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Qin G, Qu M, Jia B, Wang W, Luo Z, Song CP, Tao WA, Wang P. FAT-switch-based quantitative S-nitrosoproteomics reveals a key role of GSNOR1 in regulating ER functions. Nat Commun 2023; 14:3268. [PMID: 37277371 PMCID: PMC10241878 DOI: 10.1038/s41467-023-39078-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 05/26/2023] [Indexed: 06/07/2023] Open
Abstract
Reversible protein S-nitrosylation regulates a wide range of biological functions and physiological activities in plants. However, it is challenging to quantitively determine the S-nitrosylation targets and dynamics in vivo. In this study, we develop a highly sensitive and efficient fluorous affinity tag-switch (FAT-switch) chemical proteomics approach for S-nitrosylation peptide enrichment and detection. We quantitatively compare the global S-nitrosylation profiles in wild-type Arabidopsis and gsnor1/hot5/par2 mutant using this approach, and identify 2,121 S-nitrosylation peptides in 1,595 protein groups, including many previously unrevealed S-nitrosylated proteins. These are 408 S-nitrosylated sites in 360 protein groups showing an accumulation in hot5-4 mutant when compared to wild type. Biochemical and genetic validation reveal that S-nitrosylation at Cys337 in ER OXIDOREDUCTASE 1 (ERO1) causes the rearrangement of disulfide, resulting in enhanced ERO1 activity. This study offers a powerful and applicable tool for S-nitrosylation research, which provides valuable resources for studies on S-nitrosylation-regulated ER functions in plants.
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Affiliation(s)
- Guochen Qin
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, 200032, Shanghai, China
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, 261000, Weifang, Shandong, China
| | - Menghuan Qu
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, 200032, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Bei Jia
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, 200032, Shanghai, China
| | - Wei Wang
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, 475004, Kaifeng, China
| | - Zhuojun Luo
- Department of Biochemistry, Purdue University, West Lafayette, IN, 47907, USA
| | - Chun-Peng Song
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, 475004, Kaifeng, China
| | - W Andy Tao
- Department of Biochemistry, Purdue University, West Lafayette, IN, 47907, USA
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA
| | - Pengcheng Wang
- Institute of Advanced Biotechnology and School of Life Sciences, Southern University of Science and Technology, 518055, Shenzhen, China.
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2
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Xu G, Hou L, Liu C, Wang X, Liu L, Li N, Lin JM, Zhao RS. Fabrication of a Magnetic Fluorinated Covalent Organic Framework for the Selective Capture of Benzoylurea Insecticide Residue in Beverages. ACS APPLIED MATERIALS & INTERFACES 2021; 13:51535-51545. [PMID: 34672528 DOI: 10.1021/acsami.1c15869] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Efficient capture of benzoylurea insecticide (BU) residue in food is a vital procedure for food safe monitoring. Herein, a core-shell structured magnetic fluorinated covalent organic framework with good magnetic responsiveness and abundant fluorine affinity sites was successfully synthesized, suitable for magnetic solid-phase extraction (MSPE) of BUs. Using a room-temperature synthesis strategy, the magnetic fluorinated covalent organic framework was fabricated by in situ polymerization of 1,3,5-tris(4-aminophenyl) triazine (TAPT) and 2,3,5,6-tetrafluoroterephthaldehyde (TFTA) on the surface of carboxylated Fe3O4 nanoparticles. The competitive adsorption experiment and molecular simulation verified that this magnetic fluorinated covalent organic framework possesses favorable adsorption affinity for BUs. This magnetic fluorinated covalent organic framework could be easily regenerated and reused at least eight times with no reduction of enrichment performance. Combining this magnetic fluorinated covalent organic framework-based MSPE with high-performance liquid chromatography-tandem mass spectrometry, a novel sensitive method for the analysis of BUs was developed. In yellow wine and fruit juice samples, good linear correlations were obtained for BUs in the range of 10-2000 and 20-4000 ng·L-1, respectively. The limit of quantitation of the BUs ranged from 1.4 to 13.3 ng·L-1 in the two beverage matrices. Desirable precision was achieved, with intraday and interday relative standard deviations lower than 11%.
