1
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Wei J, Papanastasiou D, Kosmopoulou M, Smyrnakis A, Hong P, Tursumamat N, Klein JA, Xia C, Tang Y, Zaia J, Costello CE, Lin C. De novo glycan sequencing by electronic excitation dissociation MS 2-guided MS 3 analysis on an Omnitrap-Orbitrap hybrid instrument. Chem Sci 2023; 14:6695-6704. [PMID: 37350811 PMCID: PMC10284134 DOI: 10.1039/d3sc00870c] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 05/24/2023] [Indexed: 06/24/2023] Open
Abstract
Comprehensive de novo glycan sequencing remains an elusive goal due to the structural diversity and complexity of glycans. Present strategies employing collision-induced dissociation (CID) and higher energy collisional dissociation (HCD)-based multi-stage tandem mass spectrometry (MSn) or MS/MS combined with sequential exoglycosidase digestions are inherently low-throughput and difficult to automate. Compared to CID and HCD, electron transfer dissociation (ETD) and electron capture dissociation (ECD) each generate more cross-ring cleavages informative about linkage positions, but electronic excitation dissociation (EED) exceeds the information content of all other methods and is also applicable to analysis of singly charged precursors. Although EED can provide extensive glycan structural information in a single stage of MS/MS, its performance has largely been limited to FTICR MS, and thus it has not been widely adopted by the glycoscience research community. Here, the effective performance of EED MS/MS was demonstrated on a hybrid Orbitrap-Omnitrap QE-HF instrument, with high sensitivity, fragmentation efficiency, and analysis speed. In addition, a novel EED MS2-guided MS3 approach was developed for detailed glycan structural analysis. Automated topology reconstruction from MS2 and MS3 spectra could be achieved with a modified GlycoDeNovo software. We showed that the topology and linkage configurations of the Man9GlcNAc2 glycan can be accurately determined from first principles based on one EED MS2 and two CID-EED MS3 analyses, without reliance on biological knowledge, a structure database or a spectral library. The presented approach holds great promise for autonomous, comprehensive and de novo glycan sequencing.
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Affiliation(s)
- Juan Wei
- Shanghai Jiao Tong University 800 Dongchuan Road Shanghai 200240 China
- Center for Biomedical Mass Spectrometry, Boston University Chobanian & Avedisian School of Medicine Boston MA 02118 USA
| | | | | | | | - Pengyu Hong
- Department of Computer Science, Brandeis University Waltham MA 02454 USA
| | - Nafisa Tursumamat
- Shanghai Jiao Tong University 800 Dongchuan Road Shanghai 200240 China
| | - Joshua A Klein
- Center for Biomedical Mass Spectrometry, Boston University Chobanian & Avedisian School of Medicine Boston MA 02118 USA
| | - Chaoshuang Xia
- Center for Biomedical Mass Spectrometry, Boston University Chobanian & Avedisian School of Medicine Boston MA 02118 USA
| | - Yang Tang
- Center for Biomedical Mass Spectrometry, Boston University Chobanian & Avedisian School of Medicine Boston MA 02118 USA
- Department of Chemistry, Boston University Boston MA 02215 USA
| | - Joseph Zaia
- Center for Biomedical Mass Spectrometry, Boston University Chobanian & Avedisian School of Medicine Boston MA 02118 USA
| | - Catherine E Costello
- Center for Biomedical Mass Spectrometry, Boston University Chobanian & Avedisian School of Medicine Boston MA 02118 USA
- Department of Chemistry, Boston University Boston MA 02215 USA
| | - Cheng Lin
- Center for Biomedical Mass Spectrometry, Boston University Chobanian & Avedisian School of Medicine Boston MA 02118 USA
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2
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Sarbu M, Ica R, Sharon E, Clemmer DE, Zamfir AD. Glycomics by ion mobility tandem mass spectrometry of chondroitin sulfate disaccharide domain in biglycan. JOURNAL OF MASS SPECTROMETRY : JMS 2023; 58:e4908. [PMID: 36799777 DOI: 10.1002/jms.4908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 01/30/2023] [Accepted: 02/01/2023] [Indexed: 06/18/2023]
Abstract
Biglycan (BGN), a small leucine-rich repeat proteoglycan, is involved in a variety of pathological processes including malignant transformation, for which the upregulation of BGN was found related to cancer cell invasiveness. Because the functions of BGN are mediated by its chondroitin/dermatan sulfate (CS/DS) chains through the sulfates, the determination of CS/DS structure and sulfation pattern is of major importance. In this study, we have implemented an advanced glycomics method based on ion mobility separation (IMS) mass spectrometry (MS) and tandem MS (MS/MS) to characterize the CS disaccharide domains in BGN. The high separation efficiency and sensitivity of this technique allowed the discrimination of five distinct CS disaccharide motifs, of which four irregulated in their sulfation pattern. For the first time, trisulfated unsaturated and bisulfated saturated disaccharides were found in BGN, the latter species documenting the non-reducing end of the chains. The structural investigation by IMS MS/MS disclosed that in one or both of the CS/DS chains, the non-reducing end is 3-O-sulfated GlcA in a rather rare bisulfated motif having the structure 3-O-sulfated GlcA-4-O-sulfated GalNAc. Considering the role played by BGN in cancer cell spreading, the influence on this process of the newly identified sequences will be investigated in the future.
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Affiliation(s)
- Mirela Sarbu
- Department of Condensed Matter, National Institute for Research and Development in Electrochemistry and Condensed Matter, Timisoara, 300569, Romania
| | - Raluca Ica
- Department of Condensed Matter, National Institute for Research and Development in Electrochemistry and Condensed Matter, Timisoara, 300569, Romania
- Department of Physics, West University of Timisoara, Timisoara, 300223, Romania
| | - Edie Sharon
- Department of Chemistry, The College of Arts & Science, Indiana University, Bloomington, Indiana, USA
| | - David E Clemmer
- Department of Chemistry, The College of Arts & Science, Indiana University, Bloomington, Indiana, USA
| | - Alina D Zamfir
- Department of Condensed Matter, National Institute for Research and Development in Electrochemistry and Condensed Matter, Timisoara, 300569, Romania
- Department of Technical and Natural Sciences, "Aurel Vlaicu" University of Arad, Arad, 310330, Romania
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3
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Fabijanczuk K, Yu ZJ, Bakestani RM, Murtada R, Denton N, Gaspar K, Otegui T, Acosta J, Kenttämaa HI, Eshuis H, Gao J. Mechanistic Study into Free Radical-Activated Glycan Dissociations through Isotope-Labeled Cellobioses. Anal Chem 2023; 95:2932-2941. [PMID: 36715667 PMCID: PMC10129047 DOI: 10.1021/acs.analchem.2c04649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Inspired by the electron-activated dissociation technique, the most potent tool for glycan characterization, we recently developed free radical reagents for glycan structural elucidation. However, the underlying mechanisms of free radical-induced glycan dissociation remain unclear and, therefore, hinder the rational optimization of the free radical reagents and the interpretation of tandem mass spectra, especially the accurate assignment of the relatively low-abundant but information-rich ions. In this work, we selectively incorporate the 13C and/or 18O isotopes into cellobiose to study the mechanisms for free radical-induced dissociation of glycans. The eight isotope-labeled cellobioses include 1-13C, 3-13C, 1'-13C, 2'-13C, 3'-13C, 4'-13C, 5'-13C, and 1'-13C-4-18O-cellobioses. Upon one-step collisional activation, cross-ring (X ions), glycosidic bond (Y-, Z-, and B-related ions), and combinational (Y1 + 0,4X0 ion) cleavages are generated. These fragment ions can be unambiguously assigned and confirmed by the mass difference of isotope labeling. Importantly, the relatively low-abundant but information-rich ions, such as 1,5X0 + H, 1,4X0 + H, 2,4X0 + H-OH, Y1 + 0,4X0, 2,5X1-H, 3,5X0-H, 0,3X0-H, 1,4X0-H, and B2-3H, are confidently assigned. The mechanisms for the formations of these ions are investigated and supported by quantum chemical calculations. These ions are generally initiated by hydrogen abstraction followed by sequential β-elimination and/or radical migration. Here, the mechanistic study for free radical-induced glycan dissociation allows us to interpret all of the free radical-induced fragment ions accurately and, therefore, enables the differentiation of stereochemical isomers. Moreover, it provides fundamental knowledge for the subsequent development of bioinformatics tools to interpret the complex free radical-induced glycan spectra.
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Affiliation(s)
- Kimberly Fabijanczuk
- Department of Chemistry and Biochemistry, Montclair State University, 1 Normal Avenue, Montclair, New Jersey 07043, United States
| | - Zaikuan Josh Yu
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907, United States
| | - Rose M Bakestani
- Department of Chemistry and Biochemistry, Montclair State University, 1 Normal Avenue, Montclair, New Jersey 07043, United States
| | - Rayan Murtada
- Department of Chemistry and Biochemistry, Montclair State University, 1 Normal Avenue, Montclair, New Jersey 07043, United States
| | - Nicholas Denton
- Department of Chemistry and Biochemistry, Montclair State University, 1 Normal Avenue, Montclair, New Jersey 07043, United States
| | - Kaylee Gaspar
- Department of Chemistry and Biochemistry, Montclair State University, 1 Normal Avenue, Montclair, New Jersey 07043, United States
| | - Tara Otegui
- Department of Chemistry and Biochemistry, Montclair State University, 1 Normal Avenue, Montclair, New Jersey 07043, United States
| | - Jose Acosta
- Department of Chemistry and Biochemistry, Montclair State University, 1 Normal Avenue, Montclair, New Jersey 07043, United States
| | - Hilkka I Kenttämaa
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907, United States
| | - Henk Eshuis
- Department of Chemistry and Biochemistry, Montclair State University, 1 Normal Avenue, Montclair, New Jersey 07043, United States
| | - Jinshan Gao
- Department of Chemistry and Biochemistry, Montclair State University, 1 Normal Avenue, Montclair, New Jersey 07043, United States
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4
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Zappe A, Miller RL, Struwe WB, Pagel K. State-of-the-art glycosaminoglycan characterization. MASS SPECTROMETRY REVIEWS 2022; 41:1040-1071. [PMID: 34608657 DOI: 10.1002/mas.21737] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 08/02/2021] [Accepted: 09/22/2021] [Indexed: 06/13/2023]
Abstract
Glycosaminoglycans (GAGs) are heterogeneous acidic polysaccharides involved in a range of biological functions. They have a significant influence on the regulation of cellular processes and the development of various diseases and infections. To fully understand the functional roles that GAGs play in mammalian systems, including disease processes, it is essential to understand their structural features. Despite having a linear structure and a repetitive disaccharide backbone, their structural analysis is challenging and requires elaborate preparative and analytical techniques. In particular, the extent to which GAGs are sulfated, as well as variation in sulfate position across the entire oligosaccharide or on individual monosaccharides, represents a major obstacle. Here, we summarize the current state-of-the-art methodologies used for GAG sample preparation and analysis, discussing in detail liquid chromatograpy and mass spectrometry-based approaches, including advanced ion activation methods, ion mobility separations and infrared action spectroscopy of mass-selected species.
