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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: 5] [Impact Index Per Article: 5.0] [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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Jiang D, Wu S, Lv S, Qi R, Li Y, Liu J. Cerium ions immobilized magnetic graphite nitride decorated with L-Alanyl-L-Glutamine as new chelator for enrichment of phosphopeptides. Mikrochim Acta 2023; 190:452. [PMID: 37882891 DOI: 10.1007/s00604-023-06033-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 10/06/2023] [Indexed: 10/27/2023]
Abstract
Cerium ions immobilized magnetic graphite nitride material have been prepared using L-Alanyl-L-Glutamine as the new chelator. The resulting Fe3O4/g-C3N4-L-Ala-L-Gln-Ce4+, as an immobilized metal ion affinity chromatography (IMAC) sorbent, was reusable. This is due to the strong coordination interaction between L-Alanyl-L-Glutamine and cerium ions. After a series of characterizations, the magnetic nanocomposite showed high surface area, good hydrophilicity, positive electricity, and magnetic response. Fe3O4/g-C3N4-L-Ala-L-Gln-Ce4+ had high sensitivity (0.1 fmol), selectivity (α-/β-casein/bovine serum albumin, 1:1:5000), and good recyclability (10 cycles). A total of 647 unique phosphopeptides mapped to 491 phosphoproteins were identified from A549 cell lysate by nano LC-MS analysis.
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Affiliation(s)
- Dandan Jiang
- College of Chemistry and Materials Science, Inner Mongolia Key Laboratory of Carbon Nanomaterials, Nano Innovation Institute (NII), Inner Mongolia Minzu University, Tongliao, 028000, China.
| | - Siyu Wu
- College of Chemistry and Materials Science, Inner Mongolia Key Laboratory of Carbon Nanomaterials, Nano Innovation Institute (NII), Inner Mongolia Minzu University, Tongliao, 028000, China
| | - Siqi Lv
- College of Chemistry and Materials Science, Inner Mongolia Key Laboratory of Carbon Nanomaterials, Nano Innovation Institute (NII), Inner Mongolia Minzu University, Tongliao, 028000, China
| | - Ruixue Qi
- College of Chemistry and Materials Science, Inner Mongolia Key Laboratory of Carbon Nanomaterials, Nano Innovation Institute (NII), Inner Mongolia Minzu University, Tongliao, 028000, China
| | - Yangyang Li
- College of Chemistry and Materials Science, Inner Mongolia Key Laboratory of Carbon Nanomaterials, Nano Innovation Institute (NII), Inner Mongolia Minzu University, Tongliao, 028000, China
| | - Jinghai Liu
- College of Chemistry and Materials Science, Inner Mongolia Key Laboratory of Carbon Nanomaterials, Nano Innovation Institute (NII), Inner Mongolia Minzu University, Tongliao, 028000, China
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Recent advances in development of functional magnetic adsorbents for selective separation of proteins/peptides. Talanta 2023; 253:123919. [PMID: 36126523 DOI: 10.1016/j.talanta.2022.123919] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 08/26/2022] [Accepted: 09/04/2022] [Indexed: 12/13/2022]
Abstract
Nowadays, proteins separation has attracted great attention in proteomics research. Because the proteins separation is helpful for making an early diagnosis of many diseases. Magnetic nanoparticles are an interesting and useful functional material, and have attracted extensive research interest during the past decades. Because of the excellent properties such as easy surface functionalization, tunable biocompatibility, high saturation magnetization etc, magnetic microspheres have been widely used in isolation of proteins/peptides. Notably, with the rapid development of surface decoration strategies, more and more functional magnetic adsorbents have been designed and fabricated to meet the growing demands of biological separation. In this review, we have collected recent information about magnetic adsorbents applications in selective separation of proteins/peptides. Furthermore, we present a comprehensive prospects and challenges in the field of protein separation relying on magnetic nanoparticles.
