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Wang Y, Li R, Shu W, Chen X, Lin Y, Wan J. Designed Nanomaterials-Assisted Proteomics and Metabolomics Analysis for In Vitro Diagnosis. SMALL METHODS 2024; 8:e2301192. [PMID: 37922520 DOI: 10.1002/smtd.202301192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 10/12/2023] [Indexed: 11/05/2023]
Abstract
In vitro diagnosis (IVD) is pivotal in modern medicine, enabling early disease detection and treatment optimization. Omics technologies, particularly proteomics and metabolomics, offer profound insights into IVD. Despite its significance, omics analyses for IVD face challenges, including low analyte concentrations and the complexity of biological environments. In addition, the direct omics analysis by mass spectrometry (MS) is often hampered by issues like large sample volume requirements and poor ionization efficiency. Through manipulating their size, surface charge, and functionalization, as well as the nanoparticle-fluid incubation conditions, nanomaterials have emerged as a promising solution to extract biomolecules and enhance the desorption/ionization efficiency in MS detection. This review delves into the last five years of nanomaterial applications in omics, focusing on their role in the enrichment, separation, and ionization analysis of proteins and metabolites for IVD. It aims to provide a comprehensive update on nanomaterial design and application in omics, highlighting their potential to revolutionize IVD.
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Affiliation(s)
- Yanhui Wang
- School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, 200241, P. R. China
| | - Rongxin Li
- School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, 200241, P. R. China
| | - Weikang Shu
- School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, 200241, P. R. China
| | - Xiaonan Chen
- School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, 200241, P. R. China
| | - Yingying Lin
- School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, 200241, P. R. China
| | - Jingjing Wan
- School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, 200241, P. R. China
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2
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Guo Y, Hua S, Wang B, Wang B, Ding CF, Yan Y. In situ grown magnetic COF@MOF with a phosphoserine anchor for in-depth N-glycopeptide analysis in serum. Analyst 2023; 148:5864-5872. [PMID: 37906056 DOI: 10.1039/d3an01473h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
A hydrophilic phosphoserine-functionalized magnetic organic framework composite (termed Fe3O4@COF@MOF-PS) was synthesized by an in situ growth strategy for effective capture of N-glycopeptides. Fe3O4@COF@MOF-PS exhibited high sensitivity (0.2 fmol μL-1), outstanding exclusion of size capability (1 : 10 000), good selectivity (1 : 2000), and reusability (at least 10 times). It also exhibited remarkable performance in the N-glycopeptide analysis in complex biological samples. Via nano-LC-MS/MS analysis, a total of 223 N-glycopeptides with 161 glycosylation sites assigned to 91 glycoproteins and 331 N-glycopeptides with 243 glycosylation sites assigned to 134 glycoproteins were identified in sera from cervical cancer patients and normal controls, respectively. Biological processes and molecular functional analyses indicate that the captured glycoproteins are of significant relevance to cervical cancer, for example, gene coverage or expression of cell adhesion and extracellular matrix structural constituents. Thus, Fe3O4@COF@MOF-PS not only efficiently captures N-glycopeptides, but also has the possibility of screening potential disease markers and elucidating the process of cervical cancer development.
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Affiliation(s)
- Yimin Guo
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang 315211, China.
| | - Shuwen Hua
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang 315211, China.
| | - Baichun Wang
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang 315211, China.
| | - Bing Wang
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang 315211, China.
| | - Chuan-Fan Ding
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang 315211, China.
| | - Yinghua Yan
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang 315211, China.
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Wessels HJCT, Kulkarni P, van Dael M, Suppers A, Willems E, Zijlstra F, Kragt E, Gloerich J, Schmit PO, Pengelley S, Marx K, van Gool AJ, Lefeber DJ. Plasma glycoproteomics delivers high-specificity disease biomarkers by detecting site-specific glycosylation abnormalities. J Adv Res 2023:S2090-1232(23)00239-4. [PMID: 37683725 DOI: 10.1016/j.jare.2023.09.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 08/31/2023] [Accepted: 09/04/2023] [Indexed: 09/10/2023] Open
Abstract
INTRODUCTION The human plasma glycoproteome holds enormous potential to identify personalized biomarkers for diagnostics. Glycoproteomics has matured into a technology for plasma N-glycoproteome analysis but further evolution towards clinical applications depends on the clinical validity and understanding of protein- and site-specific glycosylation changes in disease. OBJECTIVES Here, we exploited the uniqueness of a patient cohort of genetic defects in well-defined glycosylation pathways to assess the clinical applicability of plasma N-glycoproteomics. METHODS Comparative glycoproteomics was performed of blood plasma from 40 controls and 74 patients with 13 different genetic diseases that impact the protein N-glycosylation pathway. Baseline glycosylation in healthy individuals was compared to reference glycome and intact transferrin protein mass spectrometry data. Use of glycoproteomics data for biomarker discovery and sample stratification was evaluated by multivariate chemometrics and supervised machine learning. Clinical relevance of site-specific glycosylation changes were evaluated in the context of genetic defects that lead to distinct accumulation or loss of specific glycans. Integrated analysis of site-specific glycoproteome changes in disease was performed using chord diagrams and correlated with intact transferrin protein mass spectrometry data. RESULTS Glycoproteomics identified 191 unique glycoforms from 58 unique peptide sequences of 34 plasma glycoproteins that span over 3 magnitudes of abundance in plasma. Chemometrics identified high-specificity biomarker signatures for each of the individual genetic defects with better stratification performance than the current diagnostic standard method. Bioinformatic analyses revealed site-specific glycosylation differences that could be explained by underlying glycobiology and protein-intrinsic factors. CONCLUSION Our work illustrates the strong potential of plasma glycoproteomics to significantly increase specificity of glycoprotein biomarkers with direct insights in site-specific glycosylation changes to better understand the glycobiological mechanisms underlying human disease.
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Affiliation(s)
- Hans J C T Wessels
- Translational Metabolic Laboratory, Department of Laboratory Medicine, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands.
| | - Purva Kulkarni
- Translational Metabolic Laboratory, Department of Laboratory Medicine, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Maurice van Dael
- Translational Metabolic Laboratory, Department of Laboratory Medicine, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Anouk Suppers
- Translational Metabolic Laboratory, Department of Laboratory Medicine, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Esther Willems
- Translational Metabolic Laboratory, Department of Laboratory Medicine, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands; Laboratory of Medical Immunology, Department of Laboratory Medicine, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Fokje Zijlstra
- Translational Metabolic Laboratory, Department of Laboratory Medicine, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Else Kragt
- Translational Metabolic Laboratory, Department of Laboratory Medicine, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Jolein Gloerich
- Translational Metabolic Laboratory, Department of Laboratory Medicine, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | | | | | | | - Alain J van Gool
- Translational Metabolic Laboratory, Department of Laboratory Medicine, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Dirk J Lefeber
- Translational Metabolic Laboratory, Department of Laboratory Medicine, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands; Department of Neurology, Donders Institute for Brain, Cognition, and Behavior, Radboud University Medical Center, Nijmegen, The Netherlands
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Zhang D, Fan Y, Sun X, Wei X, Lin Z, Zhang X, Shi J, Battino M, Gong Y, Shi B, Zou X. SERS determination of hydroxy-α-sanshool in spicy hotpot seasoning: The strategy to restrain the interference of capsaicin and its mechanism. Food Chem 2023; 413:135644. [PMID: 36773357 DOI: 10.1016/j.foodchem.2023.135644] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 02/01/2023] [Accepted: 02/03/2023] [Indexed: 02/10/2023]
Abstract
Hydroxy-α-sanshool (α-SOH) is the principal ingredient responsible for the numbing sensation in spicy hotpot. However, utilizing surface-enhanced Raman scattering (SERS) to analyze the α-SOH in hotpot seasoning is challenging due to the significant interference of capsaicin (CAP). Therefore, two schemes were proposed to address CAP interference in hotpot seasoning, namely laccase-catalyzed conversion and metal-organic framework (MOF) interaction. Among them, Fe-BTC MOF exhibited significant anti-interference effect and the underlying mechanism is elucidated. The motion of CAP aromatic ring was constrained by steric hindrance and electrostatic interactions of Fe-BTC. Additionally, the interaction between CAP aromatic ring and conjugated triene group in α-SOH was quenched, enhancing the α-SOH SERS signal. The proposed method had a significant anti-interference effect on α-SOH quantification in the presence of CAP, significantly enhancing the α-SOH SERS signal in a range of 0.85 to 4.00 × 107. The linearity and reproducibility of the proposed hotpot seasoning testing method were also validated.