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Affiliation(s)
- Andreas Zappe
- Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, Berlin, Germany
| | - Rebecca L Miller
- Department of Cellular and Molecular Medicine, Copenhagen Centre for Glycomics, University of Copenhagen, Copenhagen, Denmark
| | | | - Kevin Pagel
- Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, Berlin, Germany
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5
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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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6
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Straightforward Analysis of Sulfated Glycosaminoglycans by MALDI-TOF Mass Spectrometry from Biological Samples. BIOLOGY 2022; 11:biology11040506. [PMID: 35453706 PMCID: PMC9024577 DOI: 10.3390/biology11040506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 03/15/2022] [Accepted: 03/22/2022] [Indexed: 11/16/2022]
Abstract
Glycosaminoglycans (GAGs) are considered to be the most difficult type of glycoconjugates to analyze as they are constituted of linear long polysaccharidic chains having molecular weights reaching up to several million daltons. Bottom-up analysis of glycosaminoglycans from biological samples is a long and work-extensive procedure due to the many preparation steps involved. In addition, so far, only few research articles have been dedicated to the analysis of GAGs by means of matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF-MS) because their intact ionization can be problematic due to the presence of labile sulfate groups. In this work, we had the aim of exploring the sulfation pattern of monosulfated chondroitin/dermatan sulfate (CS/DS) disaccharides in human tissue samples because they represent the most abundant form of sulfation in disaccharides. We present here an optimized strategy to analyze on-target derivatized CS/DS disaccharides via MALDI-TOF-MS using a fast workflow that does not require any purification after enzymatic cleavage. For the first time, we show that MALDI-TOF/TOF experiments allow for discrimination between monosulfated CS disaccharide isomers via specific fragments corresponding to glycosidic linkages and to cross-ring cleavages. This proof of concept is illustrated via the analysis of CS/DS disaccharides of atherosclerotic lesions of different histological origins, in which we were able to identify their monosulfation patterns.
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7
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An Z, Zhang Z, Zhang X, Yang H, Lu H, Liu M, Shao Y, Zhao X, Zhang H. Oligosaccharide mapping analysis by HILIC-ESI-HCD-MS/MS for structural elucidation of fucoidan from sea cucumber Holothuria floridana. Carbohydr Polym 2022; 275:118694. [PMID: 34742421 DOI: 10.1016/j.carbpol.2021.118694] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 09/10/2021] [Accepted: 09/19/2021] [Indexed: 01/02/2023]
Abstract
The elucidation of precise structure of fucoidan is essential for understanding their structure-function relationship and promoting the development of marine drugs. In this work, we firstly reported the oligosaccharide mapping of fucoidan from Holothuria floridana using a combination of hydrothermal depolymerization, hydrophilic interaction liquid chromatography (HILIC) coupled with electrospray mass spectrometry (ESI-FTMS) and high energy collision-induced dissociation (HCD-MS/MS) and 2D NMR analysis. With careful selection of fully deprotonated molecular ions of fucoidan oligosaccharides and their NaBD4 reduced alditols, HILIC-ESI-HCD-MS/MS provided structurally relevant glycosidic product ions with no sulfate loss for definitive assignment of sequence and sulfation pattern of all the oligosaccharides and their isomers from dp2 to dp7 from hydrothermal depolymerization. The oligosaccharide mapping clarified the structure of fucoidan with various oligosaccharide domains with 2,4-di-O-sulfated and 2-O sulfated fucose residues.
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Affiliation(s)
- Zizhe An
- College of Food Science and Engineering, Ocean University of China, No. 5, Yushan Road, Qingdao, Shandong Province 266003, PR China
| | - Zhaohui Zhang
- College of Food Science and Engineering, Ocean University of China, No. 5, Yushan Road, Qingdao, Shandong Province 266003, PR China
| | - Xiaomei Zhang
- The Technology Center of Qingdao Customs, No. 83, Xinyue Road, Qingdao, Shandong Province 266109, PR China
| | - Huicheng Yang
- Zhejiang Marine Development Research Institute, No. 10, Lincheng Street, Zhoushan, Zhejiang Province 316021, PR China
| | - Haiyan Lu
- College of Food Science and Engineering, Ocean University of China, No. 5, Yushan Road, Qingdao, Shandong Province 266003, PR China
| | - Mengyang Liu
- College of Food Science and Engineering, Ocean University of China, No. 5, Yushan Road, Qingdao, Shandong Province 266003, PR China
| | - Ying Shao
- College of Food Science and Engineering, Ocean University of China, No. 5, Yushan Road, Qingdao, Shandong Province 266003, PR China
| | - Xue Zhao
- College of Food Science and Engineering, Ocean University of China, No. 5, Yushan Road, Qingdao, Shandong Province 266003, PR China.
| | - Hongwei Zhang
- The Technology Center of Qingdao Customs, No. 83, Xinyue Road, Qingdao, Shandong Province 266109, PR China.
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8
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Wang H, Wang Y, Hou M, Zhang C, Wang Y, Guo Z, Bu D, Li Y, Huang C, Sun S. HepParser: An Intelligent Software Program for Deciphering Low-Molecular-Weight Heparin Based on Mass Spectrometry. Front Chem 2021; 9:723149. [PMID: 34568278 PMCID: PMC8458631 DOI: 10.3389/fchem.2021.723149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 08/10/2021] [Indexed: 11/17/2022] Open
Abstract
Low-molecular-weight heparins (LMWHs) are considered to be the most successful carbohydrate-based drugs because of their wide use as anticoagulants in clinics. The efficacy of anticoagulants made by LMWHs mainly depends on the components and structures of LMWHs. Therefore, deciphering the components and identifying the structures of LMWHs are critical to developing high-efficiency anticoagulants. However, most LMWHs are mixtures of linear polysaccharides which are comprised of several disaccharide repeating units with high similarity, making it extremely challenging to separate and decipher each component in LMWHs. Here, we present a new algorithm named hepParser to decipher the main components of LMWHs automatically and precisely based on the liquid chromatography/mass spectrometry (LC/MS) data. When tested on the general LMWH using hepParser, profiling of the oligosaccharides with different degrees of polymerization (dp’s) was completed with high accuracy within 1 minute. When compared with the results of GlycReSoft on heparan sulfate samples, hepParser achieved more comprehensive and reasonable results automatically.
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Affiliation(s)
- Hui Wang
- Key Lab of Intelligent Information Processing, State Key Lab of Computer Architecture, Big-data Academy, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yu Wang
- Key Lab of Intelligent Information Processing, State Key Lab of Computer Architecture, Big-data Academy, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Meijie Hou
- Key Lab of Intelligent Information Processing, State Key Lab of Computer Architecture, Big-data Academy, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Chunming Zhang
- Key Lab of Intelligent Information Processing, State Key Lab of Computer Architecture, Big-data Academy, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China.,Phil Rivers Technology, Beijing, China
| | - Yaojun Wang
- College of Information and Electrical Engineering, China Agricultural University, Beijing, China
| | - Zhendong Guo
- University of Chinese Academy of Sciences, Beijing, China.,Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Dongbo Bu
- Key Lab of Intelligent Information Processing, State Key Lab of Computer Architecture, Big-data Academy, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yan Li
- University of Chinese Academy of Sciences, Beijing, China.,Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Chuncui Huang
- University of Chinese Academy of Sciences, Beijing, China.,Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Shiwei Sun
- Key Lab of Intelligent Information Processing, State Key Lab of Computer Architecture, Big-data Academy, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
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9
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Pepi LE, Leach FE, Klein DR, Brodbelt JS, Amster IJ. Investigation of the Experimental Parameters of Ultraviolet Photodissociation for the Structural Characterization of Chondroitin Sulfate Glycosaminoglycan Isomers. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:1759-1770. [PMID: 34096288 PMCID: PMC8377745 DOI: 10.1021/jasms.1c00119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Glycosaminoglycans (GAGs) are linear polysaccharides that participate in a broad range of biological functions. Their incomplete biosynthesis pathway leads to nonuniform chains and complex mixtures. For this reason, the characterization of GAGs has been a difficult hurdle for the analytical community. Recently, ultraviolet photodissociation (UVPD) has emerged as a useful tool for determining sites of modification within a GAG chain. Here, we investigate the ability for UVPD to distinguish chondroitin sulfate epimers and the effects of UVPD experimental parameters on fragmentation efficiency. Chondroitin sulfate A (CS-A) and chondroitin sulfate B (CS-B), commonly referred to as dermatan sulfate (DS), differ only in C-5 uronic acid stereochemistry. This uronic acid difference can influence GAG-protein binding and therefore can alter the specific biological function of a GAG chain. Prior tandem mass spectrometry methods investigated for the elucidation of GAG structures also have difficulty differentiating 4-O from 6-O sulfation in chondroitin sulfate GAGs. Preliminary data using UVPD to characterize GAGs showed a promising ability to characterize 4-O sulfation in CS-A GAGs. Here, we look in depth at the capability of UVPD to distinguish chondroitin sulfate C-5 diastereomers and the role of key experimental parameters in making this distinction. Results using a 193 nm excimer laser and a 213 nm solid-state laser are compared for this study. The effect of precursor ionization state, the number of laser pulses (193 or 213 nm UVPD), and the use of the low-pressure versus high-pressure trap are investigated.
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Affiliation(s)
- Lauren E Pepi
- Department of Chemistry, University of Georgia, Athens, Georgia 30602, United States
| | - Franklin E Leach
- Department of Chemistry, University of Georgia, Athens, Georgia 30602, United States
- Department of Environmental Health Sciences, University of Georgia, Athens, Georgia 30602, United States
| | - Dustin R Klein
- Department of Biochemistry and Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Jennifer S Brodbelt
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - I Jonathan Amster
- Department of Chemistry, University of Georgia, Athens, Georgia 30602, United States
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10
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Mendis PM, Sasiene ZJ, Ropartz D, Rogniaux H, Jackson GP. Ultra-high-performance liquid chromatography charge transfer dissociation mass spectrometry (UHPLC-CTD-MS) as a tool for analyzing the structural heterogeneity in carrageenan oligosaccharides. Anal Bioanal Chem 2021; 414:303-318. [PMID: 34050776 DOI: 10.1007/s00216-021-03396-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 04/16/2021] [Accepted: 05/07/2021] [Indexed: 02/03/2023]
Abstract
Ultra-high-performance liquid chromatography (UHPLC) with charge transfer dissociation mass spectrometry (CTD-MS) is presented for the analysis of a mixture of complex sulfated oligosaccharides. The mixture contained kappa (κ), iota (ι), and lambda (λ) carrageenans that contain anhydro bridges, different degrees of sulfation ranging from one to three per dimer, different positioning of the sulfate groups along the backbone, and varying degrees of polymerization (DP) between 4 and 12. Optimization studies using standard mixtures of carrageenans helped establish the optimal conditions for online UHPLC-CTD-MS/MS analysis. Optimization included (1) UHPLC conditions; (2) ion source conditions, such as the capillary voltage, drying gas and nebulizing gas temperature, and flow rate; and (3) CTD-MS conditions, including data-dependent CTD-MS. The UHPLC-CTD results were contrasted with UHPLC-CID results of the same mixture on the same instrument. Whereas CID tends to produce B/Y and C/Z ions with many neutral losses, CTD produced more abundant A/X ions and less abundant neutral losses, which enabled more confident structural detail. The results demonstrate that He-CTD is compatible with the timescale of UHPLC and provides more structural information about carrageenans compared to state-of-the-art methods like UHPLC-CID analysis.
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Affiliation(s)
- Praneeth M Mendis
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV, 26506-6121, USA
| | - Zachary J Sasiene
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV, 26506-6121, USA
| | - David Ropartz
- INRAE, UR BIA, 44316, Nantes, France
- INRAE, BIBS Facility, 44316, Nantes, France
| | - Hélène Rogniaux
- INRAE, UR BIA, 44316, Nantes, France
- INRAE, BIBS Facility, 44316, Nantes, France
| | - Glen P Jackson
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV, 26506-6121, USA.
- Department of Forensic and Investigative Science, West Virginia University, Morgantown, WV, 26506-6121, USA.
