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Lahkar C, Ansary A, Kashyap M, Kumar Das T, Gogoi B, Bharali D, Kumar Deka M, Jyoti Sahariah B, Majumder M. A technique based on infrared spectroscopy for determining sulfanilamide levels sustainably: Progress and comparisons of greenness and whiteness using ComplexGAPI, AGREE, and RGB. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 318:124467. [PMID: 38796892 DOI: 10.1016/j.saa.2024.124467] [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: 02/17/2024] [Revised: 05/09/2024] [Accepted: 05/12/2024] [Indexed: 05/29/2024]
Abstract
The study aimed to determine the potential of the infrared (IR) spectrophotometric technique for measuring the content of sulphanilamide with the sulfonamide group. The study aimed to obtain the IR spectra of sulfanilamide and use the -SO2 band at 1114.37 for the quantitative assay, determining its area under the curve (AUC). The study gives an alternative approach to existing analytical techniques that require vast amounts of organic solvents, which are costly and can be toxic, thus impacting the environment and increasing the analysis cost. The study evaluated the method's whiteness and greenness by utilizing the Complex green analytical procedure index, analytical GREEness calculator and Red Green Blue algorithm tool. The linierity was found to be 5 to 30 µg/ml. The present study has developed an infrared (IR) spectroscopic method that employs a straightforward sample preparation technique in methanol. The IR spectroscopic method's linearity range was determined to be 5-30 µg/ml. The p-value was 0.001 at 95 % confidence level assuring better recovery. This method is evaluated according to the Q2R1 ICH guideline. It is applicable to routine quality control analysis without pre-extraction using green IR spectroscopy. In conclusion, the study demonstrated that IR spectrophotometric techniques can quantify sulfanilamide while reducing the use of organic solvents, contributing to the green-and-white analytical chemistry approach. The developed methods are reliable, accurate, and cost-effective and have the potential to be implemented in routine analysis of sulfanilamide.
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Affiliation(s)
- Chintu Lahkar
- Department of Pharmaceutical Chemistry, NETES Institute of Pharmaceutical Science, Nemcare Group of Institution, Mirza, Kamrup 781125, Assam, India.
| | - Akramul Ansary
- Department of Pharmaceutical Chemistry, NETES Institute of Pharmaceutical Science, Nemcare Group of Institution, Mirza, Kamrup 781125, Assam, India.
| | - Manoj Kashyap
- Department of Pharmaceutical Chemistry, NETES Institute of Pharmaceutical Science, Nemcare Group of Institution, Mirza, Kamrup 781125, Assam, India.
| | - Tridib Kumar Das
- Department of Pharmaceutical Chemistry, NETES Institute of Pharmaceutical Science, Nemcare Group of Institution, Mirza, Kamrup 781125, Assam, India.
| | - Bitu Gogoi
- Department of Pharmaceutical Chemistry, NETES Institute of Pharmaceutical Science, Nemcare Group of Institution, Mirza, Kamrup 781125, Assam, India.
| | - Deepsikha Bharali
- Department of Pharmaceutical Chemistry, NETES Institute of Pharmaceutical Science, Nemcare Group of Institution, Mirza, Kamrup 781125, Assam, India.
| | - Manoj Kumar Deka
- Department of Pharmaceutics, NETES Institute of Pharmaceutical Science, Nemcare Group of Institution, Mirza, Kamrup 781125, Assam, India.
| | - Bhargab Jyoti Sahariah
- Department of Pharmaceutics, NETES Institute of Pharmaceutical Science, Nemcare Group of Institution, Mirza, Kamrup 781125, Assam, India.
| | - Manish Majumder
- Department of Pharmaceutical Chemistry, NETES Institute of Pharmaceutical Science, Nemcare Group of Institution, Mirza, Kamrup 781125, Assam, India.
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2
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Chohan DP, Biswas S, Wankhede M, Menon P, K A, Basha S, Rodrigues J, Mukunda DC, Mahato KK. Assessing Breast Cancer through Tumor Microenvironment Mapping of Collagen and Other Biomolecule Spectral Fingerprints─A Review. ACS Sens 2024. [PMID: 39175278 DOI: 10.1021/acssensors.4c00585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/24/2024]
Abstract
Breast cancer is a major challenge in the field of oncology, with around 2.3 million cases and around 670,000 deaths globally based on the GLOBOCAN 2022 data. Despite having advanced technologies, breast cancer remains the major type of cancer among women. This review highlights various collagen signatures and the role of different collagen types in breast tumor development, progression, and metastasis, along with the use of photoacoustic spectroscopy to offer insights into future cancer diagnostic applications without the need for surgery or other invasive techniques. Through mapping of the tumor microenvironment and spotlighting key components and their absorption wavelengths, we emphasize the need for extensive preclinical and clinical investigations.
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Affiliation(s)
- Diya Pratish Chohan
- Manipal School of Life Sciences, Manipal Academy of Higher Education, Karnataka, Manipal 576104, India
| | - Shimul Biswas
- Department of Biophysics, Manipal School of Life Sciences, Manipal Academy of Higher Education, Karnataka, Manipal 576104, India
| | - Mrunmayee Wankhede
- Manipal School of Life Sciences, Manipal Academy of Higher Education, Karnataka, Manipal 576104, India
| | - Poornima Menon
- Manipal School of Life Sciences, Manipal Academy of Higher Education, Karnataka, Manipal 576104, India
| | - Ameera K
- Department of Biophysics, Manipal School of Life Sciences, Manipal Academy of Higher Education, Karnataka, Manipal 576104, India
| | - Shaik Basha
- Department of Biophysics, Manipal School of Life Sciences, Manipal Academy of Higher Education, Karnataka, Manipal 576104, India
| | - Jackson Rodrigues
- Department of Biophysics, Manipal School of Life Sciences, Manipal Academy of Higher Education, Karnataka, Manipal 576104, India
| | | | - Krishna Kishore Mahato
- Department of Biophysics, Manipal School of Life Sciences, Manipal Academy of Higher Education, Karnataka, Manipal 576104, India
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3
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Yang R, Ye Y, Liu W, Liang B, He H, Li X, Ji C, Sun C. Modification of pea dietary fibre by superfine grinding assisted enzymatic modification: Structural, physicochemical, and functional properties. Int J Biol Macromol 2024; 267:131408. [PMID: 38604426 DOI: 10.1016/j.ijbiomac.2024.131408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 03/29/2024] [Accepted: 04/03/2024] [Indexed: 04/13/2024]
Abstract
Using the optimal extraction conditions determined by response surface optimisation, the yield of soluble dietary fibre (SDF) modified by superfine grinding combined with enzymatic modification (SE-SDF) was significantly increased from 4.45 % ± 0.21 % (natural pea dietary fibre) to 16.24 % ± 0.09 %. To further analyse the modification mechanism, the effects of three modification methods-superfine grinding (S), enzymatic modification (E), and superfine grinding combined with enzymatic modification (SE)-on the structural, physicochemical, and functional properties of pea SDF were studied. Nuclear magnetic resonance spectroscopy results showed that all four SDFs had α- and β-glycosidic bonds. Fourier transform infrared spectroscopy and X-ray diffraction spectroscopy results showed that the crystal structure of SE-SDF was most severely damaged. The Congo red experimental results showed that none of the four SDFs had a triple-helical structure. Scanning electron microscopy showed that SE-SDF had a looser structure and an obvious honeycomb structure than other SDFs. Thermogravimetric analysis, particle size, and zeta potential results showed that SE-SDF had the highest thermal stability, smallest particle size, and excellent solution stability compared with the other samples. The hydration properties showed that SE-SDF had the best water solubility capacity and water-holding capacity. All three modification methods (S, E, and SE) enhanced the sodium cholate adsorption capacity, cholesterol adsorption capacity, cation exchange capacity, and nitrite ion adsorption capacity of pea SDF. Among them, the SE modification had the greatest effect. This study showed that superfine grinding combined with enzymatic modification can effectively improve the SDF content and the physicochemical and functional properties of pea dietary fibre, which gives pea dietary fibre great application potential in functional foods.
