1
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Kou M, Oh YH, Lee S, Kong X. Distinguishing gas phase lactose and lactulose complexed with sodiated L-arginine by IRMPD spectroscopy and DFT calculations. Phys Chem Chem Phys 2023; 25:25116-25121. [PMID: 37676638 DOI: 10.1039/d3cp03406b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/08/2023]
Abstract
We present the origin of the observed differentiation of lactose and lactulose achieved by complexation with sodiated L-arginine (ArgNa+). We find that the infrared multiphoton dissociation (IRMPD) bands in 3600-3650 and >3650 cm-1 regimes for gas phase lactose and lactulose, respectively, vanish when forming host-guest complexes with ArgNa+. We interpret these differences in the IRMPD spectra by scrutinizing the interactions between the functional groups (guanidium, -CO2-Na+) in ArgNa+ and -OHs in lactose/lactulose. Our calculated structures and infrared spectra of lactose/ArgNa+ and lactulose/ArgNa+ host-guest pairs indicate that the functional groups interact with the low- and high-frequency -OH stretch modes of lactose and lactulose, respectively, in the 3600-3720 cm-1 window.
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Affiliation(s)
- Min Kou
- State Key Laboratory of Elemento-Organic Chemistry, Frontiers Science Center for New Organic Matter, and Tianjin Key Laboratory of Biosensing and Molecular Recognition, College of Chemistry, Nankai University, Tianjin 300071, China.
| | - Young-Ho Oh
- Department of Applied Chemistry, Kyung Hee University, Gyeonggi 17104, Republic of Korea.
| | - Sungyul Lee
- Department of Applied Chemistry, Kyung Hee University, Gyeonggi 17104, Republic of Korea.
| | - Xianglei Kong
- State Key Laboratory of Elemento-Organic Chemistry, Frontiers Science Center for New Organic Matter, and Tianjin Key Laboratory of Biosensing and Molecular Recognition, College of Chemistry, Nankai University, Tianjin 300071, China.
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2
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Grabarics M, Lettow M, Kirschbaum C, Greis K, Manz C, Pagel K. Mass Spectrometry-Based Techniques to Elucidate the Sugar Code. Chem Rev 2022; 122:7840-7908. [PMID: 34491038 PMCID: PMC9052437 DOI: 10.1021/acs.chemrev.1c00380] [Citation(s) in RCA: 61] [Impact Index Per Article: 30.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Indexed: 12/22/2022]
Abstract
Cells encode information in the sequence of biopolymers, such as nucleic acids, proteins, and glycans. Although glycans are essential to all living organisms, surprisingly little is known about the "sugar code" and the biological roles of these molecules. The reason glycobiology lags behind its counterparts dealing with nucleic acids and proteins lies in the complexity of carbohydrate structures, which renders their analysis extremely challenging. Building blocks that may differ only in the configuration of a single stereocenter, combined with the vast possibilities to connect monosaccharide units, lead to an immense variety of isomers, which poses a formidable challenge to conventional mass spectrometry. In recent years, however, a combination of innovative ion activation methods, commercialization of ion mobility-mass spectrometry, progress in gas-phase ion spectroscopy, and advances in computational chemistry have led to a revolution in mass spectrometry-based glycan analysis. The present review focuses on the above techniques that expanded the traditional glycomics toolkit and provided spectacular insight into the structure of these fascinating biomolecules. To emphasize the specific challenges associated with them, major classes of mammalian glycans are discussed in separate sections. By doing so, we aim to put the spotlight on the most important element of glycobiology: the glycans themselves.
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Affiliation(s)
- Márkó Grabarics
- Institute
of Chemistry and Biochemistry, Freie Universität
Berlin, Arnimallee 22, 14195 Berlin, Germany
- Department
of Molecular Physics, Fritz Haber Institute
of the Max Planck Society, Faradayweg 4−6, 14195 Berlin, Germany
| | - Maike Lettow
- Institute
of Chemistry and Biochemistry, Freie Universität
Berlin, Arnimallee 22, 14195 Berlin, Germany
- Department
of Molecular Physics, Fritz Haber Institute
of the Max Planck Society, Faradayweg 4−6, 14195 Berlin, Germany
| | - Carla Kirschbaum
- Institute
of Chemistry and Biochemistry, Freie Universität
Berlin, Arnimallee 22, 14195 Berlin, Germany
- Department
of Molecular Physics, Fritz Haber Institute
of the Max Planck Society, Faradayweg 4−6, 14195 Berlin, Germany
| | - Kim Greis
- Institute
of Chemistry and Biochemistry, Freie Universität
Berlin, Arnimallee 22, 14195 Berlin, Germany
- Department
of Molecular Physics, Fritz Haber Institute
of the Max Planck Society, Faradayweg 4−6, 14195 Berlin, Germany
| | - Christian Manz
- Institute
of Chemistry and Biochemistry, Freie Universität
Berlin, Arnimallee 22, 14195 Berlin, Germany
- Department
of Molecular Physics, Fritz Haber Institute
of the Max Planck Society, Faradayweg 4−6, 14195 Berlin, Germany
| | - Kevin Pagel
- Institute
of Chemistry and Biochemistry, Freie Universität
Berlin, Arnimallee 22, 14195 Berlin, Germany
- Department
of Molecular Physics, Fritz Haber Institute
of the Max Planck Society, Faradayweg 4−6, 14195 Berlin, Germany
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3
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Greis K, Kirschbaum C, von Helden G, Pagel K. Gas-phase infrared spectroscopy of glycans and glycoconjugates. Curr Opin Struct Biol 2021; 72:194-202. [PMID: 34952241 DOI: 10.1016/j.sbi.2021.11.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 11/02/2021] [Accepted: 11/21/2021] [Indexed: 11/28/2022]
Abstract
Glycans are intrinsically complex biomolecules that pose particular analytical challenges. Standard workflows for glycan analysis are based on mass spectrometry, often coupled with separation techniques such as liquid chromatography and ion mobility spectrometry. However, this approach does not yield direct structural information and cannot always distinguish between isomers. This gap might be filled in the future by gas-phase infrared spectroscopy, which has emerged as a promising structure-sensitive technique for glycan fingerprinting. This review highlights recent applications of gas-phase infrared spectroscopy for the analysis of synthetic and biological glycans and how they can be integrated into mass spectrometry-based workflows.