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Affiliation(s)
- Guiju Xu
- Shandong Analysis and Test Center, Key Laboratory for Applied Technology of Sophisticated Analytical Instruments of Shandong Province, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250014, China
| | - Longfei Hou
- College of Food Science and Engineering, Shandong Agricultural University, Taian 271018, China
| | - Chuqing Liu
- Shandong Analysis and Test Center, Key Laboratory for Applied Technology of Sophisticated Analytical Instruments of Shandong Province, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250014, China
| | - Xiaoli Wang
- Shandong Analysis and Test Center, Key Laboratory for Applied Technology of Sophisticated Analytical Instruments of Shandong Province, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250014, China
| | - Lu Liu
- College of Food Science and Engineering, Shandong Agricultural University, Taian 271018, China
| | - Na Li
- Shandong Analysis and Test Center, Key Laboratory for Applied Technology of Sophisticated Analytical Instruments of Shandong Province, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250014, China
| | - Jin-Ming Lin
- Beijing Key Laboratory of Microanalytical Methods and Instrumentation, Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Ru-Song Zhao
- Shandong Analysis and Test Center, Key Laboratory for Applied Technology of Sophisticated Analytical Instruments of Shandong Province, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250014, China
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3
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Yuan Y, Zheng X, Lin H, Li Y, Yang M, Liu X, Deng C, Fan Z. Development of a hydrophilic magnetic amino-functionalized metal-organic framework for the highly efficient enrichment of trace bisphenols in river water samples. Talanta 2020; 211:120713. [DOI: 10.1016/j.talanta.2020.120713] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 12/29/2019] [Accepted: 01/02/2020] [Indexed: 12/28/2022]
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4
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Bassanini I, Galli C, Ferrandi EE, Vallone F, Andolfo A, Romeo S. Perfluorinated Probes for Noncovalent Protein Recognition and Isolation. Bioconjug Chem 2020; 31:513-519. [PMID: 31927891 PMCID: PMC7993633 DOI: 10.1021/acs.bioconjchem.9b00846] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Perfluorinated organic compounds (PFCs) are nontoxic, biocompatible, bioavailable, and bioorthogonal species which possess the unique ability to segregate away from both polar and nonpolar solvents producing a compact fluorophilic phase. Traditional techniques of fluorous chemical proteomics are generally applied to enrich biological samples in target protein(s) exploiting this property of PFCs to build fluorinated probes able to covalently bind to protein ensembles and being selectively extracted by fluorophilic solvents. Aiming at building a strategy able to avoid irreversible modification of the analyzed biosystem, a novel fully noncovalent probe is presented as an enabling tool for the recognition and isolation of biological protein(s). In our strategy, both the fluorophilic extraction and the biorecognition of a selected protein successfully occur via the establishment of reversible but selective interactions.
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Affiliation(s)
- Ivan Bassanini
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, 20133 Milano, Italy
| | - Corinna Galli
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, 20133 Milano, Italy
| | - Erica E Ferrandi
- Istituto di Chimica del Riconoscimento Molecolare - Consiglio Nazionale delle Ricerche, 20131 Milano, Italy
| | - Fabiana Vallone
- ProMiFa, Protein Microsequencing Facility, Ospedale San Raffaele, 20132 Milano, Italy
| | - Annapaola Andolfo
- ProMiFa, Protein Microsequencing Facility, Ospedale San Raffaele, 20132 Milano, Italy
| | - Sergio Romeo
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, 20133 Milano, Italy
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5
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Yan Y, Deng C. Recent advances in nanomaterials for sample pre-treatment in phosphoproteomics research. Trends Analyt Chem 2019. [DOI: 10.1016/j.trac.2019.115655] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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6
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Tavakoli Z, Rasekh B, Yazdian F, Maghsoudi A, Soleimani M, Mohammadnejad J. One-step separation of the recombinant protein by using the amine-functionalized magnetic mesoporous silica nanoparticles; an efficient and facile approach. Int J Biol Macromol 2019; 135:600-608. [PMID: 31121232 DOI: 10.1016/j.ijbiomac.2019.05.114] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2019] [Revised: 05/16/2019] [Accepted: 05/19/2019] [Indexed: 12/14/2022]
Abstract
The separation process is the main stage of recombinant production. With the advancement of nanotechnology and the development of magnetic nanoparticles, these structures are increasingly used in different applications. In the present study, we produced the recombinant human growth hormone from Pichia pastoris and for protein separation provided the surfaces similar to chromatographic columns on the surface of magnetic nanoparticles. For this purpose, using a co-precipitation method, the core of Fe3O4 was prepared and coated by silica. To increase the protein availability, silica mesoporous formation and its amine functionalization were performed. The specific surface area and the pore size were determined 78.3189 m2/g and 7.44 nm. After the magnetic separation, the sample loading in SDS gel shows a reduction in protein band and the protein absorption at a wavelength of 280 nm. Finally, we evaluate the ability of amine functionalized nanoparticles for protein separation that demonstrate the adsorption capacity significantly increased compare with silica-coated nanoparticles. The amine functionalized nanoparticles provide the maximum adsorption capacity of 235.21 μg/mg and after the elution, protein concentration determined 476 mg/L. This work indicates the functionalized magnetic mesoporous silica nanoparticles can be used as the best candidate for the separation of different biological macromolecules.