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Affiliation(s)
- Renhui Yang
- College of Life Sciences, Yantai University, Yantai, Shandong 264005, China
| | - Ying Ye
- College of Life Sciences, Yantai University, Yantai, Shandong 264005, China
| | - Weiting Liu
- College of Life Sciences, Yantai University, Yantai, Shandong 264005, China
| | - Bin Liang
- College of Food Engineering, Ludong University, Yantai, Shandong 264025, China.
| | - Hongjun He
- College of Life Sciences, Yantai University, Yantai, Shandong 264005, China
| | - Xiulian Li
- School of Pharmacy, Binzhou Medical University, Yantai, Shandong 264003, China
| | - Changjian Ji
- Department of Physics and Electronic Engineering, Qilu Normal University, Jinan, Shandong 250200, China
| | - Chanchan Sun
- College of Life Sciences, Yantai University, Yantai, Shandong 264005, China.
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4
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Tan X, Cheng X, Ma B, Cui F, Wang D, Shen R, Li X, Li J. Characterization and Function Analysis of Soluble Dietary Fiber Obtained from Radish Pomace by Different Extraction Methods. Molecules 2024; 29:500. [PMID: 38276578 PMCID: PMC10818875 DOI: 10.3390/molecules29020500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 01/12/2024] [Accepted: 01/17/2024] [Indexed: 01/27/2024] Open
Abstract
Soluble dietary fiber (SDF) benefits human health, and different extraction methods might modify the structure and functions of the SDFs. Radish is rich in dietary fiber. To assess the impact of various extraction techniques on the properties and functions of radish SDF, the SDFs were obtained from white radish pomace using alkaline, ultrasonic-assisted, and fermentation-assisted extraction methods. Analysis was conducted on the structure, physicochemical characteristics, thermal properties, and functional attributes of the SDFs. The study revealed that various extraction techniques can impact the monosaccharides composition and functionality of the SDFs. Compared with the other two extraction methods, the surface structures of SDFs obtained by fermentation-assisted extraction were looser and more porous, and the SDF had better water solubility and water/oil holding capacity. The adsorption capacities of glucose and cholesterol of the SDFs obtained from fermentation-assisted extraction were also improved. Wickerhamomyces anomalus YFJ252 seems the most appropriate strain to ferment white radish pomace to acquire SDF; the water holding, oil holding, glucose absorption capacity, and cholesterol absorption capacity at pH 2 and pH 7 have a 3.06, 1.65, 3.19, 1.27, and 1.83 fold increase than the SDF extracted through alkaline extraction method.
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Affiliation(s)
- Xiqian Tan
- College of Food Science and Technology, Bohai University, Jinzhou 121013, China; (X.T.); (X.C.); (B.M.); (F.C.); (D.W.)
| | - Xiaoxiao Cheng
- College of Food Science and Technology, Bohai University, Jinzhou 121013, China; (X.T.); (X.C.); (B.M.); (F.C.); (D.W.)
| | - Bingyu Ma
- College of Food Science and Technology, Bohai University, Jinzhou 121013, China; (X.T.); (X.C.); (B.M.); (F.C.); (D.W.)
| | - Fangchao Cui
- College of Food Science and Technology, Bohai University, Jinzhou 121013, China; (X.T.); (X.C.); (B.M.); (F.C.); (D.W.)
| | - Dangfeng Wang
- College of Food Science and Technology, Bohai University, Jinzhou 121013, China; (X.T.); (X.C.); (B.M.); (F.C.); (D.W.)
| | - Ronghu Shen
- Hangzhou Xiaoshan Agriculture Development Co., Ltd., Xiaoshan, Hangzhou 311215, China
| | - Xuepeng Li
- College of Food Science and Technology, Bohai University, Jinzhou 121013, China; (X.T.); (X.C.); (B.M.); (F.C.); (D.W.)
| | - Jianrong Li
- College of Food Science and Technology, Bohai University, Jinzhou 121013, China; (X.T.); (X.C.); (B.M.); (F.C.); (D.W.)
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5
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Liang Z, Li K, Huang W, Li Z, Xu X, Xu H, Li S. Production, structural and functional characteristics of soluble dietary fiber from fermented okara by Penicillium expansum. Int J Biol Macromol 2023; 253:126621. [PMID: 37657574 DOI: 10.1016/j.ijbiomac.2023.126621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 08/14/2023] [Accepted: 08/28/2023] [Indexed: 09/03/2023]
Abstract
Soluble dietary fiber (SDF), an important prebiotic, has attracted growing attention, due to its great health effects and wide application. This study focused on the preparation of SDF from fermented okara. The yield of SDF obtained through Penicillium expansum fermentation (FSDF) reached 45.63 % (w/w) under the optimal conditions (pH 6.7, inoculum size 9.5 %, and time 29 h) by response surface methodology, which were 1.92 and 4.43 times higher than those of phosphate-citric acid treatment and untreated okara. Infrared spectra and X-ray diffraction indicated that three SDFs had similar spectral distribution and crystalline region. Moreover, FSDF displayed looser and more porous microstructures. Meanwhile, the composition ratio of monosaccharides has changed. FSDF exhibited higher water solubility (97.46 %), glucose adsorption capacity (203.73 mg/g), sodium cholate adsorption capacity (13.07 mg/g), cholesterol adsorption capacity (6.69- 7.62 mg/g) and radical (ABTS+, hydroxyl and DPPH) scavenging capacity. Additionally, three SDFs didn't degrade by upper gastrointestinal tract and could improve the proportion of beneficial intestinal flora in vitro, such as Lactobacillus and Bifidobacterium. Overall, the FSDF prepared in this study was a functional ingredient with great potential in foods.
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Affiliation(s)
- Zhong Liang
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211816, China
| | - Kecheng Li
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211816, China
| | - Weiwei Huang
- State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing 211816, China; College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211816, China
| | - Zhaoxia Li
- College of Marine and Biological Engineering, Yancheng Institute of Technology, Yancheng 224051, China
| | - Xiaoqi Xu
- State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing 211816, China; College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211816, China
| | - Hong Xu
- State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing 211816, China; College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211816, China
| | - Sha Li
- State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing 211816, China; College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211816, China.