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Affiliation(s)
- Kim Greis
- Institut für Chemie und Biochemie, Freie Universität Berlin, Arnimallee 22, 14195, Berlin, Germany; Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195, Berlin, Germany
| | - Carla Kirschbaum
- Institut für Chemie und Biochemie, Freie Universität Berlin, Arnimallee 22, 14195, Berlin, Germany; Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195, Berlin, Germany
| | - Gert von Helden
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195, Berlin, Germany
| | - Kevin Pagel
- Institut für Chemie und Biochemie, Freie Universität Berlin, Arnimallee 22, 14195, Berlin, Germany; Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195, Berlin, Germany.
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4
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Ho JS, Gharbi A, Schindler B, Yeni O, Brédy R, Legentil L, Ferrières V, Kiessling LL, Compagnon I. Distinguishing Galactoside Isomers with Mass Spectrometry and Gas-Phase Infrared Spectroscopy. J Am Chem Soc 2021; 143:10509-10513. [PMID: 34236183 PMCID: PMC9867933 DOI: 10.1021/jacs.0c11919] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Sequencing glycans is demanding due to their structural diversity. Compared to mammalian glycans, bacterial glycans pose a steeper challenge because they are constructed from a larger pool of monosaccharide building blocks, including pyranose and furanose isomers. Though mammalian glycans incorporate only the pyranose form of galactose (Galp), many pathogens, including Mycobacterium tuberculosis and Klebsiella pneumoniae, contain galactofuranose (Galf) residues in their cell envelope. Thus, glycan sequencing would benefit from methods to distinguish between pyranose and furanose isomers of different anomeric configurations. We used infrared multiple photon dissociation (IRMPD) spectroscopy with mass spectrometry (MS-IR) to differentiate between pyranose- and furanose-linked galactose residues. These targets pose a challenge for MS-IR because the saccharides lack basic groups, and galactofuranose residues are highly flexible. We postulated cationic groups that could complex through hydrogen bonding would offer a solution. Here, we present the first MS-IR analysis of hexose ammonium adducts. We compared their IR fingerprints with those of lithium adducts. We determined the diagnostic MS-IR signatures of the α- and β-anomers of galactose in furanose and pyranose forms. We also showed these signatures could be applied to disaccharides to assign galactose ring size. Our findings highlight the utility of MS-IR for analyzing the unique substructures that occur in bacterial glycans.
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Affiliation(s)
| | | | - Baptiste Schindler
- Univ. Lyon, Université Claude Bernard Lyon 1, F-69622 Villeurbanne, France
| | - Oznur Yeni
- Univ. Lyon, Université Claude Bernard Lyon 1, F-69622 Villeurbanne, France
| | - Richard Brédy
- Univ. Lyon, Université Claude Bernard Lyon 1, F-69622 Villeurbanne, France
| | - Laurent Legentil
- Univ. Rennes, Ecole Nationale Supérieure de Chimie de Rennes, F-35000 Rennes, France
| | - Vincent Ferrières
- Univ. Rennes, Ecole Nationale Supérieure de Chimie de Rennes, F-35000 Rennes, France
| | - Laura L. Kiessling
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Isabelle Compagnon
- Univ. Lyon, Université Claude Bernard Lyon 1, F-69622 Villeurbanne, France
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5
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Mucha E, Stuckmann A, Marianski M, Struwe WB, Meijer G, Pagel K. In-depth structural analysis of glycans in the gas phase. Chem Sci 2019; 10:1272-1284. [PMID: 30809341 PMCID: PMC6357860 DOI: 10.1039/c8sc05426f] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Accepted: 01/04/2019] [Indexed: 12/26/2022] Open
Abstract
Although there have been substantial improvements in glycan analysis over the past decade, the lack of both high-resolution and high-throughput methods hampers progress in glycomics. This perspective article highlights the current developments of liquid chromatography, mass spectrometry, ion-mobility spectrometry and cryogenic IR spectroscopy for glycan analysis and gives a critical insight to their individual strengths and limitations. Moreover, we discuss a novel concept in which ion mobility-mass spectrometry and cryogenic IR spectroscopy is combined in a single instrument such that datasets consisting of m/z, collision cross sections and IR fingerprints can be obtained. This multidimensional data will then be compared to a comprehensive reference library of intact glycans and their fragments to accurately identify unknown glycans on a high-throughput scale with minimal sample requirements. Due to the complementarity of the obtained information, this novel approach is highly diagnostic and also suitable for the identification of larger glycans; however, the workflow and instrumentation is straightforward enough to be implemented into a user-friendly setup.
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Affiliation(s)
- Eike Mucha
- Fritz Haber Institute of the Max Planck Society , Department of Molecular Physics , Faradayweg 4-6 , 14195 Berlin , Germany .
- Institute of Chemistry and Biochemistry , Freie Universität Berlin , Takustraße 3 , 14195 Berlin , Germany
| | - Alexandra Stuckmann
- Fritz Haber Institute of the Max Planck Society , Department of Molecular Physics , Faradayweg 4-6 , 14195 Berlin , Germany .