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Affiliation(s)
- Di Zhang
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Yushan Fan
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Xiaoxia Sun
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Xiaoou Wei
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Zitao Lin
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Xinai Zhang
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Jiyong Shi
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Maurizio Battino
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, China; International Research Center for Food Nutrition and Safety, Jiangsu University, Zhenjiang 212013, China; Department of Clinical Sciences, Faculty of Medicine, Polytechnic University of Marche, Ancona, Italy
| | - Yunyun Gong
- School of Food Science and Nutrition, University of Leeds, Leeds, UK
| | - Bolin Shi
- Food and Agriculture Standardization Institute, China National Institute of Standardization, Beijing 102200, China
| | - Xiaobo Zou
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, China.
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5
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Ba S, Lan F, Luo B, Wu Y. Construction of dual-hydrophilic metal-organic framework with hierarchical porous structure for efficient glycopeptide enrichment. Talanta 2023; 259:124505. [PMID: 37054618 DOI: 10.1016/j.talanta.2023.124505] [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: 01/03/2023] [Revised: 03/20/2023] [Accepted: 03/29/2023] [Indexed: 04/15/2023]
Abstract
As an important role in life activities, it is necessary and important to study protein glycosylation. The pre-enrichment of N-glycopeptides is a significant step in glycoproteomics research. According to the inherent size, hydrophilicity and other properties of N-glycopeptides, affinity materials designed to match them will be able to separate N-glycopeptides from complex samples. In this work, we designed and prepared dual-hydrophilic hierarchical porous metal-organic frameworks (MOFs) nanospheres by metal-organic assembly (MOA) based template method and post-synthesis modification strategy. The hierarchical porous structure significantly improved the diffusion rate and binding sites for N-glycopeptide enrichment. Furthermore, the combination of hydrophilic MOFs and small molecules endowed the as-prepared MOFs nanospheres excellent hydrophilicity, which is conducive to the enrichment of N-glycopeptides based on hydrophilic interaction liquid chromatography (HILIC). Therefore, the nanospheres showed surprising enrichment ability for N-glycopeptides such as excellent selectivity (1/500, human serum immunoglobulin G/bovine serum albumin, m/m) and extremely low detective limitation (0.5 fmol). Meanwhile, 550 N-glycopeptides were identified from rat liver samples, proving its application potential in glycoproteomics research and providing design idea for porous affinity materials.
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Affiliation(s)
- Shengdong Ba
- National Engineering Research Center for Biomaterials, Sichuan University, Chengdu 610064, PR China
| | - Fang Lan
- National Engineering Research Center for Biomaterials, Sichuan University, Chengdu 610064, PR China
| | - Bin Luo
- Analytical and Testing Center, Sichuan University, Chengdu 610064, PR China.
| | - Yao Wu
- National Engineering Research Center for Biomaterials, Sichuan University, Chengdu 610064, PR China.
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6
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Zhou X, Zhang H, Wang L, Lv L, Wu R. Simultaneous enrichment optimization of glycopeptides and phosphopeptides with the highly hydrophilic DZMOF-FDP. Analyst 2023; 148:1483-1491. [PMID: 36876469 DOI: 10.1039/d2an02004a] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
Abstract
Protein glycosylation and phosphorylation play essential roles in biological systems. The crosstalk of both glycosylation and phosphorylation on one protein represents an unveiled biological function. To realize the analyses of both glycopeptides and phosphopeptides, a simultaneous enrichment method of N-glycopeptides, mono-phosphopeptides and multi-phosphopeptides was developed based on a multi-functional dual-metal centered zirconium metal-organic framework that provided multiple interactions for HILIC, IMAC, and MOAC for glycopeptides and phosphopeptides. Based on a careful optimization of sample loading and elution conditions for the simultaneous enrichment of glycopeptides and phosphopeptides with the zirconium metal-organic framework, a total of 1011 N-glycopeptides derived from 410 glycoproteins and 1996 phosphopeptides including 741 multi-phosphopeptides derived from 1189 phosphoproteins could be identified from a HeLa cell digest. The simultaneous enrichment approach for glycopeptides and mono-/multi-phosphopeptides demonstrates the great potential of the combined interactions for HILIC, IMAC, and MOAC in integrated post-translational modification proteomics research.
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Affiliation(s)
- Xiaoyu Zhou
- Laboratory of High-Resolution Mass Spectrometry Technologies, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China. .,CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hongyan Zhang
- Laboratory of High-Resolution Mass Spectrometry Technologies, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China. .,CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Li Wang
- Laboratory of High-Resolution Mass Spectrometry Technologies, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China. .,CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Liting Lv
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Ren'an Wu
- Laboratory of High-Resolution Mass Spectrometry Technologies, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China. .,CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
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Harvey DJ. Analysis of carbohydrates and glycoconjugates by matrix-assisted laser desorption/ionization mass spectrometry: An update for 2019-2020. MASS SPECTROMETRY REVIEWS 2022:e21806. [PMID: 36468275 DOI: 10.1002/mas.21806] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
This review is the tenth update of the original article published in 1999 on the application of matrix-assisted laser desorption/ionization (MALDI) mass spectrometry to the analysis of carbohydrates and glycoconjugates and brings coverage of the literature to the end of 2020. Also included are papers that describe methods appropriate to analysis by MALDI, such as sample preparation techniques, even though the ionization method is not MALDI. The review is basically divided into three sections: (1) general aspects such as theory of the MALDI process, matrices, derivatization, MALDI imaging, fragmentation, quantification and the use of arrays. (2) Applications to various structural types such as oligo- and polysaccharides, glycoproteins, glycolipids, glycosides and biopharmaceuticals, and (3) other areas such as medicine, industrial processes and glycan synthesis where MALDI is extensively used. Much of the material relating to applications is presented in tabular form. The reported work shows increasing use of incorporation of new techniques such as ion mobility and the enormous impact that MALDI imaging is having. MALDI, although invented nearly 40 years ago is still an ideal technique for carbohydrate analysis and advancements in the technique and range of applications show little sign of diminishing.
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Affiliation(s)
- David J Harvey
- Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Oxford, UK
- Department of Chemistry, University of Oxford, Oxford, Oxfordshire, United Kingdom
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Li S, Wei Y, Wang Y, Liang H. Advances in hydrophilic metal-organic frameworks for N-linked glycopeptide enrichment. Front Chem 2022; 10:1091243. [PMID: 36531319 PMCID: PMC9751774 DOI: 10.3389/fchem.2022.1091243] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 11/21/2022] [Indexed: 02/06/2024] Open
Abstract
The comprehensive profiling of glycoproteins is of great significance for the timely clinical diagnosis and therapy. However, inherent obstacles hamper their direct analysis from biological samples, and specific enrichment prior to analysis is indispensable. Among the various approaches for glycopeptide enrichment, hydrophilic interaction liquid chromatography (HILIC) has attracted special focus, especially for the development of novel hydrophilic materials, which is the key of HILIC. Metal-organic frameworks (MOFs) are a type of porous materials constructed from the self-assembly of metal and organic linkers. Advantages such as high surface area, flexible pore size, and easy modification render hydrophilic MOFs as ideal candidates for HILIC, which has inspired many studies over the past years. In this review, advances in hydrophilic MOFs for N-linked glycopeptide enrichment are summarized. According to the synthesis strategies, those materials are categorized into three classes, namely pristine MOFs, MOFs with chemical modifications, and MOFs-derived composite. In each categorization, the preparation and the function of different moieties are covered, as well as the enrichment performances of sensitivity, selectivity, and practical application. Finally, a summary and future perspective on the applications of hydrophilic MOFs for N-linked glycopeptide enrichment are briefly discussed. This review is expected to raise awareness of the properties of hydrophilic MOFs and offer some valuable information to further research in glycoproteomics.
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Affiliation(s)
| | | | | | - Haoran Liang
- Chongqing Key Laboratory of Medicinal Chemistry and Molecular Pharmacology, Chongqing University of Technology, Chongqing, China
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Xie Z, Feng Q, Zhang S, Yan Y, Deng C, Ding CF. Advances in proteomics sample preparation and enrichment for phosphorylation and glycosylation analysis. Proteomics 2022; 22:e2200070. [PMID: 36100958 DOI: 10.1002/pmic.202200070] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 08/06/2022] [Accepted: 08/15/2022] [Indexed: 11/08/2022]
Abstract
As the common and significant chemical modifications, post-translational modifications (PTMs) play a key role in the functional proteome. Affected by the signal interference, low concentration, and insufficient ionization efficiency of impurities, the direct detection of PTMs by mass spectrometry (MS) still faces many challenges. Therefore, sample preparation and enrichment are an indispensable link before MS analysis of PTMs in proteomics. The rapid development of functionalized materials with diverse morphologies and compositions provides an avenue for sample preparation and enrichment for PTMs analysis. In this review, we summarize recent advances in the application of novel functionalized materials in sample preparation for phosphoproteomes and glycoproteomes analysis. In addition, this review specifically discusses the design and preparation of functionalized materials based on different enrichment mechanisms, and proposes research directions and potential challenges for proteomic PTMs research.