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6
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Zhou L, Luo J, Xie Q, Huang L, Shen D, Li G. Dietary Fiber from Navel Orange Peel Prepared by Enzymatic and Ultrasound-Assisted Deep Eutectic Solvents: Physicochemical and Prebiotic Properties. Foods 2023; 12:foods12102007. [PMID: 37238825 DOI: 10.3390/foods12102007] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 04/28/2023] [Accepted: 05/08/2023] [Indexed: 05/28/2023] Open
Abstract
Dietary fiber (DF) was extracted from navel orange peel residue by enzyme (E-DF) and ultrasound-assisted deep eutectic solvent (US-DES-DF), and its physicochemical and prebiotic properties were characterized. Based on Fourier-transform infrared spectroscopy, all DF samples exhibited typical polysaccharide absorption spectra, indicating that DES could separate lignin while leaving the chemical structure of DF unchanged, yielding significantly higher extraction yields (76.69 ± 1.68%) compared to enzymatic methods (67.27 ± 0.13%). Moreover, ultrasound-assisted DES extraction improved the properties of navel orange DFs by significantly increasing the contents of soluble dietary fiber and total dietary fiber (3.29 ± 1.33% and 10.13 ± 0.78%, respectively), as well as a notable improvement in the values of water-holding capacity, oil-holding capacity, and water swelling capacity. US-DES-DF outperformed commercial citrus fiber in stimulating the proliferation of probiotic Bifidobacteria strains in vitro. Overall, ultrasound-assisted DES extraction exhibited potential as an industrial extraction method, and US-DES-DF could serve as a valuable functional food ingredient. These results provide a new perspective on the prebiotic properties of dietary fibers and the preparation process of prebiotics.
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Affiliation(s)
- Liling Zhou
- Longping Branch, College of Biology, Hunan University, Changsha 410125, China
- Hunan Agricultural Product Processing Institute, Hunan Academy of Agricultural Sciences, Hunan Provincial Key Laboratory for Fruits and Vegetables Storage Processing and Quality Safety, Changsha 410125, China
| | - Jiaqian Luo
- Longping Branch, College of Biology, Hunan University, Changsha 410125, China
- Hunan Agricultural Product Processing Institute, Hunan Academy of Agricultural Sciences, Hunan Provincial Key Laboratory for Fruits and Vegetables Storage Processing and Quality Safety, Changsha 410125, China
| | - Qiutao Xie
- Hunan Agricultural Product Processing Institute, Hunan Academy of Agricultural Sciences, Hunan Provincial Key Laboratory for Fruits and Vegetables Storage Processing and Quality Safety, Changsha 410125, China
| | - Lvhong Huang
- Hunan Agricultural Product Processing Institute, Hunan Academy of Agricultural Sciences, Hunan Provincial Key Laboratory for Fruits and Vegetables Storage Processing and Quality Safety, Changsha 410125, China
| | - Dan Shen
- Longping Branch, College of Biology, Hunan University, Changsha 410125, China
- Hunan Agricultural Product Processing Institute, Hunan Academy of Agricultural Sciences, Hunan Provincial Key Laboratory for Fruits and Vegetables Storage Processing and Quality Safety, Changsha 410125, China
| | - Gaoyang Li
- Longping Branch, College of Biology, Hunan University, Changsha 410125, China
- Hunan Agricultural Product Processing Institute, Hunan Academy of Agricultural Sciences, Hunan Provincial Key Laboratory for Fruits and Vegetables Storage Processing and Quality Safety, Changsha 410125, China
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7
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Perez S, Makshakova O, Angulo J, Bedini E, Bisio A, de Paz JL, Fadda E, Guerrini M, Hricovini M, Hricovini M, Lisacek F, Nieto PM, Pagel K, Paiardi G, Richter R, Samsonov SA, Vivès RR, Nikitovic D, Ricard Blum S. Glycosaminoglycans: What Remains To Be Deciphered? JACS AU 2023; 3:628-656. [PMID: 37006755 PMCID: PMC10052243 DOI: 10.1021/jacsau.2c00569] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Revised: 12/05/2022] [Accepted: 12/07/2022] [Indexed: 06/19/2023]
Abstract
Glycosaminoglycans (GAGs) are complex polysaccharides exhibiting a vast structural diversity and fulfilling various functions mediated by thousands of interactions in the extracellular matrix, at the cell surface, and within the cells where they have been detected in the nucleus. It is known that the chemical groups attached to GAGs and GAG conformations comprise "glycocodes" that are not yet fully deciphered. The molecular context also matters for GAG structures and functions, and the influence of the structure and functions of the proteoglycan core proteins on sulfated GAGs and vice versa warrants further investigation. The lack of dedicated bioinformatic tools for mining GAG data sets contributes to a partial characterization of the structural and functional landscape and interactions of GAGs. These pending issues will benefit from the development of new approaches reviewed here, namely (i) the synthesis of GAG oligosaccharides to build large and diverse GAG libraries, (ii) GAG analysis and sequencing by mass spectrometry (e.g., ion mobility-mass spectrometry), gas-phase infrared spectroscopy, recognition tunnelling nanopores, and molecular modeling to identify bioactive GAG sequences, biophysical methods to investigate binding interfaces, and to expand our knowledge and understanding of glycocodes governing GAG molecular recognition, and (iii) artificial intelligence for in-depth investigation of GAGomic data sets and their integration with proteomics.
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Affiliation(s)
- Serge Perez
- Centre
de Recherche sur les Macromolecules, Vegetales,
University of Grenoble-Alpes, Centre National de la Recherche Scientifique, Grenoble F-38041 France
| | - Olga Makshakova
- FRC
Kazan Scientific Center of Russian Academy of Sciences, Kazan Institute of Biochemistry and Biophysics, Kazan 420111, Russia
| | - Jesus Angulo
- Insituto
de Investigaciones Quimicas, CIC Cartuja, CSIC and Universidad de Sevilla, Sevilla, SP 41092, Spain
| | - Emiliano Bedini
- Department
of Chemical Sciences, University of Naples
Federico II, Naples,I-80126, Italy
| | - Antonella Bisio
- Istituto
di Richerche Chimiche e Biochimiche, G. Ronzoni, Milan I-20133, Italy
| | - Jose Luis de Paz
- Insituto
de Investigaciones Quimicas, CIC Cartuja, CSIC and Universidad de Sevilla, Sevilla, SP 41092, Spain
| | - Elisa Fadda
- Department
of Chemistry and Hamilton Institute, Maynooth
University, Maynooth W23 F2H6, Ireland
| | - Marco Guerrini
- Istituto
di Richerche Chimiche e Biochimiche, G. Ronzoni, Milan I-20133, Italy
| | - Michal Hricovini
- Institute
of Chemistry, Slovak Academy of Sciences, Bratislava SK-845 38, Slovakia
| | - Milos Hricovini
- Institute
of Chemistry, Slovak Academy of Sciences, Bratislava SK-845 38, Slovakia
| | - Frederique Lisacek
- Computer
Science Department & Section of Biology, University of Geneva & Swiss Institue of Bioinformatics, Geneva CH-1227, Switzerland
| | - Pedro M. Nieto
- Insituto
de Investigaciones Quimicas, CIC Cartuja, CSIC and Universidad de Sevilla, Sevilla, SP 41092, Spain
| | - Kevin Pagel
- Institut
für Chemie und Biochemie Organische Chemie, Freie Universität Berlin, Berlin 14195, Germany
| | - Giulia Paiardi
- Molecular
and Cellular Modeling Group, Heidelberg Institute for Theoretical
Studies, Heidelberg University, Heidelberg 69118, Germany
| | - Ralf Richter
- School
of Biomedical Sciences, Faculty of Biological Sciences, School of
Physics and Astronomy, Faculty of Engineering and Physical Sciences,
Astbury Centre for Structural Molecular Biology and Bragg Centre for
Materials Research, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Sergey A. Samsonov
- Department
of Theoretical Chemistry, Faculty of Chemistry, University of Gdansk, Gdsank 80-309, Poland
| | - Romain R. Vivès
- Univ.