- Institute of Chemistry and Biochemistry , Freie Universität Berlin , Takustraße 3 , 14195 Berlin , Germany
| | - Mateusz Marianski
- Fritz Haber Institute of the Max Planck Society , Department of Molecular Physics , Faradayweg 4-6 , 14195 Berlin , Germany .
| | - Weston B Struwe
- Oxford Glycobiology Institute , Department of Biochemistry , University of Oxford , OX1 3QU Oxford , UK
| | - Gerard Meijer
- Fritz Haber Institute of the Max Planck Society , Department of Molecular Physics , Faradayweg 4-6 , 14195 Berlin , Germany .
| | - Kevin Pagel
- Fritz Haber Institute of the Max Planck Society , Department of Molecular Physics , Faradayweg 4-6 , 14195 Berlin , Germany .
- Institute of Chemistry and Biochemistry , Freie Universität Berlin , Takustraße 3 , 14195 Berlin , Germany
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6
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Lee SS, Lee JU, Oh JH, Park S, Hong Y, Min BK, Lee HHL, Kim HI, Kong X, Lee S, Oh HB. Chiral differentiation of d- and l-isoleucine using permethylated β-cyclodextrin: infrared multiple photon dissociation spectroscopy, ion-mobility mass spectrometry, and DFT calculations. Phys Chem Chem Phys 2018; 20:30428-30436. [PMID: 30499999 DOI: 10.1039/c8cp05617j] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Chiral differentiation of protonated isoleucine (Ile) using permethylated β-cyclodextrin (perCD) in the gas-phase was studied using infrared multiple photon dissociation (IRMPD) spectroscopy, ion-mobility, and density functional theory (DFT) calculations. The gaseous protonated non-covalent complexes of perCD and d-Ile or l-Ile produced by electrospray ionization were interrogated by laser pulses in the wavenumber region of 2650 to 3800 cm-1. The IRMPD spectra showed remarkably different IR spectral features for the d-Ile or l-Ile and perCD non-covalent complexes. However, drift-tube ion-mobility experiments provided only a small difference in their collision cross-sections, and thus a limited separation of the d- and l-Ile complexes. DFT calculations revealed that the chiral distinction of the d- and l-complexes by IRMPD spectroscopy resulted from local interactions of the protonated Ile with perCD. Furthermore, the theoretical results showed that the IR absorption spectra of higher energy conformers (by ∼13.7 kcal mol-1) matched best with the experimentally observed IRMPD spectra. These conformers are speculated to be formed from kinetic-trapping of the solution-phase conformers. This study demonstrated that IRMPD spectroscopy provides an excellent platform for differentiating the subtle chiral difference of a small amino acid in a cyclodextrin-complexation environment; however, drift-tube ion-mobility did not have sufficient resolution to distinguish the chiral difference.
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Affiliation(s)
- Sung-Sik Lee
- Department of Applied Chemistry, Kyung Hee University, Gyeonggi 17104, Republic of Korea.
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7
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Compagnon I, Schindler B, Renois-Predelus G, Daniel R. Lasers and ion mobility: new additions to the glycosaminoglycanomics toolkit. Curr Opin Struct Biol 2018; 50:171-180. [PMID: 30005299 DOI: 10.1016/j.sbi.2018.06.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Revised: 06/13/2018] [Accepted: 06/20/2018] [Indexed: 12/27/2022]
Abstract
Glycosaminoglycans are biopolymers present in mammalian cells or in the extracellular matrix. To address their structure, the nature of the hexuronic acids and the position of sulfate groups must be determined. Tandem mass spectrometry using collision induced dissociation or electron-based fragmentation techniques, is a well-established approach for the identification of glycans but suffers from the frequent lack of diagnostic fragments in the case of glycosaminoglycans. This review presents alternative fragmentation techniques, namely photofragmentation in the IR and the UV ranges. Alternative approaches based on the direct analysis of the molecular structure, including ion mobility spectrometry and ion spectroscopies are reviewed. The potential of future multidimensional workflows for glycosaminoglycanomics is discussed.
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Affiliation(s)
- Isabelle Compagnon
- Institut Universitaire de France IUF, 103 Boulevard St Michel, Paris F-75005, France; Univ Lyon, Université Claude Bernard Lyon 1, CNRS, Institut Lumière Matière, F-69622 Villeurbanne, France.
| | - Baptiste Schindler
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, Institut Lumière Matière, F-69622 Villeurbanne, France
| | - Gina Renois-Predelus
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, Institut Lumière Matière, F-69622 Villeurbanne, France
| | - Régis Daniel
- Université Paris-Saclay, CNRS, CEA, Univ Evry, Laboratoire Analyse et Modélisation pour la Biologie et l'Environnement, F-91025 Evry, France
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8
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Renois-Predelus G, Schindler B, Compagnon I. Analysis of Sulfate Patterns in Glycosaminoglycan Oligosaccharides by MS n Coupled to Infrared Ion Spectroscopy: the Case of GalNAc4S and GalNAc6S. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2018; 29:1242-1249. [PMID: 29700727 DOI: 10.1007/s13361-018-1955-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Revised: 03/07/2018] [Accepted: 03/20/2018] [Indexed: 06/08/2023]
Abstract
We report distinctive spectroscopic fingerprints of the monosaccharide standards GalNAc4S and GalNAc6S by coupling mass spectrometry and ion spectroscopy in the 3-μm range. The disaccharide standards CSA and CSC are used to demonstrate the applicability of a novel approach for the analysis of sulfate position in GalNAc-containing glycosaminoglycans. This approach was then used for the analysis of a sample containing CSA and CSC disaccharides. Finally, we discuss the generalization of the coupling of mass spectrometry with ion spectroscopy for the structural analysis of glycosaminoglycans on a tetrasaccharide from dermatan sulfate source. Graphical abstract ᅟ.
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Affiliation(s)
- G Renois-Predelus
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, Institut Lumière Matière (ILM), F-69622, Villeurbanne, France
| | - B Schindler
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, Institut Lumière Matière (ILM), F-69622, Villeurbanne, France
| | - I Compagnon
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, Institut Lumière Matière (ILM), F-69622, Villeurbanne, France.