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Affiliation(s)
- Zehu Xie
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang, China
| | - Quanshou Feng
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang, China
| | - Shun Zhang
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang, China
| | - Yinghua Yan
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang, China.,Department of Experimental Medical Science, HwaMei Hospital, University of Chinese Academy of Sciences, Ningbo, Zhejiang, China
| | - Chunhui Deng
- Department of Chemistry, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Chuan-Fan Ding
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang, China.,Department of Experimental Medical Science, HwaMei Hospital, University of Chinese Academy of Sciences, Ningbo, Zhejiang, China
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Sajid MS, Saleem MN, Jabeen F, Saleem S, Iqbal S, Habib S, Ashiq MN, Ressom HW, Najam-ul-Haq M. Human serum N-glycome profiling via the newly developed asparagine immobilized cellulose/polymer nanohybrid. J Sep Sci 2022; 45:4236-4244. [PMID: 36168850 PMCID: PMC9812403 DOI: 10.1002/jssc.202200179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Revised: 09/21/2022] [Accepted: 09/22/2022] [Indexed: 01/07/2023]
Abstract
Human serum N-linked glycans expression levels change during the disease progression. The low abundance, structural diversity, and coexisting matrices hinder their detection in mass spectrometry analysis. Considering the hydrophilic nature of N-glycans, cellulose/polymer (1,2-Epoxy-5-hexene) nanohybrid is fabricated with oxirane groups functionalized of asparagine to develop solid phase extraction based hydrophilic interaction liquid chromatography sorbent (cellulose/1,2-Epoxy-5-hexene/asparagine). The morphology, elemental analysis, and surface properties are studied through scanning electron microscopy, energy dispersive X-ray spectroscopy, and Fourier-transform infrared spectroscopy. The large surface area of cellulose/polymer nanohybrid (2.09 × 102 m2 /g) facilitates the high density of asparagine immobilization resulting in better hydrophilic interaction liquid chromatography enrichment under optimized conditions. The enrichment capability of nanohybrid/asparagine is assessed by the N-Linked glycans released from ovalbumin and immunoglobulin G where 23 and 13 N-glycans are detected respectively. The nanohybrid/asparagine shows selectivity of 1:1200 with spiked bovine serum albumin and sensitivity down to 100 attomole. Human serum profiling for N-glycans identifies 52 glycan structures. This new enrichment strategy enriches serum N-linked glycans in the presence of salts, proteins, endogenous serum peptides, and so forth.
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Affiliation(s)
- Muhammad Salman Sajid
- Division of Analytical Chemistry, Institute of Chemical Sciences, Bahauddin Zakariya University, Multan, 60800, Pakistan,Department of Oncology, Genomics and Epigenomics Shared Resource, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC 20057, USA
| | - Muhammad Nakash Saleem
- Division of Analytical Chemistry, Institute of Chemical Sciences, Bahauddin Zakariya University, Multan, 60800, Pakistan
| | - Fahmida Jabeen
- Division of Analytical Chemistry, Institute of Chemical Sciences, Bahauddin Zakariya University, Multan, 60800, Pakistan,Corresponding Authors: 1. Prof. Dr. M. Najam-ul-Haq, Institute of Chemical Sciences, Bahauddin Zakariya University, Multan 60800, Pakistan, Tel.: +92 306 7552653, , 2. Dr. Fahmida Jabeen, Institute of Chemical Sciences, Bahauddin Zakariya University, Multan 60800, Pakistan, Tel.: +92 333 4253409,
| | - Shafaq Saleem
- Department of Chemistry, The Women University, Kutchery Campus, L.M.Q. Road, Multan, 66000, Pakistan
| | - Sabeen Iqbal
- Division of Analytical Chemistry, Institute of Chemical Sciences, Bahauddin Zakariya University, Multan, 60800, Pakistan
| | | | - Muhammad Naeem Ashiq
- Division of Analytical Chemistry, Institute of Chemical Sciences, Bahauddin Zakariya University, Multan, 60800, Pakistan
| | - Habtom W. Ressom
- Department of Oncology, Genomics and Epigenomics Shared Resource, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC 20057, USA
| | - Muhammad Najam-ul-Haq
- Division of Analytical Chemistry, Institute of Chemical Sciences, Bahauddin Zakariya University, Multan, 60800, Pakistan,Corresponding Authors: 1. Prof. Dr. M. Najam-ul-Haq, Institute of Chemical Sciences, Bahauddin Zakariya University, Multan 60800, Pakistan, Tel.: +92 306 7552653, , 2. Dr. Fahmida Jabeen, Institute of Chemical Sciences, Bahauddin Zakariya University, Multan 60800, Pakistan, Tel.: +92 333 4253409,
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Zhang N, Huang T, Xie P, Yang Z, Zhang L, Wu X, Cai Z. Epitaxial Growth of Guanidyl-Functionalized Magnetic Metal-Organic Frameworks with Multiaffinity Sites for Selective Capture of Global Phosphopeptides. ACS APPLIED MATERIALS & INTERFACES 2022; 14:39364-39374. [PMID: 35993677 DOI: 10.1021/acsami.2c10353] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The flexible and controlled synthesis of metal-organic framework (MOF)-derived hybrid nanostructures is of great significance in fine tuning of their enrichment performance in large-scale and in-depth phosphoproteome analysis. Herein, a magnetic guanidyl-functionalized MOF hybrid coating with multiaffinity sites, denoted as Fe3O4@G-ZIF-8, was fast fabricated via a one-pot epitaxial growth strategy for the first time and applied for selective and highly efficient enrichment of global phosphopeptides. The intrinsic unsaturated metal sites of ZIF-8 endow the surface-mounted MOF coatings with immobilized metal ion affinity chromatography interaction with multiphosphorylated peptides. The oriented anchoring of bifunctional guanidineacetic acid on the magnetic MOF nanospheres provides additional affinity sites (guanidyl groups) for specific recognition of phosphopeptides by "salt bridge" interaction, as well as active site carboxyl groups for the coordination with the metal ions. The as-prepared Fe3O4@G-ZIF-8 exhibits large surface area (382.5 m2 g-1), good superparamagnetic property (41.6 emu g-1) and stability, and size-exclusion effect (1.73 nm), which can serve as a specific adsorbent for global phosphopeptide analysis with satisfactory selectivity, great detection sensitivity (1 fmol), and rapid magnetic separation. Moreover, the successful application of Fe3O4@G-ZIF-8 for selective capture of both multi- and mono-phosphopeptides from human saliva and serum demonstrated the great potential of magnetic surface-mounted MOF coatings in effective identification of low-abundance phosphopeptides by matrix-assisted laser desorption ionization time-of-flight mass spectrometry from complicated biological matrices.
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Affiliation(s)
- Ning Zhang
- Ministry of Education Key Laboratory of Analytical Science for Food Safety and Biology; College of Chemistry, Fuzhou University, Fuzhou, Fujian 350108, China
- Institute of Environmental and Analytical Science, School of Chemistry and Chemical Engineering, Henan University, Kaifeng 475004, Henan, P. R. China
| | - Ting Huang
- Ministry of Education Key Laboratory of Analytical Science for Food Safety and Biology; College of Chemistry, Fuzhou University, Fuzhou, Fujian 350108, China
| | - Peisi Xie
- State Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist University, Kowloon 999077, Hong Kong, SAR, China
| | - Zhu Yang
- State Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist University, Kowloon 999077, Hong Kong, SAR, China
| | - Lan Zhang
- Ministry of Education Key Laboratory of Analytical Science for Food Safety and Biology; College of Chemistry, Fuzhou University, Fuzhou, Fujian 350108, China
| | - Xiaoping Wu
- Ministry of Education Key Laboratory of Analytical Science for Food Safety and Biology; College of Chemistry, Fuzhou University, Fuzhou, Fujian 350108, China
| | - Zongwei Cai
- State Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist University, Kowloon 999077, Hong Kong, SAR, China
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12
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Sargazi M, Kaykhaii M. Magnetic Covalent Organic Frameworks-Fundamentals and Applications in Analytical Chemistry. Crit Rev Anal Chem 2022:1-27. [PMID: 35939351 DOI: 10.1080/10408347.2022.2107872] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
Abstract
Magnetic covalent organic frameworks are new emerging materials which, besides many other applications, have found unique applications in analytical chemistry as separating media and adsorbents. They have outstanding features such as special morphology, chemical and thermal stability, high adsorption capacity, good magnetic response, high specific surface area, uniform pore size distribution, strong π-π interactions with analytes and high reusability that makes reported studies on their properties and applications increased in the recent years. After discussing the methods of synthesis of MCOFs with different geometries that cause their special physic-chemical properties, this review focuses on their high potential which has been exhibited in various applications in extraction and pre-concentration of different analytes such as organic compounds, heavy metal ions and biological samples. The article also highlights the applications of magnetic covalent organic frameworks in other chemical analysis such as adsorbent and being used in sensors.
