1
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Metz TO, Chang CH, Gautam V, Anjum A, Tian S, Wang F, Colby SM, Nunez JR, Blumer MR, Edison AS, Fiehn O, Jones DP, Li S, Morgan ET, Patti GJ, Ross DH, Shapiro MR, Williams AJ, Wishart DS. Introducing 'identification probability' for automated and transferable assessment of metabolite identification confidence in metabolomics and related studies. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.30.605945. [PMID: 39131324 PMCID: PMC11312557 DOI: 10.1101/2024.07.30.605945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/13/2024]
Abstract
Methods for assessing compound identification confidence in metabolomics and related studies have been debated and actively researched for the past two decades. The earliest effort in 2007 focused primarily on mass spectrometry and nuclear magnetic resonance spectroscopy and resulted in four recommended levels of metabolite identification confidence - the Metabolite Standards Initiative (MSI) Levels. In 2014, the original MSI Levels were expanded to five levels (including two sublevels) to facilitate communication of compound identification confidence in high resolution mass spectrometry studies. Further refinement in identification levels have occurred, for example to accommodate use of ion mobility spectrometry in metabolomics workflows, and alternate approaches to communicate compound identification confidence also have been developed based on identification points schema. However, neither qualitative levels of identification confidence nor quantitative scoring systems address the degree of ambiguity in compound identifications in context of the chemical space being considered, are easily automated, or are transferable between analytical platforms. In this perspective, we propose that the metabolomics and related communities consider identification probability as an approach for automated and transferable assessment of compound identification and ambiguity in metabolomics and related studies. Identification probability is defined simply as 1/N, where N is the number of compounds in a reference library or chemical space that match to an experimentally measured molecule within user-defined measurement precision(s), for example mass measurement or retention time accuracy, etc. We demonstrate the utility of identification probability in an in silico analysis of multi-property reference libraries constructed from the Human Metabolome Database and computational property predictions, provide guidance to the community in transparent implementation of the concept, and invite the community to further evaluate this concept in parallel with their current preferred methods for assessing metabolite identification confidence.
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Affiliation(s)
- Thomas O. Metz
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA USA
| | - Christine H. Chang
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA USA
| | - Vasuk Gautam
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
| | - Afia Anjum
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
| | - Siyang Tian
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
| | - Fei Wang
- Department of Computing Science, University of Alberta, Edmonton, AB, Canada
- Alberta Machine Intelligence Institute, Edmonton, AB, Canada
| | - Sean M. Colby
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA USA
| | - Jamie R. Nunez
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA USA
| | - Madison R. Blumer
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA USA
| | - Arthur S. Edison
- Department of Biochemistry & Molecular Biology, Complex Carbohydrate Research Center and Institute of Bioinformatics, University of Georgia, Athens, GA, USA
| | - Oliver Fiehn
- West Coast Metabolomics Center, University of California Davis, Davis, CA, USA
| | - Dean P. Jones
- Clinical Biomarkers Laboratory, Department of Medicine, Emory University, Atlanta, Georgia, USA
| | - Shuzhao Li
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Edward T. Morgan
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Gary J. Patti
- Center for Mass Spectrometry and Metabolic Tracing, Department of Chemistry, Department of Medicine, Washington University, Saint Louis, Missouri, USA
| | - Dylan H. Ross
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA USA
| | - Madelyn R. Shapiro
- Artificial Intelligence & Data Analytics Division, Pacific Northwest National Laboratory, Richland, WA USA
| | - Antony J. Williams
- U.S. Environmental Protection Agency, Office of Research & Development, Center for Computational Toxicology & Exposure (CCTE), Research Triangle Park, NC USA
| | - David S. Wishart
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
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2
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Habibi SC, Nagy G. General Method to Obtain Collision Cross-Section Values in Multipass High-Resolution Cyclic Ion Mobility Separations. Anal Chem 2023; 95:8028-8035. [PMID: 37163363 DOI: 10.1021/acs.analchem.3c00919] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
In recent years, ion mobility spectrometry-mass spectrometry (IMS-MS) has advanced the field of omics-based research, especially with the development of high-resolution platforms; however, these separations have generally been qualitative in nature. The rotationally averaged ion neutral collision cross section (CCS) is one of the only quantitative metrics available for aiding in characterizing biomolecules in IMS-MS. However, determining the CCS of an ion for multipass IMS systems, such as in cyclic ion mobility-mass spectrometry (cIMS-MS) and structures for lossless ion manipulations, has been challenging due to the lack of methods available for calculating CCS when more than a single pass is required for separation as well as the laborious nature of requiring calibrants and unknown compounds to be subjected to identical number of passes, which may not be possible in certain instances because of peak splitting, high levels of diffusion, etc. Herein, we present a general method that uses average ion velocities for calculating CCS values in cIMS-MS-based separations. Initially, we developed calibration curves using common CCS calibrants [i.e., tetra-alkylammonium salts, polyalanine, and hexakis(fluoroalkoxy)phosphazines] at different traveling wave (TW) conditions and the calculated cIMS CCS values were within ∼1% error or less compared to previously established drift tube IMS CCS measurements. Since it has been established that glycans can split into their α/β anomers, we utilized this method for two glycan species, 2α-mannobiose and melibiose. Both glycans were analyzed at the same TW conditions as the calibrants, and we observed anomer splitting at pathlengths of 20 m for 2α-mannobiose and 40 m for melibiose and thus assigned two unique CCS values for each glycan, which is the first time this has ever been done. We have demonstrated that the use of average ion velocities is a robust approach for obtaining CCS values with good agreement to CCS measurements from the previous literature and anticipate that this methodology can be applied to any IMS-MS platform that utilizes multipass separations. Our future work aims to incorporate this methodology for the development of a high-resolution CCS database to aid in the characterization of human milk oligosaccharides.
