1
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Liew CY, Chen JL, Lin YT, Luo HS, Hung AT, Magoling BJA, Nguan HS, Lai CPK, Ni CK. Chromatograms and Mass Spectra of High-Mannose and Paucimannose N-Glycans for Rapid Isomeric Identifications. J Proteome Res 2024; 23:939-955. [PMID: 38364797 PMCID: PMC10913092 DOI: 10.1021/acs.jproteome.3c00640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 01/25/2024] [Accepted: 01/31/2024] [Indexed: 02/18/2024]
Abstract
N-Linked glycosylation is one of the most essential post-translational modifications of proteins. However, N-glycan structural determination remains challenging because of the small differences in structures between isomers. In this study, we constructed a database containing collision-induced dissociation MSn mass spectra and chromatograms of high-performance liquid chromatography for the rapid identification of high-mannose and paucimannose N-glycan isomers. These N-glycans include isomers by breaking of arbitrary numbers of glycosidic bonds at arbitrary positions of canonical Man9GlcNAc2 N-glycans. In addition, some GlcMannGlcNAc2 N-glycan isomers were included in the database. This database is particularly useful for the identification of the N-glycans not in conventional N-glycan standards. This study demonstrated the application of the database to structural assignment for high-mannose N-glycans extracted from bovine whey proteins, soybean proteins, human mammary epithelial cells, and human breast carcinoma cells. We found many N-glycans that are not expected to be generated by conventional biosynthetic pathways of multicellular eukaryotes.
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Affiliation(s)
- Chia Yen Liew
- Institute
of Atomic and Molecular Sciences, Academia Sinica, Taipei 106216, Taiwan
- International
Graduate Program of Molecular Science and Technology, National Taiwan University, Taipei 106216, Taiwan
- Molecular
Science and Technology, Taiwan International Graduate Program, Academia Sinica, Taipei 106216, Taiwan
| | - Jien-Lian Chen
- Institute
of Atomic and Molecular Sciences, Academia Sinica, Taipei 106216, Taiwan
| | - Yen-Ting Lin
- Institute
of Atomic and Molecular Sciences, Academia Sinica, Taipei 106216, Taiwan
| | - Hong-Sheng Luo
- Institute
of Atomic and Molecular Sciences, Academia Sinica, Taipei 106216, Taiwan
- Department
of Chemistry, National Taiwan Normal University, Taipei 116059, Taiwan
| | - An-Ti Hung
- Institute
of Atomic and Molecular Sciences, Academia Sinica, Taipei 106216, Taiwan
- Department
of Chemistry, National Tsing Hua University, Hsinchu 300044, Taiwan
| | - Bryan John Abel Magoling
- Institute
of Atomic and Molecular Sciences, Academia Sinica, Taipei 106216, Taiwan
- Institute
of Biochemical Sciences, College of Life Science, National Taiwan University, Taipei 106216, Taiwan
- Chemical
Biology and Molecular Biophysics Program, Taiwan International Graduate
Program, Academia Sinica, Taipei 115201, Taiwan
| | - Hock-Seng Nguan
- Institute
of Atomic and Molecular Sciences, Academia Sinica, Taipei 106216, Taiwan
| | - Charles Pin-Kuang Lai
- Institute
of Atomic and Molecular Sciences, Academia Sinica, Taipei 106216, Taiwan
- Chemical
Biology and Molecular Biophysics Program, Taiwan International Graduate
Program, Academia Sinica, Taipei 115201, Taiwan
- Genome
and Systems Biology Degree Program, National
Taiwan University and Academia Sinica, Taipei 106216, Taiwan
| | - Chi-Kung Ni
- Institute
of Atomic and Molecular Sciences, Academia Sinica, Taipei 106216, Taiwan
- Molecular
Science and Technology, Taiwan International Graduate Program, Academia Sinica, Taipei 106216, Taiwan
- Department
of Chemistry, National Tsing Hua University, Hsinchu 300044, Taiwan
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2
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Chen D, Gao J, Zheng D, Guo Z, Zhao Z. Gas Phase Conformation of Trisaccharides and Core Pentasaccharide: A Three-Step Tree-Based Sampling and Quantum Mechanical Computational Approach. Molecules 2023; 28:8093. [PMID: 38138582 PMCID: PMC10745714 DOI: 10.3390/molecules28248093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 11/23/2023] [Accepted: 12/12/2023] [Indexed: 12/24/2023] Open
Abstract
As an important component of N-linked glycoproteins, the core pentasaccharide is highly crucial to the potential application prospect of glycoprotein. However, the gas phase conformation study is a challenging one due to the size and complexity of the molecule, together with the necessity to rely on quantum chemistry modeling for relevant energetics and structures. In this paper, the structures of the trisaccharides and core pentasaccharides in N-linked glycans in the gas phase were constructed by a three-step tree-based (TSTB) sampling. Since single point energies of all the conformers are calculated at the temperature of zero, it is necessary to evaluate the stability at a high temperature. We calculate the Gibbs free energies using the standard thermochemistry model (T = 298.15 K). For trimannose, the energetic ordering at 298.15 K can be strongly changed compared to 0 K. Moreover, two structures of trimannose with high energies at 0 K are considered to provide a much better match of IR vibration signatures with the low Gibbs free energies. On this basis, the core pentasaccharide was constructed in three ways. The building configurations of core pentasaccharide were optimized to obtain reasonable low-energy stable conformers. Fortunately, the lowest-energy structure of core pentasaccharide is eventually the minimum at 0 K and 298.15 K. Furthermore, spectrum analysis of core pentasaccharide was carried out. Although poorly resolved, its contour from the experiment was in qualitative correspondence with the computed IR spectrum associated with its minimum free energy structure. A large number of strongly and weakly hydrogen-bonded hydroxyl and acetylamino groups contribute to a highly congested set of overlapping bands. Compared with traditional conformation generators, the TSTB sampling is employed to efficiently and comprehensively obtain preferred conformers of larger saccharides with lower energy.
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Affiliation(s)
- Dong Chen
- School of Physics and Electronics, Henan University, Kaifeng 475004, China; (J.G.); (D.Z.); (Z.G.)
| | - Jianming Gao
- School of Physics and Electronics, Henan University, Kaifeng 475004, China; (J.G.); (D.Z.); (Z.G.)
| | - Danting Zheng
- School of Physics and Electronics, Henan University, Kaifeng 475004, China; (J.G.); (D.Z.); (Z.G.)
| | - Zhiheng Guo
- School of Physics and Electronics, Henan University, Kaifeng 475004, China; (J.G.); (D.Z.); (Z.G.)
| | - Zuncheng Zhao
- School of Physics and Electronics, Henan University, Kaifeng 475004, China; (J.G.); (D.Z.); (Z.G.)
- Henan Province Engineering Research Center of Metal Matrix in situ Composites Based on Aluminum, Magnesium or Copper, Henan University, Kaifeng 475004, China
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3
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Liew CY, Luo HS, Yang TY, Hung AT, Magoling BJA, Lai CPK, Ni CK. Identification of the High Mannose N-Glycan Isomers Undescribed by Conventional Multicellular Eukaryotic Biosynthetic Pathways. Anal Chem 2023. [PMID: 37235553 DOI: 10.1021/acs.analchem.2c05599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
N-linked glycosylation is one of the most important post-translational modifications of proteins. Current knowledge of multicellular eukaryote N-glycan biosynthesis suggests high mannose N-glycans are generated in the endoplasmic reticulum and Golgi apparatus through conserved biosynthetic pathways. According to conventional biosynthetic pathways, four Man7GlcNAc2 isomers, three Man6GlcNAc2 isomers, and one Man5GlcNAc2 isomer are generated during this process. In this study, we applied our latest mass spectrometry method, logically derived sequence tandem mass spectrometry (LODES/MSn), to re-examine high mannose N-glycans extracted from various multicellular eukaryotes which are not glycosylation mutants. LODES/MSn identified many high mannose N-glycan isomers previously unreported in plantae, animalia, cancer cells, and fungi. A database consisting of retention time and CID MSn mass spectra was constructed for all possible MannGlcNAc2 (n = 5, 6, 7) isomers that include the isomers by removing arbitrary numbers and positions of mannose from canonical N-glycan, Man9GlcNAc2. Many N-glycans in this database are not found in current N-glycan mass spectrum libraries. The database is useful for rapid high mannose N-glycan isomeric identification.
