London, W12 0NN, UK.
| | - Robert S Plumb
- Medical and Molecular and Forensic Sciences, Murdoch University, South Street, Murdoch, WA 6150, Australia; Waters Corporation, Milford, MA, 01757, USA
| | - Lee A Gethings
- Waters Corporation, Wilmslow, Cheshire, SK9 4AX, UK; School of Biological Sciences, Division of Infection, Immunity and Respiratory Medicine, University of Manchester, Manchester, UK; Faculty of Health & Medical Sciences, University of Surrey, Guildford, UK
| | - Robert Trengove
- CHIRI, Curtin University, Kent St, Bentley, WA, 6102, Australia
| | - Garth Maker
- Medical and Molecular and Forensic Sciences, Murdoch University, South Street, Murdoch, WA 6150, Australia
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Kwantwi-Barima P, Harrilal CP, Garimella SVB, Attah IK, Smith RD, Ibrahim YM. Effect of Traveling Waveform Profiles on Collision Cross Section Measurements in Structures for Lossless Ion Manipulations. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:783-792. [PMID: 35437008 PMCID: PMC10634343 DOI: 10.1021/jasms.1c00364] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
We evaluated the effect of four different waveform profiles (Square, Sine, Triangle, and asymmetric Sawtooth) on the accuracy of collision cross section (CCS) measurements using traveling wave ion mobility spectrometry (TWIMS) separations in structures for lossless ion manipulations (SLIM). The effects of the waveform profiles on the accuracy of the CCS measurements were evaluated for four classes of compounds (lipids, peptides, steroids, and nucleosides) at different TW speeds (126-206 m/s) and amplitudes (15-89 V). For the lipids and peptides, the TWIMS-based CCS (TWCCS) deviations from the corresponding drift-tube-based CCS (DTCCS) measurements were significantly lower in experiments conducted using the Sawtooth waveform compared to the square waveform. This observation can be rationalized by the lower maximum electric field experienced by ions with a Sawtooth waveform, as compared to the other waveforms, resulting in a lower probability for significant ion heating. We also observed that given approximately comparable resolution for all four waveforms, the Sawtooth waveform resulted in lower TWCCS error and a better agreement with DTCCS values than the Square waveform. In addition, for the steroids and nucleosides, an opposite TWCCS trend was observed, with higher errors with the Sawtooth waveform and lower with the Square waveform, suggesting that these molecules tend to become slightly more compact under ion heating conditions. Under optimum conditions, all TWCCS measurements on the SLIM platform were within 0.5% of those measured in the drift tube ion mobility spectrometry.
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Affiliation(s)
- Pearl Kwantwi-Barima
- Biological Sciences Division, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99354, United States
| | - Christopher P Harrilal
- Biological Sciences Division, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99354, United States
| | - Sandilya V B Garimella
- Biological Sciences Division, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99354, United States
| | - Isaac K Attah
- Biological Sciences Division, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99354, United States
| | - Richard D Smith
- Biological Sciences Division, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99354, United States
| | - Yehia M Ibrahim
- Biological Sciences Division, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99354, United States
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5
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Meng X, Xing J, Liu S, Liu Z, Song F. Comprehensive chemical profiling and potential chemical marker’s evaluation of Tribulus terrestris by UPLC-QTOF-MS in combination with ion mobility spectrometry. J Pharm Biomed Anal 2022; 217:114839. [DOI: 10.1016/j.jpba.2022.114839] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 05/13/2022] [Accepted: 05/13/2022] [Indexed: 11/24/2022]
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Ferlenghi F, Giorgio C, Incerti M, Guidetti L, Chiodelli P, Rusnati M, Tognolini M, Vacondio F, Mor M, Lodola A. Metabolic Soft Spot and Pharmacokinetics: Functionalization of C-3 Position of an Eph-Ephrin Antagonist Featuring a Bile Acid Core as an Effective Strategy to Obtain Oral Bioavailability in Mice. Pharmaceuticals (Basel) 2021; 15:ph15010041. [PMID: 35056098 PMCID: PMC8779995 DOI: 10.3390/ph15010041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 12/23/2021] [Accepted: 12/24/2021] [Indexed: 11/16/2022] Open
Abstract
UniPR129, an L-β-homotryptophan conjugate of the secondary bile acid lithocholic acid (LCA), acts as an effective protein-protein interaction (PPI) inhibitor of the Eph-ephrin system but suffers from a poor oral bioavailability in mice. To improve UniPR129 bioavailability, a metabolic soft spot, i.e., the 3α-hydroxyl group on the LCA steroidal ring, was functionalized to 3-hydroxyimine. In vitro metabolism of UniPR129 and 3-hydroxyimine derivative UniPR500 was compared in mouse liver subcellular fractions, and main metabolites were profiled by high resolution (HR-MS) and tandem (MS/MS) mass spectrometry. In mouse liver microsomes (MLM), UniPR129 was converted into several metabolites: M1 derived from the oxidation of the 3-hydroxy group to 3-oxo, M2-M7, mono-hydroxylated metabolites, M8-M10, di-hydroxylated metabolites, and M11, a mono-hydroxylated metabolite of M1. Phase II reactions were only minor routes of in vitro biotransformation. UniPR500 shared several metabolic pathways with parent UniPR129, but it showed higher stability in MLM, with a half-life (t1/2) of 60.4 min, if compared to a t1/2 = 16.8 min for UniPR129. When orally administered to mice at the same dose, UniPR500 showed an increased systemic exposure, maintaining an in vitro valuable pharmacological profile as an EphA2 receptor antagonist and an overall improvement in its physico-chemical profile (solubility, lipophilicity), if compared to UniPR129. The present work highlights an effective strategy for the pharmacokinetic optimization of aminoacid conjugates of bile acids as small molecule Eph-ephrin antagonists.
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Affiliation(s)
- Francesca Ferlenghi
- Food and Drug Department, University of Parma, Viale delle Scienze 27/A, 43124 Parma, Italy; (F.F.); (C.G.); (M.I.); (L.G.); (M.T.); (A.L.)
| | - Carmine Giorgio
- Food and Drug Department, University of Parma, Viale delle Scienze 27/A, 43124 Parma, Italy; (F.F.); (C.G.); (M.I.); (L.G.); (M.T.); (A.L.)
| | - Matteo Incerti
- Food and Drug Department, University of Parma, Viale delle Scienze 27/A, 43124 Parma, Italy; (F.F.); (C.G.); (M.I.); (L.G.); (M.T.); (A.L.)
| | - Lorenzo Guidetti
- Food and Drug Department, University of Parma, Viale delle Scienze 27/A, 43124 Parma, Italy; (F.F.); (C.G.); (M.I.); (L.G.); (M.T.); (A.L.)
| | - Paola Chiodelli
- Experimental Oncology and Immunology, Department of Molecular and Translational Medicine, University of Brescia, 25123 Brescia, Italy; (P.C.); (M.R.)
| | - Marco Rusnati
- Experimental Oncology and Immunology, Department of Molecular and Translational Medicine, University of Brescia, 25123 Brescia, Italy; (P.C.); (M.R.)
| | - Massimiliano Tognolini
- Food and Drug Department, University of Parma, Viale delle Scienze 27/A, 43124 Parma, Italy; (F.F.); (C.G.); (M.I.); (L.G.); (M.T.); (A.L.)
| | - Federica Vacondio
- Food and Drug Department, University of Parma, Viale delle Scienze 27/A, 43124 Parma, Italy; (F.F.); (C.G.); (M.I.); (L.G.); (M.T.); (A.L.)
- Correspondence: (F.V.); (M.M.); Tel.: +39-0521-905076 (F.V.); +39-0521-905059 (M.M.)
| | - Marco Mor
- Food and Drug Department, University of Parma, Viale delle Scienze 27/A, 43124 Parma, Italy; (F.F.); (C.G.); (M.I.); (L.G.); (M.T.); (A.L.)
- Correspondence: (F.V.); (M.M.); Tel.: +39-0521-905076 (F.V.); +39-0521-905059 (M.M.)
| | - Alessio Lodola
- Food and Drug Department, University of Parma, Viale delle Scienze 27/A, 43124 Parma, Italy; (F.F.); (C.G.); (M.I.); (L.G.); (M.T.); (A.L.)