- Institut Universitaire de France IUF, 103 Blvd St Michel, 75005, Paris, France.
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9
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Martens J, Berden G, Bentlage H, Coene KLM, Engelke UF, Wishart D, van Scherpenzeel M, Kluijtmans LAJ, Wevers RA, Oomens J. Unraveling the unknown areas of the human metabolome: the role of infrared ion spectroscopy. J Inherit Metab Dis 2018; 41:367-377. [PMID: 29556837 PMCID: PMC5959965 DOI: 10.1007/s10545-018-0161-8] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Revised: 02/12/2018] [Accepted: 02/15/2018] [Indexed: 11/30/2022]
Abstract
The identification of molecular biomarkers is critical for diagnosing and treating patients and for establishing a fundamental understanding of the pathophysiology and underlying biochemistry of inborn errors of metabolism. Currently, liquid chromatography/high-resolution mass spectrometry and nuclear magnetic resonance spectroscopy are the principle methods used for biomarker research and for structural elucidation of small molecules in patient body fluids. While both are powerful techniques, several limitations exist that often make the identification of unknown compounds challenging. Here, we describe how infrared ion spectroscopy has the potential to be a valuable orthogonal technique that provides highly-specific molecular structure information while maintaining ultra-high sensitivity. Here, we characterize and distinguish two well-known biomarkers of inborn errors of metabolism, glutaric acid for glutaric aciduria and ethylmalonic acid for short-chain acyl-CoA dehydrogenase deficiency, using infrared ion spectroscopy. In contrast to tandem mass spectra, in which ion fragments can hardly be predicted, we show that the prediction of an IR spectrum allows reference-free identification in the case that standard compounds are either commercially or synthetically unavailable. Finally, we illustrate how functional group information can be obtained from an IR spectrum for an unknown and how this is valuable information to, for example, narrow down a list of candidate structures resulting from a database query. Early diagnosis in inborn errors of metabolism is crucial for enabling treatment and depends on the identification of biomarkers specific for the disorder. Infrared ion spectroscopy has the potential to play a pivotal role in the identification of challenging biomarkers.
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Affiliation(s)
- Jonathan Martens
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7c, 6525ED, Nijmegen, The Netherlands.
| | - Giel Berden
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7c, 6525ED, Nijmegen, The Netherlands
| | - Herman Bentlage
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7c, 6525ED, Nijmegen, The Netherlands
| | - Karlien L M Coene
- Department of Laboratory Medicine, Translational Metabolic Laboratory, Radboud University Medical Center, Geert Groote Plein Zuid 10, 6525, GA, Nijmegen, The Netherlands
| | - Udo F Engelke
- Department of Laboratory Medicine, Translational Metabolic Laboratory, Radboud University Medical Center, Geert Groote Plein Zuid 10, 6525, GA, Nijmegen, The Netherlands
| | - David Wishart
- Departments of Computing Science and Biological Sciences, University of Alberta, Edmonton, AB, Canada
| | - Monique van Scherpenzeel
- Department of Laboratory Medicine, Translational Metabolic Laboratory, Radboud University Medical Center, Geert Groote Plein Zuid 10, 6525, GA, Nijmegen, The Netherlands
| | - Leo A J Kluijtmans
- Department of Laboratory Medicine, Translational Metabolic Laboratory, Radboud University Medical Center, Geert Groote Plein Zuid 10, 6525, GA, Nijmegen, The Netherlands
| | - Ron A Wevers
- Department of Laboratory Medicine, Translational Metabolic Laboratory, Radboud University Medical Center, Geert Groote Plein Zuid 10, 6525, GA, Nijmegen, The Netherlands.
| | - Jos Oomens
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7c, 6525ED, Nijmegen, The Netherlands.
- Van't Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands.
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10
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Schindler B, Barnes L, Renois G, Gray C, Chambert S, Fort S, Flitsch S, Loison C, Allouche AR, Compagnon I. Anomeric memory of the glycosidic bond upon fragmentation and its consequences for carbohydrate sequencing. Nat Commun 2017; 8:973. [PMID: 29042546 PMCID: PMC5645458 DOI: 10.1038/s41467-017-01179-y] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Accepted: 08/24/2017] [Indexed: 12/17/2022] Open
Abstract
Deciphering the carbohydrate alphabet is problematic due to its unique complexity among biomolecules. Strikingly, routine sequencing technologies-which are available for proteins and DNA and have revolutionised biology-do not exist for carbohydrates. This lack of structural tools is identified as a crucial bottleneck, limiting the full development of glycosciences and their considerable potential impact for the society. In this context, establishing generic carbohydrate sequencing methods is both a major scientific challenge and a strategic priority. Here we show that a hybrid analytical approach integrating molecular spectroscopy with mass spectrometry provides an adequate metric to resolve carbohydrate isomerisms, i.e the monosaccharide content, anomeric configuration, regiochemistry and stereochemistry of the glycosidic linkage. On the basis of the spectroscopic discrimination of MS fragments, we report the unexpected demonstration of the anomeric memory of the glycosidic bond upon fragmentation. This remarkable property is applied to de novo sequencing of underivatized oligosaccharides.Establishing generic carbohydrate sequencing methods is both a major scientific challenge and a strategic priority. Here the authors show a hybrid analytical approach integrating molecular spectroscopy and mass spectrometry to resolve carbohydrate isomerism, anomeric configuration, regiochemistry and stereochemistry.