Grenoble Alpes, CNRS, CEA, IBS, Grenoble F-38044, France
| | - Dragana Nikitovic
- School
of Histology-Embriology, Medical School, University of Crete, Heraklion 71003, Greece
| | - Sylvie Ricard Blum
- University
Claude Bernard Lyon 1, CNRS, INSA Lyon, CPE, Institute of Molecular and Supramolecular Chemistry and Biochemistry,
UMR 5246, Villeurbanne F 69622 Cedex, France
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8
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Fu D, Habtegabir SG, Wang H, Feng S, Han Y. Understanding of protomers/deprotomers by combining mass spectrometry and computation. Anal Bioanal Chem 2023:10.1007/s00216-023-04574-1. [PMID: 36737499 DOI: 10.1007/s00216-023-04574-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 01/19/2023] [Accepted: 01/27/2023] [Indexed: 02/05/2023]
Abstract
Multifunctional compounds may form different prototropic isomers under different conditions, which are known as protomers/deprotomers. In biological systems, these protomer/deprotomer isomers affect the interaction modes and conformational landscape between compounds and enzymes and thus present different biological activities. Study on protomers/deprotomers is essentially the study on the acidity/basicity of each intramolecular functional group and its effect on molecular structure. In recent years, the combination of mass spectrometry (MS) and computational chemistry has been proven to be a powerful and effective means to study prototropic isomers. MS-based technologies are developed to discriminate and characterize protomers/deprotomers to provide structural information and monitor transformations, showing great superiority than other experimental methods. Computational chemistry is used to predict the thermodynamic stability of protomers/deprotomers, provide the simulated MS/MS spectra, infrared spectra, and calculate collision cross-section values. By comparing the theoretical data with the corresponding experimental results, the researchers can not only determine the protomer/deprotomer structure, but also investigate the structure-activity relationship in a given system. This review covers various MS methods and theoretical calculations and their devotion to isomer discrimination, structure identification, conformational transformation, and phase transition investigation of protomers/deprotomers.
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Affiliation(s)
- Dali Fu
- State Key Laboratory of Heavy Oil Processing, College of Chemical Engineering and Environment, China University of Petroleum-Beijing, Beijing, 102249, People's Republic of China
| | - Sara Girmay Habtegabir
- State Key Laboratory of Heavy Oil Processing, College of Chemical Engineering and Environment, China University of Petroleum-Beijing, Beijing, 102249, People's Republic of China
| | - Haodong Wang
- State Key Laboratory of Heavy Oil Processing, College of Chemical Engineering and Environment, China University of Petroleum-Beijing, Beijing, 102249, People's Republic of China
| | - Shijie Feng
- State Key Laboratory of Heavy Oil Processing, College of Chemical Engineering and Environment, China University of Petroleum-Beijing, Beijing, 102249, People's Republic of China
| | - Yehua Han
- State Key Laboratory of Heavy Oil Processing, College of Chemical Engineering and Environment, China University of Petroleum-Beijing, Beijing, 102249, People's Republic of China.
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9
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Nguan HS, Ni CK. Collision-Induced Dissociation of α-Isomaltose and α-Maltose. J Phys Chem A 2022; 126:8799-8808. [DOI: 10.1021/acs.jpca.2c04278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Affiliation(s)
- Hock-Seng Nguan
- Institute of Atomic and Molecular Sciences, Academia Sinica, P.O. Box 23-166, Taipei 10617, Taiwan
| | - Chi-Kung Ni
- Institute of Atomic and Molecular Sciences, Academia Sinica, P.O. Box 23-166, Taipei 10617, Taiwan
- Department of Chemistry, National Tsing Hua University, Hsinchu 30013, Taiwan
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10
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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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11
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Li S, Hu N, Zhu J, Zheng M, Liu H, Liu J. Influence of modification methods on physicochemical and structural properties of soluble dietary fiber from corn bran. Food Chem X 2022; 14:100298. [PMID: 35399582 PMCID: PMC8989766 DOI: 10.1016/j.fochx.2022.100298] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 03/24/2022] [Accepted: 03/30/2022] [Indexed: 11/24/2022] Open
Abstract
Soluble dietary fiber (SDF), which is a component of dietary fibers exhibit many physiological functions, biological activity, and good gel forming ability. In this study, extraction of SDF from corn bran was evaluated using twin-screw extrusion and ultrasonic treatment and the combinations of the respective methods with dual enzyme hydrolysis. The monosaccharide compositions, molecular weight, physicochemical properties, and structural and functional characteristics were determined. The results showed that ultrasonic and twin-extrusion treatments significantly increased the SDF content from 2.42 to 4.58 and 6.54%, respectively. Dual enzyme hydrolysis further increased the SDF content. Modification treatment changed the monosaccharide composition, improved physicochemical and functional properties, such as water and oil holding capacity, nitrite adsorption, and antioxidative ability. In conclusion, physical modification combined with enzyme treatment distinctly improved the extraction yield, physicochemical and functional properties of SDF. Therefore, the modified SDF is suitable as a functional food additive.