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7
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Ivashchenko DA, Cerqueira NM, Magalhães AL. Improving computational modeling coupled with ion mobility-mass spectrometry data for efficient drug metabolite structural determination. Struct Chem 2021. [DOI: 10.1007/s11224-021-01726-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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8
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Ultra-high-performance liquid chromatography high-resolution mass spectrometry variants for metabolomics research. Nat Methods 2021; 18:733-746. [PMID: 33972782 DOI: 10.1038/s41592-021-01116-4] [Citation(s) in RCA: 113] [Impact Index Per Article: 37.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 03/12/2021] [Indexed: 02/03/2023]
Abstract
Ultra-high-performance liquid chromatography high-resolution mass spectrometry (UHPLC-HRMS) variants currently represent the best tools to tackle the challenges of complexity and lack of comprehensive coverage of the metabolome. UHPLC offers flexible and efficient separation coupled with high-sensitivity detection via HRMS, allowing for the detection and identification of a broad range of metabolites. Here we discuss current common strategies for UHPLC-HRMS-based metabolomics, with a focus on expanding metabolome coverage.
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9
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Borges R, Colby SM, Das S, Edison AS, Fiehn O, Kind T, Lee J, Merrill AT, Merz KM, Metz TO, Nunez JR, Tantillo DJ, Wang LP, Wang S, Renslow RS. Quantum Chemistry Calculations for Metabolomics. Chem Rev 2021; 121:5633-5670. [PMID: 33979149 PMCID: PMC8161423 DOI: 10.1021/acs.chemrev.0c00901] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Indexed: 02/07/2023]
Abstract
A primary goal of metabolomics studies is to fully characterize the small-molecule composition of complex biological and environmental samples. However, despite advances in analytical technologies over the past two decades, the majority of small molecules in complex samples are not readily identifiable due to the immense structural and chemical diversity present within the metabolome. Current gold-standard identification methods rely on reference libraries built using authentic chemical materials ("standards"), which are not available for most molecules. Computational quantum chemistry methods, which can be used to calculate chemical properties that are then measured by analytical platforms, offer an alternative route for building reference libraries, i.e., in silico libraries for "standards-free" identification. In this review, we cover the major roadblocks currently facing metabolomics and discuss applications where quantum chemistry calculations offer a solution. Several successful examples for nuclear magnetic resonance spectroscopy, ion mobility spectrometry, infrared spectroscopy, and mass spectrometry methods are reviewed. Finally, we consider current best practices, sources of error, and provide an outlook for quantum chemistry calculations in metabolomics studies. We expect this review will inspire researchers in the field of small-molecule identification to accelerate adoption of in silico methods for generation of reference libraries and to add quantum chemistry calculations as another tool at their disposal to characterize complex samples.
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Affiliation(s)
- Ricardo
M. Borges
- Walter
Mors Institute of Research on Natural Products, Federal University of Rio de Janeiro, Rio de Janeiro 21941-901, Brazil
| | - Sean M. Colby
- Biological
Science Division, Pacific Northwest National
Laboratory, Richland, Washington 99352, United States
| | - Susanta Das
- Department
of Chemistry, Michigan State University, East Lansing, Michigan 48824, United States
| | - Arthur S. Edison
- Departments
of Genetics and Biochemistry and Molecular Biology, Complex Carbohydrate
Research Center and Institute of Bioinformatics, University of Georgia, Athens, Georgia 30602, United States
| | - Oliver Fiehn
- West
Coast Metabolomics Center for Compound Identification, UC Davis Genome
Center, University of California, Davis, California 95616, United States
| | - Tobias Kind
- West
Coast Metabolomics Center for Compound Identification, UC Davis Genome
Center, University of California, Davis, California 95616, United States
| | - Jesi Lee
- West
Coast Metabolomics Center for Compound Identification, UC Davis Genome
Center, University of California, Davis, California 95616, United States
- Department
of Chemistry, University of California, Davis, California 95616, United States
| | - Amy T. Merrill
- Department
of Chemistry, University of California, Davis, California 95616, United States
| | - Kenneth M. Merz
- Department
of Chemistry, Michigan State University, East Lansing, Michigan 48824, United States
| | - Thomas O. Metz
- Biological
Science Division, Pacific Northwest National
Laboratory, Richland, Washington 99352, United States
| | - Jamie R. Nunez
- Biological
Science Division, Pacific Northwest National
Laboratory, Richland, Washington 99352, United States
| | - Dean J. Tantillo
- Department
of Chemistry, University of California, Davis, California 95616, United States
| | - Lee-Ping Wang
- Department
of Chemistry, University of California, Davis, California 95616, United States
| | - Shunyang Wang
- West
Coast Metabolomics Center for Compound Identification, UC Davis Genome
Center, University of California, Davis, California 95616, United States
- Department
of Chemistry, University of California, Davis, California 95616, United States
| | - Ryan S. Renslow
- Biological
Science Division, Pacific Northwest National
Laboratory, Richland, Washington 99352, United States
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10
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Wei J, Xiang L, Cai Z. Emerging environmental pollutants hydroxylated polybrominated diphenyl ethers: From analytical methods to toxicology research. MASS SPECTROMETRY REVIEWS 2021; 40:255-279. [PMID: 32608069 DOI: 10.1002/mas.21640] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 05/13/2020] [Accepted: 05/23/2020] [Indexed: 06/11/2023]
Abstract
Hydroxylated polybrominated diphenyl ethers (OH-PBDEs) are of particular concern due to their ubiquitous distribution and adverse health effects. Significant progress has been made in the characterization of OH-PBDEs by using mass spectrometry (MS). In this review, we summarize applications of MS-based techniques in detection, environmental and biota distribution, and potential health risk effects, hoping to unfold an overall picture on account of current knowledge of OH-PBDEs. The analytical methodologies are discussed from sample pretreatment to MS analysis. The methods including gas chromatography-MS (GC-MS), liquid chromatography-MS (LC-MS), and ion mobility spectrometry-MS (IMS-MS) are discussed. GC-MS is the most frequently adopted method in the analysis of OH-PBDEs due to its excellent chromatographic resolution, high sensitivity, and strong ability for unknown identification. LC-MS has been widely used for its high sensitivity and capability of direct analysis. As a newly developed technique, IMS-MS provides high specificity, which greatly facilitates the identification of isomers. OH-PBDEs pervasively existed in both abiotic and biotic samples, including humans, animals, and environmental matrices. Multiple adverse health effects have been reported, such as thyroid hormone disruption, estrogen effects, and neurotoxicity. The reported potential pathological mechanisms are also reviewed. Additionally, MS-based metabolomics, lipidomics, and proteomics have been shown as promising tools to unveil the molecular mechanisms of the toxicity of OH-PBDEs. © 2020 John Wiley & Sons Ltd. Mass Spec Rev.
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Affiliation(s)
- Juntong Wei
- State Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist University, Hong Kong SAR, China
| | - Li Xiang
- State Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist University, Hong Kong SAR, China
| | - Zongwei Cai
- State Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist University, Hong Kong SAR, China
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11
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Plumb RS, Gethings LA, King A, Mullin LG, Maker G, Trengove R, Wilson ID. Hybrid organic/inorganic hybrid surface technology for increasing the performance of LC/MS(MS)-based drug metabolite identification studies: Application to gefitinib and metabolites in mouse plasma and urine. J Pharm Biomed Anal 2021; 200:114076. [PMID: 33892395 DOI: 10.1016/j.jpba.2021.114076] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 03/29/2021] [Accepted: 04/12/2021] [Indexed: 11/18/2022]
Abstract
The detection, identification and quantification of drug metabolites plays a key role in drug discovery and development. Liquid chromatography (LC) coupled to mass spectrometry (MS) has become the primary technology for these studies due to its sensitivity and specificity. However, the presence of transition metals in the chromatography system and columns can result in non-specific and unwanted interactions with the drug and/or its metabolites, via electron-pair donation, leading to poor chromatography and analyte loss. The use of a hybrid organic/inorganic surface applied to the metal surfaces of the chromatography system and column has been demonstrated to reduce or eliminate these effects. When employed for the analysis of mouse urine, derived from the oral dosing of mice with the EGFR inhibitor gefitinib, we observed more symmetrical LC peaks. This resulted in a 33 % improvement in peak capacity for a 10 min reversed - phase gradient separation, a two-fold increase in MS response, cleaner MS spectra and improved peak response reproducibility. This hybrid surface barrier appears to offer significant advantages in the analysis of low-concentration metabolites, potentially facilitating the accurate determination of the elimination phase of the pharmacokinetic (PK) curve and detection of drug metabolites in microdosing or microsampling studies.