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Affiliation(s)
- Chia Yen Liew
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei 10617, Taiwan
- International Graduate Program of Molecular Science and Technology, National Taiwan University (NTU-MST), Taipei 10617, Taiwan
- Molecular Science and Technology (MST), Taiwan International Graduate Program (TIGP), Academia Sinica, Taipei 10617, Taiwan
| | - Hong-Sheng Luo
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei 10617, Taiwan
- Department of Chemistry, National Taiwan Normal University, Taipei 11677, Taiwan
| | - Ting-Yi Yang
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei 10617, Taiwan
- Department of Chemistry, National Taiwan Normal University, Taipei 11677, Taiwan
| | - An-Ti Hung
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei 10617, Taiwan
- Department of Chemistry, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Bryan John Abel Magoling
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei 10617, Taiwan
- Institute of Biochemical Sciences, College of Life Science, National Taiwan University, Taipei 10617, Taiwan
- Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program, Academia Sinica, Taipei 11529, Taiwan
| | - Charles Pin-Kuang Lai
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei 10617, Taiwan
- Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program, Academia Sinica, Taipei 11529, Taiwan
- Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei 10617, Taiwan
| | - Chi-Kung Ni
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei 10617, Taiwan
- Molecular Science and Technology (MST), Taiwan International Graduate Program (TIGP), Academia Sinica, Taipei 10617, Taiwan
- Department of Chemistry, National Tsing Hua University, Hsinchu 30013, Taiwan
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4
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Tsai ST, Hsu HC, Ni CK. A simple tandem mass spectrometry method for structural identification of pentose oligosaccharides. Analyst 2023; 148:1712-1731. [PMID: 36929945 DOI: 10.1039/d3an00068k] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/09/2023]
Abstract
Differentiation of stereoisomers that are only dissimilar in the orientation of chemical bonds in space by mass spectrometry remains challenging. Structural determination of carbohydrates by mass spectrometry is difficult, mainly due to the large number of stereoisomers in carbohydrates. Arabinose and xylose are pentose stereoisomers typically present in plant polysaccharides and exist in α- and β-anomeric configurations of furanose and pyranose forms. Conventional methods used to determine the structures of polysaccharides include hydrolysis of polysaccharides into oligosaccharides followed by identification of these oligosaccharides' structures individually through nuclear magnetic resonance spectroscopy (NMR). Although the sensitivity of mass spectrometry is much higher than that of NMR, conventional mass spectrometry provides only limited useful information on oligosaccharide structure determination, only the linkage positions of glycosidic bonds. In this study, we demonstrated a mass spectrometry method for the identification of linkage positions, anomeric configurations, and monosaccharide stereoisomers of intact oligosaccharides consisting of arabinose and xylose. We separated arabinose and xylose monosaccharides into α-furanose, β-furanose, α-pyranose, and β-pyranose forms through high-performance liquid chromatography and obtained the corresponding collision-induced dissociation mass spectra. Using these monosaccharide spectra and a flow chart consisting of the proper CID sequences derived from the dissociation mechanisms of pentose, a simple multi-stage tandem mass spectrometry method for structural identification of intact oligosaccharides consisting of arabinose and xylose was developed. The new mass spectrometry method provides a simple method for determining the structure of polysaccharides consisting of arabinose and xylose. The flow chart can be used in computer coding for automation, an ultimate goal for oligosaccharide structure determination.
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Affiliation(s)
- Shang-Ting Tsai
- Institute of Atomic and Molecular Sciences, Academia Sinica, P. O. Box 23-166, Taipei 10617, Taiwan.
| | - Hsu-Chen Hsu
- Institute of Atomic and Molecular Sciences, Academia Sinica, P. O. Box 23-166, Taipei 10617, Taiwan.
| | - Chi-Kung Ni
- Institute of Atomic and Molecular Sciences, Academia Sinica, P. O. Box 23-166, Taipei 10617, Taiwan. .,Department of Chemistry, National Tsing Hua University, Hsinchu 30013, Taiwan
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5
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Tsou PK, Huynh HT, Phan HT, Kuo JL. A self-adapting first-principles exploration on the dissociation mechanism in sodiated aldohexose pyranoses assisted with neural network potentials. Phys Chem Chem Phys 2023; 25:3332-3342. [PMID: 36633012 DOI: 10.1039/d2cp04421h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Understanding the mechanism of collision-induced dissociation (CID) in mono-saccharides with density functional theory (DFT) is challenging because of many possible reaction paths that originate from their high structural diversity. To search for the transition state (TS) from the huge number of conformers, we propose a three-step search scheme with the assistance of neural network potential (NNP). The search starts from a cross-checking of sugars, to a global search of all possible channels, and in the end, an exhaustive exploration around the low-lying channels. The cross-checking step quickly adapts the NNP from the studied molecules to the target ones. The other two steps utilize the adapted NNP to find the available pathways via random sampling of the structures. The study of the CID reactions in all eight types of aldohexose pyranoses was applied using the search scheme. The DFT calculations on AH-0 (Glc, Gal, and Man) in the previous study were utilized to construct an NNP and provide the TS structure database for searching AH-1 (All, Alt, Gul, Ido, and Tal). In total, we identified around 5200 TSs in AH-0 and AH-1, and the final NNP covers an energy range of more than 500 kJ mol-1 with a mean absolute error of energy less than 4 kJ mol-1. The search scheme is useful not only for saccharides but also for highly flexible bio-molecules.
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Affiliation(s)
- Pei-Kang Tsou
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei, 10617, Taiwan.
| | - Hai Thi Huynh
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei, 10617, Taiwan. .,Molecular Science and Technology Program, Taiwan International Graduate Program, Academia Sinica, Taipei, 11529, Taiwan.,Department of Chemistry, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Huu Trong Phan
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei, 10617, Taiwan. .,Molecular Science and Technology Program, Taiwan International Graduate Program, Academia Sinica, Taipei, 11529, Taiwan.,Department of Chemistry, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Jer-Lai Kuo
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei, 10617, Taiwan. .,Molecular Science and Technology Program, Taiwan International Graduate Program, Academia Sinica, Taipei, 11529, Taiwan.,Department of Chemistry, National Tsing Hua University, Hsinchu 30013, Taiwan.,International Graduate Program of Molecular Science and Technology (NTU-MST), National Taiwan University, Taipei 10617, Taiwan
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6
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Harvey DJ. Analysis of carbohydrates and glycoconjugates by matrix-assisted laser desorption/ionization mass spectrometry: An update for 2017-2018. MASS SPECTROMETRY REVIEWS 2023; 42:227-431. [PMID: 34719822 DOI: 10.1002/mas.21721] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Revised: 07/26/2021] [Accepted: 07/26/2021] [Indexed: 06/13/2023]
Abstract
This review is the tenth update of the original article published in 1999 on the application of matrix-assisted laser desorption/ionization mass spectrometry (MALDI) mass spectrometry to the analysis of carbohydrates and glycoconjugates and brings coverage of the literature to the end of 2018. Also included are papers that describe methods appropriate to glycan and glycoprotein analysis by MALDI, such as sample preparation techniques, even though the ionization method is not MALDI. Topics covered in the first part of the review include general aspects such as theory of the MALDI process, new methods, matrices, derivatization, MALDI imaging, fragmentation and the use of arrays. The second part of the review is devoted to applications to various structural types such as oligo- and poly-saccharides, glycoproteins, glycolipids, glycosides, and biopharmaceuticals. Most of the applications are presented in tabular form. The third part of the review covers medical and industrial applications of the technique, studies of enzyme reactions, and applications to chemical synthesis. The reported work shows increasing use of combined new techniques such as ion mobility and highlights the impact that MALDI imaging is having across a range of diciplines. MALDI is still an ideal technique for carbohydrate analysis and advancements in the technique and the range of applications continue steady progress.