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Affiliation(s)
- Sheng Li
- College of Food Science and Engineering, Jilin Agricultural University, Changchun 130118, PR China
- National Engineering Laboratory of Wheat and Corn Deep Processing, Jilin Agricultural University, Changchun 130118, PR China
| | - Nannan Hu
- College of Food Science and Engineering, Jilin Agricultural University, Changchun 130118, PR China
- National Engineering Laboratory of Wheat and Corn Deep Processing, Jilin Agricultural University, Changchun 130118, PR China
| | - Jinying Zhu
- College of Food Science and Engineering, Jilin Agricultural University, Changchun 130118, PR China
- National Engineering Laboratory of Wheat and Corn Deep Processing, Jilin Agricultural University, Changchun 130118, PR China
| | - Mingzhu Zheng
- College of Food Science and Engineering, Jilin Agricultural University, Changchun 130118, PR China
- National Engineering Laboratory of Wheat and Corn Deep Processing, Jilin Agricultural University, Changchun 130118, PR China
| | - Huimin Liu
- College of Food Science and Engineering, Jilin Agricultural University, Changchun 130118, PR China
- National Engineering Laboratory of Wheat and Corn Deep Processing, Jilin Agricultural University, Changchun 130118, PR China
| | - Jingsheng Liu
- College of Food Science and Engineering, Jilin Agricultural University, Changchun 130118, PR China
- National Engineering Laboratory of Wheat and Corn Deep Processing, Jilin Agricultural University, Changchun 130118, PR China
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12
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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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13
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Li Y, Yu Y, Wu J, Xu Y, Xiao G, Li L, Liu H. Comparison the Structural, Physicochemical, and Prebiotic Properties of Litchi Pomace Dietary Fibers before and after Modification. Foods 2022; 11:248. [PMID: 35159400 PMCID: PMC8833994 DOI: 10.3390/foods11030248] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 01/04/2022] [Accepted: 01/14/2022] [Indexed: 01/25/2023] Open
Abstract
Litchi pomace, a by-product of litchi processing, is rich in dietary fiber. Soluble and insoluble dietary fibers were extracted from litchi pomace, and insoluble dietary fiber was modified by ultrasonic enzymatic treatment to obtain modified soluble and insoluble dietary fibers. The structural, physicochemical, and functional properties of the dietary fiber samples were evaluated and compared. It was found that all dietary fiber samples displayed typical polysaccharide absorption spectra, with arabinose being the most abundant monosaccharide component. Soluble dietary fibers from litchi pomace were morphologically fragmented and relatively smooth, with relatively high swelling capacity, whereas the insoluble dietary fibers possessed wrinkles and porous structures on the surface, as well as higher water holding capacity. Additionally, soluble dietary fiber content of litchi pomace was successfully increased by 6.32 ± 0.14% after ultrasonic enzymatic modification, and its arabinose content and apparent viscosity were also significantly increased. Further, the soluble dietary fibers exhibited superior radical scavenging ability and significantly stimulated the growth of probiotic bacterial species. Taken together, this study suggested that dietary fiber from litchi pomace could be a promising ingredient for functional foods industry.
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Affiliation(s)
- Yina Li
- Sericultural & Argi-Food Research Institute, Guangdong Academy of Agricultural Sciences/Key Laboratory of Functional Foods, Ministry of Agriculture and Rural Affairs/Guangdong Key Laboratory of Agricultural Products Processing, Guangzhou 510610, China; (Y.L.); (J.W.); (Y.X.); (G.X.); (L.L.); (H.L.)
- College of Food Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Yuanshan Yu
- Sericultural & Argi-Food Research Institute, Guangdong Academy of Agricultural Sciences/Key Laboratory of Functional Foods, Ministry of Agriculture and Rural Affairs/Guangdong Key Laboratory of Agricultural Products Processing, Guangzhou 510610, China; (Y.L.); (J.W.); (Y.X.); (G.X.); (L.L.); (H.L.)
| | - Jijun Wu
- Sericultural & Argi-Food Research Institute, Guangdong Academy of Agricultural Sciences/Key Laboratory of Functional Foods, Ministry of Agriculture and Rural Affairs/Guangdong Key Laboratory of Agricultural Products Processing, Guangzhou 510610, China; (Y.L.); (J.W.); (Y.X.); (G.X.); (L.L.); (H.L.)
| | - Yujuan Xu
- Sericultural & Argi-Food Research Institute, Guangdong Academy of Agricultural Sciences/Key Laboratory of Functional Foods, Ministry of Agriculture and Rural Affairs/Guangdong Key Laboratory of Agricultural Products Processing, Guangzhou 510610, China; (Y.L.); (J.W.); (Y.X.); (G.X.); (L.L.); (H.L.)
| | - Gengsheng Xiao
- Sericultural & Argi-Food Research Institute, Guangdong Academy of Agricultural Sciences/Key Laboratory of Functional Foods, Ministry of Agriculture and Rural Affairs/Guangdong Key Laboratory of Agricultural Products Processing, Guangzhou 510610, China; (Y.L.); (J.W.); (Y.X.); (G.X.); (L.L.); (H.L.)
| | - Lu Li
- Sericultural & Argi-Food Research Institute, Guangdong Academy of Agricultural Sciences/Key Laboratory of Functional Foods, Ministry of Agriculture and Rural Affairs/Guangdong Key Laboratory of Agricultural Products Processing, Guangzhou 510610, China; (Y.L.); (J.W.); (Y.X.); (G.X.); (L.L.); (H.L.)
| | - Haoran Liu
- Sericultural & Argi-Food Research Institute, Guangdong Academy of Agricultural Sciences/Key Laboratory of Functional Foods, Ministry of Agriculture and Rural Affairs/Guangdong Key Laboratory of Agricultural Products Processing, Guangzhou 510610, China; (Y.L.); (J.W.); (Y.X.); (G.X.); (L.L.); (H.L.)
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14
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Zamfir AD. Capillary Zone Electrophoresis-Electrospray Ionization Tandem Mass Spectrometry for Total Analysis of Chondroitin/Dermatan Sulfate Oligosaccharides. Methods Mol Biol 2022; 2531:163-184. [PMID: 35941485 DOI: 10.1007/978-1-0716-2493-7_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Proteoglycans are heavily glycosylated proteins, covalently linked to one or more glycosaminoglycan (GAG) chains, abundantly expressed in the extracellular matrix (ECM). Among GAGs, chondroitin sulfate (CS) and dermatan sulfate (DS) play an essential role at the ECM level; however, the composition of the hybrid CS/DS as well as the distribution of the sulfate groups along the chain were also shown to influence biological activities in brain. The elevated structural diversity of CS/DS motifs, in which sulfation may occur at GalNAc and/or IdoA/GlcA in various combinations, requires the development of specific high performance analytical methods for reliable elucidation. Due to its sensitivity, reproducibility, and efficiency, capillary zone electrophoresis (CZE) for separation of CS/DS oligosaccharides coupled to electrospray ionization mass spectrometry (ESI-MS) for their structure determination contributed an essential progress to this field.In the present chapter, two powerful methods based on CZE for separation and ESI-MS for identification and structural analysis of CS/DS are presented. The first part is devoted to offline CZE-ESI-MS based on fraction collection, screening by negative ion mode nanoESI, and fragmentation analysis in tandem MS using collision-induced dissociation (CID) at low ion acceleration energies. In the second part of the chapter, a strategy for online CZE-ESI-MS in normal polarity and negative mode ESI followed by tandem MS in real-time data-dependent acquisition mode for CS/DS separation, screening, and fragmentation is described in detail. The latter method entails the in-laboratory manufacturing of a simple yet sturdy interface for the online CZE coupling to ESI-MS and the optimization of the coupled system for total analysis of regularly sulfated and irregularly, i.e., under- and oversulfated CS/DS domains.
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Affiliation(s)
- Alina D Zamfir
- Mass Spectrometry Laboratory, National Institute for Research and Development in Electrochemistry and Condensed Matter, Timisoara, Romania.
- "Aurel Vlaicu" University of Arad, Arad, Romania.