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Affiliation(s)
- Robert S Plumb
- Scientific Operations, Waters Corporation, 34 Maple St, Milford, MA, 01757, USA.
| | - Lee A Gethings
- Scientific Operations, Waters Corporation, Stamford Ave, Wilmslow, Manchester, SK9 4AX, UK
| | - Adam King
- Scientific Operations, Waters Corporation, Stamford Ave, Wilmslow, Manchester, SK9 4AX, UK; Centre for Computational and Systems Medicine, Health Futures Institute, Murdoch University, South Street, Murdoch, WA, 6150, Australia
| | - Lauren G Mullin
- Scientific Operations, Waters Corporation, Stamford Ave, Wilmslow, Manchester, SK9 4AX, UK
| | - Garth Maker
- Centre for Computational and Systems Medicine, Health Futures Institute, Murdoch University, South Street, Murdoch, WA, 6150, Australia
| | - Robert Trengove
- Separations Science and Metabolomics Laboratory, Murdoch University, South Street, Murdoch, WA, 6150, Australia
| | - Ian D Wilson
- Computational & Systems Medicine, Imperial College, Exhibition Rd, London, SW7 2AZ, UK
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12
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Ross DH, Xu L. Determination of drugs and drug metabolites by ion mobility-mass spectrometry: A review. Anal Chim Acta 2021; 1154:338270. [PMID: 33736803 DOI: 10.1016/j.aca.2021.338270] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 01/25/2021] [Accepted: 01/27/2021] [Indexed: 01/04/2023]
Abstract
Ion mobility-mass spectrometry (IM-MS) has gained increased applications in the characterization and identification of drugs and drug metabolites, largely owning to the complementary separation of analyte ions based on their gas-phase size and shape in the IM dimension in addition to their mass-to-charge ratios. In this review, we discuss recent advances in such applications. We first introduce various types of IM techniques, focusing on those that allow the measurement of collision cross section (CCS), the physical property of an ion that reflects its gas-phase size and shape. Next, we discuss the IM-MS landscape of the large chemical space of drugs and multimodal distributions of certain drugs in IM separation due to the presence of protomers. We then review drug metabolism reactions and discuss the application of IM-MS in separation and identification of isomeric drug metabolites. Subsequently, we discuss various approaches to generate theoretical and predicted CCS data, including theory-based calculation methods and data-driven prediction models, and currently available resources on these approaches. Finally, current limitations and future directions of application of IM-MS are discussed.
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Affiliation(s)
- Dylan H Ross
- Department of Medicinal Chemistry, University of Washington, 1959, NE Pacific Street, HSB H-172, Seattle, WA, USA
| | - Libin Xu
- Department of Medicinal Chemistry, University of Washington, 1959, NE Pacific Street, HSB H-172, Seattle, WA, USA.
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13
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Radchenko T, Kochansky CJ, Cancilla M, Wrona MD, Mortishire-Smith RJ, Kirk J, Murray G, Fontaine F, Zamora I. Metabolite identification using an ion mobility enhanced data-independent acquisition strategy and automated data processing. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2020; 34:e8792. [PMID: 32208529 DOI: 10.1002/rcm.8792] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 03/20/2020] [Accepted: 03/21/2020] [Indexed: 06/10/2023]
Abstract
RATIONALE Liquid chromatography/mass spectrometry is an essential tool for efficient and reliable quantitative and qualitative analysis and underpins much of contemporary drug metabolism and pharmacokinetics. Data-independent acquisition methods such as MSE have reduced the potential to miss metabolites, but do not formally generate quadrupole-resolved product ion spectra. The addition of ion mobility separation to these approaches, for example, in High-Definition MSE (HDMSE ) has the potential to reduce the time needed to set up an experiment and maximize the chance that all metabolites present can be resolved and characterized. We compared High-Definition Data-Dependent Acquisition (HD-DDA), MSE and HDMSE approaches using automated software processing with Mass-MetaSite and WebMetabase. METHODS Metabolite identification was performed on incubations of glucagon-like peptide-1 (7-37) (GLP-1) and verapamil hydrochloride. The HD-DDA, MSE and HDMSE experiments were conducted on a Waters ACQUITY UPLC I-Class LC system with a VION IMS quadrupole time-of-flight (QTOF) mass spectrometer operating under UNIFI control. All acquired data were processed using MassMetaSite able to read data from UNIFI 1.9.4. WebMetabase was used to review the detected chromatographic peaks and the spectral data interpretations. RESULTS A comparison of outcomes obtained for MSE and HDMSE data demonstrated that the same structures were proposed for metabolites of both verapamil and GLP-1. The ratio of structurally matched to mismatched product ions found by MassMetaSite was slightly greater for HDMSE than for MSE , and HD-DDA, thus improving confidence in the structures proposed through the addition of ion mobility based data acquisitions. CONCLUSIONS: HDMSE data acquisition is an effective approach for the elucidation of metabolite structures for both small molecules and peptides, with excellent accuracy and quality, requiring minimal tailoring for the compound under investigation.
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Affiliation(s)
- Tatiana Radchenko
- Lead Molecular Design, S.L., Sant Cugat Del Valles, Spain
- Universitat Pompeu Fabra, Pl. de la Merce, 10-12, Barcelona, Spain
| | | | | | | | | | | | | | | | - Ismael Zamora
- Lead Molecular Design, S.L., Sant Cugat Del Valles, Spain
- Molecular Discovery Ltd, London, UK
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14
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Marshall AP, Johnson AR, Vega MM, Thomson RJ, Carlson EE. Ion Mobility Mass Spectrometry as an Efficient Tool for Identification of Streptorubin B in Streptomyces coelicolor M145. JOURNAL OF NATURAL PRODUCTS 2020; 83:159-163. [PMID: 31904955 PMCID: PMC7045693 DOI: 10.1021/acs.jnatprod.9b00828] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Ion mobility spectrometry was utilized to corroborate the identity of streptorubin B (2) as the natural product produced by Streptomyces coelicolor. Natural product 2 was initially assigned as butylcycloheptylprodigiosin (3), and only relatively recently was this assignment clarified. We present additional evidence of this assignment by comparing collisional cross sections (Ω) of synthetic standards of 2, 3, and metacycloprodigiosin (4) to the cyclic prodiginine produced by S. coelicolor. Calculated theoretical Ω values demonstrate that cyclic prodiginines could be identified without standards. This work highlights ion mobility as an efficient tool for the dereplication of natural products.
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Affiliation(s)
- Andrew P. Marshall
- Department of Chemistry, Molecular Biology and Biophysics, University of Minnesota-Twin Cities, Minneapolis, Minnesota 55455, United States
| | - Andrew R. Johnson
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Marvin M. Vega
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Regan J. Thomson
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Erin E. Carlson
- Department of Chemistry, Molecular Biology and Biophysics, University of Minnesota-Twin Cities, Minneapolis, Minnesota 55455, United States
- Department of Medicinal Chemistry, Molecular Biology and Biophysics, University of Minnesota-Twin Cities, Minneapolis, Minnesota 55455, United States
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota-Twin Cities, Minneapolis, Minnesota 55455, United States
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
- Corresponding Author:
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15
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Vissers JPC, McCullagh M. An Analytical Perspective on Protein Analysis and Discovery Proteomics by Ion Mobility-Mass Spectrometry. Methods Mol Biol 2020; 2084:161-178. [PMID: 31729660 DOI: 10.1007/978-1-0716-0030-6_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Ion mobility combined with mass spectrometry (IM-MS) is a powerful technique for the analysis of biomolecules and complex mixtures. This chapter reviews the current state-of-the-art in ion mobility technology and its application to biology, protein analysis, and quantitative discovery proteomics in particular, from an analytical perspective. IM-MS can be used as a technique to separate mixtures, to determine structural information (rotationally averaged cross-sectional area) and to enhance MS duty cycle and sensitivity. Moreover, IM-MS is ideally suited for hyphenating with liquid chromatography, or other front-end separation techniques such as, GC, microcolumn LC, capillary electrophoresis, and direct analysis, including MALDI and DESI, providing an semiorthogonal layer of separation, which affords the more unambiguous and confident detection of a wide range of analytes. To illustrate these enhancements, as well as recent developments, the principle of in-line IM separation and hyphenation to orthogonal acceleration time-of-flight mass spectrometers are discussed, in addition to the enhancement of biophysical MS-based analysis using typical proteomics and related application examples.