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Affiliation(s)
- David J Harvey
- Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Oxford, UK
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7
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Nguan HS, Ni CK. Collision-Induced Dissociation of α-Isomaltose and α-Maltose. J Phys Chem A 2022; 126:8799-8808. [DOI: 10.1021/acs.jpca.2c04278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Affiliation(s)
- Hock-Seng Nguan
- Institute of Atomic and Molecular Sciences, Academia Sinica, P.O. Box 23-166, Taipei 10617, Taiwan
| | - Chi-Kung Ni
- Institute of Atomic and Molecular Sciences, Academia Sinica, P.O. Box 23-166, Taipei 10617, Taiwan
- Department of Chemistry, National Tsing Hua University, Hsinchu 30013, Taiwan
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8
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Liew CY, Hsu HC, Nguan HS, Huang YC, Zhong YQ, Hung SC, Ni CK. The Good, the Bad, and the Ugly Memories of Carbohydrate Fragments in Collision-Induced Dissociation. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:1891-1903. [PMID: 36111786 DOI: 10.1021/jasms.2c00180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Collision-induced dissociation (CID) tandem mass spectrometry is commonly used for carbohydrate structural determinations. In the CID tandem mass spectrometry approach, carbohydrates are dissociated into fragments, and this is followed by the structural identification of fragments through subsequent CID. The success of the structural analysis depends on the structural correlation of fragments before and after dissociation, that is, structural memory of fragments. Fragments that completely lose the memory of their original structures cannot be used for structural analysis. By contrast, fragments with extremely strong correlations between the structures before and after fragmentation retain the information on their original structures as well as have memories of their precursors' entire structures. The CID spectra of these fragments depend on their own structures and on the remaining parts of the precursor structures, making structural analysis impractical. For effective structural analysis, the fragments produced from a precursor must have good structural memory, meaning that the structures of these fragments retain their original structure, and they must not be strongly affected by the remaining parts of the precursors. In this study, we found that most of the carbohydrate fragments produced by low-energy CID have good memory in terms of linkage position and anomericity. Fragments with ugly memory, where fragment structures change with the remaining parts of the precursors, can be attributed to C ion formation in a linear form. Fragments with ugly memory can be changed to have good memory by preventing linear C ion generation by using an alternative CID sequence, or the fragments of ugly memory can become useful in structural analysis when the contribution of linear C ions in fragmentation patterns is understood.
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Affiliation(s)
- Chia Yen Liew
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei 10617, Taiwan
- International Graduate Program of Molecular Science and Technology, National Taiwan University (NTU-MST), Taipei 10617, Taiwan
- Taiwan International Graduate Program (TIGP) of Molecular Science and Technology (MST), Academia Sinica, Taipei 10617, Taiwan
| | - Hsu Chen Hsu
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei 10617, Taiwan
| | - Hock-Seng Nguan
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei 10617, Taiwan
| | - Yu-Chao Huang
- Genomics Research Center, Academia Sinica, Taipei 11529, Taiwan
| | - Yong-Qing Zhong
- Genomics Research Center, Academia Sinica, Taipei 11529, Taiwan
| | | | - Chi-Kung Ni
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei 10617, Taiwan
- Taiwan International Graduate Program (TIGP) of Molecular Science and Technology (MST), Academia Sinica, Taipei 10617, Taiwan
- Department of Chemistry, National Tsing Hua University, Hsinchu 30013, Taiwan
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9
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Huynh HT, Tsai ST, Hsu PJ, Biswas A, Phan HT, Kuo JL, Ni CK, Chiu CC. Collision-induced dissociation of Na +-tagged ketohexoses: experimental and computational studies on fructose. Phys Chem Chem Phys 2022; 24:20856-20866. [PMID: 36043336 DOI: 10.1039/d2cp02313j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Collision-induced dissociation tandem mass spectrometry (CID-MSn) and computational investigation at the MP2/6-311+G(d,p) level of theory have been employed to study Na+-tagged fructose, an example of a ketohexose featuring four cyclic isomers: α-fructofuranose (αFruf), β-fructofuranose (βFruf), α-fructopyranose (αFrup), and β-fructopyranose (βFrup). The four isomers can be separated by high-performance liquid chromatography (HPLC) and they show different mass spectra, indicating that CID-MSn can distinguish the different fructose forms. Based on a simulation using a micro-kinetic model, we have obtained an overview of the mechanisms for the different dissociation pathways. It has been demonstrated that the preference for the C-C cleavage over the competing isomerization of linear fructose is the main reason for the previously reported differences between the CID-MS spectra of aldohexoses and ketohexoses. In addition, the kinetic modeling helped to confirm the assignment of the different measured mass spectra to the different fructose isomers. The previously reported assignment based on the peak intensities in the HPLC chromatogram had left some open questions as the preference for the dehydration channels did not always follow trends previously observed for aldohexoses. Setting up the kinetic model further enabled us to directly compare the computational and experimental results, which indicated that the model can reproduce most trends in the differences between the dissociation pathways of the four cyclic fructose isomers.
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Affiliation(s)
- Hai Thi Huynh
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei, 10617, Taiwan. .,Molecular Science and Technology Program, Taiwan International Graduate Program, Academia Sinica, Taipei, 11529, Taiwan.,Department of Chemistry, National Tsing Hua University, Hsinchu, 30013, Taiwan
| | - Shang-Ting Tsai
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei, 10617, Taiwan. .,Department of Applied Chemistry, National Chiayi University, Chiayi, 60004, Taiwan
| | - Po-Jen Hsu
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei, 10617, Taiwan.