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Affiliation(s)
| | - Massoud Kaykhaii
- Department of Process Engineering and Chemical Technology, Faculty of Chemistry, Gdansk University of Technology, Gdansk, Poland
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13
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Sajid MS, Saleem S, Jabeen F, Najam-Ul-Haq M, Ressom HW. Terpolymeric platform with enhanced hydrophilicity via cysteic acid for serum intact glycopeptide analysis. Mikrochim Acta 2022; 189:277. [PMID: 35829791 DOI: 10.1007/s00604-022-05343-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 05/15/2022] [Indexed: 11/29/2022]
Abstract
A new polymeric (methyl methacrylate/ethylene glycol dimethacrylate/1,2-epoxy-5-hexene) base/matrix has been fabricated and decorated with zwitterionic hydrophilic cysteic acid (Cya) for the enrichment of intact N-glycopeptides from standards and biological samples. Terpolymer-Cya provides good enrichment efficiency, improved hydrophilicity, and selectivity by virtue of better surface area (2.09 × 102 m2/g) provided by terpolymer and the zwitterionic property offered by cysteic acid. Cysteic acid-functionalized polymeric hydrophilic interaction liquid chromatography (HILIC) sorbent enriches 35 and 24 N-linked glycopeptides via SPE (solid phase extraction) mode from tryptic digests of model glycoproteins, i.e., immunoglobulin G (IgG) and horseradish peroxidase (HRP), respectively. Zwitterionic chemistry of cysteine helps in achieving higher selectivity with BSA digest (1:200), and lower detection limit down to 100 attomoles with a complete glycosylation profile of each standard digest. The recovery of 81% and good reproducibility define the application of terpolymer-Cya for complex samples like a serum. Analysis of human serum provides a profile of 807 intact N-linked glycopeptides via nano-liquid chromatography-tandem mass spectrometry (nLC-MS/MS). To the best of our knowledge, this is the highest number of glycopeptides enriched by any HILIC sorbent. Selected glycoproteins are evaluated in link to various cancers including the breast, lung, uterine, and melanoma using single-nucleotide variances (BioMuta). This study represents the complete idea of using an in-house developed strategy as a successful tool to help analyze, relate, and answer glycoprotein-based clinical issues regarding cancers.
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Affiliation(s)
- Muhammad Salman Sajid
- Division of Analytical Chemistry, Institute of Chemical Sciences, Bahauddin Zakariya University, Multan, 60800, Pakistan
- Department of Oncology, Genomics and Epigenomics Shared Resource, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC, 20057, USA
| | - Shafaq Saleem
- Department of Chemistry, The Women University, Kutchery Campus, L.M.Q. Road, Multan, 66000, Pakistan
| | - Fahmida Jabeen
- Division of Analytical Chemistry, Institute of Chemical Sciences, Bahauddin Zakariya University, Multan, 60800, Pakistan
| | - Muhammad Najam-Ul-Haq
- Division of Analytical Chemistry, Institute of Chemical Sciences, Bahauddin Zakariya University, Multan, 60800, Pakistan
| | - Habtom W Ressom
- Department of Oncology, Genomics and Epigenomics Shared Resource, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC, 20057, USA.
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14
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Zhao B, Xu W, Ma J, Jia Q. Design and fabrication of highly hydrophilic magnetic material by anchoring L-cysteine onto chitosan for efficient enrichment of glycopeptides. CHINESE CHEM LETT 2022. [DOI: 10.1016/j.cclet.2022.05.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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15
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Wu Y, Chen H, Chen Y, Sun N, Deng C. Metal organic frameworks as advanced extraction adsorbents for separation and analysis in proteomics and environmental research. Sci China Chem 2022. [DOI: 10.1007/s11426-021-1195-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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16
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Yi L, Shao Y, Fu M, Yan Y, Ding CF, Tang K. One-step preparation of magnetic zwitterionic–hydrophilic dual functional nanospheres for in-depth glycopeptides analysis in Alzheimer's disease patients' serum. J Chromatogr A 2022; 1669:462929. [DOI: 10.1016/j.chroma.2022.462929] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 03/01/2022] [Accepted: 03/02/2022] [Indexed: 01/29/2023]
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17
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Su P, Li M, Li X, Yuan X, Gong Z, Wu L, Song J, Yang Y. Glutathione functionalized magnetic covalent organic frameworks with dual-hydrophilicity for highly efficient and selective enrichment of glycopeptides. J Chromatogr A 2022; 1667:462869. [DOI: 10.1016/j.chroma.2022.462869] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 01/19/2022] [Accepted: 01/31/2022] [Indexed: 12/31/2022]
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18
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Zhu T, Gu Q, Liu Q, Zou X, Zhao H, Zhang Y, Pu C, Lan M. Nanostructure stable hydrophilic hierarchical porous metal-organic frameworks for highly efficient enrichment of glycopeptides. Talanta 2021; 240:123193. [PMID: 34979462 DOI: 10.1016/j.talanta.2021.123193] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 12/22/2021] [Accepted: 12/27/2021] [Indexed: 12/22/2022]
Abstract
Protein glycosylation plays a vital role in many physiological activities in organisms. Due to the low abundance of glycopeptides and the interference of numerous non-glycopeptides in biological samples, selective enrichment of glycopeptides is of great significance for their successful identification. Metal organic frameworks (MOFs) materials are appropriate for glycopeptides enrichment by virtue of their large specific surface area and outstanding hydrophilic properties. However, the instability of hydrophilic MOFs in acidic solutions have severely limited their applications. In this work, a rational facile strategy was established to synthesize a stable hydrophilic hierarchical porous MOF (denoted as HP-MOF-Arg@mSiO2). This new material improved the selectivity and sensitivity of enrichment for glycopeptides via modification of arginine groups. More importantly, the mesoporous silica layer was introduced to enhance the stability of MOFs in aqueous solution and achieve the size exclusion effect of large-size proteins in complex samples. Overall, owing to the unique hierarchical porous and the hydrophilic modification, the synthesized HP-MOF-Arg@mSiO2 materials showed excellent hydrophilicity and hydrolytic stability, resulting in outstanding specific separation capacity in glycopeptides enrichment. A total of 521 and 342 glycopeptides were respectively captured from 2 μL human serum digests and mouse testis tissue digests, revealing the potential of the materials in the study of glycoproteomics in complex biological samples.
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Affiliation(s)
- Tianyi Zhu
- Shanghai Key Laboratory of Functional Materials Chemistry, School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, 200237, PR China
| | - Qinying Gu
- Shanghai Key Laboratory of Functional Materials Chemistry, School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, 200237, PR China
| | - Qiannan Liu
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, 200240, PR China
| | - Xia Zou
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, 200240, PR China
| | - Hongli Zhao
- Shanghai Key Laboratory of Functional Materials Chemistry, School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, 200237, PR China.
| | - Yan Zhang
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, 200240, PR China
| | - Chenlu Pu
- Shanghai Key Laboratory of Functional Materials Chemistry, School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, 200237, PR China
| | - Minbo Lan
- Shanghai Key Laboratory of Functional Materials Chemistry, School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, 200237, PR China; Research Center of Analysis and Test, East China University of Science and Technology, Shanghai, 200237, PR China.
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19
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Zhu C, Wu J, Jin X, Yan Y, Ding CF, Tang K, Zhang Q. Graphene functionalized with structurally complementary amino acids for sensitive recognition of N-linked glycopeptides. J Chromatogr A 2021; 1655:462505. [PMID: 34500222 DOI: 10.1016/j.chroma.2021.462505] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 08/25/2021] [Accepted: 08/26/2021] [Indexed: 01/05/2023]
Abstract
Herein, a hydrophilic graphene composite functionalized with glutathione (GSH) and L(+)-Cysteine (Cys) was prepared via a simple and fast synthesis route, which was named G@S@Au@GC. The combination attack with two different zwitterionic polymers resulted in enhanced adsorption sites for glycopeptides. The obtained G@S@Au@GC exhibited excellent performance on a low limit of detection (0.2 fmol), a high selectivity (HRP: bovine serum albumin = 1:1500), a good load capacity (250 μg•mg-1) and recovery rate (93%), which was also evaluated with IgG. Subsequently, 60 glycopeptides from complex biological sample (human saliva) were identified by Nano-LC-MS/MS. The advantages of combination attack, low-cost, simple and fast synthesis, and superior enrichment performance make G@S@Au@GC composite a bright future on glycoproteomics analysis and related diseases.