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Affiliation(s)
- Sanaz C Habibi
- Department of Chemistry, University of Utah, 315 South 1400 East, Room 2020, Salt Lake City, Utah 84112, United States
| | - Gabe Nagy
- Department of Chemistry, University of Utah, 315 South 1400 East, Room 2020, Salt Lake City, Utah 84112, United States
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3
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Liu Y, Huang Y, Zhu R, Farag MA, Capanoglu E, Zhao C. Structural elucidation approaches in carbohydrates: A comprehensive review on techniques and future trends. Food Chem 2023; 400:134118. [DOI: 10.1016/j.foodchem.2022.134118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 09/01/2022] [Indexed: 10/14/2022]
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4
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Habibi SC, Nagy G. Assessing the Use of Host-Guest Chemistry in Conjunction with Cyclic Ion Mobility Separations for the Linkage-Specific Characterization of Human Milk Oligosaccharides. INTERNATIONAL JOURNAL OF MASS SPECTROMETRY 2023; 483:116977. [PMID: 36440090 PMCID: PMC9683398 DOI: 10.1016/j.ijms.2022.116977] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Human milk oligosaccharides (HMOs) are a class of glycans that are highly abundant in human milk and contribute to the healthy growth of an infant's immune system. While new advancements in analytical methodologies have been made in glycomics, the high degree of isomeric heterogeneity and lack of authentic standards have made the high-resolution separation and accurate characterization of linkage positioning of all HMO species very challenging. Herein, we present an evaluation of the use of host-guest chemistry in conjunction with cyclic ion mobility spectrometry-mass spectrometry (cIMS-MS)-based separations for the identification of linkage positioning in three pairs of di-, tetra-, and hexasaccharide HMO isomers that only differ in the positioning of one glycosidic linkage (β1,3 versus β1,4). Suitable hosts, such as α/β cyclodextrins, cucurbit[n]urils (n = 5, 7), crown ethers, cyclic peptides, and an ionophore, were used to assess host-guest inclusion complex formation as well as linkage-specific cIMS-MS trends. Our results indicated a linkage-specific trend for the [M + 2α + 2H]2+ cyclodextrin-based host-guest inclusion complexes where the β1,3 linkage-containing isomers were always higher mobility than the β1,4 linkage-containing ones as well one for the [M + α + β + 2H]2+ complexes where the β1,4 linkage-containing isomers were always higher mobility than the β1,3 linkage-containing ones. We also observed diagnostic mobility fingerprints for the cucurbituril-based complexes. We anticipate that linkage-specific and mobility fingerprint trends can potentially aid in identifying linkage positioning for other HMO isomers as well as in complex human milk samples.
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Affiliation(s)
- Sanaz C Habibi
- Department of Chemistry, University of Utah, 315 South 1400 East, Room 2020, Salt Lake City, Utah 84112, United States
| | - Gabe Nagy
- Department of Chemistry, University of Utah, 315 South 1400 East, Room 2020, Salt Lake City, Utah 84112, United States
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5
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Pellegrinelli R, Yue L, Carrascosa E, Ben Faleh A, Warnke S, Bansal P, Rizzo TR. A New Strategy Coupling Ion-Mobility-Selective CID and Cryogenic IR Spectroscopy to Identify Glycan Anomers. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:859-864. [PMID: 35437995 PMCID: PMC9074103 DOI: 10.1021/jasms.2c00043] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 04/07/2022] [Accepted: 04/07/2022] [Indexed: 05/26/2023]
Abstract
Determining the primary structure of glycans remains challenging due to their isomeric complexity. While high-resolution ion mobility spectrometry (IMS) has recently allowed distinguishing between many glycan isomers, the arrival-time distributions (ATDs) frequently exhibit multiple peaks, which can arise from positional isomers, reducing-end anomers, or different conformations. Here, we present the combination of ultrahigh-resolution ion mobility, collision-induced dissociation (CID), and cryogenic infrared (IR) spectroscopy as a systematic method to identify reducing-end anomers of glycans. Previous studies have suggested that high-resolution ion mobility of sodiated glycans is able to separate the two reducing-end anomers. In this case, Y-fragments generated from mobility-separated precursor species should also contain a single anomer at their reducing end. We confirm that this is the case by comparing the IR spectra of selected Y-fragments to those of anomerically pure mono- and disaccharides, allowing the assignment of the mobility-separated precursor and its IR spectrum to a single reducing-end anomer. The anomerically pure precursor glycans can henceforth be rapidly identified on the basis of their IR spectrum alone, allowing them to be distinguished from other isomeric forms.
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Affiliation(s)
- Robert
P. Pellegrinelli
- Laboratoire de Chimie Physique
Moléculaire, EPFL SB ISIC LCPM, École
Polytechnique Fédérale de Lausanne, Station 6, CH-1015 Lausanne, Switzerland
| | - Lei Yue
- Laboratoire de Chimie Physique
Moléculaire, EPFL SB ISIC LCPM, École
Polytechnique Fédérale de Lausanne, Station 6, CH-1015 Lausanne, Switzerland
| | - Eduardo Carrascosa
- Laboratoire de Chimie Physique
Moléculaire, EPFL SB ISIC LCPM, École
Polytechnique Fédérale de Lausanne, Station 6, CH-1015 Lausanne, Switzerland
| | - Ahmed Ben Faleh
- Laboratoire de Chimie Physique
Moléculaire, EPFL SB ISIC LCPM, École
Polytechnique Fédérale de Lausanne, Station 6, CH-1015 Lausanne, Switzerland
| | - Stephan Warnke
- Laboratoire de Chimie Physique
Moléculaire, EPFL SB ISIC LCPM, École
Polytechnique Fédérale de Lausanne, Station 6, CH-1015 Lausanne, Switzerland
| | - Priyanka Bansal
- Laboratoire de Chimie Physique
Moléculaire, EPFL SB ISIC LCPM, École
Polytechnique Fédérale de Lausanne, Station 6, CH-1015 Lausanne, Switzerland
| | - Thomas R. Rizzo
- Laboratoire de Chimie Physique
Moléculaire, EPFL SB ISIC LCPM, École
Polytechnique Fédérale de Lausanne, Station 6, CH-1015 Lausanne, Switzerland
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6
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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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7
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Bansal P, Ben Faleh A, Warnke S, Rizzo TR. Identification of N-glycan positional isomers by combining IMS and vibrational fingerprinting of structurally determinant CID fragments. Analyst 2022; 147:704-711. [PMID: 35079754 PMCID: PMC8842669 DOI: 10.1039/d1an01861b] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
While glycans are present on the surface of cells in all living organisms and play key roles in most biological processes, their isomeric complexity makes their structural characterization challenging. Of particular importance are positional isomers, for which analytical standards are difficult to obtain. We combine ultrahigh-resolution ion-mobility spectrometry with collision-induced dissociation and cryogenic infrared spectroscopy to determine the structure of N-glycan positional isomers. This approach is based on first separating the parent molecules by SLIM-based IMS, producing diagnostic fragments specific to each positional isomer, separating the fragments by IMS, and identifying them by comparing their IR fingerprints to a previously recorded spectral database. We demonstrate this strategy using a bottom-up scheme to identify the positional isomers of the N-linked glycan G0-N, in which a terminal N-acetylglucosamine (GlcNAc) is attached to either the α-3 or α-6 branch of the common N-glycan pentasaccharide core. We then use IR fingerprints of these newly identified isomers to identify the positional isomers of G1 and G1F, which are biantennary complex-type N-glycans with a terminal galactose attached to either the α-3 or α-6 branch, and in the case of G1F a fucose attached to the reducing-end GlcNAc. Starting with just a few analytical standards, this fragment-based spectroscopy method allows us to develop a database which we can use to identify positional isomers. The generalization of this approach would greatly facilitate glycan analysis. We combine high-resolution IMS-IMS with cryogenic vibrational spectroscopy for the indentification of N-glycan positional isomers.![]()
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Affiliation(s)
- Priyanka Bansal
- Laboratoire de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne, EPFL SB ISIC LCPM, Station 6, CH-1015, Lausanne, Switzerland.