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11
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Pepi LE, Amster IJ. Electron-Activated Tandem Mass Spectrometry Analysis of Glycosaminoglycans. Curr Protoc 2021; 1:e83. [PMID: 33798269 PMCID: PMC8034365 DOI: 10.1002/cpz1.83] [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] [Indexed: 11/06/2022]
Abstract
Glycosaminoglycans (GAGs) are linear polysaccharides found in a variety of organisms. GAGs contribute to biochemical pathway regulation, cell signaling, and disease progression. GAG sequence information is imperative for determining structure-function relationships. Recent advances in electron-activation techniques paired with high-resolution mass spectrometry allow for full sequencing of GAG structures. Electron detachment dissociation (EDD) and negative electron transfer dissociation (NETD) are two electron-activation methods that have been utilized for GAG characterization. Both methods produce an abundance of informative glycosidic and cross-ring fragment ions without producing a high degree of sulfate decomposition. Here, we provide detailed protocols for using EDD and NETD to sequence GAG chains. In addition to protocols directly involving performing these MS/MS methods, protocols include sample preparation, method development, internal calibration, and data analysis. © 2021 Wiley Periodicals LLC. Basic Protocol 1: Preparation of glycosaminoglycan samples Basic Protocol 2: FTICR method development Basic Protocol 3: Internal calibration with NaTFA Basic Protocol 4: Electron Detachment Dissociation (EDD) of GAG samples Basic Protocol 5: Negative electron transfer dissociation (NETD) of GAG samples Basic Protocol 6: Analysis of MS/MS data.
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Affiliation(s)
- Lauren E. Pepi
- Department of Chemistry, University of Georgia, Athens, GA 30602
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12
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Song Y, Zhang F, Linhardt RJ. Analysis of the Glycosaminoglycan Chains of Proteoglycans. J Histochem Cytochem 2021; 69:121-135. [PMID: 32623943 PMCID: PMC7841699 DOI: 10.1369/0022155420937154] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 05/29/2020] [Indexed: 12/16/2022] Open
Abstract
Glycosaminoglycans (GAGs) are heterogeneous, negatively charged, macromolecules that are found in animal tissues. Based on the form of component sugar, GAGs have been categorized into four different families: heparin/heparan sulfate, chondroitin/dermatan sulfate, keratan sulfate, and hyaluronan. GAGs engage in biological pathway regulation through their interaction with protein ligands. Detailed structural information on GAG chains is required to further understanding of GAG-ligand interactions. However, polysaccharide sequencing has lagged behind protein and DNA sequencing due to the non-template-driven biosynthesis of glycans. In this review, we summarize recent progress in the analysis of GAG chains, specifically focusing on techniques related to mass spectroscopy (MS), including separation techniques coupled to MS, tandem MS, and bioinformatics software for MS spectrum interpretation. Progress in the use of other structural analysis tools, such as nuclear magnetic resonance (NMR) and hyphenated techniques, is included to provide a comprehensive perspective.
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Affiliation(s)
- Yuefan Song
- National R & D Branch Center for Seaweed Processing, College of Food Science and Engineering, Dalian Ocean University, Dalian, P.R. China
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York
| | - Fuming Zhang
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York
| | - Robert J Linhardt
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York
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13
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Sheng A, Chen Q, Yu M, Xiao R, Zhang T, Wang Z, Linhardt RJ, Sun X, Jin L, Chi L. Coupling Liquid Chromatography and Tandem Mass Spectrometry to Electrophoresis for In-Depth Analysis of Glycosaminoglycan Drugs: Heparin and the Multicomponent Sulodexide. Anal Chem 2021; 93:1433-1442. [PMID: 33369405 DOI: 10.1021/acs.analchem.0c03330] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Glycosaminoglycans (GAGs) contribute to the treatment of many human diseases, especially in the field of thrombosis, because of their anticoagulant activity. GAGs interrupt the coagulation process by interacting with multiple coagulation factors through defined sequences within their linear and negatively charged chains, which are not fully elucidated. Numerous methods have been developed to characterize the structure of pharmaceutical GAGs, including intravenously or subcutaneously administered heparin and orally administered sulodexide. However, most currently available methods only focus on the oligosaccharide portion or analyze the whole mixture because longer-chain polysaccharides are extremely difficult to resolve by chromatographic separation. We have established two novel electrophoresis-mass spectrometry methods to provide a panoramic view of the structures of pharmaceutical GAGs. In the first method, an in-gel digestion procedure was developed to recover GAGs from the polyacrylamide gels, while in the second method, a strong anion exchange ultrafiltration procedure was developed to extract multiple GAG species from the agarose gels. Both procedures are compatible with liquid chromatography-tandem mass spectrometry, and structural information, such as disaccharide composition and chain length, can be revealed for each GAG fraction. The applications of these two methods on analysis of two different GAG drugs, heparin and sulodexide, were demonstrated. The current study offers the first robust tool to directly elucidate the structure of larger GAG chains with more biological importance rather than obtaining a vague picture of all chains as a mixture, which is fundamental for better understanding the structure-activity relationship and quality control of the GAG drugs.
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Affiliation(s)
- Anran Sheng
- National Glycoengineering Research Center, Shandong Provincial Key Laboratory of Carbohydrate Chemistry and Glycobiology, Shandong University, Qingdao 266237, China
| | - Qingqing Chen
- National Glycoengineering Research Center, Shandong Provincial Key Laboratory of Carbohydrate Chemistry and Glycobiology, Shandong University, Qingdao 266237, China
| | - Mengqi Yu
- National Glycoengineering Research Center, Shandong Provincial Key Laboratory of Carbohydrate Chemistry and Glycobiology, Shandong University, Qingdao 266237, China
| | - Ruiqi Xiao
- National Glycoengineering Research Center, Shandong Provincial Key Laboratory of Carbohydrate Chemistry and Glycobiology, Shandong University, Qingdao 266237, China
| | - Tianji Zhang
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China.,Division of Chemistry and Analytical Science, National Institute of Metrology, Beijing 100029, China
| | - Zhiyu Wang
- Department of Virology, School of Public Health, Shandong University, Jinan 250012, China
| | - Robert J Linhardt
- Department of Chemistry and Chemical Biology, Department of Chemical and Biological Engineering, Department of Biology, and Department of Biomedical Engineering, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
| | - Xiaojun Sun
- Collaborative Innovation Center for Green Chemical Manufacturing and Accurate Detection, School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, China
| | - Lan Jin
- National Glycoengineering Research Center, Shandong Provincial Key Laboratory of Carbohydrate Chemistry and Glycobiology, Shandong University, Qingdao 266237, China
| | - Lianli Chi
- National Glycoengineering Research Center, Shandong Provincial Key Laboratory of Carbohydrate Chemistry and Glycobiology, Shandong University, Qingdao 266237, China
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14
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Mendis PM, Sasiene ZJ, Ropartz D, Rogniaux H, Jackson GP. Structural Characterization of Isomeric Oligogalacturonan Mixtures Using Ultrahigh-Performance Liquid Chromatography-Charge Transfer Dissociation Mass Spectrometry. Anal Chem 2021; 93:2838-2847. [PMID: 33497195 DOI: 10.1021/acs.analchem.0c04142] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Pectins are natural polysaccharides made from galacturonic acid residues, and they are widely used as an excipient in food and pharmaceutical industries. The degree of methyl-esterification, the monomeric composition, and the linkage pattern are all important factors that influence the physical and chemical properties of pectins, such as the solubility. This work focuses on the successful online coupling of charge transfer dissociation-mass spectrometry (CTD-MS) with ultrahigh-performance liquid chromatography (UHPLC) to differentiate isomers of oligogalacturonans derived from citrus pectins. This work employed CTD fragmentation of the pectin mixtures in data-dependent acquisition mode. Compared to the UHPLC with collision-induced dissociation mass spectrometry (UHPLC-CID-MS), UHPLC-CTD-MS yielded fewer ambiguous ions and more structurally informative results. The developed UHPLC-CTD-MS method resulted in abundant cross-ring cleavages-and especially 1,4Xn, 1,5Xn, and 2,4Xn ions-which helped to identify most of the isomers. The Gal A isomers differed only in the methyl group position along the galacturonic acid backbone. The combination of CTD in real time with UHPLC provides a new tool for the structural characterization of complex mixtures of oligogalacturonans and potentially other classes of oligosaccharides.
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Affiliation(s)
- Praneeth M Mendis
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, West Virginia 26506-6121, United States
| | - Zachary J Sasiene
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, West Virginia 26506-6121, United States
| | - David Ropartz
- INRAE, UR BIA, Nantes F-44316, France.,INRAE, BIBS Facility, Nantes F-44316, France
| | - Hélène Rogniaux
- INRAE, UR BIA, Nantes F-44316, France.,INRAE, BIBS Facility, Nantes F-44316, France
| | - Glen P Jackson
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, West Virginia 26506-6121, United States.,Department of Forensic and Investigative Science, West Virginia University, Morgantown, West Virginia 26506-6121, United States
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15
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Pepi LE, Sanderson P, Stickney M, Amster IJ. Developments in Mass Spectrometry for Glycosaminoglycan Analysis: A Review. Mol Cell Proteomics 2021; 20:100025. [PMID: 32938749 PMCID: PMC8724624 DOI: 10.1074/mcp.r120.002267] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 09/15/2020] [Accepted: 09/16/2020] [Indexed: 12/11/2022] Open
Abstract
This review covers recent developments in glycosaminoglycan (GAG) analysis via mass spectrometry (MS). GAGs participate in a variety of biological functions, including cellular communication, wound healing, and anticoagulation, and are important targets for structural characterization. GAGs exhibit a diverse range of structural features due to the variety of O- and N-sulfation modifications and uronic acid C-5 epimerization that can occur, making their analysis a challenging target. Mass spectrometry approaches to the structure assignment of GAGs have been widely investigated, and new methodologies remain the subject of development. Advances in sample preparation, tandem MS techniques (MS/MS), online separations, and automated analysis software have advanced the field of GAG analysis. These recent developments have led to remarkable improvements in the precision and time efficiency for the structural characterization of GAGs.
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Affiliation(s)
- Lauren E Pepi
- Department of Chemistry, University of Georgia, Athens, Georgia, USA
| | | | - Morgan Stickney
- Department of Chemistry, University of Georgia, Athens, Georgia, USA
| | - I Jonathan Amster
- Department of Chemistry, University of Georgia, Athens, Georgia, USA.
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16
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Hogan JD, Wu J, Klein JA, Lin C, Carvalho L, Zaia J. GAGrank: Software for Glycosaminoglycan Sequence Ranking Using a Bipartite Graph Model. Mol Cell Proteomics 2021; 20:100093. [PMID: 33992776 PMCID: PMC8214146 DOI: 10.1016/j.mcpro.2021.100093] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 03/25/2021] [Accepted: 05/07/2021] [Indexed: 01/08/2023] Open
Abstract
The sulfated glycosaminoglycans (GAGs) are long, linear polysaccharide chains that are typically found as the glycan portion of proteoglycans. These GAGs are characterized by repeating disaccharide units with variable sulfation and acetylation patterns along the chain. GAG length and modification patterns have profound impacts on growth factor signaling mechanisms central to numerous physiological processes. Electron activated dissociation tandem mass spectrometry is a very effective technique for assigning the structures of GAG saccharides; however, manual interpretation of the resulting complex tandem mass spectra is a difficult and time-consuming process that drives the development of computational methods for accurate and efficient sequencing. We have recently published GAGfinder, the first peak picking and elemental composition assignment algorithm specifically designed for GAG tandem mass spectra. Here, we present GAGrank, a novel network-based method for determining GAG structure using information extracted from tandem mass spectra using GAGfinder. GAGrank is based on Google's PageRank algorithm for ranking websites for search engine output. In particular, it is an implementation of BiRank, an extension of PageRank for bipartite networks. In our implementation, the two partitions comprise every possible sequence for a given GAG composition and the tandem MS fragments found using GAGfinder. Sequences are given a higher ranking if they link to many important fragments. Using the simulated annealing probabilistic optimization technique, we optimized GAGrank's parameters on ten training sequences. We then validated GAGrank's performance on three validation sequences. We also demonstrated GAGrank's ability to sequence isomeric mixtures using two mixtures at five different ratios.