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Zeng X, Lan Y, Xiao J, Hu L, Tan L, Liang M, Wang X, Lu S, Peng T, Long F. Advances in phosphoproteomics and its application to COPD. Expert Rev Proteomics 2022; 19:311-324. [PMID: 36730079 DOI: 10.1080/14789450.2023.2176756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
INTRODUCTION Chronic obstructive pulmonary disease (COPD) was the third leading cause of global death in 2019, causing a huge economic burden to society. Therefore, it is urgent to identify specific phenotypes of COPD patients through early detection, and to promptly treat exacerbations. The field of phosphoproteomics has been a massive advancement, compelled by the developments in mass spectrometry, enrichment strategies, algorithms, and tools. Modern mass spectrometry-based phosphoproteomics allows understanding of disease pathobiology, biomarker discovery, and predicting new therapeutic modalities. AREAS COVERED In this article, we present an overview of phosphoproteomic research and strategies for enrichment and fractionation of phosphopeptides, identification of phosphorylation sites, chromatographic separation and mass spectrometry detection strategies, and the potential application of phosphorylated proteomic analysis in the diagnosis, treatment, and prognosis of COPD disease. EXPERT OPINION The role of phosphoproteomics in COPD is critical for understanding disease pathobiology, identifying potential biomarkers, and predicting new therapeutic approaches. However, the complexity of COPD requires the more comprehensive understanding that can be achieved through integrated multi-omics studies. Phosphoproteomics, as a part of these multi-omics approaches, can provide valuable insights into the underlying mechanisms of COPD.
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Affiliation(s)
- Xiaoyin Zeng
- Sino-French Hoffmann Institute, School of Basic Medical Science, State Key Laboratory of Respiratory Disease, Guangzhou Medical University, Guangzhou, China
| | - Yanting Lan
- Sino-French Hoffmann Institute, School of Basic Medical Science, State Key Laboratory of Respiratory Disease, Guangzhou Medical University, Guangzhou, China
| | - Jing Xiao
- Sino-French Hoffmann Institute, School of Basic Medical Science, State Key Laboratory of Respiratory Disease, Guangzhou Medical University, Guangzhou, China
| | - Longbo Hu
- Sino-French Hoffmann Institute, School of Basic Medical Science, State Key Laboratory of Respiratory Disease, Guangzhou Medical University, Guangzhou, China
| | - Long Tan
- Sino-French Hoffmann Institute, School of Basic Medical Science, State Key Laboratory of Respiratory Disease, Guangzhou Medical University, Guangzhou, China
| | - Mengdi Liang
- Sino-French Hoffmann Institute, School of Basic Medical Science, State Key Laboratory of Respiratory Disease, Guangzhou Medical University, Guangzhou, China
| | - Xufei Wang
- Sino-French Hoffmann Institute, School of Basic Medical Science, State Key Laboratory of Respiratory Disease, Guangzhou Medical University, Guangzhou, China
| | - Shaohua Lu
- Sino-French Hoffmann Institute, School of Basic Medical Science, State Key Laboratory of Respiratory Disease, Guangzhou Medical University, Guangzhou, China
| | - Tao Peng
- Sino-French Hoffmann Institute, School of Basic Medical Science, State Key Laboratory of Respiratory Disease, Guangzhou Medical University, Guangzhou, China.,Guangdong South China Vaccine Co. Ltd, Guangzhou, China
| | - Fei Long
- Sino-French Hoffmann Institute, School of Basic Medical Science, State Key Laboratory of Respiratory Disease, Guangzhou Medical University, Guangzhou, China
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Gök V, Topel Ö, Aksu S. Development of New Lanthanide(III) Ion-Based Magnetic Affinity Material for Phosphopeptide Enrichment. NEW J CHEM 2022. [DOI: 10.1039/d2nj02216h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Lanthanide (III) ion-based magnetic IMAC materials consisting of core-shell-like silica-coated magnetic nanoparticles as supporting material, chelidamic acid as chelating agent, and Ln3+ ions were developed in this study. Magnetic nanoparticles...