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16
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Cuyckens F. Mass spectrometry in drug metabolism and pharmacokinetics: Current trends and future perspectives. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2019; 33 Suppl 3:90-95. [PMID: 30019507 DOI: 10.1002/rcm.8235] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Revised: 07/06/2018] [Accepted: 07/08/2018] [Indexed: 06/08/2023]
Abstract
Drug Metabolism and Pharmacokinetics (DMPK) is a core scientific discipline within drug discovery and development as well as post-marketing. It helps to design and select the most promising drug candidate and obtain advanced insights on the processes that control absorption, distribution, metabolism and excretion (ADME) of the final drug candidate. Mass spectrometry is one of the key technologies applied in DMPK. Therefore, the continuous advances made in the field of mass spectrometry also directly impact the way in which we investigate the ADME properties of a compound, providing us with new tools to gather more information or improve our efficiency. An overview will be given of some important current trends and future perspectives in the field.
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Affiliation(s)
- Filip Cuyckens
- Janssen Research & Development, Turnhoutseweg 30, B-2340, Beerse, Belgium
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17
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Reinecke T, Davis AL, Clowers BH. Determination of Gas-Phase Ion Mobility Coefficients Using Voltage Sweep Multiplexing. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2019; 30:977-986. [PMID: 30989619 DOI: 10.1007/s13361-019-02182-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Revised: 02/24/2019] [Accepted: 02/25/2019] [Indexed: 06/09/2023]
Abstract
In a standard single averaged, drift tube ion mobility spectrometry (IMS) experiment, typically less than 1% of the ions are utilized, with the rest of the ions neutralizing on a closed ion gate or ion optic element. Though some efforts at lower pressures (e.g., 4 Torr) have been made to address this issue by concentrating ions prior to release into a drift cell, the ion current reaching the detector during an IMS experiment is often diminished due to this lower duty cycle. Additionally, when considering the temporal nature of the drift tube IMS experiment and the trajectory of IMS towards higher resolution separations and lower duty cycles, increased detector sampling rates are another factor also which further necessitates new modes of conducting the IMS experiment. Placing this trend in context with ion mobility-mass spectrometry instruments (IM-MS), there are numerous types of mass spectrometers that are simply incompatible with the single averaged ion mobility spectrometry experiments due to timing incompatibilities (i.e., ion traps are an order of magnitude slower than the IMS experiment). However, by utilizing a dual gate ion mobility spectrometer for ion multiplexing, ion utilization efficiency can be significantly increased while creating a measurement signal that can be recorded at low sampling rates. In this work, we present the fundamental theory and first results from proof-of-concept measurements using a new type of ion multiplexing that relies on changing the electric field within the drift cell during the course of an experiment while simultaneously opening the ion gates at a constant frequency. For brevity, this mode is termed voltage sweep multiplexing (VSM). Key variables for this type of experiment are discussed and verified with measurements from traditional signal averaged experiments. Graphical Abstract .
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Affiliation(s)
- Tobias Reinecke
- Department of Chemistry, Washington State University, Pullman, WA, 99164, USA
| | - Austen L Davis
- Department of Chemistry, Washington State University, Pullman, WA, 99164, USA
| | - Brian H Clowers
- Department of Chemistry, Washington State University, Pullman, WA, 99164, USA.
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18
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Couvillion SP, Zhu Y, Nagy G, Adkins JN, Ansong C, Renslow RS, Piehowski PD, Ibrahim YM, Kelly RT, Metz TO. New mass spectrometry technologies contributing towards comprehensive and high throughput omics analyses of single cells. Analyst 2019; 144:794-807. [PMID: 30507980 PMCID: PMC6349538 DOI: 10.1039/c8an01574k] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Mass-spectrometry based omics technologies - namely proteomics, metabolomics and lipidomics - have enabled the molecular level systems biology investigation of organisms in unprecedented detail. There has been increasing interest for gaining a thorough, functional understanding of the biological consequences associated with cellular heterogeneity in a wide variety of research areas such as developmental biology, precision medicine, cancer research and microbiome science. Recent advances in mass spectrometry (MS) instrumentation and sample handling strategies are quickly making comprehensive omics analyses of single cells feasible, but key breakthroughs are still required to push through remaining bottlenecks. In this review, we discuss the challenges faced by single cell MS-based omics analyses and highlight recent technological advances that collectively can contribute to comprehensive and high throughput omics analyses in single cells. We provide a vision of the potential of integrating pioneering technologies such as Structures for Lossless Ion Manipulations (SLIM) for improved sensitivity and resolution, novel peptide identification tactics and standards free metabolomics approaches for future applications in single cell analysis.
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Affiliation(s)
- Sneha P Couvillion
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA.
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19
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Mehmood A, Janesko BG. Predicting ion mobility collision cross sections directly from standard quantum chemistry software. JOURNAL OF MASS SPECTROMETRY : JMS 2018; 53:432-434. [PMID: 29505693 DOI: 10.1002/jms.4078] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Revised: 02/23/2018] [Accepted: 02/26/2018] [Indexed: 06/08/2023]
Abstract
A method is proposed to predict ions' collision cross-sectional area from properties that are already evaluated in standard quantum chemistry software. Computed molecular isodensity surface areas recover the predictions of existing projection approximations. Computed solvent cavity areas give comparable accuracy. This provides a simplified workflow for assigning ion-mobility mass spectra.
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Affiliation(s)
- Arshad Mehmood
- Department of Chemistry and Biochemistry, Texas Christian University, Fort Worth, TX, 76129, USA
| | - Benjamin G Janesko
- Department of Chemistry and Biochemistry, Texas Christian University, Fort Worth, TX, 76129, USA
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20
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Chen X, Kang Y, Zeng S. Analysis of stereoisomers of chiral drug by mass spectrometry. Chirality 2018; 30:609-618. [DOI: 10.1002/chir.22833] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Revised: 01/02/2018] [Accepted: 01/15/2018] [Indexed: 01/07/2023]
Affiliation(s)
- Xiaolei Chen
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research; College of Pharmaceutical Sciences, Zhejiang University; Hangzhou Zhejiang China
| | - Yu Kang
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research; College of Pharmaceutical Sciences, Zhejiang University; Hangzhou Zhejiang China
| | - Su Zeng
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research; College of Pharmaceutical Sciences, Zhejiang University; Hangzhou Zhejiang China
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21
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Ion mobility in the pharmaceutical industry: an established biophysical technique or still niche? Curr Opin Chem Biol 2018; 42:147-159. [DOI: 10.1016/j.cbpa.2017.11.008] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2017] [Revised: 11/10/2017] [Accepted: 11/15/2017] [Indexed: 01/01/2023]
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22
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Chalet C, Hollebrands B, Janssen HG, Augustijns P, Duchateau G. Identification of phase-II metabolites of flavonoids by liquid chromatography–ion-mobility spectrometry–mass spectrometry. Anal Bioanal Chem 2017; 410:471-482. [DOI: 10.1007/s00216-017-0737-4] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Revised: 10/18/2017] [Accepted: 10/30/2017] [Indexed: 10/18/2022]
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23
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Ferchaud-Roucher V, Croyal M, Moyon T, Zair Y, Krempf M, Ouguerram K. Plasma Lipidome Analysis by Liquid Chromatography-High Resolution Mass Spectrometry and Ion Mobility of Hypertriglyceridemic Patients on Extended-Release Nicotinic Acid: a Pilot Study. Cardiovasc Drugs Ther 2017; 31:269-279. [DOI: 10.1007/s10557-017-6737-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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24
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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: 142] [Impact Index Per Article: 20.3] [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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Paglia G, Astarita G. Metabolomics and lipidomics using traveling-wave ion mobility mass spectrometry. Nat Protoc 2017; 12:797-813. [PMID: 28301461 DOI: 10.1038/nprot.2017.013] [Citation(s) in RCA: 161] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Metabolomics and lipidomics aim to profile the wide range of metabolites and lipids that are present in biological samples. Recently, ion mobility spectrometry (IMS) has been used to support metabolomics and lipidomics applications to facilitate the separation and the identification of complex mixtures of analytes. IMS is a gas-phase electrophoretic technique that enables the separation of ions in the gas phase according to their charge, shape and size. Occurring within milliseconds, IMS separation is compatible with modern mass spectrometry (MS) operating with microsecond scan speeds. Thus, the time required for acquiring IMS data does not affect the overall run time of traditional liquid chromatography (LC)-MS-based metabolomics and lipidomics experiments. The addition of IMS to conventional LC-MS-based metabolomics and lipidomics workflows has been shown to enhance peak capacity, spectral clarity and fragmentation specificity. Moreover, by enabling determination of a collision cross-section (CCS) value-a parameter related to the shape of ions-IMS can improve the accuracy of metabolite identification. In this protocol, we describe how to integrate traveling-wave ion mobility spectrometry (TWIMS) into traditional LC-MS-based metabolomic and lipidomic workflows. In particular, we describe procedures for the following: tuning and calibrating a SYNAPT High-Definition MS (HDMS) System (Waters) specifically for metabolomics and lipidomics applications; extracting polar metabolites and lipids from brain samples; setting up appropriate chromatographic conditions; acquiring simultaneously m/z, retention time and CCS values for each analyte; processing and analyzing data using dedicated software solutions, such as Progenesis QI (Nonlinear Dynamics); and, finally, performing metabolite and lipid identification using CCS databases and TWIMS-derived fragmentation information.