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Affiliation(s)
- Canhong Zhu
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, School of Materials Science and Chemical Engineering, Institute of Mass Spectrometry, Ningbo University, Ningbo 315211, China
| | - Jiani Wu
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, School of Materials Science and Chemical Engineering, Institute of Mass Spectrometry, Ningbo University, Ningbo 315211, China
| | - Xueting Jin
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, School of Materials Science and Chemical Engineering, Institute of Mass Spectrometry, Ningbo University, Ningbo 315211, China
| | - Yinghua Yan
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, School of Materials Science and Chemical Engineering, Institute of Mass Spectrometry, Ningbo University, Ningbo 315211, China.
| | - Chuan-Fan Ding
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, School of Materials Science and Chemical Engineering, Institute of Mass Spectrometry, Ningbo University, Ningbo 315211, China.
| | - Keqi Tang
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, School of Materials Science and Chemical Engineering, Institute of Mass Spectrometry, Ningbo University, Ningbo 315211, China
| | - Qiaohong Zhang
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, School of Materials Science and Chemical Engineering, Institute of Mass Spectrometry, Ningbo University, Ningbo 315211, China.
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20
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Fabrication of magnetic dual-hydrophilic metal organic framework for highly efficient glycopeptide enrichment. Anal Bioanal Chem 2021; 413:5267-5278. [PMID: 34331089 DOI: 10.1007/s00216-021-03535-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 06/07/2021] [Accepted: 07/08/2021] [Indexed: 10/20/2022]
Abstract
Highly selective glycopeptide enrichment is important before mass spectrometry analysis because of the ultra-low abundance of glycopeptides in the peptide mixtures. Herein, a UiO-66-NH2-based magnetic composite was prepared and used for the hydrophilic enrichment of glycopeptides. The composite was modified with phytic acid (PA) molecules by partially replacing 2-aminoterephthalic acid ligands in UiO-66-NH2, with electrostatic interactions also promoting this modification process. Based on the hydrophilicity of both the PA molecules and the UiO-66-NH2 skeleton, the resulting material, denoted as MUiO-66-NH2/PA, showed excellent dual hydrophilicity towards glycopeptide enrichment. Compared with pure UiO-66-NH2, the specific surface area and hydrophilicity of the prepared material were increased, and MUiO-66-NH2/PA exhibited good magnetic responsiveness to facilitate a convenient enrichment procedure. HRP and IgG were used as standard proteins to evaluate the glycopeptide enrichment properties, with 21 and 34 glycopeptides enriched from their tryptic digests. Furthermore, MUiO-66-NH2/PA showed outstanding sensitivity (1 fmol/μL) and selectivity (HRP/BSA = 1:1000), and achieved remarkable glycopeptide enrichment performance for practical human serum samples. Notably, MUiO-66-NH2/PA showed perfect reusability and stability, achieving enrichment performance after five cycles similar to that of the first use. This material can be used for glycopeptide enrichment to obtain further glycosylation information, providing the possibility for cancer treatment.
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21
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Luo B, Li G, Li Z, He J, Zhou J, Wu L, Lan F, Wu Y. Construction of a magnetic covalent organic framework with synergistic affinity strategy for enhanced glycopeptide enrichment. J Mater Chem B 2021; 9:6377-6386. [PMID: 34296732 DOI: 10.1039/d1tb01168e] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Considering the inherent properties of glycopeptides, such as glycan structure, size, and hydrophilicity, affinity materials possessing suitable functional molecule-glycan interactions, matched channels with size exclusion, and surfaces with hydrophilic interactions are preferred for glycopeptide separation in biological samples. Here, a novel boronic-acid-functionalized magnetic covalent organic framework was prepared through epitaxial growth and multi-ligand strategies. The multi-ligand strategy was firstly employed to prepare functionalized magnetic covalent organic framework without any post-functionalization protocol. Notably, the proposed strategy was found to be time saving, robust, and reproducible. The versatile magnetic covalent organic framework nanocomposite was endowed with phenylboronic acid functional molecules, strong hydrophilic features, mesoporous channels, fast magnetic responsiveness, and a large surface area. Benefitting from multiple affinity interactions, namely, synergistic reversible covalent interactions and hydrophilic affinity interactions, the nanocomposite presented extremely high performance in the recognition of intact N-glycopeptides. The inherent properties endowed the nanocomposite with excellent enrichment performance for N-glycopeptides: excellent selectivity (1 : 2000, IgG/BSA, m/m), an ultralow detection limit (0.05 fmol μL-1), and a good size-exclusion effect (1 : 500, IgG digests/BSA, m/m). More excitingly, a total of 1921 unique intact glycopeptides assigned to 1154 glycoproteins were identified from rat liver tissue; this performance is superior to that of commercial products. Additionally, the nanocomposite was successfully applied to enrich intact glycopeptides of exosomes extracted from healthy individuals and renal failure patients, providing a novel concept for the design of materials using a synergistic affinity strategy for sample preparation in glycoproteomics.
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Affiliation(s)
- Bin Luo
- National Engineering Research Center for Biomaterials, Sichuan University, Chengdu 610064, P. R. China.
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22
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Flexible and hierarchical metal-organic framework composite as solid-phase media for facile affinity-tip fabrication to selectively enrich glycopeptides and phosphopeptides. Talanta 2021; 233:122576. [PMID: 34215068 DOI: 10.1016/j.talanta.2021.122576] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 05/28/2021] [Accepted: 05/29/2021] [Indexed: 01/19/2023]
Abstract
Micro-tip-based solid-phase microextraction is considered as one of the green and powerful analytical sample preparation techniques, but its efficiency is severely hampered by some basic issues such as tedious fabrication, instability of sorbent bed, and blocking of the tip, especially for biological samples due to low permeability. These issues are tackled by introducing a flexible and hierarchical substrate in the microtip, having good mechanical strength and specific functionality to capture the desired biomolecules. Considering the well-ordered and flexible structure of melamine foam, it was used as a substrate and for hydrophilic interaction chromatography (HILIC). Metal-organic framework, due to its excellent characteristics, was grafted on its surface anchored by self-assembling polydopamine. The resulting material was characterized and packed in the tip by just pressing the material in the conical structure of the tip. This affinity tip established good and tunable permeability and was used to selectively enrich glycopeptides as well as phosphopeptides. The affinity tip demonstrated excellent performance to enrich glycopeptides and phosphopeptides with a low limit of detection up to 0.5 fmol μL-1 from tryptic digests of horseradish peroxidase and β-Casein, respectively, and was stable up to 5 rounds of enrichment. Moreover, this affinity-tip also exhibited high selectivity up to up to 1:1000 (HRP digest to BSA digest) for glycopeptides and 1:200 (β-Casein digest to BSA digest) for phosphopeptides and demonstrated several other fascinating characteristics such as; excellent size exclusion effect for the omission of large-sized proteins, modest backpressure, reproducibility, reusability, smooth enrichment, and successfully applied to a human saliva sample.
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23
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Yan Y, Han R, Hou Y, Zhang H, Yu J, Gao W, Xu L, Tang K. Bowl-like mesoporous polydopamine with size exclusion for highly selective recognition of endogenous glycopeptides. Talanta 2021; 233:122468. [PMID: 34215103 DOI: 10.1016/j.talanta.2021.122468] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 04/16/2021] [Accepted: 04/23/2021] [Indexed: 01/01/2023]
Abstract
It has been confirmed that endogenous glycopeptide plays an important role in a variety of pathological and physiological processes. However, direct analysis of endogenous glycopeptide is still a great challenge owing to the low abundance of endogenous glycopeptides and the presence of a large number of interfering substances such as large-sized proteins and heteropeptides in complex biological sample. Herein, we reported a novel bowl-like mesoporous polydopamine nanoparticle modified by carrageenan (denoted as MPDA@PEI@CA) with strong hydrophilicity and size-exclusion effect for high specificity enrichment of endogenous glycopeptides. Thanks to the suitable pore channel structure as well as strong hydrophilic surface, the as-prepared MPDA@PEI@CA nanoparticles exhibited prominent performance in enrichment of N-linked glycopeptide with ultrahigh selectivity (1:5000 M ratio of horseradish peroxidase (HRP) digests/bovine serum albumin (BSA) digests), low detection limit (5 fmol μL-1), outstanding size-exclusion ability (1:1000 mass of HRP/BSA), and unique reusability (five times). 125 N-glycosylation sites of 134 glycopeptides from 65 glycoproteins were identified from 2 μL sample of human serum treated with the MPDA@PEI@CA nanoparticles, which manifested the ability to enrich endogenous N-linked glycopeptides from complex biological samples. These results indicated that the bowl-like MPDA@PEI@CA nanoparticles with novel structure prepared in this work had great potential for glycopeptidome analysis.