| | - Anik Biswas
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei, 10617, Taiwan. .,Department of Chemical Engineering, Indian Institute of Technology Bombay, Mumbai, 400076, India
| | - Huu Trong Phan
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei, 10617, Taiwan. .,Molecular Science and Technology Program, Taiwan International Graduate Program, Academia Sinica, Taipei, 11529, Taiwan.,Department of Chemistry, National Tsing Hua University, Hsinchu, 30013, Taiwan
| | - Jer-Lai Kuo
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei, 10617, Taiwan. .,Molecular Science and Technology Program, Taiwan International Graduate Program, Academia Sinica, Taipei, 11529, Taiwan.,Department of Chemistry, National Tsing Hua University, Hsinchu, 30013, Taiwan.,International Graduate Program of Molecular Science and Technology (NTU-MST), National Taiwan University, Taipei, 10617, Taiwan
| | - Chi-Kung Ni
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei, 10617, Taiwan. .,Molecular Science and Technology Program, Taiwan International Graduate Program, Academia Sinica, Taipei, 11529, Taiwan.,Department of Chemistry, National Tsing Hua University, Hsinchu, 30013, Taiwan
| | - Cheng-Chau Chiu
- Department of Chemistry, National Sun Yat-sen University, Kaohsiung, 80424, Taiwan. .,Center for Theoretical and Computational Physics, National Sun Yat-sen University, Kaohsiung, 80424, Taiwan
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10
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Unusual free oligosaccharides in human bovine and caprine milk. Sci Rep 2022; 12:10790. [PMID: 35750794 PMCID: PMC9232581 DOI: 10.1038/s41598-022-15140-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 06/20/2022] [Indexed: 11/23/2022] Open
Abstract
Free oligosaccharides are abundant macronutrients in milk and involved in prebiotic functions and antiadhesive binding of viruses and pathogenic bacteria to colonocytes. Despite the importance of these oligosaccharides, structural determination of oligosaccharides is challenging, and milk oligosaccharide biosynthetic pathways remain unclear. Oligosaccharide structures are conventionally determined using a combination of chemical reactions, exoglycosidase digestion, nuclear magnetic resonance spectroscopy, and mass spectrometry. Most reported free oligosaccharides are highly abundant and have lactose at the reducing end, and current oligosaccharide biosynthetic pathways in human milk are proposed based on these oligosaccharides. In this study, a new mass spectrometry technique, which can identify linkages, anomericities, and stereoisomers, was applied to determine the structures of free oligosaccharides in human, bovine, and caprine milk. Oligosaccharides that do not follow the current biosynthetic pathways and are not synthesized by any discovered enzymes were found, indicating the existence of undiscovered biosynthetic pathways and enzymes.
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11
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Wong HTK, Chen X, Wu R, Wong YLE, Hung YLW, Chan TWD. Dissociation of Mannose-Rich Glycans Using Collision-Based and Electron-Based Ion Activation Methods. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:803-812. [PMID: 35380839 DOI: 10.1021/jasms.1c00385] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Three dissociation methods, including collision-induced dissociation (CID), electron capture dissociation (ECD), and electronic excitation dissociation (EED), were evaluated for the dissociation of doubly charged glycans using sodium or magnesium ions as charge carriers. CID produced mainly glycosidic cleavages, although more cross-ring fragment ions could be obtained at higher intensities when magnesium ions were used as charge carriers [M + Mg]2+. The 0,2A3, 0,3A3, and 0,4A3 ions provided structural information on the 3 → 1 and 6 → 1 linkages of the mannoses. Some internal fragment ions, such as 2,4A5_Y3β, were also produced in high abundance, thus providing additional information on the glycan structure. ECD produced limited fragments compared to other dissociation methods when either of the metal ions were used as charge carriers. Cross-ring fragments were obtained in relatively high abundance, with the charge mainly retained on the nonreducing end. EED produced extensive glycosidic and cross-ring cleavages when either metal charge carrier was used. A higher fragmentation efficiency was achieved and more structural-specific fragments were produced when Na+ was used as the charge carrier. Of the 31 possible cross-ring cleavages, including 0,2-, 0,4-, 1,5-, 2,4-, and 3,5-cleavages, 25 were found, thus providing extensive linkage information. A wide range of fragment ions could be obtained in all dissociation methods when Mg2+ was used as the charge carrier. Two specific analytical approaches were found to produce extensively structural-specific information on the glycans studied, namely CID of magnesiated glycans and EED of sodiated glycans. These two methods were selected to further analyze the larger mannose-rich glycans Man6GlcNAc2 and Man8GlcNAc2 and generated extensive structural information.
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Affiliation(s)
- H-T Kitty Wong
- Department of Chemistry, The Chinese University of Hong Kong, Hong Kong, P. R. China
| | - Xiangfeng Chen
- Department of Chemistry, The Chinese University of Hong Kong, Hong Kong, P. R. China
- Shandong Analysis and Test Centre, School of Pharmaceutical Science, Qilu University of Technology (Shandong Academy of Sciences), Jinan, Shandong 250014, P. R. China
| | - Ri Wu
- Department of Chemistry, The Chinese University of Hong Kong, Hong Kong, P. R. China
| | - Y-L Elaine Wong
- Department of Chemistry, The Chinese University of Hong Kong, Hong Kong, P. R. China
| | - Y-L Winnie Hung
- Department of Chemistry, The Chinese University of Hong Kong, Hong Kong, P. R. China
| | - T-W Dominic Chan
- Department of Chemistry, The Chinese University of Hong Kong, Hong Kong, P. R. China
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12
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Nguan HS, Tsai ST, Ni CK. Collision-Induced Dissociation of Cellobiose and Maltose. J Phys Chem A 2022; 126:1486-1495. [PMID: 35212541 DOI: 10.1021/acs.jpca.1c10046] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Structure determination is a longstanding bottleneck of carbohydrate research. Tandem mass spectrometry (MS/MS) is one of the most widely used methods for carbohydrate structure determination. However, the effectiveness of MS/MS depends on how the precursor structures are derived from the observed fragments. Understanding the dissociation mechanisms is crucial for MS/MS-based structure determination. Herein, we investigate the collision-induced dissociation mechanism of β-cellobiose and β-maltose sodium adducts using quantum chemical calculations and experimental measurements. Four dissociation channels are studied. Dehydration mainly occurs through the transfer of an H atom to O1 of the sugar at the reducing end, followed by a C1-O1 bond cleavage; cross-ring dissociation starts with a ring-opening reaction, which occurs through the transfer of an H atom from O1 to O5 of the sugar at the reducing end. These two dissociation channels are analogous to that of glucose monosaccharide. The third channel, generation of B1 and Y1 ions, occurs through the transfer of an H atom from O3 (cellobiose) or O2 (maltose) to O1 of the sugar at the nonreducing end, followed by a glycosidic bond cleavage. The fourth channel, C1-Z1 fragmentation, has two mechanisms: (1) the transfer of an H atom from O3 or O2 to O4 of the sugar at the reducing end to generate C ions in the ring form and (2) the transfer of an H atom from O3 of the sugar at the reducing end to O5 of the sugar at the nonreducing end to produce C ions in the linear form. The results of calculations are supported by experimental collision-induced dissociation spectral measurements.
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Affiliation(s)
- Hock-Seng Nguan
- Institute of Atomic and Molecular Sciences, Academia Sinica, P.O. Box 23-166, Taipei 10617, Taiwan
| | - Shang-Ting Tsai
- Institute of Atomic and Molecular Sciences, Academia Sinica, P.O. Box 23-166, Taipei 10617, Taiwan
| | - Chi-Kung Ni
- Institute of Atomic and Molecular Sciences, Academia Sinica, P.O. Box 23-166, Taipei 10617, Taiwan.,Department of Chemistry, National Tsing Hua University, Hsinchu 30013, Taiwan
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13
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Lin HY, Ni CK. Structural Determination of Polysaccharides Lichenin Using Logically Derived Sequence Tandem Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:335-346. [PMID: 34965721 DOI: 10.1021/jasms.1c00325] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
A new mass spectrometry method, logically derived sequence (LODES) tandem mass spectrometry (MSn), was applied to determine the primary structure of polysaccharide lichenin. Conventional polysaccharide structural analysis requires complex processes, including derivation, permethylation, gas chromatography-mass spectrometry, and nuclear magnetic resonance spectrometry. Many of these processes can be replaced by LODES/MSn. In this new method, polysaccharides are hydrolyzed into monosaccharides, disaccharides, and oligosaccharides, and structures of these molecules are determined using LODES/MSn. The application of LODES/MSn for determination of primary structure of polysaccharide lichenin was demonstrated. The repeating unit of lichenin was determined to be An-Bn, where A represents β-Glc-(1 → 4)-β-Glc-(1 → 4)-β-Glc-(1 → 3)-Glc, B represents β-Glc-(1 → 4)-β-Glc-(1 → 4)-β-Glc-(1 → 4)-β-Glc-(1 → 3)-Glc, n is an integral, and n ≥ 2 exists but n = 1 cannot be excluded. LODES/MSn, which substantially reduces the time, effort, and sample quantity necessary for structural determination of oligosaccharides, is a powerful tool for polysaccharide primary structural determination.