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Affiliation(s)
- Baptiste Schindler
- Université de Lyon, F-69622, Lyon, France
- Université Lyon 1, Villeurbanne, France
- Institut Lumière Matière, UMR5306 Université Lyon 1-CNRS, Université de Lyon, 69622, Villeurbanne Cedex, France
| | - Loïc Barnes
- Université de Lyon, F-69622, Lyon, France
- Université Lyon 1, Villeurbanne, France
- Institut Lumière Matière, UMR5306 Université Lyon 1-CNRS, Université de Lyon, 69622, Villeurbanne Cedex, France
| | - Gina Renois
- Université de Lyon, F-69622, Lyon, France
- Université Lyon 1, Villeurbanne, France
- Institut Lumière Matière, UMR5306 Université Lyon 1-CNRS, Université de Lyon, 69622, Villeurbanne Cedex, France
| | - Christopher Gray
- School of Chemistry & Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Stéphane Chambert
- Université de Lyon, F-69622, Lyon, France
- Université Lyon 1, Villeurbanne, France
- Laboratoire de Chimie Organique et Bioorganique, INSA Lyon, CNRS, UMR5246, ICBMS, Bât. J. Verne, 20 Avenue A. Einstein, 69621, Villeurbanne Cedex, France
| | - Sébastien Fort
- Université de Grenoble Alpes, CERMAV, F-38000, Grenoble, France
- CNRS, CERMAV, F-38000, Grenoble, France
| | - Sabine Flitsch
- School of Chemistry & Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Claire Loison
- Université de Lyon, F-69622, Lyon, France
- Université Lyon 1, Villeurbanne, France
- Institut Lumière Matière, UMR5306 Université Lyon 1-CNRS, Université de Lyon, 69622, Villeurbanne Cedex, France
| | - Abdul-Rahman Allouche
- Université de Lyon, F-69622, Lyon, France
- Université Lyon 1, Villeurbanne, France
- Institut Lumière Matière, UMR5306 Université Lyon 1-CNRS, Université de Lyon, 69622, Villeurbanne Cedex, France
| | - Isabelle Compagnon
- Université de Lyon, F-69622, Lyon, France.
- Université Lyon 1, Villeurbanne, France.
- Institut Lumière Matière, UMR5306 Université Lyon 1-CNRS, Université de Lyon, 69622, Villeurbanne Cedex, France.
- Institut Universitaire de France IUF, 103 Blvd St Michel, 75005, Paris, France.
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11
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Tan Y, Zhao N, Liu J, Li P, Stedwell CN, Yu L, Polfer NC. Vibrational Signatures of Isomeric Lithiated N-acetyl-D-hexosamines by Gas-Phase Infrared Multiple-Photon Dissociation (IRMPD) Spectroscopy. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:539-550. [PMID: 28050874 DOI: 10.1007/s13361-016-1575-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Revised: 11/22/2016] [Accepted: 11/25/2016] [Indexed: 05/14/2023]
Abstract
Three lithiated N-acetyl-D-hexosamine (HexNAc) isomers, N-acetyl-D-glucosamine (GlcNAc), N-acetyl-D-galactosamine (GalNAc), and N-acetyl-D-mannosamine (ManNAc) are investigated as model monosaccharide derivatives by gas-phase infrared multiple-photon dissociation (IRMPD) spectroscopy. The hydrogen stretching region, which is attributed to OH and NH stretching modes, reveals some distinguishing spectral features of the lithium-adducted complexes that are useful in terms of differentiating these isomers. In order to understand the effect of lithium coordination on saccharide structure, and therefore anomericity, chair configuration, and hydrogen bonding networks, the conformational preferences of lithiated GlcNAc, GalNAc, and ManNAc are studied by comparing the experimental measurements with density functional theory (DFT) calculations. The experimental results of lithiated GlcNAc and GalNAc show a good match to the theoretical spectra of low-energy structures adopting a 4 C 1 chair conformation, consistent with this motif being the dominant conformation in condensed-phase monosaccharides. The epimerization effect upon going to lithiated ManNAc is significant, as in this case the 1 C 4 chair conformers give a more compelling match with the experimental results, consistent with their lower calculated energies. A contrasting computational study of these monosaccharides in their neutral form suggests that the lithium cation coordination with Lewis base oxygens can play a key role in favoring particular structural motifs (e.g., a 4 C 1 versus 1 C 4 ) and disrupting hydrogen bond networks, thus exhibiting specific IR spectral features between these closely related lithium-chelated complexes. Graphical Abstract ᅟ.
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Affiliation(s)
- Yanglan Tan
- Department of Chemistry, University of Florida, Gainesville, FL, 32611, USA
- Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Ning Zhao
- Department of Chemistry, University of Florida, Gainesville, FL, 32611, USA
| | - Jinfeng Liu
- State Key Laboratory of Precision Spectroscopy, Institute of Theoretical and Computational Science, East China Normal University, Shanghai, 200062, China
| | - Pengfei Li
- Department of Chemistry, Michigan State University, East Lansing, MI, 48824, USA
| | - Corey N Stedwell
- Department of Chemistry, University of Florida, Gainesville, FL, 32611, USA
| | - Long Yu
- Department of Chemistry, University of Florida, Gainesville, FL, 32611, USA
| | - Nicolas C Polfer
- Department of Chemistry, University of Florida, Gainesville, FL, 32611, USA.
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12
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Zeng Z, Bernstein ER. Anionic fructose-related conformational and positional isomers assigned through PES experiments and DFT calculations. Phys Chem Chem Phys 2017; 19:23325-23344. [DOI: 10.1039/c7cp03492j] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Fructose− exists as an open chain structure with substrate dependent specific conformational isomers. (Fructose-H2O)− evidences two types of positional isomers.