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Affiliation(s)
- John D Hogan
- Program in Bioinformatics, Boston University, Boston, Massachusetts, USA; Department of Biochemistry, Center for Biomedical Mass Spectrometry, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Jiandong Wu
- Department of Biochemistry, Center for Biomedical Mass Spectrometry, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Joshua A Klein
- Program in Bioinformatics, Boston University, Boston, Massachusetts, USA; Department of Biochemistry, Center for Biomedical Mass Spectrometry, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Cheng Lin
- Department of Biochemistry, Center for Biomedical Mass Spectrometry, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Luis Carvalho
- Program in Bioinformatics, Boston University, Boston, Massachusetts, USA; Department of Mathematics & Statistics, Boston University, Boston, Massachusetts, USA
| | - Joseph Zaia
- Program in Bioinformatics, Boston University, Boston, Massachusetts, USA; Department of Biochemistry, Center for Biomedical Mass Spectrometry, Boston University School of Medicine, Boston, Massachusetts, USA.
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17
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Pepi LE, Sasiene ZJ, Mendis PM, Jackson GP, Amster IJ. Structural Characterization of Sulfated Glycosaminoglycans Using Charge-Transfer Dissociation. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:2143-2153. [PMID: 32820910 PMCID: PMC8045215 DOI: 10.1021/jasms.0c00252] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Glycosaminoglycans (GAGs) participate in a broad range of physiological processes, and their structures are of interest to researchers in structural biology and medicine. Although they are abundant in tissues and extracellular matrices, their structural heterogeneity makes them challenging analytes. Mass spectrometry, and more specifically, tandem mass spectrometry, is particularly well suited for their analysis. Many tandem mass spectrometry techniques have been examined for their suitability toward the structural characterization of GAGs. Threshold activation methods such as collision-induced dissociation (CID) produce mainly glycosidic cleavages and do not yield a broad range of structurally informative cross-ring fragments. Considerable research efforts have been directed at finding other means of dissociating gas-phase GAG ions to produce more comprehensive structural information. Here, we compare the structural information on GAGs obtained by charge-transfer dissociation (CTD) and electron detachment dissociation (EDD). EDD has previously been applied to GAGs and is known to produce both glycosidic and cross-ring cleavages in similar abundance. CTD has not previously been used to analyze GAGs but has been shown to produce abundant cross-ring cleavages and no sulfate loss when applied to another class of sulfated carbohydrates like algal polysaccharides. In contrast to EDD, which is restricted to FTICR mass spectrometers, CTD can be implemented on other platforms, such as ion trap mass spectrometers (ITMS). Here, we show the capability of CTD-ITMS to produce structurally significant details of the sites of modification in both heparan sulfate (HS) and chondroitin sulfate (CS) standards ranging in length from degree of polymerization (dp) 4 to dp6. EDD and CTD both yield more structural information than CID and yield similar fractional abundances to one another for glycosidic fragments, cross-ring fragments, and neutral losses.
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Affiliation(s)
- Lauren E Pepi
- Department of Chemistry, University of Georgia, Athens, Georgia 30602, United States
| | - Zachary J Sasiene
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, West Virginia 26506, United States
| | - Praneeth M Mendis
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, West Virginia 26506, United States
| | - Glen P Jackson
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, West Virginia 26506, United States
- Department of Forensic and Investigative Science, West Virginia University, Morgantown, West Virginia 26506, United States
| | - I Jonathan Amster
- Department of Chemistry, University of Georgia, Athens, Georgia 30602, United States
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18
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Ultraviolet photodissociation of fondaparinux generates signature antithrombin-like 3-O-sulfated -GlcNS3S6S- monosaccharide fragment (Y3/C3). Anal Bioanal Chem 2020; 412:7925-7935. [DOI: 10.1007/s00216-020-02925-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Revised: 07/27/2020] [Accepted: 08/28/2020] [Indexed: 12/22/2022]
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19
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Bayat P, Lesage D, Cole RB. TUTORIAL: ION ACTIVATION IN TANDEM MASS SPECTROMETRY USING ULTRA-HIGH RESOLUTION INSTRUMENTATION. MASS SPECTROMETRY REVIEWS 2020; 39:680-702. [PMID: 32043643 DOI: 10.1002/mas.21623] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Accepted: 01/23/2020] [Indexed: 05/16/2023]
Abstract
Tandem mass spectrometry involves isolation of specific precursor ions and their subsequent excitation through collision-, photon-, or electron-mediated activation techniques in order to induce unimolecular dissociation leading to formation of fragment ions. These powerful ion activation techniques, typically used in between mass selection and mass analysis steps for structural elucidation, have not only found a wide variety of analytical applications in chemistry and biology, but they have also been used to study the fundamental properties of ions in the gas phase. In this tutorial paper, a brief overview is presented of the theories that have been used to describe the activation of ions and their subsequent unimolecular dissociation. Acronyms of the presented techniques include CID, PQD, HCD, SORI, SID, BIRD, IRMPD, UVPD, EPD, ECD, EDD, ETD, and EID. The fundamental principles of these techniques are discussed in the context of their implementation on ultra-high resolution tandem mass spectrometers. © 2020 John Wiley & Sons Ltd. Mass Spec Rev.
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Affiliation(s)
- Parisa Bayat
- Faculté des Sciences et Ingénierie, Sorbonne Université, IPCM (UMR 8232), F-75252, Paris, France
| | - Denis Lesage
- Faculté des Sciences et Ingénierie, Sorbonne Université, IPCM (UMR 8232), F-75252, Paris, France
| | - Richard B Cole
- Faculté des Sciences et Ingénierie, Sorbonne Université, IPCM (UMR 8232), F-75252, Paris, France
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20
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Peters-Clarke TM, Quan Q, Brademan DR, Hebert AS, Westphall MS, Coon JJ. Ribonucleic Acid Sequence Characterization by Negative Electron Transfer Dissociation Mass Spectrometry. Anal Chem 2020; 92:4436-4444. [PMID: 32091202 PMCID: PMC7161943 DOI: 10.1021/acs.analchem.9b05388] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Modified oligonucleotides represent a promising avenue for drug development, with small interfering RNAs (siRNA) and microRNAs gaining traction in the therapeutic market. Mass spectrometry (MS)-based analysis offers many benefits for characterizing modified nucleic acids. Negative electron transfer dissociation (NETD) has proven valuable in sequencing oligonucleotide anions, particularly because it can retain modifications while generating sequence-informative fragments. We show that NETD can be successfully implemented on a widely available quadrupole-Orbitrap-linear ion trap mass spectrometer that uses a front-end glow discharge source to generate radical fluoranthene reagent cations. We characterize both unmodified and modified ribonucleic acids and present the first application of activated-ion negative electron transfer dissociation (AI-NETD) to nucleic acids. AI-NETD achieved 100% sequence coverage for both a 6-mer (5'-rGmUrArCmUrG-3') with 2'-O-methyl modifications and a 21-mer (5'-rCrArUrCrCrUrCrUrArGrArGrGrArUrArGrArArUrG-3'), the luciferase antisense siRNA. Both NETD and AI-NETD afforded complete sequence coverage of these molecules while maintaining a relatively low degree of undesired base-loss products and internal products relative to collision-based methods.
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Affiliation(s)
| | - Qiuwen Quan
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Dain R. Brademan
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | | | | | - Joshua J. Coon
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
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21
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Glycosaminoglycan Domain Mapping of Cellular Chondroitin/Dermatan Sulfates. Sci Rep 2020; 10:3506. [PMID: 32103093 PMCID: PMC7044218 DOI: 10.1038/s41598-020-60526-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Accepted: 02/12/2020] [Indexed: 12/22/2022] Open
Abstract
Glycosaminoglycans (GAGs) are polysaccharides produced by most mammalian cells and involved in a variety of biological processes. However, due to the size and complexity of GAGs, detailed knowledge about the structure and expression of GAGs by cells, the glycosaminoglycome, is lacking. Here we report a straightforward and versatile approach for structural domain mapping of complex mixtures of GAGs, GAGDoMa. The approach is based on orthogonal enzymatic depolymerization of the GAGs to generate internal, terminating, and initiating domains, and nanoflow reversed-phase ion-pairing chromatography with negative mode higher-energy collision dissociation (HCD) tandem mass spectrometry (MS/MS) for structural characterization of the individual domains. GAGDoMa provides a detailed structural insight into the glycosaminoglycome, and offers an important tool for deciphering the complexity of GAGs in cellular physiology and pathology.
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22
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Han X, Sanderson P, Nesheiwat S, Lin L, Yu Y, Zhang F, Amster IJ, Linhardt RJ. Structural analysis of urinary glycosaminoglycans from healthy human subjects. Glycobiology 2020; 30:143-151. [PMID: 31616929 PMCID: PMC7415306 DOI: 10.1093/glycob/cwz088] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 10/07/2019] [Accepted: 10/09/2019] [Indexed: 11/12/2022] Open
Abstract
Urinary glycosaminoglycans (GAGs) can reflect the health condition of a human being, and the GAGs composition can be directly related to various diseases. In order to effectively utilize such information, a detailed understanding of urinary GAGs in healthy individuals can provide insight into the levels and structures of human urinary GAGs. In this study, urinary GAGs were collected and purified from healthy males and females of adults and young adults. The total creatinine-normalized urinary GAG content, molecular weight distribution and disaccharide compositions were determined. Using capillary zone electrophoresis (CZE)-mass spectrometry (MS) and CZE-MS/MS relying on negative electron transfer dissociation, the major components of healthy human urinary GAGs were determined. The structures of 10 GAG oligosaccharides representing the majority of human urinary GAGs were determined.