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Affiliation(s)
- Hou-Yu Lin
- Institute of Atomic and Molecular Sciences, Academia Sinica, No. 1, Sec. 4, Roosevelt Road, Taipei 10617, Taiwan
- Department of Chemistry, National Taiwan University, No. 1, Sec. 4, Roosevelt Road, Taipei 10617, Taiwan
| | - Chi-Kung Ni
- Institute of Atomic and Molecular Sciences, Academia Sinica, No. 1, Sec. 4, Roosevelt Road, Taipei 10617, Taiwan
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14
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Liew CY, Chan CK, Huang SP, Cheng YT, Tsai ST, Hsu HC, Wang CC, Ni CK. De novo structural determination of oligosaccharide isomers in glycosphingolipids using logically derived sequence tandem mass spectrometry. Analyst 2021; 146:7345-7357. [PMID: 34766961 DOI: 10.1039/d1an01448j] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Despite the importance of carbohydrates in biological systems, structural determination of carbohydrates remains difficult because of the large number of isomers. In this study, a new mass spectrometry method, namely logically derived sequence tandem mass spectrometry (LODES/MSn), was developed to characterize oligosaccharide structures. In this approach, sequential collision-induced dissociation (CID) of oligosaccharides is performed in an ion trap mass spectrometer to identify the linkage position, anomeric configuration, and stereoisomers of each monosaccharide in the oligosaccharides. The CID sequences are derived from carbohydrate dissociation mechanisms. LODES/MSn does not require oligosaccharide standards or the prior knowledge of the rules and principles of biosynthetic pathways; thus LODES/MSn is particularly useful for the investigation of undiscovered oligosaccharides. We demonstrated that the structure of core oligosaccharides in glycosphingolipids can be identified from more than 500 000 isomers using LODES/MSn. The same method can be applied for determining the structures of other oligosaccharides, such as N-, and O-glycans, and free oligosaccharides in milk.
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Affiliation(s)
- Chia Yen Liew
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei, 10617, Taiwan.,International Graduate Program of Molecular Science and Technology, National Taiwan University (NTU-MST), Taipei, 10617, Taiwan.,an International Graduate Program (TIGP) of Molecular Science and Technology (MST), Academia Sinica, Taiw, Taipei, 10617, Taiwan
| | - Chieh-Kai Chan
- Institute of Chemistry, Academia Sinica, Taipei, 11529, Taiwan
| | - Shih-Pei Huang
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei, 10617, Taiwan
| | - Yu-Ting Cheng
- Institute of Chemistry, Academia Sinica, Taipei, 11529, Taiwan
| | - Shang-Ting Tsai
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei, 10617, Taiwan
| | - Hsu Chen Hsu
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei, 10617, Taiwan
| | | | - Chi-Kung Ni
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei, 10617, Taiwan.,Department of Chemistry, National Tsing Hua University, Hsinchu 30013, Taiwan.
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15
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Wang J, Zhao J, Nie S, Xie M, Li S. Mass spectrometry for structural elucidation and sequencing of carbohydrates. Trends Analyt Chem 2021. [DOI: 10.1016/j.trac.2021.116436] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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16
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Tsai S, Ni C. Differentiation of aldohexoses and ketohexoses through collision‐induced dissociation. J CHIN CHEM SOC-TAIP 2021. [DOI: 10.1002/jccs.202100257] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Shang‐Ting Tsai
- Institute of Atomic and Molecular Sciences, Academia Sinica Taipei Taiwan
| | - Chi‐Kung Ni
- Institute of Atomic and Molecular Sciences, Academia Sinica Taipei Taiwan
- Department of Chemistry National Tsing Hua University Hsinchu Taiwan
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17
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Castillo JJ, Galermo AG, Amicucci MJ, Nandita E, Couture G, Bacalzo N, Chen Y, Lebrilla CB. A Multidimensional Mass Spectrometry-Based Workflow for De Novo Structural Elucidation of Oligosaccharides from Polysaccharides. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:2175-2185. [PMID: 34261322 PMCID: PMC8344699 DOI: 10.1021/jasms.1c00133] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 06/09/2021] [Accepted: 07/06/2021] [Indexed: 06/13/2023]
Abstract
Carbohydrates play essential roles in a variety of biological processes that are dictated by their structures. However, characterization of carbohydrate structures remains extremely difficult and generally unsolved. In this work, a de novo mass spectrometry-based workflow was developed to isolate and structurally elucidate oligosaccharides to provide sequence, monosaccharide compositions, and glycosidic linkage positions. The approach employs liquid chromatography-tandem mass spectrometry (LC-MS/MS)-based methods in a 3-dimensional concept: one high performance liquid chromatography-quadrupole time-of-flight mass spectrometry (HPLC-QTOF MS) analysis for oligosaccharide sequencing and two ultra high performance liquid chromatography-triple quadrupole mass spectrometry (UHPLC-QqQ MS) analyses on fractionated oligosaccharides to determine their monosaccharides and linkages compositions. The workflow was validated by applying the procedure to maltooligosaccharide standards. The approach was then used to determine the structures of oligosaccharides derived from polysaccharide standards and whole food products. The integrated LC-MS workflow will reveal the in-depth structures of oligosaccharides.
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Affiliation(s)
- Juan Jose Castillo
- Department of Chemistry, University of
California Davis, Davis, California 95616, United
States
| | - Ace G. Galermo
- Department of Chemistry, University of
California Davis, Davis, California 95616, United
States
| | - Matthew J. Amicucci
- Department of Chemistry, University of
California Davis, Davis, California 95616, United
States
- Agricultural and Environmental Chemistry Graduate
Group, University of California Davis, Davis, California 95616,
United States
| | - Eshani Nandita
- Department of Chemistry, University of
California Davis, Davis, California 95616, United
States
| | - Garret Couture
- Department of Chemistry, University of
California Davis, Davis, California 95616, United
States
| | - Nikita Bacalzo
- Department of Chemistry, University of
California Davis, Davis, California 95616, United
States
| | - Ye Chen
- Department of Chemistry, University of
California Davis, Davis, California 95616, United
States
| | - Carlito B. Lebrilla
- Department of Chemistry, University of
California Davis, Davis, California 95616, United
States
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18
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Tsai ST, Nguan HS, Ni CK. Identification of Anomericity and Linkage of Arabinose and Ribose through Collision-Induced Dissociation. J Phys Chem A 2021; 125:6109-6121. [PMID: 34256570 DOI: 10.1021/acs.jpca.1c03854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Arabinose and ribose are two common pentoses that exist in both furanose and pyranose forms in plant and bacteria oligosaccharides. In this study, each pentose isomer, namely α-furanose, β-furanose, α-pyranose, and β-pyranose, was first separated through high-performance liquid chromatography followed by an investigation of collision-induced dissociation in an ion trap mass spectrometer. The major dissociation channels, dehydration and cross-ring dissociation, were analyzed by using high-level quantum chemistry calculations and transition state theory. The branching ratio of major dissociation channels was governed by two geometrical features: one being the cis or trans configuration of O1 and O2 atoms determining dehydration preferability and the other being the number of hydroxyl groups on the same side of the ring as the O1 atom determining the preferability of cross-ring dissociation. The relative branching ratios of the major channels were used to identify anomericity and the linkages of arabinose and ribose. Arabinose in the β-configuration and ribose in the α-configuration are predicted to have larger relative dehydration branching ratios than arabinose in the α-configuration and ribose in the β-configuration, respectively. Arabinose and ribose at the reducing end of oligosaccharides with 1 → 2 (pyranose and furanose), 1 → 3 (pyranose and furanose), 1 → 4 (pyranose only), and 1 → 5 (furanose only) linkages are predicted to undergo 0,2X, 0,3X, 0,2A, and 0,2A/0,3A cross-ring dissociation, respectively. Application of the dissociation mechanism to the disaccharide linkage determination is demonstrated.