| | - Ahmed Ben Faleh
- Laboratoire de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne, EPFL SB ISIC LCPM, Station 6, CH-1015, Lausanne, Switzerland.
| | - Stephan Warnke
- Laboratoire de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne, EPFL SB ISIC LCPM, Station 6, CH-1015, Lausanne, Switzerland.
| | - Thomas R Rizzo
- Laboratoire de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne, EPFL SB ISIC LCPM, Station 6, CH-1015, Lausanne, Switzerland.
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8
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Hong T, Yin JY, Nie SP, Xie MY. Applications of infrared spectroscopy in polysaccharide structural analysis: Progress, challenge and perspective. Food Chem X 2021; 12:100168. [PMID: 34877528 PMCID: PMC8633561 DOI: 10.1016/j.fochx.2021.100168] [Citation(s) in RCA: 114] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 11/16/2021] [Accepted: 11/19/2021] [Indexed: 12/31/2022] Open
Abstract
Functional properties of polysaccharides depend on their structural features. IR spectroscopy is widely used in polysaccharide structural analysis. Classical applications of IR spectroscopy in polysaccharide are reviewed. IR integrating techniques can considerably expand its application scope.
Polysaccharides are important biomacromolecules with numerous beneficial functions and a wide range of industrial applications. Functions and properties of polysaccharides are closely related to their structural features. Infrared (IR) spectroscopy is a well-established technique which has been widely applied in polysaccharide structural analysis. In this paper, the principle of IR and interpretation of polysaccharide IR spectrum are briefly introduced. Classical applications of IR spectroscopy in polysaccharide structural elucidation are reviewed from qualitative and quantitative aspects. Some advanced IR techniques including integrating with mass spectrometry (MS), microscopy and computational chemistry are introduced and their applications are emphasized. These emerging techniques can considerably expand application scope of IR, thus exert a more important effect on carbohydrate characterization. Overall, this review seeks to provide a comprehensive insight to applications of IR spectroscopy in polysaccharide structural analysis and highlights the importance of advanced IR-integrating techniques.
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Affiliation(s)
- Tao Hong
- State Key Laboratory of Food Science and Technology, China-Canada Joint Laboratory of Food Science and Technology (Nanchang), Nanchang University, 235 Nanjing East Road, Nanchang, Jiangxi 330047, People's Republic of China
| | - Jun-Yi Yin
- State Key Laboratory of Food Science and Technology, China-Canada Joint Laboratory of Food Science and Technology (Nanchang), Nanchang University, 235 Nanjing East Road, Nanchang, Jiangxi 330047, People's Republic of China
| | - Shao-Ping Nie
- State Key Laboratory of Food Science and Technology, China-Canada Joint Laboratory of Food Science and Technology (Nanchang), Nanchang University, 235 Nanjing East Road, Nanchang, Jiangxi 330047, People's Republic of China
| | - Ming-Yong Xie
- State Key Laboratory of Food Science and Technology, China-Canada Joint Laboratory of Food Science and Technology (Nanchang), Nanchang University, 235 Nanjing East Road, Nanchang, Jiangxi 330047, People's Republic of China
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9
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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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10
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Abikhodr AH, Yatsyna V, Ben Faleh A, Warnke S, Rizzo TR. Identifying Mixtures of Isomeric Human Milk Oligosaccharides by the Decomposition of IR Spectral Fingerprints. Anal Chem 2021; 93:14730-14736. [PMID: 34704745 PMCID: PMC8581968 DOI: 10.1021/acs.analchem.1c03190] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 10/19/2021] [Indexed: 12/17/2022]
Abstract
The analysis of glycans presents a significant challenge that arises from their isomeric heterogeneity. While high-resolution ion mobility spectrometry (IMS) has shown the ability to resolve subtly different glycan isomers, their unambiguous assignment remains difficult. Here, we demonstrate an infrared (IR) spectroscopic approach for identifying isomers in a glycan mixture. To display the feasibility of this approach, we have constructed a small database of cryogenic spectra of five lacto-N-fucopentaose (LNFP) and six disaccharide isomers and demonstrated that in the cases where they cannot be separated by IMS, we can use a cryogenic IR spectrum to identify the isomeric components of a mixture.