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Affiliation(s)
- Xiaorui Han
- Departments of Chemistry and Chemical Biology, Biology, Chemical and Biological Engineering and Biomedical Engineering, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, 110 8 Street, Troy, NY 12180, USA
| | - Patience Sanderson
- Department of Chemistry, University of Georgia, 140 Cedar St, Athens, GA 30602, USA
| | - Sara Nesheiwat
- Departments of Chemistry and Chemical Biology, Biology, Chemical and Biological Engineering and Biomedical Engineering, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, 110 8 Street, Troy, NY 12180, USA
| | - Lei Lin
- Departments of Chemistry and Chemical Biology, Biology, Chemical and Biological Engineering and Biomedical Engineering, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, 110 8 Street, Troy, NY 12180, USA
| | - Yanlei Yu
- Departments of Chemistry and Chemical Biology, Biology, Chemical and Biological Engineering and Biomedical Engineering, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, 110 8 Street, Troy, NY 12180, USA
| | - Fuming Zhang
- Departments of Chemistry and Chemical Biology, Biology, Chemical and Biological Engineering and Biomedical Engineering, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, 110 8 Street, Troy, NY 12180, USA
| | - I Jonathan Amster
- Department of Chemistry, University of Georgia, 140 Cedar St, Athens, GA 30602, USA
| | - Robert J Linhardt
- Departments of Chemistry and Chemical Biology, Biology, Chemical and Biological Engineering and Biomedical Engineering, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, 110 8 Street, Troy, NY 12180, USA
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23
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Glycosaminoglycans in biological samples – Towards identification of novel biomarkers. Trends Analyt Chem 2020. [DOI: 10.1016/j.trac.2019.115732] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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24
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Lettow M, Grabarics M, Mucha E, Thomas DA, Polewski Ł, Freyse J, Rademann J, Meijer G, von Helden G, Pagel K. IR action spectroscopy of glycosaminoglycan oligosaccharides. Anal Bioanal Chem 2019; 412:533-537. [PMID: 31853603 PMCID: PMC6992547 DOI: 10.1007/s00216-019-02327-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 11/04/2019] [Accepted: 11/11/2019] [Indexed: 02/06/2023]
Abstract
Glycosaminoglycans (GAGs) are a physio- and pharmacologically highly relevant class of complex saccharides, possessing a linear sequence and strongly acidic character. Their repetitive linear core makes them seem structurally simple at first glance, yet differences in sulfation and epimerization lead to an enormous structural diversity with only a few GAGs having been successfully characterized to date. Recent infrared action spectroscopic experiments on sulfated mono- and disaccharide ions show great promise. Here, we assess the potential of two types of gas-phase action spectroscopy approaches in the range from 1000 to 1800 cm−1 for the structural analysis of complex GAG oligosaccharides. Synthetic tetra- and pentasaccharides were chosen as model compounds for this benchmark study. Utilizing infrared multiple photon dissociation action spectroscopy at room temperature, diagnostic bands are largely unresolved. In contrast, cryogenic infrared action spectroscopy of ions trapped in helium nanodroplets yields resolved infrared spectra with diagnostic features for monosaccharide composition and sulfation pattern. The analysis of GAGs could therefore significantly benefit from expanding the conventional MS-based toolkit with gas-phase cryogenic IR spectroscopy. Graphical abstract ![]()
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Affiliation(s)
- Maike Lettow
- Department of Molecular Physics, Fritz Haber Institute of the Max Planck Society, Faradayweg 4-6, 14195, Berlin, Germany
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Takustraße 3, 14195, Berlin, Germany
| | - Márkó Grabarics
- Department of Molecular Physics, Fritz Haber Institute of the Max Planck Society, Faradayweg 4-6, 14195, Berlin, Germany
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Takustraße 3, 14195, Berlin, Germany
| | - Eike Mucha
- Department of Molecular Physics, Fritz Haber Institute of the Max Planck Society, Faradayweg 4-6, 14195, Berlin, Germany
| | - Daniel A Thomas
- Department of Molecular Physics, Fritz Haber Institute of the Max Planck Society, Faradayweg 4-6, 14195, Berlin, Germany
| | - Łukasz Polewski
- Department of Molecular Physics, Fritz Haber Institute of the Max Planck Society, Faradayweg 4-6, 14195, Berlin, Germany
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Takustraße 3, 14195, Berlin, Germany
| | - Joanna Freyse
- Institute of Pharmacy, Medicinal Chemistry, Freie Universität Berlin, Königin-Luise-Str. 2+4, 14195, Berlin, Germany
| | - Jörg Rademann
- Institute of Pharmacy, Medicinal Chemistry, Freie Universität Berlin, Königin-Luise-Str. 2+4, 14195, Berlin, Germany
| | - Gerard Meijer
- Department of Molecular Physics, Fritz Haber Institute of the Max Planck Society, Faradayweg 4-6, 14195, Berlin, Germany
| | - Gert von Helden
- Department of Molecular Physics, Fritz Haber Institute of the Max Planck Society, Faradayweg 4-6, 14195, Berlin, Germany
| | - Kevin Pagel
- Department of Molecular Physics, Fritz Haber Institute of the Max Planck Society, Faradayweg 4-6, 14195, Berlin, Germany.
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Takustraße 3, 14195, Berlin, Germany.
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25
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Duan J, Pepi L, Amster IJ. A Scoring Algorithm for the Automated Analysis of Glycosaminoglycan MS/MS Data. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2019; 30:2692-2703. [PMID: 31673949 PMCID: PMC6917907 DOI: 10.1007/s13361-019-02338-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Revised: 08/20/2019] [Accepted: 08/20/2019] [Indexed: 06/10/2023]
Abstract
The role of glycosaminoglycans (GAGs) in major biological functions is numerous and diverse, yet structural characterization of them by mass spectrometric techniques proves to be challenging. Characterization of GAG structure from tandem mass spectrometry is a tedious and time-consuming process but one that can be automated in a database-independent, high-throughput fashion through the assistance of software implementing a genetic algorithm (J. Am. Soc. Mass Spectrom. 29, 1802-1911, 2018). This work presents the manner in which this data is interpreted by the software, specifically addressing the development of a scoring algorithm. The significance of glycosidic and cross-ring fragment ions and the implications that specific fragments provide for assigning the positions of modifications are discussed. The scoring algorithm is tested for statistical merit using the widely accepted expectation value as the criterion for quality. Using MS/MS data for well-characterized standards, this scoring approach is shown to assign the correct structure, with a low likelihood (1 in 1012 chances) that the assigned structure matches the data due to random chance. The integrated software that automates the structure assignment is called Glycosaminoglycan-Unambiguous Identification Technology (G-UNIT).
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Affiliation(s)
- Jiana Duan
- Department of Chemistry, University of Georgia, Athens, GA, 30602, USA
| | - Lauren Pepi
- Department of Chemistry, University of Georgia, Athens, GA, 30602, USA
| | - I Jonathan Amster
- Department of Chemistry, University of Georgia, Athens, GA, 30602, USA.
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26
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Stickney M, Sanderson P, Leach FE, Zhang F, Linhardt RJ, Amster IJ. Online Capillary Zone Electrophoresis Negative Electron Transfer Dissociation Tandem Mass Spectrometry of Glycosaminoglycan Mixtures. INTERNATIONAL JOURNAL OF MASS SPECTROMETRY 2019; 445:116209. [PMID: 32641905 PMCID: PMC7343235 DOI: 10.1016/j.ijms.2019.116209] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Glycosaminoglycans (GAGs) are important biological molecules that are highly anionic and occur in nature as complex mixtures. A platform that combines capillary zone electrophoresis (CZE) separations with mass spectrometry (MS) and gas-phase sequencing by using negative electron transfer dissociation (NETD) is shown to be efficacious for the structural analysis of GAG mixtures. CZE is a separation method well suited to the highly negatively charged nature of GAGs. NETD is an electron-based ion activation method that enables the generation of informative fragments with retention of the labile sulfate half-ester modification that determine specific GAG function. Here we combine for the first time NETD and CZE for assigning the structures of GAG oligomers present in mixtures. The speed of ion activation by NETD is found to couple well with the narrow peaks resulting from CZE migration. The platform was optimized with mixtures of GAG tetrasaccharide standards. The potential of the platform is demonstrated by the analysis of enoxaparin, a complex mixture of low molecular weight heparins, which was separated by CZE within 30 minutes and characterized by NETD MS/MS in one online experiment. 37 unique molecular compositions have been identified in enoxaparin using CZE-MS and 9 structures have been assigned with CZE-NETD-MS/MS.
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Affiliation(s)
- Morgan Stickney
- Department of Chemistry, University of Georgia, Athens, GA 30602
| | | | - Franklin E. Leach
- Department of Environmental Health Science, University of Georgia, Athens, GA 30602
| | - Fuming Zhang
- Center for Biotechnology & Interdisciplinary Studies, Departments of Chemistry and Chemical Engineering, Rensselaer Polytechnic Institute, Troy, NY 12180
| | - Robert J. Linhardt
- Center for Biotechnology & Interdisciplinary Studies, Departments of Chemistry and Chemical Engineering, Rensselaer Polytechnic Institute, Troy, NY 12180
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27
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Klein DR, Leach FE, Amster IJ, Brodbelt JS. Structural Characterization of Glycosaminoglycan Carbohydrates Using Ultraviolet Photodissociation. Anal Chem 2019; 91:6019-6026. [PMID: 30932467 DOI: 10.1021/acs.analchem.9b00521] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Structural characterization of sulfated glycosaminoglycans (GAGs) by mass spectrometry has long been a formidable analytical challenge owing to their high structural variability and the propensity for sulfate decomposition upon activation with low-energy ion activation methods. While derivatization and complexation workflows have aimed to generate informative spectra using low-energy ion activation methods, alternative ion activation methods present the opportunity to obtain informative spectra from native GAG structures. Both electron- and photon-based activation methods, including electron detachment dissociation (EDD), negative electron transfer dissociation (NETD), and extreme ultraviolet photon activation, have been explored previously to overcome the limitations associated with low-energy activation methods for GAGs and other sulfated oligosaccharides. Further, implementation of such methods on high-resolution mass spectrometers has aided the interpretation of the complex spectra generated. Here, we explore ultraviolet photodissociation (UVPD) implemented on an Orbitrap mass spectrometer as another option for structural characterization of GAGs. UVPD spectra for both dermatan and heparan sulfate structures display extensive fragmentation including both glycosidic and cross-ring cleavages with the extent of sulfate retention comparable to that observed by EDD and NETD. In addition, the relatively short activation time of UVPD makes it promising for higher throughput analysis of GAGs in complex mixtures.
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Affiliation(s)
- Dustin R Klein
- Department of Chemistry , The University of Texas at Austin , Austin , Texas 78712 , United States
| | - Franklin E Leach
- Department of Environmental Health Science , The University of Georgia , Athens , Georgia 30602 , United States
| | - I Jonathan Amster
- Department of Chemistry , The University of Georgia , Athens , Georgia 30602 , United States
| | - Jennifer S Brodbelt
- Department of Chemistry , The University of Texas at Austin , Austin , Texas 78712 , United States
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28
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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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29
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Jang I, Jeon A, Lim SG, Hong DK, Kim MS, Jo JH, Lee ST, Moon B, Oh HB. Free Radical-Initiated Peptide Sequencing Mass Spectrometry for Phosphopeptide Post-translational Modification Analysis. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2019; 30:538-547. [PMID: 30414067 DOI: 10.1007/s13361-018-2100-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Revised: 10/23/2018] [Accepted: 10/23/2018] [Indexed: 06/08/2023]
Abstract
Free radical-initiated peptide sequencing mass spectrometry (FRIPS MS) was employed to analyze a number of representative singly or doubly protonated phosphopeptides (phosphoserine and phosphotyrosine peptides) in positive ion mode. In contrast to collision-activated dissociation (CAD) results, a loss of a phosphate group occurred to a limited degree for both phosphoserine and phosphotyrosine peptides, and thus, localization of a phosphorylated site was readily achieved. Considering that FRIPS MS supplies a substantial amount of collisional energy to peptides, this result was quite unexpected because a labile phosphate group was conserved. Analysis of the resulting peptide fragments revealed the extensive production of a-, c-, x-, and z-type fragments (with some minor b- and y-type fragments), suggesting that radical-driven peptide fragmentation was the primary mechanism involved in the FRIPS MS of phosphopeptides. Results of this study clearly indicate that FRIPS MS is a promising tool for the characterization of post-translational modifications such as phosphorylation. Graphical Abstract.
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Affiliation(s)
- Inae Jang
- Department of Chemistry, Sogang University, Seoul, 04107, Republic of Korea
| | - Aeran Jeon
- Department of Chemistry, Sogang University, Seoul, 04107, Republic of Korea
| | - Suk Gyu Lim
- Seoul Science High School, Seoul, 03066, Republic of Korea
- Seoul National University, Seoul, 08826, Republic of Korea
| | - Duk Ki Hong
- Seoul Science High School, Seoul, 03066, Republic of Korea
- Seoul National University, Seoul, 08826, Republic of Korea
| | - Min Soo Kim
- Seoul Science High School, Seoul, 03066, Republic of Korea
- Korea University, Seoul, 02841, Republic of Korea
| | - Jae Hyeong Jo
- Seoul Science High School, Seoul, 03066, Republic of Korea
- Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea
| | - Sang Tak Lee
- Department of Chemistry, Sogang University, Seoul, 04107, Republic of Korea
| | - Bongjin Moon
- Department of Chemistry, Sogang University, Seoul, 04107, Republic of Korea
| | - Han Bin Oh
- Department of Chemistry, Sogang University, Seoul, 04107, Republic of Korea.