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Affiliation(s)
- Zahra Tavakoli
- Department of Life Science Engineering, Faculty of New Sciences and Technologies, University of Tehran, Tehran, Iran
| | - Behnam Rasekh
- Microbiology and Biotechnology Research Group, Research Institute of Petroleum Industry, Tehran, Iran
| | - Fatemeh Yazdian
- Department of Life Science Engineering, Faculty of New Sciences and Technologies, University of Tehran, Tehran, Iran.
| | | | - Mehdi Soleimani
- Department of Biotechnology, Faculty of Chemical Engineering, Tarbiat Modares University, Tehran, Iran
| | - Javad Mohammadnejad
- Department of Life Science Engineering, Faculty of New Sciences and Technologies, University of Tehran, Tehran, Iran
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7
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Huang T, Armbruster MR, Coulton JB, Edwards JL. Chemical Tagging in Mass Spectrometry for Systems Biology. Anal Chem 2018; 91:109-125. [DOI: 10.1021/acs.analchem.8b04951] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Tianjiao Huang
- Department of Chemistry, Saint Louis University, 3501 Laclede Avenue, St. Louis, Missouri 63103, United States
| | - Michael R. Armbruster
- Department of Chemistry, Saint Louis University, 3501 Laclede Avenue, St. Louis, Missouri 63103, United States
| | - John B. Coulton
- Department of Chemistry, Saint Louis University, 3501 Laclede Avenue, St. Louis, Missouri 63103, United States
| | - James L. Edwards
- Department of Chemistry, Saint Louis University, 3501 Laclede Avenue, St. Louis, Missouri 63103, United States
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8
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Yao J, Sun N, Deng C. Recent advances in mesoporous materials for sample preparation in proteomics research. Trends Analyt Chem 2018. [DOI: 10.1016/j.trac.2017.11.016] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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9
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Zhang C, Tao T, Yuan W, Zhang L, Zhang X, Yao J, Zhang Y, Lu H. Fluorous Solid-Phase Extraction Technique Based on Nanographite Fluoride. Anal Chem 2017; 89:4566-4572. [DOI: 10.1021/acs.analchem.6b05071] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Cheng Zhang
- Shanghai
Cancer Center and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, P. R. China
- Department
of Chemistry, Fudan University, Shanghai, 200433, P. R. China
| | - Tao Tao
- Shanghai
Cancer Center and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, P. R. China
- Department
of Chemistry, Fudan University, Shanghai, 200433, P. R. China
| | - Wenjuan Yuan
- Shanghai
Cancer Center and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, P. R. China
- Department
of Chemistry, Fudan University, Shanghai, 200433, P. R. China
| | - Lei Zhang
- Shanghai
Cancer Center and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, P. R. China
| | - Xiaoqin Zhang
- Shanghai
Cancer Center and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, P. R. China
- Department
of Chemistry, Fudan University, Shanghai, 200433, P. R. China
| | - Jun Yao
- Shanghai
Cancer Center and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, P. R. China
| | - Ying Zhang
- Shanghai
Cancer Center and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, P. R. China
| | - Haojie Lu
- Shanghai
Cancer Center and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, P. R. China
- Department
of Chemistry, Fudan University, Shanghai, 200433, P. R. China
- Key
Laboratory of Glycoconjugates Research Ministry of Public Health, Fudan University, Shanghai, 200032, P. R. China
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10
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Fabrication and evaluation of a fluorophilic adsorbent for multiple monolithic fiber solid-phase microextraction of fluorobenzenes. J Chromatogr A 2017; 1492:12-18. [DOI: 10.1016/j.chroma.2017.03.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Revised: 03/01/2017] [Accepted: 03/02/2017] [Indexed: 12/13/2022]
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11
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Yuan W, Zhang Y, Xiong Y, Tao T, Wang Y, Yao J, Zhang L, Yan G, Bao H, Lu H. Highly Selective and Large Scale Mass Spectrometric Analysis of 4-Hydroxynonenal Modification via Fluorous Derivatization and Fluorous Solid-Phase Extraction. Anal Chem 2017; 89:3093-3100. [DOI: 10.1021/acs.analchem.6b04850] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Wenjuan Yuan