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Affiliation(s)
- Ali H. Abikhodr
- Laboratoire
de Chimie Physique Moléculaire, École Polytechnique
Fédérale de Lausanne, EPFL SB ISIC LCPM, Station 6, CH-1015 Lausanne, Switzerland
| | - Vasyl Yatsyna
- Laboratoire
de Chimie Physique Moléculaire, École Polytechnique
Fédérale de Lausanne, EPFL SB ISIC LCPM, Station 6, CH-1015 Lausanne, Switzerland
- Department
of Physics, University of Gothenburg, 412 96 Gothenburg, Sweden
| | - Ahmed Ben Faleh
- Laboratoire
de Chimie Physique Moléculaire, École Polytechnique
Fédérale de Lausanne, EPFL SB ISIC LCPM, Station 6, CH-1015 Lausanne, Switzerland
| | - Stephan Warnke
- Laboratoire
de Chimie Physique Moléculaire, École Polytechnique
Fédérale de Lausanne, EPFL SB ISIC LCPM, Station 6, CH-1015 Lausanne, Switzerland
| | - Thomas R. Rizzo
- Laboratoire
de Chimie Physique Moléculaire, École Polytechnique
Fédérale de Lausanne, EPFL SB ISIC LCPM, Station 6, CH-1015 Lausanne, Switzerland
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11
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Peterson TL, Nagy G. Toward Sequencing the Human Milk Glycome: High-Resolution Cyclic Ion Mobility Separations of Core Human Milk Oligosaccharide Building Blocks. Anal Chem 2021; 93:9397-9407. [PMID: 34185494 DOI: 10.1021/acs.analchem.1c00942] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Human milk oligosaccharides (HMOs) are an unconjugated class of glycans that have been implicated for their role in promoting the healthy development of the brain-gut axes of infants. Production of HMOs is ever-changing and specifically tailored for each infant in response to various biological factors (e.g., cognitive development, diseases, or allergies). While every HMO consists of up to only five monosaccharides, their structures can be composed of many possible glycosidic linkage positions and corresponding α/β anomericities, linear or branched chains, and potential fucosylation/sialylation modifications, thus leading to a tremendous degree of isomeric heterogeneity. With limited availability of authentic standards for every putative HMO structure (estimated to be >200 total), new analytical methods are needed for their accurate characterization. Complete sequencing of the human milk glycome would enable a better understanding of their infant-specific biological roles and potentially lead to their widespread incorporation into infant formula. Herein, we explore the use of our high-resolution cyclic ion mobility spectrometry-mass spectrometry (cIMS-MS)-based platform for the separation of core disaccharide and trisaccharide isomer building blocks as a first step toward the sequencing of larger HMOs. By utilizing the flexible capabilities of the cIMS array, separation pathlengths were extended up to 40 m, thus enabling the resolution of all seven sets of sialylated, fucosylated galactosyllactose and lactosamine HMO building block isomers. Additionally, we assessed the utility of pre-/post-cIMS tandem mass spectrometry (MS/MS) and tandem cIMS (cIMS/cIMS) for the characterization of HMOs based on their diagnostic fragmentation patterns and mobility fingerprints. We anticipate that our presented cIMS-MS-based methodology will enable the better characterization of larger, unknown HMOs when incorporated into an overall workflow that also includes online liquid chromatography and enzymatic hydrolyses.
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Affiliation(s)
- Tyler L Peterson
- Department of Chemistry, University of Utah, 315 South 1400 East, Room 2020, Salt Lake City, Utah 84112, United States
| | - Gabe Nagy
- Department of Chemistry, University of Utah, 315 South 1400 East, Room 2020, Salt Lake City, Utah 84112, United States
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12
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Rabus JM, Pellegrinelli RP, Khodr AHA, Bythell BJ, Rizzo TR, Carrascosa E. Unravelling the structures of sodiated β-cyclodextrin and its fragments. Phys Chem Chem Phys 2021; 23:13714-13723. [PMID: 34128027 PMCID: PMC8220536 DOI: 10.1039/d1cp01058a] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 06/05/2021] [Indexed: 12/29/2022]
Abstract
We present cryogenic infrared spectra of sodiated β-cyclodextrin [β-CD + Na]+, a common cyclic oligosaccharide, and its main dissociation products upon collision-induced dissociation (CID). We characterize the parent ions using high-resolution ion mobility spectrometry and cryogenic infrared action spectroscopy, while the fragments are characterized by their mass and cryogenic infrared spectra. We observe sodium-cationized fragments that differ in mass by 162 u, corresponding to Bn/Zm ions. For the m/z 347 product ion, electronic structure calculations are consistent with formation of the lowest energy 2-ketone B2 ion structure. For the m/z 509 product ion, both the calculated 2-ketone B3 and the Z3 structures show similarities with the experimental spectrum. The theoretical structure most consistent with the spectrum of the m/z 671 ions is a slightly higher energy 2-ketone B4 structure. Overall, the data suggest a consistent formation mechanism for all the observed fragments.
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Affiliation(s)
- Jordan M Rabus
- Department of Chemistry and Biochemistry, Ohio University, 391 Clippinger Laboratories, Athens, Ohio 45701, USA
| | - Robert P Pellegrinelli
- Laboratoire de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne, EPFL SB ISIC LCPM, Station 6, CH-1015 Lausanne, Switzerland.
| | - Ali Hassan Abi Khodr
- Laboratoire de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne, EPFL SB ISIC LCPM, Station 6, CH-1015 Lausanne, Switzerland.
| | - Benjamin J Bythell
- Department of Chemistry and Biochemistry, Ohio University, 391 Clippinger Laboratories, Athens, Ohio 45701, USA
| | - Thomas R Rizzo
- Laboratoire de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne, EPFL SB ISIC LCPM, Station 6, CH-1015 Lausanne, Switzerland.
| | - Eduardo Carrascosa
- Laboratoire de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne, EPFL SB ISIC LCPM, Station 6, CH-1015 Lausanne, Switzerland.