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15
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Hong T, Yin JY, Nie SP, Xie MY. Applications of infrared spectroscopy in polysaccharide structural analysis: Progress, challenge and perspective. Food Chem X 2021; 12:100168. [PMID: 34877528 PMCID: PMC8633561 DOI: 10.1016/j.fochx.2021.100168] [Citation(s) in RCA: 112] [Impact Index Per Article: 37.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 11/16/2021] [Accepted: 11/19/2021] [Indexed: 12/31/2022] Open
Abstract
Functional properties of polysaccharides depend on their structural features. IR spectroscopy is widely used in polysaccharide structural analysis. Classical applications of IR spectroscopy in polysaccharide are reviewed. IR integrating techniques can considerably expand its application scope.
Polysaccharides are important biomacromolecules with numerous beneficial functions and a wide range of industrial applications. Functions and properties of polysaccharides are closely related to their structural features. Infrared (IR) spectroscopy is a well-established technique which has been widely applied in polysaccharide structural analysis. In this paper, the principle of IR and interpretation of polysaccharide IR spectrum are briefly introduced. Classical applications of IR spectroscopy in polysaccharide structural elucidation are reviewed from qualitative and quantitative aspects. Some advanced IR techniques including integrating with mass spectrometry (MS), microscopy and computational chemistry are introduced and their applications are emphasized. These emerging techniques can considerably expand application scope of IR, thus exert a more important effect on carbohydrate characterization. Overall, this review seeks to provide a comprehensive insight to applications of IR spectroscopy in polysaccharide structural analysis and highlights the importance of advanced IR-integrating techniques.
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Affiliation(s)
- Tao Hong
- State Key Laboratory of Food Science and Technology, China-Canada Joint Laboratory of Food Science and Technology (Nanchang), Nanchang University, 235 Nanjing East Road, Nanchang, Jiangxi 330047, People's Republic of China
| | - Jun-Yi Yin
- State Key Laboratory of Food Science and Technology, China-Canada Joint Laboratory of Food Science and Technology (Nanchang), Nanchang University, 235 Nanjing East Road, Nanchang, Jiangxi 330047, People's Republic of China
| | - Shao-Ping Nie
- State Key Laboratory of Food Science and Technology, China-Canada Joint Laboratory of Food Science and Technology (Nanchang), Nanchang University, 235 Nanjing East Road, Nanchang, Jiangxi 330047, People's Republic of China
| | - Ming-Yong Xie
- State Key Laboratory of Food Science and Technology, China-Canada Joint Laboratory of Food Science and Technology (Nanchang), Nanchang University, 235 Nanjing East Road, Nanchang, Jiangxi 330047, People's Republic of China
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16
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Greis K, Kirschbaum C, von Helden G, Pagel K. Gas-phase infrared spectroscopy of glycans and glycoconjugates. Curr Opin Struct Biol 2021; 72:194-202. [PMID: 34952241 DOI: 10.1016/j.sbi.2021.11.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 11/02/2021] [Accepted: 11/21/2021] [Indexed: 11/28/2022]
Abstract
Glycans are intrinsically complex biomolecules that pose particular analytical challenges. Standard workflows for glycan analysis are based on mass spectrometry, often coupled with separation techniques such as liquid chromatography and ion mobility spectrometry. However, this approach does not yield direct structural information and cannot always distinguish between isomers. This gap might be filled in the future by gas-phase infrared spectroscopy, which has emerged as a promising structure-sensitive technique for glycan fingerprinting. This review highlights recent applications of gas-phase infrared spectroscopy for the analysis of synthetic and biological glycans and how they can be integrated into mass spectrometry-based workflows.
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Affiliation(s)
- Kim Greis
- Institut für Chemie und Biochemie, Freie Universität Berlin, Arnimallee 22, 14195, Berlin, Germany; Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195, Berlin, Germany
| | - Carla Kirschbaum
- Institut für Chemie und Biochemie, Freie Universität Berlin, Arnimallee 22, 14195, Berlin, Germany; Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195, Berlin, Germany
| | - Gert von Helden
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195, Berlin, Germany
| | - Kevin Pagel
- Institut für Chemie und Biochemie, Freie Universität Berlin, Arnimallee 22, 14195, Berlin, Germany; Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195, Berlin, Germany.
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17
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Warnke S, Ben Faleh A, Rizzo TR. Toward High-Throughput Cryogenic IR Fingerprinting of Mobility-Separated Glycan Isomers. ACS MEASUREMENT SCIENCE AU 2021; 1:157-164. [PMID: 34939078 PMCID: PMC8679095 DOI: 10.1021/acsmeasuresciau.1c00018] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Indexed: 05/10/2023]
Abstract
Infrared (IR) spectroscopy is a powerful tool used to infer detailed structural information on molecules, often in conjunction with quantum-chemical calculations. When applied to cryogenically cooled ions, IR spectra provide unique fingerprints that can be used for biomolecular identification. This is particularly important in the analysis of isomeric biopolymers, which are difficult to distinguish using mass spectrometry. However, IR spectroscopy typically requires laser systems that need substantial user attention and measurement times of tens of minutes, which limits its analytical utility. We report here the development of a new high-throughput instrument that combines ultrahigh-resolution ion-mobility spectrometry with cryogenic IR spectroscopy and mass spectrometry, and we apply it to the analysis of isomeric glycans. The ion mobility step, which is based on structures for lossless ion manipulations (SLIM), separates glycan isomers, and an IR fingerprint spectrum identifies them. An innovative cryogenic ion trap allows multiplexing the acquisition of analyte IR fingerprints following mobility separation, and using a turn-key IR laser, we can obtain spectra and identify isomeric species in less than a minute. This work demonstrates the potential of IR fingerprinting methods to impact the analysis of isomeric biomolecules and more specifically glycans.
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18
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Gaigeot MP. Some opinions on MD-based vibrational spectroscopy of gas phase molecules and their assembly: An overview of what has been achieved and where to go. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2021; 260:119864. [PMID: 34052762 DOI: 10.1016/j.saa.2021.119864] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Revised: 04/13/2021] [Accepted: 04/18/2021] [Indexed: 06/12/2023]
Abstract
We hereby review molecular dynamics simulations for anharmonic gas phase spectroscopy and provide some of our opinions of where the field is heading. With these new directions, the theoretical IR/Raman spectroscopy of large (bio)-molecular systems will be more easily achievable over longer time-scale MD trajectories for an increase in accuracy of the MD-IR and MD-Raman calculated spectra. With the new directions presented here, the high throughput 'decoding' of experimental IR/Raman spectra into 3D-structures should thus be possible, hence advancing e.g. the field of MS-IR for structural characterization by spectroscopy. We also review the assignment of vibrational spectra in terms of anharmonic molecular modes from the MD trajectories, and especially introduce our recent developments based on Graph Theory algorithms. Graph Theory algorithmic is also introduced in this review for the identification of the molecular 3D-structures sampled over MD trajectories.
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Affiliation(s)
- Marie-Pierre Gaigeot
- Université Paris-Saclay, Univ Evry, CNRS, LAMBE UMR8587, 91025 Evry-Courcouronnes, France.