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Low TY, Mohtar MA, Lee PY, Omar N, Zhou H, Ye M. WIDENING THE BOTTLENECK OF PHOSPHOPROTEOMICS: EVOLVING STRATEGIES FOR PHOSPHOPEPTIDE ENRICHMENT. MASS SPECTROMETRY REVIEWS 2021; 40:309-333. [PMID: 32491218 DOI: 10.1002/mas.21636] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 05/11/2020] [Accepted: 05/12/2020] [Indexed: 06/11/2023]
Abstract
Phosphorylation is a form of protein posttranslational modification (PTM) that regulates many biological processes. Whereas phosphoproteomics is a scientific discipline that identifies and quantifies the phosphorylated proteome using mass spectrometry (MS). This task is extremely challenging as ~30% of the human proteome is phosphorylated; and each phosphoprotein may exist as multiple phospho-isoforms that are present in low abundance and stoichiometry. Hence, phosphopeptide enrichment techniques are indispensable to (phospho)proteomics laboratories. These enrichment methods encompass widely-adopted techniques such as (i) affinity-based chromatography; (ii) ion exchange and mixed-mode chromatography (iii) enrichment with phospho-specific antibodies and protein domains, and (iv) functionalized polymers and other less common but emerging technologies such as hydroxyapatite chromatography and precipitation with inorganic ions. Here, we review these techniques, their history, continuous development and evaluation. Besides, we outline associating challenges of phosphoproteomics that are linked to experimental design, sample preparation, and proteolytic digestion. In addition, we also discuss about the future outlooks in phosphoproteomics, focusing on elucidating the noncanonical phosphoproteome and deciphering the "dark phosphoproteome". © 2020 John Wiley & Sons Ltd.
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Affiliation(s)
- Teck Yew Low
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, 56000, Kuala Lumpur, Malaysia
| | - M Aiman Mohtar
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, 56000, Kuala Lumpur, Malaysia
| | - Pey Yee Lee
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, 56000, Kuala Lumpur, Malaysia
| | - Nursyazwani Omar
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, 56000, Kuala Lumpur, Malaysia
| | - Houjiang Zhou
- Medical Research Council (MRC) Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH, United Kingdom
| | - Mingliang Ye
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Centre, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
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Núñez C, Chantada-Vázquez MDP, Bravo SB, Vázquez-Estévez S. Novel functionalized nanomaterials for the effective enrichment of proteins and peptides with post-translational modifications. J Proteomics 2018; 181:170-189. [DOI: 10.1016/j.jprot.2018.04.017] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Revised: 04/02/2018] [Accepted: 04/09/2018] [Indexed: 02/07/2023]
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Hong Y, Pu C, Zhao H, Sheng Q, Zhan Q, Lan M. Yolk-shell magnetic mesoporous TiO 2 microspheres with flowerlike NiO nanosheets for highly selective enrichment of phosphopeptides. NANOSCALE 2017; 9:16764-16772. [PMID: 29072763 DOI: 10.1039/c7nr05330d] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
In this work, we fabricated a yolk-shell magnetic composite that contains mesoporous TiO2 as the inner shell and flowerlike NiO as the outer shell (denoted as Fe3O4@H-TiO2@f-NiO) to reduce the limitations of single-component metal oxides in phosphopeptide enrichment. The NiO nanosheets play a synergistic role in phosphopeptide enrichment. And the unique flowerlike structure of NiO with sufficient space can facilitate the reversible insertion/extraction of peptides, which will have less impact on the enrichment process of the inner TiO2 shell. The yolk-shell structure and two types of porous nanostructures endowed this composite with a high surface area (156.58 m2 g-1) and a large pore volume (0.37 cm3 g-1). Owing to the high surface area and combined properties of TiO2 and NiO, the Fe3O4@H-TiO2@f-NiO microspheres showed a better performance for phosphopeptide enrichment than the same material without NiO nanosheets (Fe3O4@H-TiO2). According to the LC-MS/MS results, 972 unique phosphopeptides were identified from HeLa cell extracts with a high selectivity (91.9%) by Fe3O4@H-TiO2@f-NiO relative to 837 phosphopeptides (selectivity: 60.2%) by Fe3O4@H-TiO2. The results demonstrated that, compared with single-component metal oxides, composite metal oxides could enhance the selectivity and sensitivity for phosphopeptide enrichment.