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Affiliation(s)
- Zhen Zeng
- Department of Chemistry
- NSF ERC for Extreme Ultraviolet Science and Technology
- Colorado State University
- Fort Collins
- USA
| | - Elliot R. Bernstein
- Department of Chemistry
- NSF ERC for Extreme Ultraviolet Science and Technology
- Colorado State University
- Fort Collins
- USA
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13
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Schindler B, Joshi J, Allouche AR, Simon D, Chambert S, Brites V, Gaigeot MP, Compagnon I. Distinguishing isobaric phosphated and sulfated carbohydrates by coupling of mass spectrometry with gas phase vibrational spectroscopy. Phys Chem Chem Phys 2015; 16:22131-8. [PMID: 25211353 DOI: 10.1039/c4cp02898h] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
An original application of the coupling of mass spectrometry with vibrational spectroscopy, used for the first time to discriminate isobaric bioactive saccharides with sulfate and phosphate functional modifications, is presented. Whereas their nominal masses and fragmentation patterns are undifferentiated by sole mass spectrometry, their distinctive OH stretching modes at 3595 cm(-1) and 3666 cm(-1), respectively, provide a reliable spectroscopic diagnostic for distinguishing their sulfate or phosphate functionalization. A detailed analysis of the 6-sulfated and 6-phosphated d-glucosamine conformations is presented, together with theoretical scaled harmonic spectra and anharmonic spectra (VPT2 and DFT-based molecular dynamics simulations). Strong anharmonic effects are observed in the case of the phosphated species, resulting in a dramatic enhancement of its phosphate diagnostic mode.
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14
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Pearson WL, Contreras C, Powell D, Berden G, Oomens J, Bendiak B, Eyler JR. Differentiation of Rubidiated Methyl-d-Glycoside Stereoisomers by Infrared Multiple-Photon Dissociation Spectroscopy in the O–H and C–H Stretching Regions. J Phys Chem B 2015; 119:12970-81. [DOI: 10.1021/acs.jpcb.5b06563] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Wright L. Pearson
- Department
of Chemistry, University of Florida, Gainesville, Florida 32611-7200, United States
| | - Cesar Contreras
- Department
of Chemistry, University of Florida, Gainesville, Florida 32611-7200, United States
| | - David Powell
- Department
of Chemistry, University of Florida, Gainesville, Florida 32611-7200, United States
| | - Giel Berden
- Radboud University, Institute for Molecules and
Materials, FELIX Laboratory, Toernooiveld 7c, 6525 ED Nijmegen, The Netherlands
| | - Jos Oomens
- Radboud University, Institute for Molecules and
Materials, FELIX Laboratory, Toernooiveld 7c, 6525 ED Nijmegen, The Netherlands
- University of Amsterdam, Science
Park 904, 1098XH Amsterdam, The Netherlands
| | - Brad Bendiak
- Department
of Cell and Developmental Biology and Program in Structural Biology
and Biochemistry, University of Colorado Health Sciences Center, Denver, Colorado 80045, United States
| | - John R. Eyler
- Department
of Chemistry, University of Florida, Gainesville, Florida 32611-7200, United States
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15
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Kleisath E, Marta RA, Martens S, Martens J, McMahon T. Structures and Energetics of Protonated Clusters of Methylamine with Phenylalanine Analogs, Characterized by Infrared Multiple Photon Dissociation Spectroscopy and Electronic Structure Calculations. J Phys Chem A 2015; 119:6689-702. [DOI: 10.1021/acs.jpca.5b02794] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Elizabeth Kleisath
- Department
of Chemistry, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Rick A. Marta
- Department
of Chemistry, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Sabrina Martens
- Department
of Chemistry, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Jon Martens
- Department
of Chemistry, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Terry McMahon
- Department
of Chemistry, University of Waterloo, Waterloo, ON N2L 3G1, Canada
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16
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Barnes L, Schindler B, Allouche AR, Simon D, Chambert S, Oomens J, Compagnon I. Anharmonic simulations of the vibrational spectrum of sulfated compounds: application to the glycosaminoglycan fragment glucosamine 6-sulfate. Phys Chem Chem Phys 2015; 17:25705-13. [DOI: 10.1039/c5cp02079d] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Anharmonic behavior of sulfated glucosamine resolved by hybrid GVPT2 approach.
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Affiliation(s)
- Loïc Barnes
- Université de Lyon
- Lyon
- France
- Université Lyon 1
- Villeurbanne
| | | | | | - Daniel Simon
- Université de Lyon
- Lyon
- France
- Université Lyon 1
- Villeurbanne
| | | | - Jos Oomens
- Radboud University
- Institute for Molecules and Materials
- FELIX Laboratory
- 6525ED Nijmegen
- The Netherlands
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17
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Patrick AL, Stedwell CN, Polfer NC. Differentiating sulfopeptide and phosphopeptide ions via resonant infrared photodissociation. Anal Chem 2014; 86:5547-52. [PMID: 24823797 DOI: 10.1021/ac500992f] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The post-translational modifications sulfation and phosphorylation pose special challenges to mass spectral analysis due to their isobaric nature and their lability in the gas phase, as both types of peptides dissociate through similar channels upon collisional activation. Here, we present resonant infrared photodissociation based on diagnostic sulfate and phosphate OH stretches, as a means to differentiate sulfated from phosphorylated peptides within the framework of a mass spectrometry platform. The approach is demonstrated for a number of tyrosine-containing peptides, ranging from dipeptides (YG, pYG, and sYG) over tripeptides (GYR, GpYR, and GsYR), to more biologically relevant enkephalin peptides (YGGFL, pYGGFL, and sYGGFL). In all cases, the diagnostic ranges for sulfate OH stretches are established as 3580-3600 cm(-1) and can thus be distinguished from other characteristic hydrogen stretches, such as carboxylic acid OH, alcohol OH, and phosphate OH stretches.