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Affiliation(s)
- Yuyan Yan
- Zhejiang Provincial Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis, PR China; Institute of Mass Spectrometry, School of Materials Science & Chemical Engineering, Ningbo University, Ningbo, 315211, PR China
| | - Renlu Han
- Zhejiang Provincial Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis, PR China; Institute of Mass Spectrometry, School of Materials Science & Chemical Engineering, Ningbo University, Ningbo, 315211, PR China.
| | - Yafei Hou
- Department of Microelectronic Science and Engineering, Ningbo University, Ningbo, 315211, PR China
| | - Huijun Zhang
- Zhejiang Provincial Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis, PR China; Institute of Mass Spectrometry, School of Materials Science & Chemical Engineering, Ningbo University, Ningbo, 315211, PR China
| | - Jiancheng Yu
- Faculty of Electrical Engineering and Computer Science, Ningbo University, Ningbo, 315211, PR China
| | - Wenqing Gao
- Zhejiang Provincial Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis, PR China; Institute of Mass Spectrometry, School of Materials Science & Chemical Engineering, Ningbo University, Ningbo, 315211, PR China
| | - Long Xu
- Zhejiang Provincial Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis, PR China; Institute of Mass Spectrometry, School of Materials Science & Chemical Engineering, Ningbo University, Ningbo, 315211, PR China
| | - Keqi Tang
- Zhejiang Provincial Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis, PR China; Institute of Mass Spectrometry, School of Materials Science & Chemical Engineering, Ningbo University, Ningbo, 315211, PR China.
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24
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Zhang C, Jin X, Wang L, Jin C, Han X, Ma W, Li X, Teng G. Hollow MnFe 2O 4@C@APBA Nanospheres with Size Exclusion and pH Response for Efficient Enrichment of Endogenous Glycopeptides. ACS APPLIED MATERIALS & INTERFACES 2021; 13:9714-9728. [PMID: 33600144 DOI: 10.1021/acsami.0c22221] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Enrichment and detection of glycopeptides are an important clinical measure for the diagnosis of complex diseases. Enrichment materials play a key role in this process; they must have an effective sample-screening ability to eliminate the interference of nonglycopeptides. In this work, novel hollow MnFe2O4@C@APBA nanospheres (HMCAs) with magnetic and pH responsiveness were prepared for glycopeptide enrichment. The as-prepared composites have a suitable hollow structure and large specific surface area, and the boron hydroxyl group in their cavities can fix or disconnect the hydrophilic groups of the glycopeptides at different pH, so the glycopeptides can be adsorbed or desorbed in a controllable way. Enrichment results showed that the HMCAs exhibited an excellent enrichment performance: ultralow limit of detection (approximately 0.5 fmol μL-1), perfect size-exclusion effect (HRP/BSA, 1:800, w/w), favorable universality (HRP, IgG, and RNase B), and high binding capacity (150 mg/g). In order to verify the application of materials in practice, the HMCAs were used for the analysis of complex samples and it was found that 474 glycopeptides were identified from 210 glycoproteins in three replicate analyses of 2 μL of human serum. The results showed that the HMCAs could be used as a promising enrichment material for glycopeptide characterization in MS-based glycoproteomics and related fields.
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Affiliation(s)
- Chun Zhang
- School of Chemical and Biological Engineering, Lanzhou Jiaotong University, Lanzhou 730070, P. R. China
| | - Xiaodong Jin
- School of Chemical and Biological Engineering, Lanzhou Jiaotong University, Lanzhou 730070, P. R. China
| | - Liping Wang
- School of Chemical and Biological Engineering, Lanzhou Jiaotong University, Lanzhou 730070, P. R. China
| | - Chengzhao Jin
- School of Chemical and Biological Engineering, Lanzhou Jiaotong University, Lanzhou 730070, P. R. China
| | - Xiaoqian Han
- School of Chemical and Biological Engineering, Lanzhou Jiaotong University, Lanzhou 730070, P. R. China
| | - Weigang Ma
- School of Aerospace Engineering, Tsinghua University, Beijing 100084, P. R. China
| | - Xingang Li
- School of Chemical and Biological Engineering, Lanzhou Jiaotong University, Lanzhou 730070, P. R. China
- Tianjin Key Laboratory of Applied Catalysis Science and Engineering, Tianjin University, Tianjin 300072, China
| | - Guixiang Teng
- College of Life Science, Northwest Normal University, Lanzhou 730070, P. R. China
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Zhong H, Li Y, Huang Y, Zhao R. Metal-organic frameworks as advanced materials for sample preparation of bioactive peptides. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2021; 13:862-873. [PMID: 33543184 DOI: 10.1039/d0ay02193h] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Development of novel affinity materials and separation techniques is crucial for the progress of modern proteomics and peptidomics. Detection of peptides and proteins from complex matrices still remains a challenging task due to the highly complicated biological composition, low abundance of target molecules, and large dynamic range of proteins. As an emerging area of analytical science, metal-organic framework (MOF)-based separation of proteins and peptides is attracting growing interest. This minireview summarizes the recent advances in MOF-based affinity materials for the sample preparation of proteins and peptides. Some newly emerging MOF nanoreactors for the degradation of peptides and proteins are introduced. An update of MOF-based affinity materials for the isolation of glycopeptides, phosphopeptides and low-abundance endogenous peptides in the last two years is focused on. The separation mechanism is discussed along with the chemical structures of MOFs. Finally, the remaining challenges and future development of MOFs in analyzing peptides and proteins in complicated biological samples are discussed.
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Affiliation(s)
- Huifei Zhong
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Analytical Chemistry for Living Biosystems, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China.
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Ali MM, Zhu Z, Wang M, Hussain D, Gao X, Wang J, Du Z. Melamine foam assisted in-tip packed amine-functionalized titanium metal-organic framework for the selective enrichment of endogenous glycopeptides. J Chromatogr A 2020; 1636:461711. [PMID: 33316563 DOI: 10.1016/j.chroma.2020.461711] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 11/04/2020] [Accepted: 11/09/2020] [Indexed: 12/16/2022]
Abstract
Endogenous glycopeptides are significantly important in diverse pathological and physiological systems, but their direct analysis is severely hampered by their low abundance and presence of interfering species in biological fluids. In this study, we synthesized the amine-functionalized titanium metal-organic framework (NH2-MIL-125(Ti)) by a simple hydrothermal method, characterized and used for glycopeptides enrichment. The designed separation media is highly hydrophilic and stable which is suitable for hydrophilic interaction chromatography (HILIC). To make the process smooth, simple, reliable, and robust, NH2-MIL-125(Ti) crystals were packed in pipette-tip using hydrophilic melamine foam, as supporting frit. Free amine groups, present in the structure imparted hydrophilicity and a unique pattern of porosity, contributing to the size exclusion effect that excluded the large-sized proteins up to 1:700 peptide to protein ratio. The prepared MOF particles possessed regular porosity, high surface area, good hydrophilicity, and offered an in-tip flow-based set-up enhanced the enrichment performance for N-linked glycopeptides. The affinity material showed a detection limit of 1 fmol.µL-1 and selectivity up to 1:1000 (HRP digest to BSA digest). Moreover, repeatability and reusability were evaluated up to five rounds of enrichment using the same affinity tip, and scanning electron microscopic images revealed no structural changes in the MOF crystals. Finally, the MOF packed in pipette tip was applied to selectively capture the N-linked endogenous glycopeptides from a healthy saliva sample and 64 unique endogenous glycopeptides were identified. These results demonstrated the excellent potential of NH2-MIL-125(Ti) based affinity tip for glycopeptides which can be used to enrich trace glycopeptide biomarkers from the biological fluids.
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Affiliation(s)
- Muhammad Mujahid Ali
- College of Chemistry, Beijing Key Laboratory of Environmentally Harmful Chemical Analysis, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Zhiyuan Zhu
- College of Chemistry, Beijing Key Laboratory of Environmentally Harmful Chemical Analysis, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Mengyu Wang
- College of Chemistry, Beijing Key Laboratory of Environmentally Harmful Chemical Analysis, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Dilshad Hussain
- HEJ Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan
| | - Xia Gao
- Beijing Center for Physical and Chemical Analysis, Beijing Engineering Research Center of Food Safety Analysis, Beijing 100089, China
| | - Jianfeng Wang
- College of Chemistry, Beijing Key Laboratory of Environmentally Harmful Chemical Analysis, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Zhenxia Du
- College of Chemistry, Beijing Key Laboratory of Environmentally Harmful Chemical Analysis, Beijing University of Chemical Technology, Beijing, 100029, China.