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Affiliation(s)
- Yayun Hong
- Shanghai Key Laboratory of Functional Materials Chemistry, School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, 200237, People's Republic of China.
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Porous α-Fe2O3 microflowers: Synthesis, structure, and enhanced acetone sensing performances. J Colloid Interface Sci 2017; 505:1039-1046. [DOI: 10.1016/j.jcis.2017.07.007] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Revised: 06/30/2017] [Accepted: 07/02/2017] [Indexed: 11/22/2022]
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Jiang J, Sun X, Li Y, Deng C, Duan G. Facile synthesis of Fe 3O 4@PDA core-shell microspheres functionalized with various metal ions: A systematic comparison of commonly-used metal ions for IMAC enrichment. Talanta 2017; 178:600-607. [PMID: 29136869 DOI: 10.1016/j.talanta.2017.09.071] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Revised: 09/20/2017] [Accepted: 09/26/2017] [Indexed: 01/04/2023]
Abstract
Metal ions differed greatly in affinity towards phosphopeptides, and thus it is essential to systematically compare the phosphopeptides enrichment ability of different metal ions usually used in the IMAC techniques. In this work, for the first time, eight metal ions, including Nb5+, Ti4+, Zr4+, Ga3+, Y3+, In3+, Ce4+, Fe3+, were immobilized on the polydopamine (PDA)-coated Fe3O4 (denoted as Fe3O4@PDA-Mn+), and systematically compared by the real biosamples, in addition to standard phosphopeptides. Fe3O4 microspheres were synthesized via the solvothermal reaction, followed by self-polymerization of dopamine on the surface. Then through taking advantage of the hydroxyl and amino group of PDA, the eight metal ions were easily adhered to the surface of Fe3O4@PDA. After characterization, the resultant Fe3O4@PDA-Mn+ microspheres were applied to phosphopeptides enrichment based on the binding affinity between metal ions and phosphopeptides. According to the results, different metal ions presented diverse phosphopeptides enrichment efficiency in terms of selectivity, sensitivity and the enrichment ability from real complex samples, and Fe3O4@PDA-Nb5+ and Fe3O4@PDA-Ti4+ showed obvious advantages of the phosphopeptides enrichment effect after the comparison. This systematic comparison may provide certain reference for the use and development of IMAC materials in the future.
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Affiliation(s)
- Jiebing Jiang
- Pharmaceutical Analysis Department, School of Pharmacy, Fudan University, Shanghai 201203, China
| | - Xueni Sun
- Institute of Functional Genomics, University of Regensburg, Am BioPark 9, 93053 Regensburg, Germany
| | - Yan Li
- Pharmaceutical Analysis Department, School of Pharmacy, Fudan University, Shanghai 201203, China.