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Affiliation(s)
- Amanda L Patrick
- Department of Chemistry, University of Florida , P.O. Box 117200, Gainesville, Florida 32611, United States
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18
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Rijs AM, Oomens J. IR Spectroscopic Techniques to Study Isolated Biomolecules. Top Curr Chem (Cham) 2014; 364:1-42. [DOI: 10.1007/128_2014_621] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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19
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Abstract
Although carbohydrates represent one of the most important families of biomolecules, they remain under-studied in comparison to the other biomolecular families (peptides, nucleobases). Beyond their best-known function of energy source in living systems, they act as mediator of molecular recognition processes, carrying molecular information in the so-called "sugar code," just to name one of their countless functions. Owing to their high conformational flexibility, they encode extremely rich information conveyed via the non-covalent hydrogen bonds within the carbohydrate and with other biomolecular assemblies, such as peptide subunits of proteins. Over the last decade there has been tremendous progress in the study of the conformational preferences of neutral oligosaccharides, and of the interactions between carbohydrates and various molecular partners (water, aromatic models, and peptide models), using vibrational spectroscopy as a sensitive probe. In parallel, other spectroscopic techniques have recently become available to the study of carbohydrates in the gas phase (microwave spectroscopy, IRMPD on charged species).
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Affiliation(s)
- Emilio J Cocinero
- Departamento de Química Física, Facultad de Ciencia y Tecnología, Universidad del País Vasco (UPV - EHU), Apartado 644, 48940, Bilbao, Spain,
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20
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Stedwell CN, Galindo JF, Roitberg AE, Polfer NC. Structures of biomolecular ions in the gas phase probed by infrared light sources. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2013; 6:267-285. [PMID: 23560933 DOI: 10.1146/annurev-anchem-062012-092700] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Infrared (IR) spectroscopy of biomolecular ions combines mass spectrometry's high sensitivity and ability to analyze complex mixtures with the enhanced structural information available from vibrational spectroscopy. IR spectroscopy is in principle well placed to distinguish isomers and allow chemical classification of unknown molecules. This review gives an outline of current instrumentation, spectroscopic approaches, and potential bottlenecks. We discuss the most promising applications in bioanalytical mass spectrometry in view of recent experimental results, as well as future applications based on bioinformatics.
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Affiliation(s)
- Corey N Stedwell
- Department of Chemistry, University of Florida, Gainesville, Florida 32611-7200, USA.
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21
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22
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Burt MB, Decker SGA, Fridgen TD. Water binding energies of [Pb(amino acid-H)H2O]+ complexes determined by blackbody infrared radiative dissociation. Phys Chem Chem Phys 2012; 14:15118-26. [DOI: 10.1039/c2cp41440f] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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23
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Fentabil MA, Daneshfar R, Kitova EN, Klassen JS. Blackbody infrared radiative dissociation of protonated oligosaccharides. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2011; 22:2171-2178. [PMID: 21952784 DOI: 10.1007/s13361-011-0243-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2011] [Revised: 08/27/2011] [Accepted: 08/30/2011] [Indexed: 05/31/2023]
Abstract
The dissociation pathways, kinetics, and energetics of protonated oligosaccharides in the gas phase were investigated using blackbody infrared radiative dissociation (BIRD). Time-resolved BIRD measurements were performed on singly protonated ions of cellohexaose (Cel(6)), which is composed of β-(1→4)-linked glucopyranose rings, and five malto-oligosaccharides (Mal(x), where x=4-8), which are composed of α-(1→4)-linked glucopyranose units. At the temperatures investigated (85-160 °C), the oligosaccharides dissociate at the glycosidic linkages or by the loss of a water molecule to produce B- or Y-type ions. The Y ions dissociate to smaller Y or B ions, while the B ions yield exclusively smaller B ions. The sequential loss of water molecules from the smallest B ions (B(1) and B(2)) also occurs. Rate constants for dissociation of the protonated oligosaccharides and the corresponding Arrhenius activation parameters (E(a) and A) were determined. The E(a) and A-factors measured for protonated Mal(x) (x>4) are indistinguishable within error (~19 kcal mol(-1), 10(10) s(-1)), which is consistent with the ions being in the rapid energy exchange limit. In contrast, the Arrhenius parameters for protonated Cel(6) (24 kcal mol(-1), 10(12) s(-1)) are significantly larger. These results indicate that both the energy and entropy changes associated with the glycosidic bond cleavage are sensitive to the anomeric configuration. Based on the results of this study, it is proposed that formation of B and Y ions occurs through a common dissociation mechanism, with the position of the proton establishing whether a B or Y ion is formed upon glycosidic bond cleavage.