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30
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Wei J, Wu J, Tang Y, Ridgeway ME, Park MA, Costello CE, Zaia J, Lin C. Characterization and Quantification of Highly Sulfated Glycosaminoglycan Isomers by Gated-Trapped Ion Mobility Spectrometry Negative Electron Transfer Dissociation MS/MS. Anal Chem 2019; 91:2994-3001. [PMID: 30649866 DOI: 10.1021/acs.analchem.8b05283] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Glycosaminoglycans (GAGs) play vital roles in many biological processes and are naturally present as complex mixtures of polysaccharides with tremendous structural heterogeneity, including many structural isomers. Mass spectrometric analysis of GAG isomers, in particular highly sulfated heparin (Hep) and heparan sulfate (HS), is challenging because of their structural similarity and facile sulfo losses during analysis. Herein, we show that highly sulfated Hep/HS isomers may be resolved by gated-trapped ion mobility spectrometry (gated-TIMS) with negligible sulfo losses. Subsequent negative electron transfer dissociation (NETD) tandem mass spectrometry (MS/MS) analysis of TIMS-separated Hep/HS isomers generated extensive glycosidic and cross-ring fragments for confident isomer differentiation and structure elucidation. The high mobility resolution and preservation of labile sulfo modifications afforded by gated-TIMS MS analysis also allowed relative quantification of highly sulfated heparin isomers. These results show that the gated-TIMS-NETD MS/MS approach is useful for both qualitative and quantitative analysis of highly sulfated Hep/HS compounds in a manner not possible with other techniques.
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Affiliation(s)
- Juan Wei
- Center for Biomedical Mass Spectrometry , Boston University School of Medicine , Boston , Massachusetts 02118 , United States
| | - Jiandong Wu
- 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
| | - Mark E Ridgeway
- Bruker Daltonics , Billerica , Massachusetts 01821 , United States
| | - Melvin A Park
- Bruker Daltonics , Billerica , Massachusetts 01821 , 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
| | - Joseph Zaia
- Center for Biomedical Mass Spectrometry , Boston University School of Medicine , Boston , Massachusetts 02118 , United States
| | - Cheng Lin
- Center for Biomedical Mass Spectrometry , Boston University School of Medicine , Boston , Massachusetts 02118 , United States
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31
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Zhang T, Liu X, Li H, Wang Z, Chi L, Li JP, Tan T. Characterization of epimerization and composition of heparin and dalteparin using a UHPLC-ESI-MS/MS method. Carbohydr Polym 2019; 203:87-94. [DOI: 10.1016/j.carbpol.2018.08.108] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Revised: 08/24/2018] [Accepted: 08/25/2018] [Indexed: 10/28/2022]
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32
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Chen X, Wang Z, Wong YLE, Wu R, Zhang F, Chan TWD. Electron-ion reaction-based dissociation: A powerful ion activation method for the elucidation of natural product structures. MASS SPECTROMETRY REVIEWS 2018; 37:793-810. [PMID: 29603345 DOI: 10.1002/mas.21563] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Accepted: 02/12/2018] [Indexed: 05/16/2023]
Abstract
The structural elucidation of natural products (NPs) remains a challenge due to their structurally diversities and unpredictable functionalities, motifs, and scaffolds. Tandem mass spectrometry (MS/MS) is an effective method that assists the full elucidation of complicated NP structures. Ion activation methods play a key role in determining the fragmentation pathways and the structural information obtained from MS/MS. Electron-ion reaction-based dissociation (ExD) methods, including electron capture dissociation (ECD), electron transfer dissociation (ETD), electron-induced dissociation (EID), and electron detachment dissociation (EDD), can induce the breakage of specific chemical bonds and the generation of distinct fragment ions. This review article provides an overview of the mechanisms, instrumentation, and typical applications related to ExD MS/MS in the structural elucidation of NPs, primarly including lipids, oligosaccharides, glycoconjugates, metabolites, and pharmaceutical drugs. This work aims to reveal the capacity and potential of ExD mass spectrometry in analyzing NPs and consequently helping the NP communities to utilize the modern capabilities of MS/MS in the discovery and evaluation of novel NPs.
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Affiliation(s)
- Xiangfeng Chen
- Key Laboratory for Applied Technology of Sophisticated Analytical Instruments, Shandong Analysis and Test Centre, Qilu University of Technology (Shandong Academy of Science), Shandong, P.R. China
- Department of Chemistry, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, P.R. China
| | - Ze Wang
- Department of Chemistry, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, P.R. China
| | - Y-L Elaine Wong
- Department of Chemistry, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, P.R. China
| | - Ri Wu
- Department of Chemistry, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, P.R. China
| | - Feng Zhang
- Chinese Academy of Inspection and Quarantine, Beijing, P. R. China
| | - T-W Dominic Chan
- Department of Chemistry, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, P.R. China
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33
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Riggs DL, Hofmann J, Hahm HS, Seeberger PH, Pagel K, Julian RR. Glycan Isomer Identification Using Ultraviolet Photodissociation Initiated Radical Chemistry. Anal Chem 2018; 90:11581-11588. [PMID: 30179447 PMCID: PMC11216535 DOI: 10.1021/acs.analchem.8b02958] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Glycans are fundamental biological macromolecules, yet despite their prevalence and recognized importance, a number of unique challenges hinder routine characterization. The multiplicity of OH groups in glycan monomers easily afford branched structures and alternate linkage sites, which can result in isomeric structures that differ by minute details. Herein, radical chemistry is employed in conjunction with mass spectrometry to enable rapid, accurate, and high throughput identification of a challenging series of closely related glycan isomers. The results are compared with analysis by collision-induced dissociation, higher-energy collisional dissociation, and ultraviolet photodissociation (UVPD) at 213 nm. In general, collision-based activation struggles to produce characteristic fragmentation patterns, while UVPD and radical-directed dissociation (RDD) can distinguish all isomers. In the case of RDD, structural differentiation derives from radical mobility and subsequent fragmentation. For glycans, the energetic landscape for radical migration is flat, increasing the importance of the three-dimensional structure. RDD is therefore a powerful and straightforward method for characterizing glycan isomers.
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Affiliation(s)
- Dylan L. Riggs
- Department of Chemistry, University of California, Riverside, 501 Big Springs Road, Riverside, CA 92521, USA
| | - Johanna Hofmann
- Department of Molecular Physics, Fritz Haber Institute of the Max Planck Society Faradayweg 4-6, 14195 Berlin, Germany
- Institute for Chemistry and Biochemistry, Freie Universitaet Berlin, Takustrasse 3, 14195 Berlin, Germany
| | - Heung S. Hahm
- Department for Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14476 Potsdam, Germany
| | - Peter H. Seeberger
- Department for Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14476 Potsdam, Germany
- Institute for Chemistry and Biochemistry, Freie Universitaet Berlin, Takustrasse 3, 14195 Berlin, Germany
| | - Kevin Pagel
- Department of Molecular Physics, Fritz Haber Institute of the Max Planck Society Faradayweg 4-6, 14195 Berlin, Germany
- Institute for Chemistry and Biochemistry, Freie Universitaet Berlin, Takustrasse 3, 14195 Berlin, Germany
| | - Ryan R. Julian
- Department of Chemistry, University of California, Riverside, 501 Big Springs Road, Riverside, CA 92521, USA
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34
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Duan J, Jonathan Amster I. An Automated, High-Throughput Method for Interpreting the Tandem Mass Spectra of Glycosaminoglycans. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2018; 29:1802-1811. [PMID: 29790112 PMCID: PMC6087482 DOI: 10.1007/s13361-018-1969-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 04/06/2018] [Accepted: 04/14/2018] [Indexed: 05/03/2023]
Abstract
The biological interactions between glycosaminoglycans (GAGs) and other biomolecules are heavily influenced by structural features of the glycan. The structure of GAGs can be assigned using tandem mass spectrometry (MS2), but analysis of these data, to date, requires manually interpretation, a slow process that presents a bottleneck to the broader deployment of this approach to solving biologically relevant problems. Automated interpretation remains a challenge, as GAG biosynthesis is not template-driven, and therefore, one cannot predict structures from genomic data, as is done with proteins. The lack of a structure database, a consequence of the non-template biosynthesis, requires a de novo approach to interpretation of the mass spectral data. We propose a model for rapid, high-throughput GAG analysis by using an approach in which candidate structures are scored for the likelihood that they would produce the features observed in the mass spectrum. To make this approach tractable, a genetic algorithm is used to greatly reduce the search-space of isomeric structures that are considered. The time required for analysis is significantly reduced compared to an approach in which every possible isomer is considered and scored. The model is coded in a software package using the MATLAB environment. This approach was tested on tandem mass spectrometry data for long-chain, moderately sulfated chondroitin sulfate oligomers that were derived from the proteoglycan bikunin. The bikunin data was previously interpreted manually. Our approach examines glycosidic fragments to localize SO3 modifications to specific residues and yields the same structures reported in literature, only much more quickly. Graphical Abstract ᅟ.
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Affiliation(s)
- Jiana Duan
- Department of Chemistry, University of Georgia, Athens, GA, 30606, USA
| | - I Jonathan Amster
- Department of Chemistry, University of Georgia, Athens, GA, 30606, USA.
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35
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Compagnon I, Schindler B, Renois-Predelus G, Daniel R. Lasers and ion mobility: new additions to the glycosaminoglycanomics toolkit. Curr Opin Struct Biol 2018; 50:171-180. [PMID: 30005299 DOI: 10.1016/j.sbi.2018.06.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Revised: 06/13/2018] [Accepted: 06/20/2018] [Indexed: 12/27/2022]
Abstract
Glycosaminoglycans are biopolymers present in mammalian cells or in the extracellular matrix. To address their structure, the nature of the hexuronic acids and the position of sulfate groups must be determined. Tandem mass spectrometry using collision induced dissociation or electron-based fragmentation techniques, is a well-established approach for the identification of glycans but suffers from the frequent lack of diagnostic fragments in the case of glycosaminoglycans. This review presents alternative fragmentation techniques, namely photofragmentation in the IR and the UV ranges. Alternative approaches based on the direct analysis of the molecular structure, including ion mobility spectrometry and ion spectroscopies are reviewed. The potential of future multidimensional workflows for glycosaminoglycanomics is discussed.
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Affiliation(s)
- Isabelle Compagnon
- Institut Universitaire de France IUF, 103 Boulevard St Michel, Paris F-75005, France; Univ Lyon, Université Claude Bernard Lyon 1, CNRS, Institut Lumière Matière, F-69622 Villeurbanne, France.
| | - Baptiste Schindler
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, Institut Lumière Matière, F-69622 Villeurbanne, France
| | - Gina Renois-Predelus
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, Institut Lumière Matière, F-69622 Villeurbanne, France
| | - Régis Daniel
- Université Paris-Saclay, CNRS, CEA, Univ Evry, Laboratoire Analyse et Modélisation pour la Biologie et l'Environnement, F-91025 Evry, France
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36
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Renois-Predelus G, Schindler B, Compagnon I. Analysis of Sulfate Patterns in Glycosaminoglycan Oligosaccharides by MS n Coupled to Infrared Ion Spectroscopy: the Case of GalNAc4S and GalNAc6S. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2018; 29:1242-1249. [PMID: 29700727 DOI: 10.1007/s13361-018-1955-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Revised: 03/07/2018] [Accepted: 03/20/2018] [Indexed: 06/08/2023]
Abstract
We report distinctive spectroscopic fingerprints of the monosaccharide standards GalNAc4S and GalNAc6S by coupling mass spectrometry and ion spectroscopy in the 3-μm range. The disaccharide standards CSA and CSC are used to demonstrate the applicability of a novel approach for the analysis of sulfate position in GalNAc-containing glycosaminoglycans. This approach was then used for the analysis of a sample containing CSA and CSC disaccharides. Finally, we discuss the generalization of the coupling of mass spectrometry with ion spectroscopy for the structural analysis of glycosaminoglycans on a tetrasaccharide from dermatan sulfate source. Graphical abstract ᅟ.