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Affiliation(s)
- Giuseppe Paglia
- Center for Biomedicine, European Academy of Bolzano/Bozen, Bolzano, Italy
| | - Giuseppe Astarita
- Department of Biochemistry and Molecular &Cellular Biology, Georgetown University, Washington, DC, USA
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27
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Gonzales GB, Smagghe G, Coelus S, Adriaenssens D, De Winter K, Desmet T, Raes K, Van Camp J. Collision cross section prediction of deprotonated phenolics in a travelling-wave ion mobility spectrometer using molecular descriptors and chemometrics. Anal Chim Acta 2016; 924:68-76. [DOI: 10.1016/j.aca.2016.04.020] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Revised: 03/29/2016] [Accepted: 04/15/2016] [Indexed: 02/02/2023]
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28
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Lapthorn C, Pullen FS, Chowdhry BZ, Wright P, Perkins GL, Heredia Y. How useful is molecular modelling in combination with ion mobility mass spectrometry for 'small molecule' ion mobility collision cross-sections? Analyst 2016; 140:6814-23. [PMID: 26131453 DOI: 10.1039/c5an00411j] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Ion mobility mass spectrometry is used to measure the drift-time of an ion. The drift-time of an ion can be used to calculate the collision cross-section (CCS) in travelling wave ion mobility (e.g. Waters Synapt and Vion instruments) or directly determine the experimental CCS (e.g. Agilent 6560 instrument and many drift-tube instruments). A comparison of the experimental CCS and theoretical CCS values obtained from trajectory method He(g) parameterised MOBCAL and N2(g) parameterised MOBCAL software, for a range of 20 'small molecules' is presented. This study utilises density functional theory B3LYP methods and the 6-31G+(d,p) basis set to calculate theoretical CCS values. This study seeks to assess the accuracy of a common procedure using CCS calibration with poly-(d/l)-alanine derived from drift-cell measurements and the original release of MOBCAL software and compare it with recent improvements with a drug-like molecule calibration set and a revision of MOBCAL parameterised for N2(g) drift gas. This study represents one of the first quantitative evaluations of the agreement between theoretical CCS and experimental CCS values for a range of small pharmaceutically relevant molecules using travelling wave ion mobility mass spectrometry. Accurate theoretical CCS may allow optimisation of ion mobility separations in silico, provide CCS databases that can confirm structures without the need for alternative analytical tools such as nuclear magnetic resonance spectroscopy (NMR) and assignment of unknowns and positional isomers without requiring reference materials.
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Affiliation(s)
- Cris Lapthorn
- Faculty of Engineering & Science, University of Greenwich, Medway Campus, Chatham, Kent ME4 4TB, UK.
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29
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Reading E, Munoz-Muriedas J, Roberts AD, Dear GJ, Robinson CV, Beaumont C. Elucidation of Drug Metabolite Structural Isomers Using Molecular Modeling Coupled with Ion Mobility Mass Spectrometry. Anal Chem 2016; 88:2273-80. [DOI: 10.1021/acs.analchem.5b04068] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Eamonn Reading
- Department
of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford OX1 3QZ, U.K
| | - Jordi Munoz-Muriedas
- Chemical
Sciences, Computational Chemistry, GlaxoSmithKline, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Andrew D. Roberts
- Drug
Metabolism and Pharmacokinetics, GlaxoSmithKline, Ware, Hertfordshire SG12 0DP, U.K
| | - Gordon J. Dear
- Drug
Metabolism and Pharmacokinetics, GlaxoSmithKline, Ware, Hertfordshire SG12 0DP, U.K
| | - Carol V. Robinson
- Department
of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford OX1 3QZ, U.K
| | - Claire Beaumont
- Drug
Metabolism and Pharmacokinetics, GlaxoSmithKline, Ware, Hertfordshire SG12 0DP, U.K
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30
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Zhang JT, Wang HY, Zhang X, Zhang F, Guo YL. Study of short-lived and early reaction intermediates in organocatalytic asymmetric amination reactions by ion-mobility mass spectrometry. Catal Sci Technol 2016. [DOI: 10.1039/c6cy01051b] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A study of the reactive intermediates in organocatalytic asymmetric amination reactions by reactive SAESI coupled to ion-mobility mass spectrometry.
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Affiliation(s)
- Jun-Ting Zhang
- State Key Laboratory of Organometallic Chemistry and National Center for Organic Mass Spectrometry in Shanghai
- Shanghai Institute of Organic Chemistry
- Chinese Academy of Sciences
- Shanghai 200032
- China
| | - Hao-Yang Wang
- State Key Laboratory of Organometallic Chemistry and National Center for Organic Mass Spectrometry in Shanghai
- Shanghai Institute of Organic Chemistry
- Chinese Academy of Sciences
- Shanghai 200032
- China
| | - Xiang Zhang
- Department of Applied Chemistry
- Zhejiang Gongshang University
- Hangzhou 310035
- China
| | - Fang Zhang
- State Key Laboratory of Organometallic Chemistry and National Center for Organic Mass Spectrometry in Shanghai
- Shanghai Institute of Organic Chemistry
- Chinese Academy of Sciences
- Shanghai 200032
- China
| | - Yin-Long Guo
- State Key Laboratory of Organometallic Chemistry and National Center for Organic Mass Spectrometry in Shanghai
- Shanghai Institute of Organic Chemistry
- Chinese Academy of Sciences
- Shanghai 200032
- China
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31
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Boschmans J, Jacobs S, Williams JP, Palmer M, Richardson K, Giles K, Lapthorn C, Herrebout WA, Lemière F, Sobott F. Combining density functional theory (DFT) and collision cross-section (CCS) calculations to analyze the gas-phase behaviour of small molecules and their protonation site isomers. Analyst 2016; 141:4044-54. [DOI: 10.1039/c5an02456k] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Computational methods are employed to study the protomers in ESI-IM-MS.