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Affiliation(s)
- Shang-Ting Tsai
- Institute of Atomic and Molecular Sciences, Academia Sinica, P.O. Box 23-166, Taipei 10617, Taiwan
| | - Hock-Seng Nguan
- Institute of Atomic and Molecular Sciences, Academia Sinica, P.O. Box 23-166, Taipei 10617, Taiwan
| | - Chi-Kung Ni
- Institute of Atomic and Molecular Sciences, Academia Sinica, P.O. Box 23-166, Taipei 10617, Taiwan.,Department of Chemistry, National Tsing Hua University, Hsinchu 30013, Taiwan
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19
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Structural identification of N-glycan isomers using logically derived sequence tandem mass spectrometry. Commun Chem 2021; 4:92. [PMID: 36697781 PMCID: PMC9814355 DOI: 10.1038/s42004-021-00532-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 05/19/2021] [Indexed: 01/28/2023] Open
Abstract
N-linked glycosylation is one of the most important protein post-translational modifications. Despite the importance of N-glycans, the structural determination of N-glycan isomers remains challenging. Here we develop a mass spectrometry method, logically derived sequence tandem mass spectrometry (LODES/MSn), to determine the structures of N-glycan isomers that cannot be determined using conventional mass spectrometry. In LODES/MSn, the sequences of successive collision-induced dissociation are derived from carbohydrate dissociation mechanisms and apply to N-glycans in an ion trap for structural determination. We validate LODES/MSn using synthesized N-glycans and subsequently applied this method to N-glycans extracted from soybean, ovalbumin, and IgY. Our method does not require permethylation, reduction, and labeling of N-glycans, or the mass spectrum databases of oligosaccharides and N-glycan standards. Moreover, it can be applied to all types of N-glycans (high-mannose, hybrid, and complex), as well as the N-glycans degraded from larger N-glycans by any enzyme or acid hydrolysis.
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20
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Bruni PS, Schürch S. Fragmentation mechanisms of protonated cyclodextrins in tandem mass spectrometry. Carbohydr Res 2021; 504:108316. [PMID: 33892257 DOI: 10.1016/j.carres.2021.108316] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 03/05/2021] [Accepted: 04/06/2021] [Indexed: 12/20/2022]
Abstract
Tandem mass spectrometry has found widespread application as a powerful tool for the characterization of linear and branched oligosaccharides. Though the technique has been applied to the analysis of cyclic oligosaccharides as well, the underlying fragmentation mechanisms have hardly been investigated. This study focuses on the mechanistic aspects of the gas-phase dissociation of protonated β-cyclodextrins. Elucidation of the dissociation mechanisms is supported by tandem mass spectrometric experiments and by experiments on di- and trimethylated cyclodextrin derivatives. The fragmentation pathway comprises the linearization of the macrocyclic structure as the initial step of the decomposition, followed by the elimination of glucose subunits and the subsequent release of water and formaldehyde moieties from the glucose monomer and dimer fragment ions. Linearization of the macrocycle occurs due to proton-driven scission of the glycosidic bond adjacent to carbon atom C1 in conjunction with the formation of a new hydroxy group. The resulting ring-opened structure further decomposes in charge-independent processes forming either zwitterionic fragments, a 1,4-anhydroglucose moiety, or a new macrocyclic structure, that is lost as a neutral, and an oxonium ion. Since the hydroxy group formed at the ring-opening site can be regarded as the non-reducing end of the linearized structure, the fragment ion nomenclature commonly used for linear and branched oligosaccharides, which relies on the designation of a reducing and a non-reducing end, can also be applied to the description of fragment ions derived from cyclic structures.
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Affiliation(s)
- Pia S Bruni
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland.
| | - Stefan Schürch
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland.
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21
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Nguan HS, Tsai ST, Chen JL, Hsu PJ, Kuo JL, Ni CK. Collision-induced dissociation of xylose and its applications in linkage and anomericity identification. Phys Chem Chem Phys 2021; 23:3485-3495. [DOI: 10.1039/d0cp05868h] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Different dehydration barrier heights result in different branching ratio, a simple and fast anomeric configuration identification for xylose.
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Affiliation(s)
- Hock-Seng Nguan
- Institute of Atomic and Molecular Sciences
- Academia Sinica
- Taipei 10617
- Taiwan
| | - Shang-Ting Tsai
- Institute of Atomic and Molecular Sciences
- Academia Sinica
- Taipei 10617
- Taiwan
| | - Jien-Lian Chen
- Institute of Atomic and Molecular Sciences
- Academia Sinica
- Taipei 10617
- Taiwan
| | - Po-Jen Hsu
- Institute of Atomic and Molecular Sciences
- Academia Sinica
- Taipei 10617
- Taiwan
| | - Jer-Lai Kuo
- Institute of Atomic and Molecular Sciences
- Academia Sinica
- Taipei 10617
- Taiwan
| | - Chi-Kung Ni
- Institute of Atomic and Molecular Sciences
- Academia Sinica
- Taipei 10617
- Taiwan
- Department of Chemistry
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22
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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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23
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Huang SP, Hsu HC, Liew CY, Tsai ST, Ni CK. Logically derived sequence tandem mass spectrometry for structural determination of Galactose oligosaccharides. Glycoconj J 2020; 38:177-189. [PMID: 32062823 DOI: 10.1007/s10719-020-09915-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 12/30/2019] [Accepted: 02/03/2020] [Indexed: 12/30/2022]
Abstract
Mass spectrometry has high sensitivity and is widely used in the identification of molecular structures, however, the structural determination of oligosaccharides through mass spectrometry is still challenging. A novel method, namely the logically derived sequence (LODES) tandem mass spectrometry (MSn), for the structural determination of underivatized oligosaccharides was developed. This method, which is based on the dissociation mechanisms, involves sequential low-energy collision-induced dissociation (CID) of sodium ion adducts, a logical sequence for identifying the structurally decisive product ions for subsequent CID, and a specially prepared disaccharide CID spectrum database. In this work, we reported the assignment of the specially prepared galactose disaccharide CID spectra. We used galactose trisaccharides and tetrasaccharides as examples to demonstrate LODES/MSn is a general method that can be used for the structural determination of hexose oligosaccharides. LODES/MSn has the potential to be extended to oligosaccharides containing other monosaccharides provided the dissociation mechanisms are understood and the corresponding disaccharide database is available.