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Affiliation(s)
- Messele A Fentabil
- Alberta Innovates Centre for Carbohydrate Science and Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada T6G 2G2
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24
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Brown DJ, Stefan SE, Berden G, Steill JD, Oomens J, Eyler JR, Bendiak B. Direct evidence for the ring opening of monosaccharide anions in the gas phase: photodissociation of aldohexoses and aldohexoses derived from disaccharides using variable-wavelength infrared irradiation in the carbonyl stretch region. Carbohydr Res 2011; 346:2469-81. [DOI: 10.1016/j.carres.2011.06.018] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2011] [Revised: 06/14/2011] [Accepted: 06/15/2011] [Indexed: 12/30/2022]
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25
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Burt MB, Decker SGA, Atkins CG, Rowsell M, Peremans A, Fridgen TD. Structures of bare and hydrated [Pb(aminoacid-H)]+ complexes using infrared multiple photon dissociation spectroscopy. J Phys Chem B 2011; 115:11506-18. [PMID: 21875029 DOI: 10.1021/jp2068655] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Infrared multiple-photon dissociation (IRMPD) spectroscopy was used to determine the gas-phase structures of deprotonated Pb(2+)/amino acid (Aa) complexes with and without a solvent molecule present. Five amino acid complexes with side chains containing only carbon and hydrogen (Ala, Val, Leu, Ile, Pro) and one with a basic side chain (Lys) were compared. These experiments demonstrated that all [Pb(Aa-H)](+) complexes have Pb(2+) covalently bound between the amine nitrogen and carbonyl oxygen. The nonhydrated complexes containing Ala, Val, Leu, Ile, and Pro are amine-deprotonated, whereas the one containing Lys is deprotonated at its carboxylic acid. The difference is attributed to the polar and basic side chain of lysine, which helps stabilize Pb(2+). IRMPD spectroscopy was also performed on the monohydrated analogues of the [Pb(Aa-H)](+) complexes. The [Pb(Aa-H)H(2)O](+) complexes, where Aa = Ala, Val, Leu, and Ile, exhibited two N-H stretches as well as a carboxylic acid O-H and a PbO-H stretch. Hence, their structures are monohydrated versions of the amine-deprotonated [Pb(Aa-H)](+) complexes where a proton transfer has occurred from the lead-bound water to the deprotonated amine. The IRMPD spectrum and calculations suggest that [Pb(Pro-H)H(2)O](+) has a hydrated carboxylate salt structure. The structure of [Pb(Lys-H)H(2)O](+) was also carboxyl-deprotonated, but Pb(2+) is bound to the carbonyl oxygen and the amine nitrogen, with one of the protons belonging to the water transferred to the basic side chain. This results in an intramolecular hydrogen bond that does not absorb in the region of the spectrum probed in these experiments. The IRMPD spectra and structural characterizations were confirmed and aided by infrared spectra calculated at the B3LYP/6-31+G(d,p) level of theory and 298 K enthalpies and Gibbs energies using the MP2(full)/6-311++G(2d,2p) method on the B3LYP geometries.
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Affiliation(s)
- Michael B Burt
- Department of Chemistry, Memorial University of Newfoundland, St. John's, Newfoundland and Labrador, Canada, A1B 3X7
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26
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Wang D, Gulyuz K, Stedwell CN, Polfer NC. Diagnostic NH and OH vibrations for oxazolone and diketopiperazine structures: b2 from protonated triglycine. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2011; 22:1197-1203. [PMID: 21953102 DOI: 10.1007/s13361-011-0147-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2011] [Revised: 04/03/2011] [Accepted: 04/04/2011] [Indexed: 05/31/2023]
Abstract
We present infrared multiple photon dissociation (IRMPD) spectra in the hydrogen stretching region of the simplest b fragment, b(2) from protonated triglycine, contrasted to that of protonated cyclo(Gly-Gly). Both spectra confirm the presence of intense, diagnostic vibrations linked to the site of proton attachment. Protonated cyclo(Gly-Gly) serves as a reference spectrum for the diketopiperazine structure, showing a diagnostic O-H(+) stretch of the protonated carbonyl group at 3585 cm(-1). Conversely, b(2) from protonated triglycine exhibits a strong band at 3345 cm(-1), associated with the N-H stretching mode of the protonated oxazolone ring structure. Other weaker N-H stretches can also be discerned, such as the amino NH(2) and amide NH bands. These results demonstrate the usefulness of the hydrogen stretching region, and hence benchtop optical parametric oscillator/amplifier (OPO/A) set-ups, in making structural assignments of product ions in collision-induced dissociation (CID) of peptides.
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Affiliation(s)
- Da Wang
- Department of Chemistry, University of Florida, Gainesville, FL 32611-7200, USA
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27
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Gulyuz K, Stedwell CN, Wang D, Polfer NC. Hybrid quadrupole mass filter∕quadrupole ion trap∕time-of-flight-mass spectrometer for infrared multiple photon dissociation spectroscopy of mass-selected ions. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2011; 82:054101. [PMID: 21639521 DOI: 10.1063/1.3585982] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
We present a laboratory-constructed mass spectrometer optimized for recording infrared multiple photon dissociation (IRMPD) spectra of mass-selected ions using a benchtop tunable infrared optical parametric oscillator∕amplifier (OPO∕A). The instrument is equipped with two ionization sources, an electrospray ionization source, as well as an electron ionization source for troubleshooting. This hybrid mass spectrometer is composed of a quadrupole mass filter for mass selection, a reduced pressure (∼10(-5) Torr) quadrupole ion trap (QIT) for OPO irradiation, and a reflectron time-of-flight drift tube for detecting the remaining precursor and photofragment ions. A helium gas pulse is introduced into the QIT to temporarily increase the pressure and hence enhance the trapping efficiency of axially injected ions. After a brief pump-down delay, the compact ion cloud is subjected to the focused output from the continuous wave OPO. In a recent study, we implemented this setup in the study of protonated tryptophan, TrpH(+), as well as collision-induced dissociation products of this protonated amino acid [W. K. Mino, Jr., K. Gulyuz, D. Wang, C. N. Stedwell, and N. C. Polfer, J. Phys. Chem. Lett. 2, 299 (2011)]. Here, we give a more detailed account on the figures of merit of such IRMPD experiments. The appreciable photodissociation yields in these measurements demonstrate that IRMPD spectroscopy of covalently bound ions can be routinely carried out using benchtop OPO setups.
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Affiliation(s)
- Kerim Gulyuz
- Department of Chemistry, University of Florida, P.O. Box 117200, Gainesville, Florida 32611, USA
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28
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Polfer NC. Infrared multiple photon dissociation spectroscopy of trapped ions. Chem Soc Rev 2011; 40:2211-21. [DOI: 10.1039/c0cs00171f] [Citation(s) in RCA: 229] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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29
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Assignment of the stereochemistry and anomeric configuration of structurally informative product ions derived from disaccharides: infrared photodissociation of glycosyl-glycolaldehydes in the negative ion mode. Carbohydr Res 2010; 345:2390-400. [DOI: 10.1016/j.carres.2010.09.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2010] [Revised: 08/29/2010] [Accepted: 09/01/2010] [Indexed: 12/30/2022]
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