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Affiliation(s)
- G Renois-Predelus
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, Institut Lumière Matière (ILM), F-69622, Villeurbanne, France
| | - B Schindler
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, Institut Lumière Matière (ILM), F-69622, Villeurbanne, France
| | - I Compagnon
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, Institut Lumière Matière (ILM), F-69622, Villeurbanne, France.
- Institut Universitaire de France IUF, 103 Blvd St Michel, 75005, Paris, France.
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37
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Sanderson P, Stickney M, Leach FE, Xia Q, Yu Y, Zhang F, Linhardt RJ, Amster IJ. Heparin/heparan sulfate analysis by covalently modified reverse polarity capillary zone electrophoresis-mass spectrometry. J Chromatogr A 2018; 1545:75-83. [PMID: 29501428 PMCID: PMC5862776 DOI: 10.1016/j.chroma.2018.02.052] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Revised: 02/17/2018] [Accepted: 02/24/2018] [Indexed: 12/21/2022]
Abstract
Reverse polarity capillary zone electrophoresis coupled to negative ion mode mass spectrometry (CZE-MS) is shown to be an effective and sensitive tool for the analysis of glycosaminoglycan mixtures. Covalent modification of the inner wall of the separation capillary with neutral or cationic reagents produces a stable and durable surface that provides reproducible separations. By combining CZE-MS with a cation-coated capillary and a sheath flow interface, a rapid and reliable method has been developed for the analysis of sulfated oligosaccharides from dp4 to dp12. Several different mixtures have been separated and detected by mass spectrometry. The mixtures were selected to test the capability of this approach to resolve subtle differences in structure, such as sulfation position and epimeric variation of the uronic acid. The system was applied to a complex mixture of heparin/heparan sulfate oligosaccharides varying in chain length from dp3 to dp12 and more than 80 molecular compositions were identified by accurate mass measurement.
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Affiliation(s)
- Patience Sanderson
- Department of Chemistry, University of Georgia, Athens, GA 30602, United States
| | - Morgan Stickney
- Department of Chemistry, University of Georgia, Athens, GA 30602, United States
| | - Franklin E Leach
- Department of Chemistry, University of Georgia, Athens, GA 30602, United States
| | - Qiangwei Xia
- 760 Parkside Avenue, STE 211, CMP Scientific, Corp., Brooklyn, NY, 11226, United States
| | - Yanlei Yu
- Biotech 4005, 110 8th Street, Rensselaer Polytechnic Institute, Troy, NY, 12180, United States
| | - Fuming Zhang
- Biotech 4005, 110 8th Street, Rensselaer Polytechnic Institute, Troy, NY, 12180, United States
| | - Robert J Linhardt
- Biotech 4005, 110 8th Street, Rensselaer Polytechnic Institute, Troy, NY, 12180, United States
| | - I Jonathan Amster
- Department of Chemistry, University of Georgia, Athens, GA 30602, United States.
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38
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Tang Y, Pu Y, Gao J, Hong P, Costello CE, Lin C. De Novo Glycan Sequencing by Electronic Excitation Dissociation and Fixed-Charge Derivatization. Anal Chem 2018; 90:3793-3801. [PMID: 29443510 DOI: 10.1021/acs.analchem.7b04077] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Detailed glycan structural characterization is frequently achieved by collisionally activated dissociation (CAD) based sequential tandem mass spectrometry (MS n) analysis of permethylated glycans. However, it is challenging to implement MS n ( n > 2) during online glycan separation, and this has limited its application to analysis of complex glycan mixtures from biological samples. Further, permethylation can reduce liquid chromatographic (LC) resolution of isomeric glycans. Here, we studied the electronic excitation dissociation (EED) fragmentation behavior of native glycans with a reducing-end fixed charge tag and identified key spectral features that are useful for topology and linkage determination. We also developed a de novo glycan sequencing software that showed remarkable accuracy in glycan topology elucidation based on the EED spectra of fixed charge-derivatized glycans. The ability to obtain glycan structural details at the MS2 level, without permethylation, via a combination of fixed charge derivatization, EED, and de novo spectral interpretation, makes the present approach a promising tool for comprehensive and rapid characterization of glycan mixtures.
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Affiliation(s)
- 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
| | - Yi Pu
- 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
| | - Jinshan Gao
- Department of Chemistry and Biochemistry , Montclair State University , Montclair , New Jersey 07043 , United States
| | - Pengyu Hong
- Department of Computer Science, Brandeis University , Waltham , Massachusetts 02453 , 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
| | - Cheng Lin
- Center for Biomedical Mass Spectrometry , Boston University School of Medicine , Boston , Massachusetts 02118 , United States
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39
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40
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Hong P, Sun H, Sha L, Pu Y, Khatri K, Yu X, Tang Y, Lin C. GlycoDeNovo - an Efficient Algorithm for Accurate de novo Glycan Topology Reconstruction from Tandem Mass Spectra. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:2288-2301. [PMID: 28786094 PMCID: PMC5647224 DOI: 10.1007/s13361-017-1760-6] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Revised: 07/03/2017] [Accepted: 07/09/2017] [Indexed: 05/15/2023]
Abstract
A major challenge in glycomics is the characterization of complex glycan structures that are essential for understanding their diverse roles in many biological processes. We present a novel efficient computational approach, named GlycoDeNovo, for accurate elucidation of the glycan topologies from their tandem mass spectra. Given a spectrum, GlycoDeNovo first builds an interpretation-graph specifying how to interpret each peak using preceding interpreted peaks. It then reconstructs the topologies of peaks that contribute to interpreting the precursor ion. We theoretically prove that GlycoDeNovo is highly efficient. A major innovative feature added to GlycoDeNovo is a data-driven IonClassifier which can be used to effectively rank candidate topologies. IonClassifier is automatically learned from experimental spectra of known glycans to distinguish B- and C-type ions from all other ion types. Our results showed that GlycoDeNovo is robust and accurate for topology reconstruction of glycans from their tandem mass spectra. Graphical Abstract ᅟ.
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Affiliation(s)
- Pengyu Hong
- Department of Computer Science, Brandeis University, Waltham, MA, 02453, USA.
| | - Hui Sun
- Department of Computer Science, Brandeis University, Waltham, MA, 02453, USA
| | - Long Sha
- Department of Computer Science, Brandeis University, Waltham, MA, 02453, USA
| | - Yi Pu
- Department of Chemistry, Boston University, Boston, MA, 02215, USA
| | - Kshitij Khatri
- Department of Biochemistry, Boston University School of Medicine, Boston, MA, 02118, USA
| | - Xiang Yu
- Department of Biochemistry, Boston University School of Medicine, Boston, MA, 02118, USA
| | - Yang Tang
- Department of Chemistry, Boston University, Boston, MA, 02215, USA
| | - Cheng Lin
- Department of Biochemistry, Boston University School of Medicine, Boston, MA, 02118, USA.
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41
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Leach FE, Riley NM, Westphall MS, Coon JJ, Amster IJ. Negative Electron Transfer Dissociation Sequencing of Increasingly Sulfated Glycosaminoglycan Oligosaccharides on an Orbitrap Mass Spectrometer. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:1844-1854. [PMID: 28589488 PMCID: PMC5711533 DOI: 10.1007/s13361-017-1709-9] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Revised: 05/04/2017] [Accepted: 05/07/2017] [Indexed: 05/03/2023]
Abstract
The structural characterization of sulfated glycosaminoglycan (GAG) carbohydrates remains an important target for analytical chemists attributable to challenges introduced by the natural complexity of these mixtures and the defined need for molecular-level details to elucidate biological structure-function relationships. Tandem mass spectrometry has proven to be the most powerful technique for this purpose. Previously, electron detachment dissociation (EDD), in comparison to other methods of ion activation, has been shown to provide the largest number of useful cleavages for de novo sequencing of GAG oligosaccharides, but such experiments are restricted to Fourier transform ion cyclotron resonance mass spectrometers (FTICR-MS). Negative electron transfer dissociation (NETD) provides similar fragmentation results, and can be achieved on any mass spectrometry platform that is designed to accommodate ion-ion reactions. Here, we examine for the first time the effectiveness of NETD-Orbitrap mass spectrometry for the structural analysis of GAG oligosaccharides. Compounds ranging in size from tetrasaccharides to decasaccharides were dissociated by NETD, producing both glycosidic and cross-ring cleavages that enabled the location of sulfate modifications. The highly-sulfated, heparin-like synthetic GAG, ArixtraTM, was also successfully sequenced by NETD. In comparison to other efforts to sequence GAG chains without fully ionized sulfate constituents, the occurrence of sulfate loss peaks is minimized by judicious precursor ion selection. The results compare quite favorably to prior results with electron detachment dissociation (EDD). Significantly, the duty cycle of the NETD experiment is sufficiently short to make it an effective tool for on-line separations, presenting a straightforward path for selective, high-throughput analysis of GAG mixtures. Graphical Abstract ᅟ.
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Affiliation(s)
| | - Nicholas M Riley
- Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Michael S Westphall
- Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Joshua J Coon
- Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Morgridge Institute for Research, Madison, WI, USA
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42
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Agyekum I, Zong C, Boons GJ, Amster IJ. Single Stage Tandem Mass Spectrometry Assignment of the C-5 Uronic Acid Stereochemistry in Heparan Sulfate Tetrasaccharides using Electron Detachment Dissociation. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:1741-1750. [PMID: 28389983 PMCID: PMC5632119 DOI: 10.1007/s13361-017-1643-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Revised: 02/14/2017] [Accepted: 02/24/2017] [Indexed: 05/03/2023]
Abstract
The analysis of heparan sulfate (HS) glycosaminoglycans presents many challenges, due to the high degree of structural heterogeneity arising from their non-template biosynthesis. Complete structural elucidation of glycosaminoglycans necessitates the unambiguous assignments of sulfo modifications and the C-5 uronic acid stereochemistry. Efforts to develop tandem mass spectrometric-based methods for the structural analysis of glycosaminoglycans have focused on the assignment of sulfo positions. The present work focuses on the assignment of the C-5 stereochemistry of the uronic acid that lies closest to the reducing end. Prior work with electron-based tandem mass spectrometry methods, specifically electron detachment dissociation (EDD), have shown great promise in providing stereo-specific product ions, such as the B3´ -CO2, which has been found to distinguish glucuronic acid (GlcA) from iduronic acid (IdoA) in some HS tetrasaccharides. The previously observed diagnostic ions are generally not observed with 2-O-sulfo uronic acids or for more highly sulfated heparan sulfate tetrasaccharides. A recent study using electron detachment dissociation and principal component analysis revealed a series of ions that correlate with GlcA versus IdoA for a set of 2-O-sulfo HS tetrasaccharide standards. The present work comprehensively investigates the efficacy of these ions for assigning the C-5 stereochemistry of the reducing end uronic acid in 33 HS tetrasaccharides. A diagnostic ratio can be computed from the sum of the ions that correlate to GlcA to those that correlate to IdoA. Graphical Abstract ᅟ.
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Affiliation(s)
- Isaac Agyekum
- Department of Chemistry, University of Georgia, Athens, GA, 30602, USA
| | - Chengli Zong
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, 30602, USA
| | - Geert-Jan Boons
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, 30602, USA
| | - I Jonathan Amster
- Department of Chemistry, University of Georgia, Athens, GA, 30602, USA.