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13
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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: 41] [Impact Index Per Article: 13.7] [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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14
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Xie C, Li L, Wu Q, Guan P, Wang C, Yu J, Tang K. Effective separation of carbohydrate isomers using metal cation and halogen anion complexes in trapped ion mobility spectrometry. Talanta 2021; 225:121903. [DOI: 10.1016/j.talanta.2020.121903] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 11/09/2020] [Accepted: 11/15/2020] [Indexed: 11/17/2022]
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15
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Hayen SM, Knulst AC, Garssen J, Otten HG, Willemsen LEM. Fructo-Oligosaccharides Modify Human DC Maturation and Peanut-Induced Autologous T-Cell Response of Allergic Patients In Vitro. Front Immunol 2021; 11:600125. [PMID: 33658990 PMCID: PMC7917053 DOI: 10.3389/fimmu.2020.600125] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Accepted: 12/24/2020] [Indexed: 11/13/2022] Open
Abstract
Background Dendritic cells (DCs) play an important role in antigen presentation, and are an interesting target for immune-modulation in allergies. Short- and long-chain fructo-oligosaccharides (scFOS/lcFOS, FF) have immunomodulatory capacities, and may influence the outcome of DC antigen presentation. Objective This study investigated the effect of FF during DC maturation and allergen presentation using cells of peanut-allergic patients in an autologous DC-T cell assay. Methods CD14+ and CD4+ T cells were isolated from peanut-allergic patients. CD14+ monocytes were differentiated into immature DCs (imDCs), and matured (matDCs) in the presence or absence of crude peanut-extract (CPE) and/or FF, and co-cultured in an autologous DC-T cell assay. T cell polarization, proliferation and cytokine production were measured. Results Expression of maturation surface molecule markers on matDCs was not affected by CPE and/or FF. By contrast, the IL-10 secretion by matDCs increased compared to imDCs, upon exposure to CPE and FF compared to CPE alone. Also the IP-10 secretion increased in CPE/FF-matDCs compared to imDC. CPE-matDCs enhanced IL-13 release in the DC-T-cell assay and Treg polarization in presence or absence of FF. CPE/FF-DCs tended to increase the Treg/Th1 and Treg/Th2 ratios compared to matDCs. The proliferation of both Treg and Th2 cells tended to increase when T cells were co-cultured with CPE-matDCs compared to matDCs, which became significant when CPE-matDCs were also exposed to FF and a same tendency was shown for Th1 proliferation. Conclusion Only in the presence of FF, CPE-matDCs produced increased regulatory and Th1-related mediators. CPE-matDCs modified T cell polarization and proliferation, and additional exposure to FF tended to enhance Treg/Th2 and Treg/Th1 ratios instructed by CPE/FF-matDCs. However this effect was not strong enough to suppress CPE-matDCs induced IL-13 release by Th-cells. This indicates the ability of FF to modify DC maturation in the presence of an allergen supporting a more Treg/Th1 prone direction of the successive allergen specific Th2 cell response.
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Affiliation(s)
- Simone M Hayen
- Department of Dermatology/Allergology, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands.,Laboratory of Translational Immunology, University Medical Center Utrecht, Utrecht, Netherlands
| | - André C Knulst
- Department of Dermatology/Allergology, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Johan Garssen
- Division of Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Faculty of Science, Utrecht University, Utrecht, Netherlands.,Department of Immunology, Nutricia Research B.V., Utrecht, Netherlands
| | - Henny G Otten
- Laboratory of Translational Immunology, University Medical Center Utrecht, Utrecht, Netherlands
| | - Linette E M Willemsen
- Division of Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Faculty of Science, Utrecht University, Utrecht, Netherlands
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Mookherjee A, Uppal SS, Murphree TA, Guttman M. Linkage Memory in Underivatized Protonated Carbohydrates. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:581-589. [PMID: 33350817 PMCID: PMC8136833 DOI: 10.1021/jasms.0c00440] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Carbohydrates are among the most complex class of biomolecules, and even subtle variations in their structures are attributed to diverse biological functions. Mass spectrometry has been essential for large scale glycomics and glycoproteomics studies, but the gas-phase structures and sometimes anomalous fragmentation properties of carbohydrates present long-standing challenges. Here we investigate the gas-phase properties of a panel of isomeric protonated disaccharides differing in their linkage configurations. Multiple conformations were evident for most of the structures based on their fragment ion abundances by tandem mass spectrometry, their ion mobilities in several gases, and their deuterium uptake kinetics by gas-phase hydrogen-deuterium exchange. Most notably, we find that the properties of the Y-ion fragments are characteristically influenced by the precursor carbohydrate's linkage configuration. This study reveals how protonated carbohydrate fragment ions can retain "linkage memory" that provides structural insight into their intact precursor.
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17
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To KC, Ben-Jaber S, Parkin IP. Recent Developments in the Field of Explosive Trace Detection. ACS NANO 2020; 14:10804-10833. [PMID: 32790331 DOI: 10.1021/acsnano.0c01579] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Explosive trace detection (ETD) technologies play a vital role in maintaining national security. ETD remains an active research area with many analytical techniques in operational use. This review details the latest advances in animal olfactory, ion mobility spectrometry (IMS), and Raman and colorimetric detection methods. Developments in optical, biological, electrochemical, mass, and thermal sensors are also covered in addition to the use of nanomaterials technology. Commercially available systems are presented as examples of current detection capabilities and as benchmarks for improvement. Attention is also drawn to recent collaborative projects involving government, academia, and industry to highlight the emergence of multimodal screening approaches and applications. The objective of the review is to provide a comprehensive overview of ETD by highlighting challenges in ETD and providing an understanding of the principles, advantages, and limitations of each technology and relating this to current systems.
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Affiliation(s)
- Ka Chuen To
- Department of Chemistry, University College London, 20 Gordon Street, Bloomsbury, London WC1H 0AJ, United Kingdom
| | - Sultan Ben-Jaber
- Department of Science and Forensics, King Fahad Security College, Riyadh 13232, Saudi Arabia
| | - Ivan P Parkin
- Department of Chemistry, University College London, 20 Gordon Street, Bloomsbury, London WC1H 0AJ, United Kingdom
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18
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From lab bench to formulated ingredient: Characterization, production, and commercialization of human milk oligosaccharides. J Funct Foods 2020. [DOI: 10.1016/j.jff.2020.104052] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
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19
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Warnke S, Ben Faleh A, Pellegrinelli RP, Yalovenko N, Rizzo TR. Combining ultra-high resolution ion mobility spectrometry with cryogenic IR spectroscopy for the study of biomolecular ions. Faraday Discuss 2020; 217:114-125. [PMID: 30993271 PMCID: PMC6657637 DOI: 10.1039/c8fd00180d] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
We explore the capability of SLIM-based IMS for isomer selectivity in combination with cryogenic, messenger-tagging IR spectroscopy.