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19
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Analytical challenges of glycosaminoglycans at biological interfaces. Anal Bioanal Chem 2021; 414:85-93. [PMID: 34647134 PMCID: PMC8514262 DOI: 10.1007/s00216-021-03705-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 09/24/2021] [Accepted: 09/28/2021] [Indexed: 11/15/2022]
Abstract
The analysis of glycosaminoglycans (GAGs) is a challenging task due to their high structural heterogeneity, which results in diverse GAG chains with similar chemical properties. Simultaneously, it is of high importance to understand their role and behavior in biological systems. It has been known for decades now that GAGs can interact with lipid molecules and thus contribute to the onset of atherosclerosis, but their interactions at and with biological interfaces, such as the cell membrane, are yet to be revealed. Here, analytical approaches that could yield important knowledge on the GAG-cell membrane interactions as well as the synthetic and analytical advances that make their study possible are discussed. Due to recent developments in laser technology, we particularly focus on nonlinear spectroscopic methods, especially vibrational sum-frequency generation spectroscopy, which has the potential to unravel the structural complexity of heterogeneous biological interfaces in contact with GAGs, in situ and in real time.
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20
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Schiller J, Lemmnitzer K, Dürig JN, Rademann J. Insights into structure, affinity, specificity, and function of GAG-protein interactions through the chemoenzymatic preparation of defined sulfated oligohyaluronans. Biol Chem 2021; 402:1375-1384. [PMID: 34291624 DOI: 10.1515/hsz-2021-0165] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 07/04/2021] [Indexed: 11/15/2022]
Abstract
High amounts of glycosaminoglycans (GAG) such as hyaluronan (HA) occur in connective tissues. There is nowadays increasing evidence that a "sulfation code" exists which mediates numerous GAG functions. High molecular weight and inhomogeneity of GAG, however, aggravated detailed studies. Thus, synthetic oligosaccharides were urgently required. We will review here chemoenzymatic and analytic strategies to provide defined sulfated and anomerically modified GAG oligosaccharides of the HA type. Representative studies of protein/GAG interactions by (bio)chemical and biophysical methods are reported yielding novel insights into GAG-protein binding. Finally, the biological conclusions and in vivo applications of defined sulfated GAG oligosaccharides will be discussed.
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Affiliation(s)
- Jürgen Schiller
- Faculty of Medicine, Institute of Medical Physics and Biophysics, University of Leipzig, Härtelstraße 16-18, 04107Leipzig, Germany
| | - Katharina Lemmnitzer
- Faculty of Medicine, Institute of Medical Physics and Biophysics, University of Leipzig, Härtelstraße 16-18, 04107Leipzig, Germany
| | - Jan-Niklas Dürig
- Department of Biology, Chemistry, and Pharmacy, Institute of Pharmacy, Pharmaceutical and Medicinal Chemistry, Freie Universität Berlin, Königin-Luise-Str. 2+4, 14195Berlin, Germany
| | - Jörg Rademann
- Department of Biology, Chemistry, and Pharmacy, Institute of Pharmacy, Pharmaceutical and Medicinal Chemistry, Freie Universität Berlin, Königin-Luise-Str. 2+4, 14195Berlin, Germany
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21
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Lettow M, Greis K, Grabarics M, Horlebein J, Miller RL, Meijer G, von Helden G, Pagel K. Chondroitin Sulfate Disaccharides in the Gas Phase: Differentiation and Conformational Constraints. J Phys Chem A 2021; 125:4373-4379. [PMID: 33979516 PMCID: PMC8279649 DOI: 10.1021/acs.jpca.1c02463] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
![]()
Glycosaminoglycans
(GAGs) are a family of complex carbohydrates
vital to all mammalian organisms and involved in numerous biological
processes. Chondroitin and dermatan sulfate, an important class of
GAGs, are linear macromolecules consisting of disaccharide building
blocks of N-acetylgalactosamine and two different
uronic acids. The varying degree and the site of sulfation render
their characterization challenging. Here, we combine mass spectrometry
with cryogenic infrared spectroscopy in the wavenumber range from
1000 to 1800 cm–1. Fingerprint spectra were recorded
for a comprehensive set of disaccharides bearing all known motifs
of sulfation. In addition, state-of-the-art quantum chemical calculations
were performed to aid the understanding of the differences in the
experimental fingerprint spectra. The results show that the degree
and position of charged sulfate groups define the size of the conformational
landscape in the gas phase. The detailed understanding of cryogenic
infrared spectroscopy for acidic and often highly sulfated glycans
may pave the way to utilize the technique in fragment-based sequencing
approaches.
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Affiliation(s)
- Maike Lettow
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195 Berlin, Germany.,Institut für Chemie und Biochemie, Freie Universität Berlin, Arnimallee 22, 14195 Berlin, Germany
| | - Kim Greis
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195 Berlin, Germany.,Institut für Chemie und Biochemie, Freie Universität Berlin, Arnimallee 22, 14195 Berlin, Germany
| | - Márkó Grabarics
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195 Berlin, Germany.,Institut für Chemie und Biochemie, Freie Universität Berlin, Arnimallee 22, 14195 Berlin, Germany
| | - Jan Horlebein
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195 Berlin, Germany.,Institut für Chemie und Biochemie, Freie Universität Berlin, Arnimallee 22, 14195 Berlin, Germany
| | - Rebecca L Miller
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark
| | - Gerard Meijer
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195 Berlin, Germany
| | - Gert von Helden
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195 Berlin, Germany
| | - Kevin Pagel
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195 Berlin, Germany.,Institut für Chemie und Biochemie, Freie Universität Berlin, Arnimallee 22, 14195 Berlin, Germany
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22
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Bilong M, Bayat P, Bourderioux M, Jérôme M, Giuliani A, Daniel R. Mammal Hyaluronidase Activity on Chondroitin Sulfate and Dermatan Sulfate: Mass Spectrometry Analysis of Oligosaccharide Products. Glycobiology 2021; 31:751-761. [PMID: 33442722 DOI: 10.1093/glycob/cwab004] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 12/28/2020] [Accepted: 12/28/2020] [Indexed: 11/13/2022] Open
Abstract
Mammalian hyaluronidases are endo-N-acetyl-D-hexosaminidases involved in the catabolism of hyaluronic acid (HA) but their role in the catabolism of chondroitin sulfate (CS) is also examined. HA and CS are glycosaminoglycans (GAGs) implicated in several physiological and pathological processes, and understanding their metabolism is of significant importance. Data have been previously reported on the degradation of CS under the action of hyaluronidase, yet a detailed structural investigation of CS depolymerization products remains necessary to improve our knowledge of the CS depolymerizyng activity of hyaluronidase. For that purpose, the fine structural characterization of CS oligosaccharides formed upon the enzymatic depolymerization of various CS sub-types by hyaluronidase has been carried out by high resolution Orbitrap mass spectrometry and extreme UV (XUV) photodissociation tandem mass spectrometry. The exact mass measurements show the formation of wide size range of even oligosaccharides upon digestion of CS-A and CS-C comprising hexa- and octa-saccharides among the main digestion products, as well as formation of small quantities of odd-numbered oligosaccharides, while no hyaluronidase activity was detected on CS-B. In addition, slight differences have been observed in the distribution of oligosaccharides in the digestion mixture of CS-A and CS-C, the contribution of longer oligosaccharides being significantly higher for CS-C. The sequence of CS oligosaccharide products determined XUV photodissociation experiments verifies the selective β(1 → 4) glycosidic bond cleavage catalyzed by mammal hyaluronidase. The ability of the mammal hyaluronidase to produce hexa- and higher oligosaccharides supports its role in the catabolism of CS anchored to membrane proteoglycans and in extra-cellular matrix.