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Affiliation(s)
- Shih-Pei Huang
- Institute of Atomic and Molecular Sciences, Academia Sinica, P. O. Box 23-166, Taipei, 10617, Taiwan
| | - Hsu Chen Hsu
- Institute of Atomic and Molecular Sciences, Academia Sinica, P. O. Box 23-166, Taipei, 10617, Taiwan
| | - Chia Yen Liew
- Institute of Atomic and Molecular Sciences, Academia Sinica, P. O. Box 23-166, Taipei, 10617, Taiwan.,Molecular Science and Technology, Taiwan International Graduate Program, Academia Sinica and National Taiwan University, Taipei, 10617, Taiwan
| | - Shang-Ting Tsai
- Institute of Atomic and Molecular Sciences, Academia Sinica, P. O. Box 23-166, Taipei, 10617, Taiwan
| | - Chi-Kung Ni
- Institute of Atomic and Molecular Sciences, Academia Sinica, P. O. Box 23-166, Taipei, 10617, Taiwan. .,Department of Chemistry, National Tsing Hua University, Hsinchu, 30013, Taiwan.
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24
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Wei J, Tang Y, Bai Y, Zaia J, Costello CE, Hong P, Lin C. Toward Automatic and Comprehensive Glycan Characterization by Online PGC-LC-EED MS/MS. Anal Chem 2020; 92:782-791. [PMID: 31829560 PMCID: PMC7082718 DOI: 10.1021/acs.analchem.9b03183] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Despite the recent advances in mass spectrometry (MS)-based methods for glycan structural analysis, characterization of glycomes remains a significant analytical challenge, in part due to the widespread presence of isomeric structures and the need to define the many structural variables for each glycan. Interpretation of the complex tandem mass spectra of glycans is often laborious and requires substantial expertise. Broad adoption of MS methods for glycomics, within and outside the glycoscience community, has been hindered by the shortage of bioinformatics tools for rapid and accurate glycan sequencing. Here, we developed an online porous graphitic carbon liquid chromatography (PGC-LC)-electronic excitation dissociation (EED) MS/MS method that takes advantage of the superior isomer resolving power of PGC and the structural details provided by EED MS/MS for characterization of glycan mixtures. We also made improvements to GlycoDeNovo, our de novo glycan sequencing algorithm, so that it can automatically and accurately identify glycan topologies from EED tandem mass spectra acquired online. The majority of linkages can also be determined de novo, although in some cases, biological insight may be needed to fully define the glycan structure. Application of this method to the analysis of N-glycans released from ribonuclease B not only revealed the presence of 18 high-mannose structures, including new isomers not previously reported, but also provided relative quantification for each isomeric structure. With fully automated data acquisition and topology analysis, the approach presented here holds great potential for automated and comprehensive glycan characterization.
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Affiliation(s)
- Juan Wei
- Center for Biomedical Mass Spectrometry, Boston University School of Medicine, Boston, Massachusetts 02118, United States
| | - Yang Tang
- Center for Biomedical Mass Spectrometry, Boston University School of Medicine, Boston, Massachusetts 02118, United States
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, United States
| | - Yu Bai
- Beijing National Laboratory for Molecular Sciences, Institute of Analytical Chemistry, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Joseph Zaia
- Center for Biomedical Mass Spectrometry, Boston University School of Medicine, Boston, Massachusetts 02118, United States
| | - Catherine E. Costello
- Center for Biomedical Mass Spectrometry, Boston University School of Medicine, Boston, Massachusetts 02118, United States
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, United States
| | - Pengyu Hong
- Department of Computer Science, Brandeis University, Waltham, Massachusetts 02454, United States
| | - Cheng Lin
- Center for Biomedical Mass Spectrometry, Boston University School of Medicine, Boston, Massachusetts 02118, United States
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25
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Chiu CC, Lin CK, Kuo JL. Improved agreement between experimental and computational results for collision-induced dissociation mass spectrometry of cation-tagged hexoses. Phys Chem Chem Phys 2020; 22:6928-6941. [DOI: 10.1039/d0cp00286k] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Low exact exchange DFT methods underestimate the dehydration barriers as the charge localization in such transition states is challenging to describe.
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Affiliation(s)
- Cheng-chau Chiu
- Institute of Atomic and Molecular Sciences
- Academia Sinica
- Taipei City 10617
- Taiwan
| | - Chih-Kai Lin
- Institute of Atomic and Molecular Sciences
- Academia Sinica
- Taipei City 10617
- Taiwan
| | - Jer-Lai Kuo
- Institute of Atomic and Molecular Sciences
- Academia Sinica
- Taipei City 10617
- Taiwan
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26
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Tsai S, Liew CY, Hsu C, Huang S, Weng W, Kuo Y, Ni C. Automatic Full Glycan Structural Determination through Logically Derived Sequence Tandem Mass Spectrometry. Chembiochem 2019; 20:2351-2359. [DOI: 10.1002/cbic.201900228] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Indexed: 12/12/2022]
Affiliation(s)
- Shang‐Ting Tsai
- Institute of Atomic and Molecular SciencesAcademia Sinica P. O. Box 23-166 Taipei 10617 Taiwan
| | - Chia Yen Liew
- Institute of Atomic and Molecular SciencesAcademia Sinica P. O. Box 23-166 Taipei 10617 Taiwan
- Molecular Science and Technology International Graduate ProgramAcademia Sinica and National University Taipei 10617 Taiwan
| | - Chen Hsu
- Institute of Atomic and Molecular SciencesAcademia Sinica P. O. Box 23-166 Taipei 10617 Taiwan
| | - Shih‐Pei Huang
- Institute of Atomic and Molecular SciencesAcademia Sinica P. O. Box 23-166 Taipei 10617 Taiwan
| | - Wei‐Chien Weng
- Institute of Atomic and Molecular SciencesAcademia Sinica P. O. Box 23-166 Taipei 10617 Taiwan
| | - Yu‐Hsiang Kuo
- Institute of Atomic and Molecular SciencesAcademia Sinica P. O. Box 23-166 Taipei 10617 Taiwan
| | - Chi‐Kung Ni
- Institute of Atomic and Molecular SciencesAcademia Sinica P. O. Box 23-166 Taipei 10617 Taiwan
- Department of ChemistryNational Tsing Hua University Hsinchu 30013 Taiwan
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27
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Chiu CC, Huynh HT, Tsai ST, Lin HY, Hsu PJ, Phan HT, Karumanthra A, Thompson H, Lee YC, Kuo JL, Ni CK. Toward Closing the Gap between Hexoses and N-Acetlyhexosamines: Experimental and Computational Studies on the Collision-Induced Dissociation of Hexosamines. J Phys Chem A 2019; 123:6683-6700. [DOI: 10.1021/acs.jpca.9b04143] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Cheng-chau Chiu
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei, 10617, Taiwan
| | - Hai Thi Huynh
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei, 10617, Taiwan
- Molecular Science and Technology Program, Taiwan International Graduate Program, Academia Sinica, Taipei, 11529, Taiwan
- Department of Chemistry, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Shang-Ting Tsai
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei, 10617, Taiwan
| | - Hou-Yu Lin
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei, 10617, Taiwan
- Department of Chemistry, National Taiwan University, Taipei, 10617, Taiwan
| | - Po-Jen Hsu
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei, 10617, Taiwan
| | - Huu Trong Phan
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei, 10617, Taiwan
- Molecular Science and Technology Program, Taiwan International Graduate Program, Academia Sinica, Taipei, 11529, Taiwan
- Department of Chemistry, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Arya Karumanthra