Double-resonance spectroscopic schemes in combination with cryogenic ion traps are the go-to techniques when isomer-specific high-resolution spectra are required for analysis of molecular ions. Their limitation lies in the requirement for well-resolved, isomer-specific absorption bands as well as in the potentially time-consuming steps to identify each isomer. We present an alternative approach where isomeric species are readily separated using ion mobility spectrometry (IMS) and selected prior to cryogenic spectroscopic analysis. To date, most IMS approaches suffer from relatively low resolution, however, recent technological developments in the field of travelling-wave ion mobility using structures for lossless ion manipulation (SLIM) permit the use of extremely long drift paths, which greatly enhances the resolution. We demonstrate the power of combining this type of ultra-high resolution IMS with cryogenic vibrational spectroscopy by comparing mobility-resolved IR spectra of a disaccharide to those acquired using IR–IR double resonance. This new approach is especially promising for the investigation of larger molecules where spectral congestion interferes with double resonance techniques.
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Affiliation(s)
- Stephan Warnke
- Laboratoire de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne, EPFL SB ISIC LCPM, Station 6, CH-1015 Lausanne, Switzerland.
| | - Ahmed Ben Faleh
- Laboratoire de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne, EPFL SB ISIC LCPM, Station 6, CH-1015 Lausanne, Switzerland.
| | - Robert P Pellegrinelli
- Laboratoire de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne, EPFL SB ISIC LCPM, Station 6, CH-1015 Lausanne, Switzerland.
| | - Natalia Yalovenko
- Laboratoire de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne, EPFL SB ISIC LCPM, Station 6, CH-1015 Lausanne, Switzerland.
| | - Thomas R Rizzo
- Laboratoire de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne, EPFL SB ISIC LCPM, Station 6, CH-1015 Lausanne, Switzerland.
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20
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Pellegrinelli RP, Yue L, Carrascosa E, Warnke S, Ben Faleh A, Rizzo TR. How General Is Anomeric Retention during Collision-Induced Dissociation of Glycans? J Am Chem Soc 2020; 142:5948-5951. [DOI: 10.1021/jacs.0c00264] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Robert P. Pellegrinelli
- Laboratoire de Chimie Physique Moléculaire, Ecole Polytechnique Fédérale de Lausanne, EPFL SB ISIC LCPM, Station 6, CH-1015 Lausanne, Switzerland
| | - Lei Yue
- Laboratoire de Chimie Physique Moléculaire, Ecole Polytechnique Fédérale de Lausanne, EPFL SB ISIC LCPM, Station 6, CH-1015 Lausanne, Switzerland
| | - Eduardo Carrascosa
- Laboratoire de Chimie Physique Moléculaire, Ecole Polytechnique Fédérale de Lausanne, EPFL SB ISIC LCPM, Station 6, CH-1015 Lausanne, Switzerland
| | - Stephan Warnke
- Laboratoire de Chimie Physique Moléculaire, Ecole Polytechnique Fédérale de Lausanne, EPFL SB ISIC LCPM, Station 6, CH-1015 Lausanne, Switzerland
| | - Ahmed Ben Faleh
- Laboratoire de Chimie Physique Moléculaire, Ecole Polytechnique Fédérale de Lausanne, EPFL SB ISIC LCPM, Station 6, CH-1015 Lausanne, Switzerland
| | - Thomas R. Rizzo
- Laboratoire de Chimie Physique Moléculaire, Ecole Polytechnique Fédérale de Lausanne, EPFL SB ISIC LCPM, Station 6, CH-1015 Lausanne, Switzerland
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21
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Gray CJ, Compagnon I, Flitsch SL. Mass spectrometry hybridized with gas-phase InfraRed spectroscopy for glycan sequencing. Curr Opin Struct Biol 2020; 62:121-131. [PMID: 31981952 DOI: 10.1016/j.sbi.2019.12.014] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 12/12/2019] [Accepted: 12/23/2019] [Indexed: 11/29/2022]
Abstract
Precise structural differentiation of often isomeric glycans is important given their roles in numerous biological processes. Mass spectrometry (MS) (and tandem MS) is one of the analytical techniques at the forefront of glycan analysis given its speed, sensitivity in producing structural information as well as the fact it can be coupled to other orthogonal analytical techniques such as liquid chromatography (LC) and ion mobility spectrometry (IMS). This review describes another family of techniques that are more commonly being hybridized to MS(/MS) namely gas-phase infrared (IR) spectroscopy, whose rise is in part due to the development and improved accessibility of tunable IR lasers. Gas-phase IR can often differentiate fine isomeric differences ubiquitous within carbohydrates that MS may be 'blind' to. There are also examples of cryogenic gas-phase IR spectroscopy with much greater spectral resolution as well as hybridizing with separative methods (LC, IMS). Furthermore, collision-induced dissociation (CID) product ions can also be probed by IR, which may be beneficial to deconvolute spectra, aid analysis and build spectral libraries, thus generating novel opportunities for fragment-based approaches to analyze glycans.
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Affiliation(s)
- Christopher John Gray
- School of Chemistry & Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK
| | - Isabelle Compagnon
- Univ. Lyon, Université Claude Bernard Lyon 1, CNRS, Institut Lumière Matière, F-69622 Villeurbanne, France.
| | - Sabine L Flitsch
- School of Chemistry & Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.
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22
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Yalovenko N, Yatsyna V, Bansal P, AbiKhodr AH, Rizzo TR. Analyzing glycans cleaved from a biotherapeutic protein using ultrahigh-resolution ion mobility spectrometry together with cryogenic ion spectroscopy. Analyst 2020; 145:6493-6499. [DOI: 10.1039/d0an01206h] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
A new approach for analysis of cleaved glycans.