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Hu X, Wu Y, Deng C. Recognition of urinary N-linked glycopeptides in kidney cancer patients by hydrophilic carbohydrate functionalized magnetic metal organic framework combined with LC-MS/MS. Mikrochim Acta 2020; 187:616. [PMID: 33073321 DOI: 10.1007/s00604-020-04595-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 10/07/2020] [Indexed: 12/20/2022]
Abstract
A hydrophilic carbohydrate functionalized magnetic metal organic framework (Mag Zr-MOF@G6P) was synthesized via a facile one-step modification strategy for selective glycopeptide capture in virtue of hydrophilic interaction chromatography technique. The inherently hydrophilic Zr-MOF layer not only provides selective size-sieving pore structures but also offers large specific surface area to afford abundant affinity sites. Hydroxyl-rich glucose-6-phosphate was immobilized onto the Zr-MOF via a straightforward coordination manner to regulate its surface property, for the purpose of enhancing its hydrophilicity. Benefitting from the merits of Zr-MOF and glucose-6-phosphate, the as-designed composite exhibits good selectivity (the mass ratio of HRP digests to BSA digests was up to1:200) and low limit of detection (0.1 fmol μL-1) towards the recognition of glycopeptides from standard samples. More excitingly, glycopeptides in urine of healthy people and patients with kidney cancer were successfully enriched and identified by the combined liquid chromatography-mass spectrometry/mass spectrometry technology (LC-MS/MS). Further gene ontology analysis of molecular function and biological process revealed that 13 original glycoproteins of the identified glycopeptides from urine of patients significantly participate in diverse cancer-associated events, including collagen binding, immunoglobulin receptor binding, antigen binding, and complement activation process. Graphical abstract.
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Affiliation(s)
- Xufang Hu
- Department of Chemistry, Department of Gastroenterology and Hepatology, Zhongshan Hospital, Institutes of Biomedical Sciences, Fudan University, 200433, Shanghai, China
| | - Yonglei Wu
- Department of Chemistry, Department of Gastroenterology and Hepatology, Zhongshan Hospital, Institutes of Biomedical Sciences, Fudan University, 200433, Shanghai, China
| | - Chunhui Deng
- Department of Chemistry, Department of Gastroenterology and Hepatology, Zhongshan Hospital, Institutes of Biomedical Sciences, Fudan University, 200433, Shanghai, China.
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Li J, Huan W, Xu K, Wang B, Zhang J, Zhu B, Wu M, Wang J. Gold nanoparticle-glutathione-functionalized porous graphene oxide-based hydrophilic beads for the selective enrichment of N-linked glycopeptides. Mikrochim Acta 2020; 187:518. [PMID: 32851535 DOI: 10.1007/s00604-020-04519-w] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Accepted: 08/18/2020] [Indexed: 12/17/2022]
Abstract
A three-dimensional structured porous graphene oxide-polyethylenimine bead (pGP) is synthesized for immobilizing gold nanoparticles and modifying glutathione molecules (denoted as pGP/AuG). The pGP/AuG has open pore structure, honeycomb-like channels, and excellent hydrophilicity. By taking advantages of the porous structure, abundant binding sites, and multivalent interactions between glycopeptides and both glutathione molecules and free amino groups, the pGP/AuG is adopted to the selective enrichment of N-linked glycopeptides with low limit of detection (2 fmol), high enrichment selectivity (1:500), binding capacity (333.3 mg/g), recovery yield (91.3 ± 2.1%), and repeatability (< 6.0% RSD) using matrix-assisted laser desorption/ionization time of flight mass spectrometry detection method. Furthermore, the practical applicability of pGP/AuG is evaluated, in which 209 N-glycosylated peptides corresponding to 128 N-glycosylated proteins are identified from 1 μL human serum in three independent analysis procedures, suggesting the great potential for application in glycoproteome fields.Graphical abstract Schematic presentation of preparation for porous graphene oxide-based hydrophilic beads (pGP/AuG) with honeycomb-like microstructure. The pGP/AuG was successfully used for enriching and identifying glycopeptides from actual biological sample.
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Affiliation(s)
- Jie Li
- Zhejiang Provincial Key Laboratory of Chemical Utilization of Forestry Biomass, Zhejiang A& F University, Lin'an, Hangzhou, 311300, China.
| | - Weiwei Huan
- Zhejiang Provincial Key Laboratory of Chemical Utilization of Forestry Biomass, Zhejiang A& F University, Lin'an, Hangzhou, 311300, China
| | - Kaiwei Xu
- Department of Radiology, The Affiliated Hospital of Medical School of Ningbo University, Ningbo, 315020, China
| | - Buchuan Wang
- Zhejiang Provincial Key Laboratory of Chemical Utilization of Forestry Biomass, Zhejiang A& F University, Lin'an, Hangzhou, 311300, China
| | - Jingshu Zhang
- Safety Assessment and Research Center for Drug, Pesticide and Veterinary Drug of Jiangsu Province, Nanjing Medical University, Nanjing, 211166, China
| | - Binbin Zhu
- Department of Radiology, The Affiliated Hospital of Medical School of Ningbo University, Ningbo, 315020, China
| | - Minjie Wu
- Zhejiang Provincial Key Laboratory of Chemical Utilization of Forestry Biomass, Zhejiang A& F University, Lin'an, Hangzhou, 311300, China
| | - Jianhua Wang
- Department of Radiology, The Affiliated Hospital of Medical School of Ningbo University, Ningbo, 315020, China.
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Zheng H, Guan S, Wang X, Zhao J, Gao M, Zhang X. Deconstruction of Heterogeneity of Size-Dependent Exosome Subpopulations from Human Urine by Profiling N-Glycoproteomics and Phosphoproteomics Simultaneously. Anal Chem 2020; 92:9239-9246. [PMID: 32495629 DOI: 10.1021/acs.analchem.0c01572] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The heterogeneous populations of exosomes with distinct nanosize have impeded our understanding of their corresponding function as intercellular communication agents. Profiling signaling proteins packaged in each size-dependent subtype can disclose this heterogeneity of exosomes. Herein, new strategy was developed for deconstructing heterogeneity of distinct-size urine exosome subpopulations by profiling N-glycoproteomics and phosphoproteomics simultaneously. Two-dimension size exclusion liquid chromatography (SEC) was utilized to isolate large exosomes (L-Exo), medium exosomes (M-Exo), and small exosomes (S-Exo) from human urine samples. Then, hydrophilic carbonyl-functionalized magnetic zirconium-organic framework (CFMZOF) was developed as probe for capturing the two kinds of post-translational modification (PTM) peptides simultaneously. Finally, liquid chromatography-tandem mass spectrometry (LC-MS/MS) combined with database search was used to characterize PTM protein contents. We identified 144 glycoproteins and 44 phosphoproteins from L-Exo, 156 glycoproteins, and 46 phosphoproteins from M-Exo and 134 glycoproteins and 10 phosphoproteins from S-Exo. The ratio of the proteins with simultaneous glycosylation and phosphorylation is 11%, 9%, and 3% in L-Exo, M-Exo, and S-Exo, respectively. Based on label-free quantification intensity results, both principal component analysis and Pearson's correlation coefficients indicate that distinct-size exosome subpopulations exist significant differences in PTM protein contents. Analysis of high abundance PTM proteins in each exosome subset reveals that the preferentially packaged PTM proteins in L-Exo, M-Exo, and S-Exo are associated with immune response, biological metabolism, and molecule transport processes, respectively. Our PTM proteomics study based on size-dependent exosome subtypes opens a new avenue for deconstructing the heterogeneity of exosomes.