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Affiliation(s)
- Mélanie Bilong
- Université Paris-Saclay, Univ Evry, CNRS, LAMBE, 91025 Evry-Courcouronnes, France
| | - Parisa Bayat
- Université Paris-Saclay, Univ Evry, CNRS, LAMBE, 91025 Evry-Courcouronnes, France
| | - Matthieu Bourderioux
- Université Paris-Saclay, Univ Evry, CNRS, LAMBE, 91025 Evry-Courcouronnes, France
| | - Murielle Jérôme
- Université Paris-Saclay, Univ Evry, CNRS, LAMBE, 91025 Evry-Courcouronnes, France
| | - Alexandre Giuliani
- SOLEIL, l'Orme des Merisiers, St Aubin, BP48, 91192 Gif sur Yvette Cedex, France.,UAR1008, Transform, INRAe, Rue de la Géraudière, 44316 Nantes, France
| | - Régis Daniel
- Université Paris-Saclay, Univ Evry, CNRS, LAMBE, 91025 Evry-Courcouronnes, France
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23
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Dong W, Wang D, Hu R, Long Y, Lv L. Chemical composition, structural and functional properties of soluble dietary fiber obtained from coffee peel using different extraction methods. Food Res Int 2020; 136:109497. [DOI: 10.1016/j.foodres.2020.109497] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Revised: 06/19/2020] [Accepted: 06/23/2020] [Indexed: 11/28/2022]
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24
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Lettow M, Grabarics M, Greis K, Mucha E, Thomas DA, Chopra P, Boons GJ, Karlsson R, Turnbull JE, Meijer G, Miller RL, von Helden G, Pagel K. Cryogenic Infrared Spectroscopy Reveals Structural Modularity in the Vibrational Fingerprints of Heparan Sulfate Diastereomers. Anal Chem 2020; 92:10228-10232. [PMID: 32658472 DOI: 10.1021/acs.analchem.0c02048] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Heparan sulfate and heparin are highly acidic polysaccharides with a linear sequence, consisting of alternating glucosamine and hexuronic acid building blocks. The identity of hexuronic acid units shows a variability along their sequence, as d-glucuronic acid and its C5 epimer, l-iduronic acid, can both occur. The resulting backbone diversity represents a major challenge for an unambiguous structural assignment by mass spectrometry-based techniques. Here, we employ cryogenic infrared spectroscopy on mass-selected ions to overcome this challenge and distinguish isomeric heparan sulfate tetrasaccharides that differ only in the configuration of their hexuronic acid building blocks. High-resolution infrared spectra of a systematic set of synthetic heparan sulfate stereoisomers were recorded in the fingerprint region from 1000 to 1800 cm-1. The experiments reveal a characteristic combination of spectral features for each of the four diastereomers studied and imply structural modularity in the vibrational fingerprints. Strong spectrum-structure correlations were found and rationalized by state-of-the-art quantum chemical calculations. The findings demonstrate the potential of cryogenic infrared spectroscopy to extend the mass spectrometry-based toolkit for the sequencing of heparan sulfate and structurally related biomolecules.
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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.,Institut für Chemie und Biochemie, Freie Universität Berlin, Arnimallee 22, 14195 Berlin, Germany
| | - Márkó Grabarics
- Department of Molecular Physics, Fritz Haber Institute of the Max Planck Society, Faradayweg 4-6, 14195 Berlin, Germany.,Institut für Chemie und Biochemie, Freie Universität Berlin, Arnimallee 22, 14195 Berlin, Germany
| | - Kim Greis
- Department of Molecular Physics, Fritz Haber Institute of the Max Planck Society, Faradayweg 4-6, 14195 Berlin, Germany.,Institut für Chemie und Biochemie, Freie Universität Berlin, Arnimallee 22, 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
| | - Pradeep Chopra
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens, Georgia 30602, United States
| | - Geert-Jan Boons
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens, Georgia 30602, United States.,Department of Chemical Biology and Drug Discovery, Utrecht Institute for Pharmaceutical Science, and Bijvoet Center for Biomolecular Research, Utrecht University, Universiteitsweg 99, 3584 CG Utrecht, The Netherlands
| | - Richard Karlsson
- Copenhagen Centre for Glycomics, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen N 2200, Denmark
| | - Jeremy E Turnbull
- Copenhagen Centre for Glycomics, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen N 2200, Denmark.,Centre for Glycobiology, Department of Biochemistry, University of Liverpool, Liverpool L69 7ZB, United Kingdom
| | - Gerard Meijer
- Department of Molecular Physics, Fritz Haber Institute of the Max Planck Society, Faradayweg 4-6, 14195 Berlin, Germany
| | - Rebecca L Miller
- Copenhagen Centre for Glycomics, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen N 2200, Denmark
| | - 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.,Institut für Chemie und Biochemie, Freie Universität Berlin, Arnimallee 22, 14195 Berlin, Germany
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25
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Yalovenko N, Yatsyna V, Bansal P, AbiKhodr AH, Rizzo TR. Analyzing glycans cleaved from a biotherapeutic protein using ultrahigh-resolution ion mobility spectrometry together with cryogenic ion spectroscopy. Analyst 2020; 145:6493-6499. [DOI: 10.1039/d0an01206h] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
A new approach for analysis of cleaved glycans.
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Affiliation(s)
- Natalia Yalovenko
- Laboratoire de Chimie Physique Moléculaire
- École Polytechnique Fédérale de Lausanne
- EPFL SB ISIC LCPM
- CH-1015 Lausanne
- Switzerland
| | - Vasyl Yatsyna
- Laboratoire de Chimie Physique Moléculaire
- École Polytechnique Fédérale de Lausanne
- EPFL SB ISIC LCPM
- CH-1015 Lausanne
- Switzerland
| | - Priyanka Bansal
- Laboratoire de Chimie Physique Moléculaire
- École Polytechnique Fédérale de Lausanne
- EPFL SB ISIC LCPM
- CH-1015 Lausanne
- Switzerland
| | - Ali H. AbiKhodr
- Laboratoire de Chimie Physique Moléculaire
- École Polytechnique Fédérale de Lausanne
- EPFL SB ISIC LCPM
- CH-1015 Lausanne
- Switzerland
| | - Thomas R. Rizzo
- Laboratoire de Chimie Physique Moléculaire
- École Polytechnique Fédérale de Lausanne
- EPFL SB ISIC LCPM
- CH-1015 Lausanne
- Switzerland
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