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Affiliation(s)
- Jasper Boschmans
- Biomolecular & Analytical Mass Spectrometry group
- Department of Chemistry
- University of Antwerp
- Antwerp
- Belgium
| | - Sam Jacobs
- Molecular Spectroscopy group
- Department of Chemistry
- University of Antwerp
- Antwerp
- Belgium
| | | | | | | | | | - Cris Lapthorn
- Faculty of Engineering & Science
- University of Greenwich
- Chatham
- UK
| | - Wouter A. Herrebout
- Molecular Spectroscopy group
- Department of Chemistry
- University of Antwerp
- Antwerp
- Belgium
| | - Filip Lemière
- Biomolecular & Analytical Mass Spectrometry group
- Department of Chemistry
- University of Antwerp
- Antwerp
- Belgium
| | - Frank Sobott
- Biomolecular & Analytical Mass Spectrometry group
- Department of Chemistry
- University of Antwerp
- Antwerp
- Belgium
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Chendo C, Moreira G, Tintaru A, Posocco P, Laurini E, Lefay C, Gigmes D, Viel S, Pricl S, Charles L. Anomerization of Acrylated Glucose During Traveling Wave Ion Mobility Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2015; 26:1483-1493. [PMID: 26041082 DOI: 10.1007/s13361-015-1170-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Revised: 04/16/2015] [Accepted: 04/18/2015] [Indexed: 06/04/2023]
Abstract
Anomerization of simple sugars in the liquid phase is known as an acid- and base-catalyzed process, which highly depends on solvent polarity. This reaction is reported here to occur in the gas phase, during traveling wave ion mobility spectrometry (TWIMS) experiments aimed at separating α- and β-anomers of penta-acrylated glucose generated as ammonium adducts in electrospray ionization. This compound was available in two samples prepared from glucose dissolved in solvents of different polarity, namely tetrahydrofuran (THF) and N,N-dimethylacetamide (DMAC), and analyzed by electrospray tandem mass spectrometry (ESI-MS/MS) as well as traveling wave ion mobility (ESI-TWIMS-MS). In MS/MS, an anchimerically-assisted process was found to be unique to the electrosprayed α-anomer, and was only observed for the THF sample. In ESI-TWIMS-MS, a signal was measured at the drift time expected for the α-anomer for both the THF and DMAC samples, in apparent contradiction to the MS/MS results, which indicated that the α-anomer was not present in the DMAC sample. However, MS/MS experiments performed after TWIMS separation revealed that ammonium adducts of the α-anomer produced from each sample, although exhibiting the same collision cross section, were clearly different. Indeed, while the α-anomer actually present in the THF sample was electrosprayed with the ammonium adducted at the C2 acrylate, its homologue only observed when the DMAC sample was subjected to TWIMS hold the adducted ammonium at the C1 acrylate. These findings were explained by a β/α inter-conversion upon injection in the TWIMS cell, as supported by theoretical calculation and dynamic molecular modeling.
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Affiliation(s)
- Christophe Chendo
- Aix-Marseille Université - CNRS, UMR 7273, Institut de Chimie Radicalaire, Marseille, France
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Abstract
Drug metabolism can produce metabolites with physicochemical and pharmacological properties that differ substantially from those of the parent drug, and consequently has important implications for both drug safety and efficacy. To reduce the risk of costly clinical-stage attrition due to the metabolic characteristics of drug candidates, there is a need for efficient and reliable ways to predict drug metabolism in vitro, in silico and in vivo. In this Perspective, we provide an overview of the state of the art of experimental and computational approaches for investigating drug metabolism. We highlight the scope and limitations of these methods, and indicate strategies to harvest the synergies that result from combining measurement and prediction of drug metabolism.
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34
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Applications of ion-mobility mass spectrometry for lipid analysis. Anal Bioanal Chem 2015; 407:4995-5007. [PMID: 25893801 DOI: 10.1007/s00216-015-8664-8] [Citation(s) in RCA: 132] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Revised: 03/19/2015] [Accepted: 03/26/2015] [Indexed: 12/28/2022]
Abstract
The high chemical complexity of the lipidome is one of the major challenges in lipidomics research. Ion-mobility spectrometry (IMS), a gas-phase electrophoretic technique, makes possible the separation of ions in the gas phase according to their charge, shape, and size. IMS can be combined with mass spectrometry (MS), adding three major benefits to traditional lipidomic approaches. First, IMS-MS allows the determination of the collision cross section (CCS), a physicochemical measure related to the conformational structure of lipid ions. The CCS is used to improve the confidence of lipid identification. Second, IMS-MS provides a new set of hybrid fragmentation experiments. These experiments, which combine collision-induced dissociation with ion-mobility separation, improve the specificity of MS/MS-based approaches. Third, IMS-MS improves the peak capacity and signal-to-noise ratio of traditional analytical approaches. In doing so, it allows the separation of complex lipid extracts from interfering isobaric species. Developing in parallel with advances in instrumentation, informatics solutions enable analysts to process and exploit IMS-MS data for qualitative and quantitative applications. Here we review the current approaches for lipidomics research based on IMS-MS, including liquid chromatography-MS and direct-MS analyses of "shotgun" lipidomics and MS imaging.
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Cumeras R, Figueras E, Davis CE, Baumbach JI, Gràcia I. Review on ion mobility spectrometry. Part 2: hyphenated methods and effects of experimental parameters. Analyst 2015; 140:1391-410. [PMID: 25465248 PMCID: PMC4331244 DOI: 10.1039/c4an01101e] [Citation(s) in RCA: 103] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Ion Mobility Spectrometry (IMS) is a widely used and 'well-known' technique of ion separation in the gaseous phase based on the differences of ion mobilities under an electric field. This technique has received increased interest over the last several decades as evidenced by the pace and advances of new IMS devices available. In this review we explore the hyphenated techniques that are used with IMS, specifically mass spectrometry as an identification approach and a multi-capillary column as a pre-separation approach. Also, we will pay special attention to the key figures of merit of the ion mobility spectrum and how data sets are treated, and the influences of the experimental parameters on both conventional drift time IMS (DTIMS) and miniaturized IMS also known as high Field Asymmetric IMS (FAIMS) in the planar configuration. The present review article is preceded by a companion review article which details the current instrumentation and contains the sections that configure both conventional DTIMS and FAIMS devices. These reviews will give the reader an insightful view of the main characteristics and aspects of the IMS technique.
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Affiliation(s)
- R Cumeras
- Institut de Microelectrònica de Barcelona, IMB-CNM (CSIC), Esfera UAB, Campus UAB s/n, E-08193 Bellaterra, Barcelona, Spain.
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36
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Paglia G, Angel P, Williams JP, Richardson K, Olivos HJ, Thompson JW, Menikarachchi L, Lai S, Walsh C, Moseley A, Plumb RS, Grant D, Palsson BO, Langridge J, Geromanos S, Astarita G. Ion mobility-derived collision cross section as an additional measure for lipid fingerprinting and identification. Anal Chem 2015; 87:1137-44. [PMID: 25495617 PMCID: PMC4302848 DOI: 10.1021/ac503715v] [Citation(s) in RCA: 204] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2014] [Accepted: 12/13/2014] [Indexed: 02/07/2023]
Abstract
Despite recent advances in analytical and computational chemistry, lipid identification remains a significant challenge in lipidomics. Ion-mobility spectrometry provides an accurate measure of the molecules' rotationally averaged collision cross-section (CCS) in the gas phase and is thus related to ionic shape. Here, we investigate the use of CCS as a highly specific molecular descriptor for identifying lipids in biological samples. Using traveling wave ion mobility mass spectrometry (MS), we measured the CCS values of over 200 lipids within multiple chemical classes. CCS values derived from ion mobility were not affected by instrument settings or chromatographic conditions, and they were highly reproducible on instruments located in independent laboratories (interlaboratory RSD < 3% for 98% of molecules). CCS values were used as additional molecular descriptors to identify brain lipids using a variety of traditional lipidomic approaches. The addition of CCS improved the reproducibility of analysis in a liquid chromatography-MS workflow and maximized the separation of isobaric species and the signal-to-noise ratio in direct-MS analyses (e.g., "shotgun" lipidomics and MS imaging). These results indicate that adding CCS to databases and lipidomics workflows increases the specificity and selectivity of analysis, thus improving the confidence in lipid identification compared to traditional analytical approaches. The CCS/accurate-mass database described here is made publicly available.