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei, 10617, Taiwan
- Undergraduate Programme, Indian Institute of Science, Bangalore, 560012, India
| | - Hayden Thompson
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei, 10617, Taiwan
- Department of Chemistry, University of Bath, Bath BA2 7AY, United Kingdom
| | - Yu-Chi Lee
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei, 10617, Taiwan
| | - Jer-Lai Kuo
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei, 10617, Taiwan
| | - Chi-Kung Ni
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei, 10617, Taiwan
- Department of Chemistry, National Tsing Hua University, Hsinchu 30013, Taiwan
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De novo structural determination of mannose oligosaccharides by using a logically derived sequence for tandem mass spectrometry. Anal Bioanal Chem 2019; 411:3241-3255. [DOI: 10.1007/s00216-019-01817-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Revised: 03/04/2019] [Accepted: 03/28/2019] [Indexed: 10/26/2022]
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29
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Chiu CC, Tsai ST, Hsu PJ, Huynh HT, Chen JL, Phan HT, Huang SP, Lin HY, Kuo JL, Ni CK. Unexpected Dissociation Mechanism of Sodiated N-Acetylglucosamine and N-Acetylgalactosamine. J Phys Chem A 2019; 123:3441-3453. [DOI: 10.1021/acs.jpca.9b00934] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Cheng-chau Chiu
- Institute of Atomic and Molecular Sciences, Academia Sinica, P.O. Box 23-166, Taipei 10617, Taiwan
| | - Shang-Ting Tsai
- Institute of Atomic and Molecular Sciences, Academia Sinica, P.O. Box 23-166, Taipei 10617, Taiwan
| | - Po-Jen Hsu
- Institute of Atomic and Molecular Sciences, Academia Sinica, P.O. Box 23-166, Taipei 10617, Taiwan
| | - Hai Thi Huynh
- Institute of Atomic and Molecular Sciences, Academia Sinica, P.O. Box 23-166, Taipei 10617, Taiwan
- Molecular Science and Technology, Taiwan International Graduate Program, Academia Sinica, Taipei 10617, Taiwan
- Department of Chemistry, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Jien-Lian Chen
- Institute of Atomic and Molecular Sciences, Academia Sinica, P.O. Box 23-166, Taipei 10617, Taiwan
| | - Huu Trong Phan
- Institute of Atomic and Molecular Sciences, Academia Sinica, P.O. Box 23-166, Taipei 10617, Taiwan
- Molecular Science and Technology, Taiwan International Graduate Program, Academia Sinica, Taipei 10617, Taiwan
- Department of Chemistry, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Shih-Pei Huang
- Institute of Atomic and Molecular Sciences, Academia Sinica, P.O. Box 23-166, Taipei 10617, Taiwan
| | - Hou-Yu Lin
- Institute of Atomic and Molecular Sciences, Academia Sinica, P.O. Box 23-166, Taipei 10617, Taiwan
- Department of Chemistry, National Taiwan University, Taipei 10617, Taiwan
| | - Jer-Lai Kuo
- Institute of Atomic and Molecular Sciences, Academia Sinica, P.O. Box 23-166, Taipei 10617, Taiwan
| | - Chi-Kung Ni
- Institute of Atomic and Molecular Sciences, Academia Sinica, P.O. Box 23-166, Taipei 10617, Taiwan
- Department of Chemistry, National Tsing Hua University, Hsinchu 30013, Taiwan
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30
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Shen YH, Tsai ST, Liew CY, Ni CK. Mass spectrometry-based identification of carbohydrate anomeric configuration to determine the mechanism of glycoside hydrolases. Carbohydr Res 2019; 476:53-59. [DOI: 10.1016/j.carres.2019.03.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2018] [Revised: 03/10/2019] [Accepted: 03/11/2019] [Indexed: 10/27/2022]
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31
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Klukowski P, Schubert M. Chemical shift-based identification of monosaccharide spin-systems with NMR spectroscopy to complement untargeted glycomics. Bioinformatics 2018; 35:293-300. [DOI: 10.1093/bioinformatics/bty465] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Accepted: 06/10/2018] [Indexed: 11/13/2022] Open
Affiliation(s)
- Piotr Klukowski
- Department of Computer Science, Faculty of Computer Science and Management, Wrocław University of Science and Technology, 50-370 Wrocław, Poland
| | - Mario Schubert
- Department of Biosciences, University of Salzburg, Salzburg, Austria
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32
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Simple Method for De Novo Structural Determination of Underivatised Glucose Oligosaccharides. Sci Rep 2018; 8:5562. [PMID: 29615745 PMCID: PMC5882935 DOI: 10.1038/s41598-018-23903-4] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Accepted: 03/22/2018] [Indexed: 12/04/2022] Open
Abstract
Carbohydrates have various functions in biological systems. However, the structural analysis of carbohydrates remains challenging. Most of the commonly used methods involve derivatization of carbohydrates or can only identify part of the structure. Here, we report a de novo method for completely structural identification of underivatised oligosaccharides. This method, which can provide assignments of linkages, anomeric configurations, and branch locations, entails low-energy collision-induced dissociation (CID) of sodium ion adducts that enable the cleavage of selective chemical bonds, a logical procedure to identify structurally decisive fragment ions for subsequent CID, and the specially prepared disaccharide CID spectrum databases. This method was first applied to determine the structures of four underivatised glucose oligosaccharides. Then, high-performance liquid chromatography and a mass spectrometer with a built-in logical procedure were established to demonstrate the capability of the in situ CID spectrum measurement and structural determination of the oligosaccharides in chromatogram. This consolidation provides a simple, rapid, sensitive method for the structural determination of glucose oligosaccharides, and applications to oligosaccharides containing hexoses other than glucose can be made provided the corresponding disaccharide databases are available.
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33
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Huynh HT, Phan HT, Hsu PJ, Chen JL, Nguan HS, Tsai ST, Roongcharoen T, Liew CY, Ni CK, Kuo JL. Collision-induced dissociation of sodiated glucose, galactose, and mannose, and the identification of anomeric configurations. Phys Chem Chem Phys 2018; 20:19614-19624. [DOI: 10.1039/c8cp03753a] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Different dehydration barrier heights of cis and trans configurations between O1 and O2 provide a simple and fast anomeric configuration identification.
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Affiliation(s)
- Hai Thi Huynh
- Institute of Atomic and Molecular Sciences
- Academia Sinica
- Taipei 10617
- Taiwan
- Molecular Science and Technology
| | - Huu Trong Phan
- Institute of Atomic and Molecular Sciences
- Academia Sinica
- Taipei 10617
- Taiwan
- Molecular Science and Technology
| | - Po-Jen Hsu
- Institute of Atomic and Molecular Sciences
- Academia Sinica
- Taipei 10617
- Taiwan
| | - Jien-Lian Chen
- Institute of Atomic and Molecular Sciences
- Academia Sinica
- Taipei 10617
- Taiwan
| | - Hock Seng Nguan
- Institute of Atomic and Molecular Sciences
- Academia Sinica
- Taipei 10617
- Taiwan
| | - Shang-Ting Tsai
- Institute of Atomic and Molecular Sciences
- Academia Sinica
- Taipei 10617
- Taiwan
| | - Thantip Roongcharoen
- Institute of Atomic and Molecular Sciences
- Academia Sinica
- Taipei 10617
- Taiwan
- Department of Chemistry
| | - Chia Yen Liew
- Institute of Atomic and Molecular Sciences
- Academia Sinica
- Taipei 10617
- Taiwan
| | - Chi-Kung Ni
- Institute of Atomic and Molecular Sciences
- Academia Sinica
- Taipei 10617
- Taiwan
- Department of Chemistry
| | - Jer-Lai Kuo
- Institute of Atomic and Molecular Sciences
- Academia Sinica
- Taipei 10617
- Taiwan
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