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Affiliation(s)
- Haoyang Zheng
- Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200433, China
| | - Sheng Guan
- Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200433, China
| | - Xuantang Wang
- Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200433, China
| | - Jiandong Zhao
- Department of Radiation Oncology, Fudan University Shanghai Cancer Center; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Mingxia Gao
- Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200433, China
| | - Xiangmin Zhang
- Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200433, China
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Peng J, Zhang H, Niu H, Wu R. Peptidomic analyses: The progress in enrichment and identification of endogenous peptides. Trends Analyt Chem 2020. [DOI: 10.1016/j.trac.2020.115835] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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Liu B, Wang B, Yan Y, Tang K, Ding CF. Postsynthesis of zwitterionic hydrophilic composites for enhanced enrichment of N-linked glycopeptides from human serum. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2020; 34:e8607. [PMID: 31657490 DOI: 10.1002/rcm.8607] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2019] [Revised: 09/19/2019] [Accepted: 09/20/2019] [Indexed: 06/10/2023]
Abstract
RATIONALE Glycosylation of proteins plays an important role in life activities, but the concentration of naturally occurring glycopeptides is usually relatively low, and glycosylation has microfacies heterogeneity, so direct mass spectrometry is not feasible. Therefore, selective enrichment of glycopeptides before mass spectrometry has turned into an urgent problem to be resolved. METHODS Herein, the zwitterionic L-cysteine functionalized hydrophilic graphene oxide composite (GO@PDA@MIL-125-NH2 @Au@L-Cys) was prepared via a postsynthetic method. The obtained material was used for glycopeptide enrichment. The enriched peptides were then detected using matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOFMS) to demonstrate the enrichment performance of the material. RESULTS In the actual enrichment process, GO@PDA@MIL-125-NH2 @Au@L-Cys nanomaterials exhibited high selectivity (1:1000), outstanding sensitivity (0.5 fmol), and excellent repeatability for the enrichment of glycopeptides. In addition, the proposed material showed good performance in the enrichment of glycopeptides from complex biosamples; 56 glycopeptides were detected from 2 μL of human serum using MALDI-TOFMS. CONCLUSIONS The experimental results showed that GO@PDA@MIL-125-NH2 @Au@L-Cys exhibited excellent performance on glycopeptide analysis. It has great potential in the enrichment of glycopeptides and provides new ideas for synthetic materials with better enrichment properties in the future.
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Affiliation(s)
- Bin Liu
- School of Materials Science and Chemical Engineering, Institute of Mass Spectrometry, Ningbo University, Ningbo, China
| | - Baichun Wang
- School of Materials Science and Chemical Engineering, Institute of Mass Spectrometry, Ningbo University, Ningbo, China
| | - Yinghua Yan
- School of Materials Science and Chemical Engineering, Institute of Mass Spectrometry, Ningbo University, Ningbo, China
| | - Keqi Tang
- School of Materials Science and Chemical Engineering, Institute of Mass Spectrometry, Ningbo University, Ningbo, China
| | - Chuan-Fan Ding
- School of Materials Science and Chemical Engineering, Institute of Mass Spectrometry, Ningbo University, Ningbo, China
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Wu Y, Sun N, Deng C. Construction of Magnetic Covalent Organic Frameworks with Inherent Hydrophilicity for Efficiently Enriching Endogenous Glycopeptides in Human Saliva. ACS APPLIED MATERIALS & INTERFACES 2020; 12:9814-9823. [PMID: 32011110 DOI: 10.1021/acsami.9b22601] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
In this work, a magnetic covalent organic framework (COF) with inherent hydrophilicity (denoted mCTpBD) was synthesized through interface deposition of a hydrophilic COF shell on amino group-functionalized magnetite particles via the reaction between a carboxyl group-containing monomer and benzidine. Thanks to the superior hydrophilicity, appropriate porous structure, and easy magnetic separation, the resulting mCTpBD exhibited excellent performance in conveniently enriching glycopeptides from standard samples with a high sensitivity of 0.5 fmol μL-1 and strong size-exclusion effect of up to 1:1000 (w/w). Furthermore, by using the mCTpBD adsorbent, endogenous glycopeptides in saliva of healthy people and patients with inflammatory bowel disease were successfully enriched and identified by the combined liquid chromatography-mass spectrometry/mass spectrometry technology, which indicates a promising prospective of core-shell magnetic composite microspheres with a hydrophilic COF shell in glycoproteomics research.
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Affiliation(s)
- Yonglei Wu
- Department of Chemistry, The Fifth People's Hospital of Shanghai, Institutes of Biomedical Sciences, Collaborative Innovation Center of Genetics and Development , Fudan University , Shanghai 200433 , China
| | - Nianrong Sun
- Department of Gastroenterology and Hepatology, Zhongshan Hospital , Fudan University , Shanghai 200433 , China
| | - Chunhui Deng
- Department of Chemistry, The Fifth People's Hospital of Shanghai, Institutes of Biomedical Sciences, Collaborative Innovation Center of Genetics and Development , Fudan University , Shanghai 200433 , China
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Zheng H, Jia J, Li Z, Jia Q. Bifunctional Magnetic Supramolecular-Organic Framework: A Nanoprobe for Simultaneous Enrichment of Glycosylated and Phosphorylated Peptides. Anal Chem 2020; 92:2680-2689. [DOI: 10.1021/acs.analchem.9b04691] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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Luo B, He J, Li Z, Lan F, Wu Y. Glutathione-Functionalized Magnetic Covalent Organic Framework Microspheres with Size Exclusion for Endogenous Glycopeptide Recognition in Human Saliva. ACS APPLIED MATERIALS & INTERFACES 2019; 11:47218-47226. [PMID: 31750645 DOI: 10.1021/acsami.9b15905] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Endogenous glycopeptides have been confirmed to play a significant role in multifarious pathological and physiological processes. The low abundance of endogenous glycopeptides and abundant interferents (e.g., large-size proteins and heteropeptides) in complex biological matrices render the direct analysis of endogenous glycopeptides difficult. Reported here is a novel glutathione-functionalized magnetic covalent organic framework microsphere (denoted as MCNC@COF@GSH) endowed with size-exclusion effect and strong hydrophilicity for selective and efficient enrichment of N-linked glycopeptides. The as-prepared MCNC@COF@GSH microspheres possessed fast magnetic responsiveness, regular porosity, large surface areas, and good hydrophilicity, resulting in remarkable performances in N-linked glycopeptide enrichment with low detection limit (0.01 fmol μL-1), high selectivity (1:5000, human immunoglobulin G (IgG) digests to bovine serum albumin digests), excellent size-exclusion effect (IgG digests/IgG/bovine serum albumin (BSA), 1:500:500), and reusability (at least five times). More excitingly, 143 endogenous N-linked glycopeptides were clearly identified from 10 μL sample of human saliva treated with the MCNC@COF@GSH microspheres, which is the unprecedented high efficiency in endogenous N-linked glycopeptide enrichment from human saliva. In addition to providing a strategy for versatile functionalization of magnetic covalent organic frameworks (COFs), this study may be used to develop application of endogenous glycoproteome analysis.
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Affiliation(s)
- Bin Luo
- National Engineering Research Center for Biomaterials , Sichuan University , Chengdu 610064 , P. R. China
| | - Jia He
- National Engineering Research Center for Biomaterials , Sichuan University , Chengdu 610064 , P. R. China
| | - Zhiyu Li
- National Engineering Research Center for Biomaterials , Sichuan University , Chengdu 610064 , P. R. China
| | - Fang Lan
- National Engineering Research Center for Biomaterials , Sichuan University , Chengdu 610064 , P. R. China
| | - Yao Wu
- National Engineering Research Center for Biomaterials , Sichuan University , Chengdu 610064 , P. R. China
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Qi H, Li Z, Zheng H, Fu L, Jia Q. Facile preparation of hydrophilic glutathione modified magnetic nanomaterials for specific enrichment of glycopeptides. CHINESE CHEM LETT 2019. [DOI: 10.1016/j.cclet.2019.06.046] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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Li Y, Sun N, Hu X, Li Y, Deng C. Recent advances in nanoporous materials as sample preparation techniques for peptidome research. Trends Analyt Chem 2019. [DOI: 10.1016/j.trac.2019.115658] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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Sun N, Wu H, Chen H, Shen X, Deng C. Advances in hydrophilic nanomaterials for glycoproteomics. Chem Commun (Camb) 2019; 55:10359-10375. [PMID: 31414669 DOI: 10.1039/c9cc04124a] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Owing to the formidable challenge posed by microheterogeneities in glycosylation sites, macroheterogeneity of the modification number of glycans, and low abundance and ionization efficiency of glycosylation, the crucial premise for conducting in-depth profiling of the glycoproteome is to develop highly efficient technology for separation and enrichment. The appearance of hydrophilic interaction chromatography (HILIC) has considerably accelerated the progress in glycoproteomics. In particular, additional hydrophilic nanomaterials have been developed for glycoproteomics research in the recent years. In this review, we mainly summarize the recent progresses made in the design and synthesis of different hydrophilic nanomaterials, as well as their applications in glycoproteomics, according to the classification of the main hydrophilic functional molecules on the surface. Further, we briefly illustrate the potential retention mechanism of the HILIC mode and discuss the limits and barriers of hydrophilic nanomaterials in glycoproteomics, as well as propose their possible development trends in the future.
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Affiliation(s)
- Nianrong Sun
- Department of Gastroenterology, Zhongshan Hospital of Fudan University, Shanghai 200032, China.
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