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Affiliation(s)
- Giuseppe Paglia
- Istituto
Zooprofilattico Sperimentale della Puglia e Della Basilicata, Foggia, Italy
- Center
for Systems Biology, University of Iceland, Reykjavik, Iceland
| | - Peggi Angel
- Protea
Biosciences Group, Inc., Morgantown, West Virginia 26505, United States
| | | | | | | | - J. Will Thompson
- Duke
Proteomics Core Facility, Durham, North Carolina 27708, United States
| | - Lochana Menikarachchi
- Department
of Pharmaceutical Sciences, University of
Connecticut, Storrs, Connecticut 06268, United States
| | - Steven Lai
- Waters
Corporation, Milford, Massachusetts 01757, United States
| | - Callee Walsh
- Protea
Biosciences Group, Inc., Morgantown, West Virginia 26505, United States
| | - Arthur Moseley
- Duke
Proteomics Core Facility, Durham, North Carolina 27708, United States
| | - Robert S. Plumb
- Waters
Corporation, Milford, Massachusetts 01757, United States
- Computational
and Systems Medicine, Department of Surgery and Cancer, Faculty of
Medicine, Imperial College London, London, United Kingdom
| | - David
F. Grant
- Department
of Pharmaceutical Sciences, University of
Connecticut, Storrs, Connecticut 06268, United States
| | - Bernhard O. Palsson
- Computational
and Systems Medicine, Department of Surgery and Cancer, Faculty of
Medicine, Imperial College London, London, United Kingdom
| | - James Langridge
- Waters
Corporation, Milford, Massachusetts 01757, United States
| | - Scott Geromanos
- Waters
Corporation, Milford, Massachusetts 01757, United States
| | - Giuseppe Astarita
- Waters
Corporation, Milford, Massachusetts 01757, United States
- Department
of Biochemistry and Molecular & Cellular Biology, Georgetown University, Washington, DC 20057, United States
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37
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Coupling ultra-high-pressure liquid chromatography with mass spectrometry for in-vitro drug-metabolism studies. Trends Analyt Chem 2014. [DOI: 10.1016/j.trac.2014.06.021] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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38
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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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39
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Separation of steroid isomers by ion mobility mass spectrometry. J Chromatogr A 2013; 1310:133-7. [DOI: 10.1016/j.chroma.2013.08.056] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2013] [Revised: 08/13/2013] [Accepted: 08/15/2013] [Indexed: 11/18/2022]
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40
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Lalli PM, Corilo YE, Fasciotti M, Riccio MF, de Sa GF, Daroda RJ, Souza GHMF, McCullagh M, Bartberger MD, Eberlin MN, Campuzano IDG. Baseline resolution of isomers by traveling wave ion mobility mass spectrometry: investigating the effects of polarizable drift gases and ionic charge distribution. JOURNAL OF MASS SPECTROMETRY : JMS 2013; 48:989-997. [PMID: 24078238 DOI: 10.1002/jms.3245] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2013] [Revised: 05/28/2013] [Accepted: 06/06/2013] [Indexed: 06/02/2023]
Abstract
We have studied the behavior of isomers and analogues by traveling wave ion mobility mass spectrometry (TWIM-MS) using drift-gases with varying masses and polarizabilities. Despite the reduced length of the cell (18 cm), a pair of constitutional isomers, N-butylaniline and para-butylaniline, with theoretical collision cross-section values in helium (ΩHe ) differing by as little as 1.2 Å(2) (1.5%) but possessing contrasting charge distribution, showed baseline peak-to-peak resolution (Rp-p ) for their protonated molecules, using carbon dioxide (CO2), nitrous oxide (N2O) and ethene (C2H4 ) as the TWIM drift-gas. Near baseline Rp-p was also obtained in CO2 for a group of protonated haloanilines (para-chloroaniline, para-bromoaniline and para-iodoaniline) which display contrasting masses and theoretical ΩHe , which differ by as much as 15.7 Å(2) (19.5%) but similar charge distributions. The deprotonated isomeric pair of trans-oleic acid and cis-oleic acid possessing nearly identical theoretical ΩHe and ΩN2 as well as similar charge distributions, remained unresolved. Interestingly, an inversion of drift-times were observed for the 1,3-dialkylimidazolium ions when comparing He, N2 and N2O. Using density functional theory as a means of examining the ions electronic structure, and He and N2-based trajectory method algorithm, we discuss the effect of the long-range charge induced dipole attractive and short-range Van der Waals forces involved in the TWIM separation in drift-gases of differing polarizabilities. We therefore propose that examining the electronic structure of the ions under investigation may potentially indicate whether the use of more polarizable drift-gases could improve separation and the overall success of TWIM-MS analysis.
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Affiliation(s)
- Priscila M Lalli
- ThoMSon Mass Spectrometry Laboratory, Institute of Chemistry, University of Campinas - UNICAMP, 13084-970, Campinas, SP, Brazil
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41
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Shimizu A, Chiba M. Ion Mobility Spectrometry–Mass Spectrometry Analysis for the Site of Aromatic Hydroxylation. Drug Metab Dispos 2013; 41:1295-9. [DOI: 10.1124/dmd.113.051953] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
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42
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Zhang T, Zhang J, Derreumaux P, Mu Y. Molecular mechanism of the inhibition of EGCG on the Alzheimer Aβ(1-42) dimer. J Phys Chem B 2013; 117:3993-4002. [PMID: 23537203 DOI: 10.1021/jp312573y] [Citation(s) in RCA: 162] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Growing evidence supports that amyloid β (Aβ) oligomers are the major causative agents leading to neural cell death in Alzheimer's disease. The polyphenol (-)-epigallocatechin gallate (EGCG) was recently reported to inhibit Aβ fibrillization and redirect Aβ aggregation into unstructured, off-pathway oligomers. Given the experimental challenge to characterize the structures of Aβ/EGCG complexes, we performed extensive atomistic replica exchange molecular dynamics simulations of Aβ1-42 dimer in the present and absence of EGCG in explicit solvent. Our equilibrium Aβ dimeric structures free of EGCG are consistent with the collision cross section from ion-mobility mass spectrometry and the secondary structure composition from circular dichroism experiment. In the presence of EGCG, the Aβ structures are characterized by increased inter-center-of-mass distances, reduced interchain and intrachain contacts, reduced β-sheet content, and increased coil and α-helix contents. Analysis of the free energy surfaces reveals that the Aβ dimer with EGCG adopts new conformations, affecting therefore its propensity to adopt fibril-prone states. Overall, this study provides, for the first time, insights on the equilibrium structures of Aβ1-42 dimer in explicit aqueous solution and an atomic picture of the EGCG-mediated conformational change on Aβ dimer.
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Affiliation(s)
- Tong Zhang
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
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43
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Menikarachchi LC, Hamdalla MA, Hill DW, Grant DF. Chemical structure identification in metabolomics: computational modeling of experimental features. Comput Struct Biotechnol J 2013; 5:e201302005. [PMID: 24688698 PMCID: PMC3962140 DOI: 10.5936/csbj.201302005] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2012] [Revised: 12/20/2012] [Accepted: 12/24/2012] [Indexed: 11/30/2022] Open
Abstract
The identification of compounds in complex mixtures remains challenging despite recent advances in analytical techniques. At present, no single method can detect and quantify the vast array of compounds that might be of potential interest in metabolomics studies. High performance liquid chromatography/mass spectrometry (HPLC/MS) is often considered the analytical method of choice for analysis of biofluids. The positive identification of an unknown involves matching at least two orthogonal HPLC/MS measurements (exact mass, retention index, drift time etc.) against an authentic standard. However, due to the limited availability of authentic standards, an alternative approach involves matching known and measured features of the unknown compound with computationally predicted features for a set of candidate compounds downloaded from a chemical database. Computationally predicted features include retention index, ECOM50 (energy required to decompose 50% of a selected precursor ion in a collision induced dissociation cell), drift time, whether the unknown compound is biological or synthetic and a collision induced dissociation (CID) spectrum. Computational predictions are used to filter the initial “bin” of candidate compounds. The final output is a ranked list of candidates that best match the known and measured features. In this mini review, we discuss cheminformatics methods underlying this database search-filter identification approach.
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Affiliation(s)
- Lochana C Menikarachchi
- Department of Pharmaceutical Sciences, University of Connecticut, 69 N Eagleville Rd, Storrs, CT 06269, United States
| | - Mai A Hamdalla
- Department of Computer Science & Engineering, University of Connecticut, 371 Fairfield Road, Unit 2155 Storrs, CT 06269, United States
| | - Dennis W Hill
- Department of Pharmaceutical Sciences, University of Connecticut, 69 N Eagleville Rd, Storrs, CT 06269, United States
| | - David F Grant
- Department of Pharmaceutical Sciences, University of Connecticut, 69 N Eagleville Rd, Storrs, CT 06269, United States
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44
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Metabolite structure analysis by high-resolution MS: supporting drug-development studies. Bioanalysis 2013; 5:463-79. [DOI: 10.4155/bio.13.3] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Effective characterization of drug metabolites in complex biological matrices is facilitated by mass spectrometers with high resolving power, mass accuracy and sensitivity. This review begins with an overview of high-resolution MS terminology and the different types of instrumentation that are currently available. Metabolite structure analysis offers unique challenges and, therefore, the different types of approaches used to solve problems are highlighted through specific examples. Overall, this review describes the value that high-resolution MS brings to drug-metabolism studies.