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Affiliation(s)
- Natalia Yalovenko
- Laboratoire de Chimie Physique Moléculaire
- École Polytechnique Fédérale de Lausanne
- EPFL SB ISIC LCPM
- CH-1015 Lausanne
- Switzerland
| | - Vasyl Yatsyna
- Laboratoire de Chimie Physique Moléculaire
- École Polytechnique Fédérale de Lausanne
- EPFL SB ISIC LCPM
- CH-1015 Lausanne
- Switzerland
| | - Priyanka Bansal
- Laboratoire de Chimie Physique Moléculaire
- École Polytechnique Fédérale de Lausanne
- EPFL SB ISIC LCPM
- CH-1015 Lausanne
- Switzerland
| | - Ali H. AbiKhodr
- Laboratoire de Chimie Physique Moléculaire
- École Polytechnique Fédérale de Lausanne
- EPFL SB ISIC LCPM
- CH-1015 Lausanne
- Switzerland
| | - Thomas R. Rizzo
- Laboratoire de Chimie Physique Moléculaire
- École Polytechnique Fédérale de Lausanne
- EPFL SB ISIC LCPM
- CH-1015 Lausanne
- Switzerland
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23
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Warnke S, Ben Faleh A, Scutelnic V, Rizzo TR. Separation and Identification of Glycan Anomers Using Ultrahigh-Resolution Ion-Mobility Spectrometry and Cryogenic Ion Spectroscopy. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2019; 30:2204-2211. [PMID: 31520337 DOI: 10.1007/s13361-019-02333-0] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 08/29/2019] [Accepted: 08/29/2019] [Indexed: 05/14/2023]
Abstract
The analysis of carbohydrates, or glycans, is challenging for established structure-sensitive gas-phase methods. The multitude of possible stereo-, regio-, and structural isomers makes them substantially more complex to analyze than DNA or proteins, and no one method is currently able to fully resolve them. While the combination of tandem mass spectrometry (MS) and ion-mobility spectrometry (IMS) have made important inroads in glycan analysis, in many cases, this approach is still not able to identify the precise isomeric form. To advance the techniques available for glycan analysis, we employ two important innovations. First, we perform ultrahigh-resolution mobility separation using structures for lossless ion manipulations (SLIM) for isomer separation and pre-selection. We then complement this IMS-MS stage with a cryogenic IR spectroscopic dimension since a glycan's vibrational spectrum provides a fingerprint that is extremely sensitive to the precise isomeric form. Using this unique approach in conjunction with oxygen-18 isotopic labeling, we show on a range of disaccharides how the two α and β anomers that every reducing glycan adopts in solution can be readily separated by mobility and identified based on their IR spectra. In addition to highlighting the power of our technique to detect minute differences in the structure of isomeric carbohydrates, these results provide the means to determine if and when anomericity is retained during collision-induced dissociation (CID) of larger glycans.
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Affiliation(s)
- Stephan Warnke
- Laboratoire de Chimie Physique Moléculaire, EPFL SB ISIC LCPM, École Polytechnique Fédérale de Lausanne, Station 6, CH-1015, Lausanne, Switzerland
| | - Ahmed Ben Faleh
- Laboratoire de Chimie Physique Moléculaire, EPFL SB ISIC LCPM, École Polytechnique Fédérale de Lausanne, Station 6, CH-1015, Lausanne, Switzerland
| | - Valeriu Scutelnic
- Laboratoire de Chimie Physique Moléculaire, EPFL SB ISIC LCPM, École Polytechnique Fédérale de Lausanne, Station 6, CH-1015, Lausanne, Switzerland
- Department of Chemistry, University of California, Berkeley, CA, 94720, USA
| | - Thomas R Rizzo
- Laboratoire de Chimie Physique Moléculaire, EPFL SB ISIC LCPM, École Polytechnique Fédérale de Lausanne, Station 6, CH-1015, Lausanne, Switzerland.
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24
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Zhang W, Wang T, Chen X, Pang X, Zhang S, Obaroakpo JU, Shilong J, Lu J, Lv J. Absolute quantification of twelve oligosaccharides in human milk using a targeted mass spectrometry-based approach. Carbohydr Polym 2019; 219:328-333. [DOI: 10.1016/j.carbpol.2019.04.092] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2019] [Revised: 04/18/2019] [Accepted: 04/30/2019] [Indexed: 02/08/2023]
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25
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Gray CJ, Migas LG, Barran PE, Pagel K, Seeberger PH, Eyers CE, Boons GJ, Pohl NLB, Compagnon I, Widmalm G, Flitsch SL. Advancing Solutions to the Carbohydrate Sequencing Challenge. J Am Chem Soc 2019; 141:14463-14479. [PMID: 31403778 DOI: 10.1021/jacs.9b06406] [Citation(s) in RCA: 90] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Carbohydrates possess a variety of distinct features with stereochemistry playing a particularly important role in distinguishing their structure and function. Monosaccharide building blocks are defined by a high density of chiral centers. Additionally, the anomericity and regiochemistry of the glycosidic linkages carry important biological information. Any carbohydrate-sequencing method needs to be precise in determining all aspects of this stereodiversity. Recently, several advances have been made in developing fast and precise analytical techniques that have the potential to address the stereochemical complexity of carbohydrates. This perspective seeks to provide an overview of some of these emerging techniques, focusing on those that are based on NMR and MS-hybridized technologies including ion mobility spectrometry and IR spectroscopy.