| | - Chunhui Deng
- Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai 200433, China
| | - Gengli Duan
- Pharmaceutical Analysis Department, School of Pharmacy, Fudan University, Shanghai 201203, China
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Lv N, Zhang J, Li G, Wang X, Ni J. Pyrophosphate-Imprinted Magnetic Mesoporous Silica Microspheres for Recognition, Enrichment and MS Detection of Phosphopeptides. ChemistrySelect 2017. [DOI: 10.1002/slct.201700035] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Nan Lv
- State Key Laboratory of Rare Earth Resource Utilization; Changchun Institute of Applied Chemistry; Changchun 130022 P. R. China
- University of Chinese Academy of Sciences; Beijing 100049 P. R. China
| | - Jilin Zhang
- State Key Laboratory of Rare Earth Resource Utilization; Changchun Institute of Applied Chemistry; Changchun 130022 P. R. China
| | - Guangming Li
- State Key Laboratory of Rare Earth Resource Utilization; Changchun Institute of Applied Chemistry; Changchun 130022 P. R. China
- University of Chinese Academy of Sciences; Beijing 100049 P. R. China
| | - Xun Wang
- State Key Laboratory of Rare Earth Resource Utilization; Changchun Institute of Applied Chemistry; Changchun 130022 P. R. China
- University of Chinese Academy of Sciences; Beijing 100049 P. R. China
| | - Jiazuan Ni
- State Key Laboratory of Rare Earth Resource Utilization; Changchun Institute of Applied Chemistry; Changchun 130022 P. R. China
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Salimi K, Usta DD, Çelikbıçak Ö, Pınar A, Salih B, Tuncel A. Highly selective enrichment of phosphopeptides by titanium (IV) attached monodisperse-porous poly(vinylphosphonic acid- co -ethylene dimethacrylate) microspheres. J Chromatogr A 2017; 1496:9-19. [DOI: 10.1016/j.chroma.2017.03.052] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2016] [Revised: 03/17/2017] [Accepted: 03/20/2017] [Indexed: 11/15/2022]
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13
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Dai L, Jin S, Fan M, Zhou P. Preparation of quaternized cellulose/chitosan microspheres for selective enrichment of phosphopeptides. Anal Bioanal Chem 2017; 409:3309-3317. [PMID: 28258465 DOI: 10.1007/s00216-017-0273-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2016] [Revised: 02/08/2017] [Accepted: 02/21/2017] [Indexed: 01/09/2023]
Abstract
As one of the most important posttranslational modifications, protein phosphorylation plays an important role in vital movement. However, an efficiency enrichment treatment prior to MS detection is still a crucial step to protein phosphorylation analysis. In this work, a novel hybrid microsphere for efficient phosphopeptide enrichment was prepared by reverse-phase suspension polymerization of cellulose derivative and chitosan. The microspheres bore different kinds of amine groups and the main enrichment mechanism was based on anion exchange. This approach exhibited high selectivity for phosphopeptides from β-casein, α-casein, and non-fat milk. Three phosphopeptides could still be detected when the amount of β-casein was as low as 10 fmol. This study demonstrated a new attractive solid-phase support for phosphopeptide enrichment to meet the increasing need of phosphoproteomics analysis.
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Affiliation(s)
- Lili Dai
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, Hubei, 430072, China
| | - Shanxia Jin
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, Hubei, 430072, China
| | - Mengying Fan
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, Hubei, 430072, China
| | - Ping Zhou
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, Hubei, 430072, China.
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Qi X, Chen L, Zhang C, Xu X, Zhang Y, Bai Y, Liu H. NiCoMnO4: A Bifunctional Affinity Probe for His-Tagged Protein Purification and Phosphorylation Sites Recognition. ACS APPLIED MATERIALS & INTERFACES 2016; 8:18675-18683. [PMID: 27381638 DOI: 10.1021/acsami.6b04280] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
A bifunctional affinity probe NiCoMnO4 was designed and prepared with controllable morphology and size using facile methods. It was observed that the probe could be applied in His-tagged proteins purification and phosphopeptides enrichment simply through the buffer modulation. NiCoMnO4 particles showed satisfactory cycling performance for His-tagged proteins purification and broad pH-tolerance of loading buffer for phosphopeptides affinity. Therefore, a high-throughput, cost-effective, and efficient protein/peptide purification method was developed within 10 min based on the novel bifunctional affinity probe.