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45
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Lapthorn C, Pullen F, Chowdhry BZ. Ion mobility spectrometry-mass spectrometry (IMS-MS) of small molecules: separating and assigning structures to ions. MASS SPECTROMETRY REVIEWS 2013; 32:43-71. [PMID: 22941854 DOI: 10.1002/mas.21349] [Citation(s) in RCA: 183] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2011] [Revised: 01/29/2012] [Accepted: 03/08/2012] [Indexed: 05/11/2023]
Abstract
The phenomenon of ion mobility (IM), the movement/transport of charged particles under the influence of an electric field, was first observed in the early 20th Century and harnessed later in ion mobility spectrometry (IMS). There have been rapid advances in instrumental design, experimental methods, and theory together with contributions from computational chemistry and gas-phase ion chemistry, which have diversified the range of potential applications of contemporary IMS techniques. Whilst IMS-mass spectrometry (IMS-MS) has recently been recognized for having significant research/applied industrial potential and encompasses multi-/cross-disciplinary areas of science, the applications and impact from decades of research are only now beginning to be utilized for "small molecule" species. This review focuses on the application of IMS-MS to "small molecule" species typically used in drug discovery (100-500 Da) including an assessment of the limitations and possibilities of the technique. Potential future developments in instrumental design, experimental methods, and applications are addressed. The typical application of IMS-MS in relation to small molecules has been to separate species in fairly uniform molecular classes such as mixture analysis, including metabolites. Separation of similar species has historically been challenging using IMS as the resolving power, R, has been low (3-100) and the differences in collision cross-sections that could be measured have been relatively small, so instrument and method development has often focused on increasing resolving power. However, IMS-MS has a range of other potential applications that are examined in this review where it displays unique advantages, including: determination of small molecule structure from drift time, "small molecule" separation in achiral and chiral mixtures, improvement in selectivity, identification of carbohydrate isomers, metabonomics, and for understanding the size and shape of small molecules. This review provides a broad but selective overview of current literature, concentrating on IMS-MS, not solely IMS, and small molecule applications.
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Affiliation(s)
- Cris Lapthorn
- School of Science, University of Greenwich, Medway Campus, Chatham, Kent ME4 4TB, UK
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46
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Menikarachchi LC, Cawley S, Hill DW, Hall LM, Hall L, Lai S, Wilder J, Grant DF. MolFind: a software package enabling HPLC/MS-based identification of unknown chemical structures. Anal Chem 2012; 84:9388-94. [PMID: 23039714 PMCID: PMC3523192 DOI: 10.1021/ac302048x] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
In this paper, we present MolFind, a highly multithreaded pipeline type software package for use as an aid in identifying chemical structures in complex biofluids and mixtures. MolFind is specifically designed for high-performance liquid chromatography/mass spectrometry (HPLC/MS) data inputs typical of metabolomics studies where structure identification is the ultimate goal. MolFind enables compound identification by matching HPLC/MS-based experimental data obtained for an unknown compound with computationally derived HPLC/MS values for candidate compounds downloaded from chemical databases such as PubChem. The downloaded "bins" consist of all compounds matching the monoisotopic molecular weight of the unknown. The computational HPLC/MS values predicted include retention index (RI), ECOM(50) (energy required to fragment 50% of a selected precursor ion), drift time, and collision induced dissociation (CID) spectrum. RI, ECOM(50), and drift-time models are used for filtering compounds downloaded from PubChem. The remaining candidates are then ranked based on CID spectra matching. Current RI and ECOM(50) models allow for the removal of about 28% of compounds from PubChem bins. Our estimates suggest that this could be improved to as much as 87% with additional chemical structures included in the computational models. Quantitative structure property relationship-based modeling of drift times showed a better correlation with experimentally determined drift times than did Mobcal cross-sectional areas. In 23 of 35 example cases, filtering PubChem bins with RI and ECOM(50) predictive models resulted in improved ranking of the unknown compounds compared to previous studies using CID spectra matching alone. In 19 of 35 examples, the correct candidate was ranked within the top 20 compounds in bins containing an average of 1635 compounds.
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Affiliation(s)
- Lochana C. Menikarachchi
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, Connecticut, United States
| | - Shannon Cawley
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, Connecticut, United States
| | - Dennis W. Hill
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, Connecticut, United States
| | - L. Mark Hall
- Hall Associates Consulting, Quincy, Massachusetts, United States
| | - Lowell Hall
- Department of Chemistry, Eastern Nazarene College, Quincy, Massachusetts, United States
| | - Steven Lai
- Waters Corporation, Beverly, Massachusetts, United States
| | - Janine Wilder
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, Connecticut, United States
| | - David F. Grant
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, Connecticut, United States
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47
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Donegan M, Browning M. A REVIEW RECENT DEVELOPMENTS IN SAMPLE IONIZATION INTERFACES USED IN MASS SPECTROMETRY. J LIQ CHROMATOGR R T 2012. [DOI: 10.1080/10826076.2012.714595] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
| | - Marc Browning
- a Bristol-Myers Squibb , Wallingford , Connecticut , USA
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48
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Recent developments in liquid chromatography–mass spectrometry and related techniques. J Chromatogr A 2012; 1259:3-15. [DOI: 10.1016/j.chroma.2012.08.072] [Citation(s) in RCA: 228] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2012] [Revised: 08/22/2012] [Accepted: 08/23/2012] [Indexed: 11/22/2022]
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49
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Bush MF, Campuzano IDG, Robinson CV. Ion Mobility Mass Spectrometry of Peptide Ions: Effects of Drift Gas and Calibration Strategies. Anal Chem 2012; 84:7124-30. [DOI: 10.1021/ac3014498] [Citation(s) in RCA: 254] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Matthew F. Bush
- University of Washington, Department of Chemistry,
Box 351700, Seattle, Washington 98195-1700, United States
| | - Iain D. G. Campuzano
- Department of Molecular Structure, Amgen, Thousand Oaks, California 91320, United States
| | - Carol V. Robinson
- Department of Chemistry, Physical
and Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom
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50
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Shimizu A, Ohe T, Chiba M. A novel method for the determination of the site of glucuronidation by ion mobility spectrometry-mass spectrometry. Drug Metab Dispos 2012; 40:1456-9. [PMID: 22611068 DOI: 10.1124/dmd.112.045435] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Glucuronidation not only plays a detoxifying role in living body, but it also can complicate pharmacological and toxicological profiles of new drug candidates by forming active and reactive conjugated metabolites. The opportunity to elucidate structure of conjugated metabolites has increased in drug metabolism studies at the early development stage. General methodologies for the structure elucidation of glucuronide conjugate(s) include liquid chromatography-tandem mass spectrometry (LC-MS/MS) and NMR spectroscopy. In many cases, LC-MS/MS alone cannot unequivocally identify the site(s) of conjugation in isomeric glucuronidations. In the present study, we established a new strategy for the structure elucidation of glucuronide conjugates using ion mobility spectrometry (IMS)-mass spectrometry. Linear correlation between calculated collision cross-sections (CCS) and actual drift times from IMS was found for each set of parent compound (raloxifene, losartan, telmisartan, and estradiol) and the corresponding MS/MS product ions. Thus, obtained regression lines accurately and selectively projected the actual drift times of authentic standards of glucuronide conjugate based on the theoretical CCS values. The established method was used for the accurate assignment of predominant formation of phenolic glucuronide conjugate (SCH 60663) in the isomeric (phenolic and benzylic) glucuronidations of ezetimibe in the incubated sample with cryopreserved human hepatocytes. This application demonstrates the potential to facilitate the structure identification of glucuronide conjugates at the early development stage of new drug candidates.
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Affiliation(s)
- Atsushi Shimizu
- Discovery Drug Metabolism & Pharmacokinetics, Tsukuba Research Center, Taiho Pharmaceutical Co., Ltd., 3 Okubo, Tsukuba, Ibaraki 300-2611, Japan.
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