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Affiliation(s)
- Christopher J Gray
- School of Chemistry & Manchester Institute of Biotechnology , The University of Manchester , 131 Princess Street , Manchester M1 7DN , U.K
| | - Lukasz G Migas
- School of Chemistry & Manchester Institute of Biotechnology , The University of Manchester , 131 Princess Street , Manchester M1 7DN , U.K
| | - Perdita E Barran
- School of Chemistry & Manchester Institute of Biotechnology , The University of Manchester , 131 Princess Street , Manchester M1 7DN , U.K
| | - Kevin Pagel
- Institute for Chemistry and Biochemistry , Freie Universität Berlin , Takustraße 3 , 14195 Berlin , Germany
| | - Peter H Seeberger
- Biomolecular Systems Department , Max Planck Institute for Colloids and Interfaces , Am Muehlenberg 1 , 14476 Potsdam , Germany
| | - Claire E Eyers
- Department of Biochemistry, Institute of Integrative Biology , University of Liverpool , Crown Street , Liverpool L69 7ZB , U.K
| | - Geert-Jan Boons
- Complex Carbohydrate Research Center , University of Georgia , Athens , Georgia 30602 , United States
| | - Nicola L B Pohl
- Department of Chemistry , Indiana University , Bloomington , Indiana 47405 , United States
| | - Isabelle Compagnon
- 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
| | - Göran Widmalm
- Department of Organic Chemistry, Arrhenius Laboratory , Stockholm University , S-106 91 Stockholm , Sweden
| | - Sabine L Flitsch
- School of Chemistry & Manchester Institute of Biotechnology , The University of Manchester , 131 Princess Street , Manchester M1 7DN , U.K
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Ujma J, Ropartz D, Giles K, Richardson K, Langridge D, Wildgoose J, Green M, Pringle S. Cyclic Ion Mobility Mass Spectrometry Distinguishes Anomers and Open-Ring Forms of Pentasaccharides. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2019; 30:1028-1037. [PMID: 30977045 PMCID: PMC6517361 DOI: 10.1007/s13361-019-02168-9] [Citation(s) in RCA: 85] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 02/21/2019] [Accepted: 02/21/2019] [Indexed: 05/11/2023]
Abstract
There is increasing biopharmaceutical interest in oligosaccharides and glycosylation. A key requirement for these sample types is the ability to characterize the chain length, branching, type of monomers, and importantly stereochemistry and anomeric configuration. Herein, we showcase the multi-function capability of a cyclic ion mobility (cIM) separator embedded in a quadrupole/time-of-flight mass spectrometer (Q-ToF MS). The instrument design enables selective activation of mobility-separated precursors followed by cIM separation of product ions, an approach analogous to MSn. Using high cIM resolution, we demonstrate the separation of three isomeric pentasaccharides and, moreover, that three components are present for each compound. We show that structural differences between product ions reflect the precursor differences in some cases but not others. These findings are corroborated by a heavy oxygen labelling approach. Using this methodology, the identity of fragment ions may be assigned. This enables us to postulate that the two main components observed for each pentasaccharide are anomeric forms. The remaining low abundance component is assigned as an open-ring form.
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Affiliation(s)
- Jakub Ujma
- Waters Corporation, Stamford Avenue, Altrincham Road, Wilmslow, SK9 4AX, UK
| | - David Ropartz
- INRA, UR1268 Biopolymers Interactions Assemblies, Rue de la Géraudière, B.P. 71627, F-44316, Nantes, France
| | - Kevin Giles
- Waters Corporation, Stamford Avenue, Altrincham Road, Wilmslow, SK9 4AX, UK.
| | - Keith Richardson
- Waters Corporation, Stamford Avenue, Altrincham Road, Wilmslow, SK9 4AX, UK
| | - David Langridge
- Waters Corporation, Stamford Avenue, Altrincham Road, Wilmslow, SK9 4AX, UK
| | - Jason Wildgoose
- Waters Corporation, Stamford Avenue, Altrincham Road, Wilmslow, SK9 4AX, UK
| | - Martin Green
- Waters Corporation, Stamford Avenue, Altrincham Road, Wilmslow, SK9 4AX, UK
| | - Steven Pringle
- Waters Corporation, Stamford Avenue, Altrincham Road, Wilmslow, SK9 4AX, UK
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Ben Faleh A, Warnke S, Rizzo TR. Combining Ultrahigh-Resolution Ion-Mobility Spectrometry with Cryogenic Infrared Spectroscopy for the Analysis of Glycan Mixtures. Anal Chem 2019; 91:4876-4882. [PMID: 30835102 DOI: 10.1021/acs.analchem.9b00659] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The isomeric complexity of glycans make their analysis by traditional techniques particularly challenging. While the recent combination of ion mobility spectrometry (IMS) with cryogenic IR spectroscopy has demonstrated promise as a new technique for glycan analysis, this approach has been limited by the modest resolution of the ion mobility stage. In this work we report results from a newly developed instrument that combines ultrahigh-resolution IMS with cryogenic IR spectroscopy for glycan analysis. This apparatus makes use of the recent development in traveling-wave IMS called structures for lossless ion manipulation. The IMS stage allows the selection of glycan isomers that differ in collisional cross section by as little as 0.2% before injecting them into a cryogenic ion trap for IR spectral analysis. We compare our results to those using drift-tube IMS and highlight the advantages of the substantial increase in resolution. Application of this approach to glycan mixtures demonstrates our ability to isolate individual components, measure a cryogenic IR spectrum, and identify them using a spectroscopic database.
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Affiliation(s)
- Ahmed Ben Faleh
- Laboratoire de Chimie Physique Moléculaire , École Polytechnique Fédérale de Lausanne , EPFL SB ISIC LCPM, Station 6 , CH-1015 Lausanne , Switzerland
| | - Stephan Warnke
- Laboratoire de Chimie Physique Moléculaire , École Polytechnique Fédérale de Lausanne , EPFL SB ISIC LCPM, Station 6 , CH-1015 Lausanne , Switzerland
| | - Thomas R Rizzo
- Laboratoire de Chimie Physique Moléculaire , École Polytechnique Fédérale de Lausanne , EPFL SB ISIC LCPM, Station 6 , CH-1015 Lausanne , Switzerland
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Chouinard CD, Nagy G, Smith RD, Baker ES. Ion Mobility-Mass Spectrometry in Metabolomic, Lipidomic, and Proteomic Analyses. ADVANCES IN ION MOBILITY-MASS SPECTROMETRY: FUNDAMENTALS, INSTRUMENTATION AND APPLICATIONS 2019. [DOI: 10.1016/bs.coac.2018.11.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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Nagy G, Attah IK, Garimella SVB, Tang K, Ibrahim YM, Baker ES, Smith RD. Unraveling the isomeric heterogeneity of glycans: ion mobility separations in structures for lossless ion manipulations. Chem Commun (Camb) 2018; 54:11701-11704. [PMID: 30264832 DOI: 10.1039/c8cc06966b] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
To address the challenges associated with glycan analyses, we have implemented a structures for lossless ion manipulations (SLIM) serpentine ultra-long path with extended routing (SUPER) ion mobility-mass spectrometry (i.e. SLIM SUPER IM-MS) platform to achieve much higher resolution of isomeric glycoforms. We have demonstrated the potential of this platform as a future component of the glycomics toolbox.
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Affiliation(s)
- Gabe Nagy
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA.
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