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Affiliation(s)
- Xiaoyue Qi
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University , Beijing 100871, China
| | - Long Chen
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University , Beijing 100871, China
| | - Chaoqun Zhang
- Beijing Nuclear Magnetic Resonance Center, College of Life Science, Peking University , Beijing 100871, China
| | - Xinyuan Xu
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University , Beijing 100871, China
| | - Yiding Zhang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University , Beijing 100871, China
| | - Yu Bai
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University , Beijing 100871, China
| | - Huwei Liu
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University , Beijing 100871, China
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15
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Li XS, Yuan BF, Feng YQ. Recent advances in phosphopeptide enrichment: Strategies and techniques. Trends Analyt Chem 2016. [DOI: 10.1016/j.trac.2015.11.001] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Preparation of core-shell structure Fe3O4@SiO2superparamagnetic microspheres immoblized with iminodiacetic acid as immobilized metal ion affinity adsorbents for His-tag protein purification. Biomed Chromatogr 2015; 30:566-73. [DOI: 10.1002/bmc.3584] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Revised: 07/26/2015] [Accepted: 08/04/2015] [Indexed: 01/23/2023]
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17
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Chen Y, Xiong Z, Peng L, Gan Y, Zhao Y, Shen J, Qian J, Zhang L, Zhang W. Facile Preparation of Core-Shell Magnetic Metal-Organic Framework Nanoparticles for the Selective Capture of Phosphopeptides. ACS APPLIED MATERIALS & INTERFACES 2015; 7:16338-16347. [PMID: 26156207 DOI: 10.1021/acsami.5b03335] [Citation(s) in RCA: 137] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
In regard to the phosphoproteome, highly specific and efficient capture of heteroideous kinds of phosphopeptides from intricate biological sample attaches great significance to comprehensive and in-depth phosphorylated proteomics research. However, until now, it has been a challenge. In this study, a new-fashioned porous immobilized metal ion affinity chromatography (IMAC) material was designed and fabricated to promote the selectivity and detection limit for phosphopeptides by covering a metal-organic frameworks (MOFs) shell onto Fe3O4 nanoparticles, taking advantage of layer-by-layer method (the synthesized nanoparticle denoted as Fe3O4@MIL-100 (Fe)). The thick layer renders the nanoparticles with perfect hydrophilic character, super large surface area, large immobilization of the Fe(3+) ions and the special porous structure. Specifically, the as-synthesized MOF-decorated magnetic nanoparticles own an ultra large surface area which is up to 168.66 m(2) g(-1) as well as two appropriate pore sizes of 1.93 and 3.91 nm with a narrow grain-size distribution and rapid separation under the magnetic circumstance. The unique features vested the synthesized nanoparticles an excellent ability for phosphopeptides enrichment with high selectivity for β-casein (molar ratio of β-casein/BSA, 1:500), large enrichment capacity (60 mg g(-1)), low detection limit (0.5 fmol), excellent phosphopeptides recovery (above 84.47%), fine size-exclusion of high molecular weight proteins, good reusability, and desirable batch-to-batch repeatability. Furthermore, encouraged by the experimental results, we successfully performed the as-prepared porous IMAC nanoparticle in the specific capture of phosphopeptides from the human serum (both the healthy and unhealthy) and nonfat milk, which proves itself to be a good candidate for the enrichment and detection of the low-abundant phosphopeptides from complicated biological samples.
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Affiliation(s)
- Yajing Chen
- Shanghai Key Laboratory of Functional Materials Chemistry, Department of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Zhichao Xiong
- Shanghai Key Laboratory of Functional Materials Chemistry, Department of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Li Peng
- Shanghai Key Laboratory of Functional Materials Chemistry, Department of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Yangyang Gan
- Shanghai Key Laboratory of Functional Materials Chemistry, Department of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Yiman Zhao
- Shanghai Key Laboratory of Functional Materials Chemistry, Department of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Jie Shen
- Shanghai Key Laboratory of Functional Materials Chemistry, Department of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Junhong Qian
- Shanghai Key Laboratory of Functional Materials Chemistry, Department of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Lingyi Zhang
- Shanghai Key Laboratory of Functional Materials Chemistry, Department of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Weibing Zhang
- Shanghai Key Laboratory of Functional Materials Chemistry, Department of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai 200237, China
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Wang ZG, Lv N, Bi WZ, Zhang JL, Ni JZ. Development of the affinity materials for phosphorylated proteins/peptides enrichment in phosphoproteomics analysis. ACS APPLIED MATERIALS & INTERFACES 2015; 7:8377-92. [PMID: 25845677 DOI: 10.1021/acsami.5b01254] [Citation(s) in RCA: 97] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Reversible protein phosphorylation is a key event in numerous biological processes. Mass spectrometry (MS) is the most powerful analysis tool in modern phosphoproteomics. However, the direct MS analysis of phosphorylated proteins/peptides is still a big challenge because of the low abundance and insufficient ionization of phosphorylated proteins/peptides as well as the suppression effects of nontargets. Enrichment of phosphorylated proteins/peptides by affinity materials from complex biosamples is the most widely used strategy to enhance the MS detection. The demand of efficiently enriching phosphorylated proteins/peptides has spawned diverse affinity materials based on different enrichment principles (e.g., electronic attraction, chelating). In this review, we summarize the recent development of various affinity materials for phosphorylated proteins/peptides enrichment. We will highlight the design and fabrication of these affinity materials, discuss the enrichment mechanisms involved in different affinity materials, and suggest the future challenges and research directions in this field.