- Shanghai
Cancer Center and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, P. R. China
- Department
of Chemistry, Fudan University, Shanghai 200433, P. R. China
| | - Ying Zhang
- Shanghai
Cancer Center and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, P. R. China
| | - Yun Xiong
- Shanghai
Cancer Center and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, P. R. China
| | - Tao Tao
- Shanghai
Cancer Center and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, P. R. China
- Department
of Chemistry, Fudan University, Shanghai 200433, P. R. China
| | - Yi Wang
- Shanghai
Cancer Center and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, P. R. China
| | - Jun Yao
- Shanghai
Cancer Center and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, P. R. China
| | - Lei Zhang
- Shanghai
Cancer Center and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, P. R. China
| | - Guoquan Yan
- Department
of Chemistry, Fudan University, Shanghai 200433, P. R. China
| | - Huimin Bao
- Department
of Chemistry, Fudan University, Shanghai 200433, P. R. China
| | - Haojie Lu
- Shanghai
Cancer Center and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, P. R. China
- Department
of Chemistry, Fudan University, Shanghai 200433, P. R. China
- Key
Laboratory of Glycoconjugates Research Ministry of Public Health, Fudan University, Shanghai 200032, P. R. China
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12
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Li X, Chen X, Tan J, Liang X, Wu J. Palladium modified porous silicon as multi-functional MALDI chip for serum peptide detection. Analyst 2017; 142:586-590. [DOI: 10.1039/c6an02165d] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Interest in using mesoporous materials for peptidomic research has increased recently.
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Affiliation(s)
- Xiao Li
- Institute of Microanalytical System
- Department of Chemistry
- Zhejiang University
- Hangzhou
- China
| | - Xiaoming Chen
- Institute of Microanalytical System
- Department of Chemistry
- Zhejiang University
- Hangzhou
- China
| | - Jie Tan
- Institute of Microanalytical System
- Department of Chemistry
- Zhejiang University
- Hangzhou
- China
| | - Xiao Liang
- Department of General Surgery
- Sir Run Run Shaw Hospital
- School of Medicine
- Zhejiang University
- Hangzhou
| | - Jianmin Wu
- Institute of Microanalytical System
- Department of Chemistry
- Zhejiang University
- Hangzhou
- China
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13
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Zhao M, Deng C. Fluorous modified magnetic mesoporous silica composites-incorporated fluorous solid-phase extraction for the specific enrichment of N-linked glycans with simultaneous exclusion of proteins. Talanta 2016; 159:111-116. [PMID: 27474286 DOI: 10.1016/j.talanta.2016.06.017] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Revised: 06/01/2016] [Accepted: 06/05/2016] [Indexed: 12/31/2022]
Abstract
Taking advantage of fluorine-fluorine interactions, fluorous solid-phase extraction (FSPE) is emerging as a novel approach in proteomics research. Notably, silica gel bound with perfluoroalkyl groups was applied to the FSPE of N-linked glycans. Based on previous studies, mesoporous silica coated magnetic nanoparticles bound with perfluoroalkyl groups were synthesized for the specific enrichment of N-linked glycans in this study. The magnetic nanoparticles-incorporated FSPE strategy successfully identified 22 N-linked glycans from the OVA digest with a concentration of 0.5μg/μL, and achieved a detection limit of 5ng/μL (with 16 N-linked glycans identified). It also showed good day-to-day reproducibility. Its selectivity towards BSA protein is 1:200 (molar ratio), showing excellent size-exclusion effect. In addition, the present method proved to be effective for the analysis of the human serum digest, opening up new prospect for the identification of glycans and proteins with other post-translational modifications in biological environment.
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Affiliation(s)
- Man Zhao
- Department of Chemistry and Institutes of Biomedical Sciences, Collaborative Innovation Center of Genetics and Development, Fudan University, Shanghai 200433, China
| | - Chunhui Deng
- Department of Chemistry and Institutes of Biomedical Sciences, Collaborative Innovation Center of Genetics and Development, Fudan University, Shanghai 200433, China.
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