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43
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Miller RL, Guimond SE, Prescott M, Turnbull JE, Karlsson N. Versatile Separation and Analysis of Heparan Sulfate Oligosaccharides Using Graphitized Carbon Liquid Chromatography and Electrospray Mass Spectrometry. Anal Chem 2017; 89:8942-8950. [DOI: 10.1021/acs.analchem.7b01417] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Rebecca L. Miller
- Centre
for Glycobiology, Department of Biochemistry, Institute of Integrative
Biology, University of Liverpool, Crown Street, Liverpool, L69 7ZB, U.K
- Oncology
Department, University of Oxford, Old Road Campus Research Building, Oxford, OX3 7DQ, U.K
| | - Scott E. Guimond
- Centre
for Glycobiology, Department of Biochemistry, Institute of Integrative
Biology, University of Liverpool, Crown Street, Liverpool, L69 7ZB, U.K
| | - Mark Prescott
- Centre
for Glycobiology, Department of Biochemistry, Institute of Integrative
Biology, University of Liverpool, Crown Street, Liverpool, L69 7ZB, U.K
| | - Jeremy E. Turnbull
- Centre
for Glycobiology, Department of Biochemistry, Institute of Integrative
Biology, University of Liverpool, Crown Street, Liverpool, L69 7ZB, U.K
| | - Niclas Karlsson
- Department
of Medical Biochemistry and Cell Biology, Institute of Biomedicine,
Sahlgrenska Academy, University of Gothenburg, Box 440, 40530 Gothenburg, Sweden
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Khanal N, Masellis C, Kamrath MZ, Clemmer DE, Rizzo TR. Glycosaminoglycan Analysis by Cryogenic Messenger-Tagging IR Spectroscopy Combined with IMS-MS. Anal Chem 2017; 89:7601-7606. [PMID: 28636333 PMCID: PMC5675075 DOI: 10.1021/acs.analchem.7b01467] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
We combine ion mobility spectrometry with cryogenic, messenger-tagging, infrared spectroscopy and mass spectrometry to identify different isomeric disaccharides of chondroitin sulfate (CS) and heparan sulfate (HS), which are representatives of two major subclasses of glycosaminoglycans. Our analysis shows that while CS and HS disaccharide isomers have similar drift times, they can be uniquely distinguished by their vibrational spectrum between ∼3200 and 3700 cm-1 due to their different OH hydrogen-bonding patterns. We suggest that this combination of techniques is well suited to identify and characterize glycan isomers directly, which presents tremendous challenges for existing methods.
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Affiliation(s)
- Neelam Khanal
- Department of Chemistry, Indiana University, 800 East Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Chiara Masellis
- Laboratoire de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne, EPFL SB ISIC LCPM, Station 6, CH-1015 Lausanne, Switzerland
| | - Michael Z. Kamrath
- Laboratoire de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne, EPFL SB ISIC LCPM, Station 6, CH-1015 Lausanne, Switzerland
| | - David E. Clemmer
- Department of Chemistry, Indiana University, 800 East Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - 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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Ropartz D, Li P, Jackson GP, Rogniaux H. Negative Polarity Helium Charge Transfer Dissociation Tandem Mass Spectrometry: Radical-Initiated Fragmentation of Complex Polysulfated Anions. Anal Chem 2017; 89:3824-3828. [PMID: 28300396 DOI: 10.1021/acs.analchem.7b00473] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
This work provides the first use of helium charge transfer dissociation (He-CTD) tandem mass spectrometry (MS/MS) in negative polarity mode. Three sulfated oligosaccharides of natural origin were chosen as representative structures that are difficult to solve by conventional MS/MS approaches. Negative polarity He-CTD provided a full set of structurally informative fragments, which permitted the unambiguous determination of the complete structures of these molecules, including the characterization of labile sulfated functional groups. Despite close structural features, the three molecules led to distinct fragmentation patterns depending on the position of the sulfate group in the heterocycle. The observed fragments showed a consistent radical-initiated mechanism of dissociation, which shares similarities with fragment types produced in electron detachment dissociation (EDD), negative electron transfer dissociation (NETD), or extreme UV photodissociation (XUV-PD). Short times of data collection and the fact that the technique can be affordably implementable in any standard laboratory and with a classical ion trap mass spectrometer were other remarkable characteristics of negative polarity He-CTD.
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Affiliation(s)
- David Ropartz
- INRA, UR1268 Biopolymers Interactions Assemblies, Rue de la Géraudière B.P. 71627, F-44316 Nantes, France
| | - Pengfei Li
- C. Eugene Bennett Department of Chemistry, West Virginia University , Morgantown, West Virginia 26506, United States
| | - Glen P Jackson
- C. Eugene Bennett Department of Chemistry, West Virginia University , Morgantown, West Virginia 26506, United States.,Department of Forensic and Investigative Science, West Virginia University , Morgantown, West Virginia 26506-6121, United States
| | - Hélène Rogniaux
- INRA, UR1268 Biopolymers Interactions Assemblies, Rue de la Géraudière B.P. 71627, F-44316 Nantes, France
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Ropartz D, Li P, Fanuel M, Giuliani A, Rogniaux H, Jackson GP. Charge Transfer Dissociation of Complex Oligosaccharides: Comparison with Collision-Induced Dissociation and Extreme Ultraviolet Dissociative Photoionization. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2016; 27:1614-9. [PMID: 27582116 DOI: 10.1007/s13361-016-1453-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2016] [Revised: 07/11/2016] [Accepted: 07/12/2016] [Indexed: 05/04/2023]
Abstract
The structural characterization of oligosaccharides still challenges the field of analytical chemistry. Tandem mass spectrometry offers many advantages toward this aim, although the generic fragmentation method (low-energy collision-induced dissociation) shows clear limitations and is often insufficient to retrieve some essential structural information on these molecules. In this work, we present the first application of helium charge transfer dissociation (He-CTD) to characterize the structure of complex oligosaccharides. We compare this method with low-energy collision-induced dissociation and extreme-ultraviolet dissociative photoionization (XUV-DPI), which was shown previously to ensure the successful characterization of complex glycans. Similarly to what could be obtained by XUV-DPI, He-CTD provides a complete description of the investigated structures by producing many informative cross-ring fragments and no ambiguous fragmentation. Unlike XUV-DPI, which is performed at a synchrotron source, He-CTD has the undeniable advantage of being implementable in a conventional benchtop ion trap in a conventional laboratory setting. Graphical Abstract ᅟ.
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Affiliation(s)
- David Ropartz
- INRA, UR1268 Biopolymers Interactions Assemblies, 44316, Nantes, France
| | - Pengfei Li
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV, 26506, USA
| | - Mathieu Fanuel
- INRA, UR1268 Biopolymers Interactions Assemblies, 44316, Nantes, France
| | - Alexandre Giuliani
- Synchrotron SOLEIL, L'Orme des Merisiers, 91190, Gif-sur-Yvette, France
- UAR 1008 CEPIA, INRA, 44316, Nantes, France
| | - Hélène Rogniaux
- INRA, UR1268 Biopolymers Interactions Assemblies, 44316, Nantes, France.
| | - Glen P Jackson
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV, 26506, USA
- Department of Forensic and Investigative Science, West Virginia University, Morgantown, WV, 26506-6121, USA
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48
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Sionkowska A, Kaczmarek B, Lewandowska K, Grabska S, Pokrywczyńska M, Kloskowski T, Drewa T. 3D composites based on the blends of chitosan and collagen with the addition of hyaluronic acid. Int J Biol Macromol 2016; 89:442-8. [DOI: 10.1016/j.ijbiomac.2016.04.085] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Revised: 04/23/2016] [Accepted: 04/29/2016] [Indexed: 11/29/2022]
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49
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Pu Y, Ridgeway ME, Glaskin RS, Park MA, Costello CE, Lin C. Separation and Identification of Isomeric Glycans by Selected Accumulation-Trapped Ion Mobility Spectrometry-Electron Activated Dissociation Tandem Mass Spectrometry. Anal Chem 2016; 88:3440-3. [PMID: 26959868 PMCID: PMC4821751 DOI: 10.1021/acs.analchem.6b00041] [Citation(s) in RCA: 93] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
One of the major challenges in structural characterization of oligosaccharides is the presence of many structural isomers in most naturally occurring glycan mixtures. Although ion mobility spectrometry (IMS) has shown great promise in glycan isomer separation, conventional IMS separation occurs on the millisecond time scale, largely restricting its implementation to fast time-of-flight (TOF) analyzers which often lack the capability to perform electron activated dissociation (ExD) tandem MS analysis and the resolving power needed to resolve isobaric fragments. The recent development of trapped ion mobility spectrometry (TIMS) provides a promising new tool that offers high mobility resolution and compatibility with high-performance Fourier transform ion cyclotron resonance (FTICR) mass spectrometers when operated under the selected accumulation-TIMS (SA-TIMS) mode. Here, we present our initial results on the application of SA-TIMS-ExD-FTICR MS to the separation and identification of glycan linkage isomers.
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Affiliation(s)
- Yi Pu
- Center for Biomedical Mass Spectrometry, Boston University School of Medicine, Boston, MA 02118, US
| | | | - Rebecca S. Glaskin
- Center for Biomedical Mass Spectrometry, Boston University School of Medicine, Boston, MA 02118, US
| | | | - Catherine E. Costello
- Center for Biomedical Mass Spectrometry, Boston University School of Medicine, Boston, MA 02118, US
| | - Cheng Lin
- Center for Biomedical Mass Spectrometry, Boston University School of Medicine, Boston, MA 02118, US
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50
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Huang Y, Pu Y, Yu X, Costello CE, Lin C. Mechanistic Study on Electronic Excitation Dissociation of the Cellobiose-Na(+) Complex. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2016; 27:319-28. [PMID: 26432580 PMCID: PMC4724539 DOI: 10.1007/s13361-015-1277-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Revised: 09/02/2015] [Accepted: 09/05/2015] [Indexed: 05/04/2023]
Abstract
The recent development of electron activated dissociation (ExD) techniques has opened the door for high-throughput, detailed glycan structural elucidation. Among them, ExD methods employing higher-energy electrons offer several advantages over low-energy electron capture dissociation (ECD), owing to their applicability towards chromophore-labeled glycans and singly charged ions, and ability to provide more extensive structural information. However, a lack of understanding of these processes has hindered rational optimization of the experimental conditions for more efficient fragmentation as well as the development of informatics tools for interpretation of the complex glycan ExD spectra. Here, cellobiose-Na(+) was used as the model system to investigate the fragmentation behavior of metal-adducted glycans under irradiation of electrons with energy exceeding their ionization potential, and served as the basis on which a novel electronic excitation dissociation (EED) mechanism was proposed. It was found that ionization of the glycan produces a mixture of radical cations and ring-opened distonic ions. These distonic ions then capture a low-energy electron to produce diradicals with trivial singlet-triplet splitting, and subsequently undergo radical-induced dissociation to produce a variety of fragment ions, the abundances of which are influenced by the stability of the distonic ions from which they originate. Graphical Abstract ᅟ.
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Affiliation(s)
- Yiqun Huang
- Mass Spectrometry Resource, Boston University School of Medicine, Boston, MA, 02118, USA
- Department of Biochemistry, Boston University School of Medicine, Boston, MA, 02118, USA
| | - Yi Pu
- Mass Spectrometry Resource, Boston University School of Medicine, Boston, MA, 02118, USA
- Department of Chemistry, Boston University, Boston, MA, 02215, USA
| | - Xiang Yu
- Mass Spectrometry Resource, Boston University School of Medicine, Boston, MA, 02118, USA
- Department of Biochemistry, Boston University School of Medicine, Boston, MA, 02118, USA
| | - Catherine E Costello
- Mass Spectrometry Resource, Boston University School of Medicine, Boston, MA, 02118, USA
- Department of Biochemistry, Boston University School of Medicine, Boston, MA, 02118, USA
- Department of Chemistry, Boston University, Boston, MA, 02215, USA
| | - Cheng Lin
- Mass Spectrometry Resource, Boston University School of Medicine, Boston, MA, 02118, USA.
- Department of Biochemistry, Boston University School of Medicine, Boston, MA, 02118, USA.
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