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Affiliation(s)
- Zhi-Gang Wang
- †State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, P. R. China
- ‡University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Nan Lv
- †State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, P. R. China
- ‡University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Wen-Zhi Bi
- †State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, P. R. China
- ‡University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Ji-Lin Zhang
- †State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, P. R. China
| | - Jia-Zuan Ni
- †State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, P. R. China
- §College of Life Science, Shenzhen University, Shenzhen 518060, P. R. China
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Xiong Z, Chen Y, Zhang L, Ren J, Zhang Q, Ye M, Zhang W, Zou H. Facile synthesis of guanidyl-functionalized magnetic polymer microspheres for tunable and specific capture of global phosphopeptides or only multiphosphopeptides. ACS APPLIED MATERIALS & INTERFACES 2014; 6:22743-22750. [PMID: 25466400 DOI: 10.1021/am506882b] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The highly selective and efficient capture of heterogeneous types of phosphopeptides is critical for comprehensive and in-depth phosphoproteome analysis, but it still remains a challenge since the lack of affinity material with large binding capacity and controllable specificity. Here, a new affinity material was prepared to improve the enrichment capacity and endue the tunable specificity by introducing guanidyl onto poly(glycidyl methacrylate) (PGMA) modified Fe3O4 microsphere (denoted as Fe3O4@PGMA-Guanidyl). The thick polymer shell endows the composite microsphere with large amount of guanidyl and is beneficial to enhancing the affinity interaction between phosphopeptides and the material. Interestingly, the Fe3O4@PGMA-Guanidyl possesses tunable enriching ability for global phosphopeptides or only multiphosphopeptides through simple regulation of buffer composition. The composite has large enrichment capacity (200 mg g(-1)), extremely high detection sensitivity (0.5 fmol), high enrichment recovery (91.30%), great specificity, and rapid magnetic separation. Moreover, the result of the application to capture of phosphopeptides from tryptic digest of nonfat milk has demonstrated the great potential of Fe3O4@PGMA-Guanidyl in detection and identification of low-abundance phosphopeptides of interest in biological sample.
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Affiliation(s)
- Zhichao Xiong
- Shanghai Key Laboratory of Functional Materials Chemistry, Department of Chemistry and Molecular Engineering, East China University of Science and Technology , Shanghai 200237, China
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Magnetic separation techniques in sample preparation for biological analysis: A review. J Pharm Biomed Anal 2014; 101:84-101. [DOI: 10.1016/j.jpba.2014.04.017] [Citation(s) in RCA: 187] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2014] [Revised: 04/10/2014] [Accepted: 04/14/2014] [Indexed: 11/16/2022]
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Li G, Liu M, Zhang Z, Geng C, Wu Z, Zhao X. Extraction of methylmercury and ethylmercury from aqueous solution using surface sulfhydryl-functionalized magnetic mesoporous silica nanoparticles. J Colloid Interface Sci 2014; 424:124-31. [DOI: 10.1016/j.jcis.2014.03.026] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2013] [Revised: 03/06/2014] [Accepted: 03/10/2014] [Indexed: 10/25/2022]
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