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Wang K, Yu A, Gao Y, Chen M, Yuan H, Zhang S, Ouyang G. A nitrogen-doped graphene tube composite based on immobilized metal affinity chromatography for the capture of phosphopeptides. Talanta 2023; 261:124617. [PMID: 37187026 DOI: 10.1016/j.talanta.2023.124617] [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: 03/28/2023] [Revised: 04/24/2023] [Accepted: 04/28/2023] [Indexed: 05/17/2023]
Abstract
A novel immobilized metal affinity chromatography (IMAC) functional composite, mNi@N-GrT@PDA@Ti4+, was fabricated based on ultrathin magnetic nitrogen-doped graphene tube (mNi@N-GrT) after chelated Ti4+ with polydopamine, following as a magnetic solid-phase extraction sorbent for rapidly selective enrichment and mass spectrometry identification of phosphorylated peptides. After optimized, the composite exhibited high specificity in the enrichment of phosphopeptides from the digest mixture of β-casein and bovine serum albumin (BSA). The robust method presented the low detection limits (1 fmol, 200 μL) and excellent selectivity (1:100) in the molar ration mixture of β-casein and BSA digests. Furthermore, the selective enrichment of phosphopeptides in the complex bio-samples, was successfully carried out. The results showed that 28 phosphopeptides were finally detected in mouse brain, and 2087 phosphorylated peptides were identified in the HeLa cells extracts with specific selectivity of 95.6%. The enrichment performance of mNi@N-GrT@PDA@Ti4+ was satisfactory, suggesting that the functional composite provided a potential application in the enrichment of trace phosphorylated peptides from the complex biological matrix.
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Affiliation(s)
- Kexuan Wang
- College of Chemistry, Key Laboratory of Molecular Sensing and Harmful Substances Detection Technology, Zhengzhou University, Kexue Avenue 100, Zhengzhou, Henan, 450001, PR China
| | - Ajuan Yu
- College of Chemistry, Key Laboratory of Molecular Sensing and Harmful Substances Detection Technology, Zhengzhou University, Kexue Avenue 100, Zhengzhou, Henan, 450001, PR China.
| | - Yu Gao
- High & New Technology Research Center of Henan Academy of Sciences, Zhengzhou, Henan Province, 450002, PR China
| | - Miao Chen
- College of Chemistry, Key Laboratory of Molecular Sensing and Harmful Substances Detection Technology, Zhengzhou University, Kexue Avenue 100, Zhengzhou, Henan, 450001, PR China
| | - Hang Yuan
- Center of Advanced Analysis and Gene Sequencing, Key Laboratory of Molecular Sensing and Harmful Substances Detection Technology, Zhengzhou University, Kexue Avenue 100, Zhengzhou, Henan, 450001, PR China
| | - Shusheng Zhang
- Center of Advanced Analysis and Gene Sequencing, Key Laboratory of Molecular Sensing and Harmful Substances Detection Technology, Zhengzhou University, Kexue Avenue 100, Zhengzhou, Henan, 450001, PR China.
| | - Gangfeng Ouyang
- Center of Advanced Analysis and Gene Sequencing, Key Laboratory of Molecular Sensing and Harmful Substances Detection Technology, Zhengzhou University, Kexue Avenue 100, Zhengzhou, Henan, 450001, PR China
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He Y, Zhang S, Zhong C, Yang Y, Li G, Ji Y, Lin Z. Facile synthesis of Ti 4+-immobilized magnetic covalent organic frameworks for enhanced phosphopeptide enrichment. Talanta 2021; 235:122789. [PMID: 34517647 DOI: 10.1016/j.talanta.2021.122789] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 07/31/2021] [Accepted: 08/04/2021] [Indexed: 10/20/2022]
Abstract
In this work, core-shell structured Ti4+-immobilized magnetic covalent organic frameworks (denoted as Fe3O4@TAPTDHTA-Ti4+ composites) were prepared for enhanced phosphopeptide enrichment by one-pot synthesis of COFs shell with inherent bifunctional groups on Fe3O4 NPs and further Ti4+ immobilization. The widely distributed bifunctional groups could provide abundant chelating sites for Ti4+ immobilizing. Combining with the high specific surface area and mesoporous structure, the Fe3O4@TAPTDHTA-Ti4+ composites exhibited excellent enrichment efficiency for phosphopeptides, such as low detection limit (0.05 fmol μL-1), high selectivity (1:5000 of molar ratio of β-casein/bovine serum albumin (BSA) tryptic digests), high adsorption capacity (62.9 μg mg-1) and strong size-exclusive effect (1:250:250 of molar ratio of β-casein tryptic digest/β-casein/BSA). In addition, this method was general for immobilizing other metal ions (Zr4+ and Fe3+). Notably, the Fe3O4@TAPTDHTA-Fe3+ composites exhibited controllable affinity towards mono-phosphopeptides and multi-phosphopeptides. Furthermore, the Fe3O4@TAPTDHTA-Ti4+ composites were successfully applied to selectively capture phosphopeptides from complex biological samples including the tryptic digest of nonfat milk, human serum and human saliva. More significantly, 3333 phosphopeptides derived from 1409 phosphoproteins with 3492 phosphorylation sites were clearly identified from the tryptic digest of HeLa cell lysate. In addition to providing a potential excellent enrichment probe for comprehensive phosphoproteomic analysis, this study also offers a new perspective for the functionalization of COFs.
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Affiliation(s)
- Yanting He
- Ministry of Education Key Laboratory of Analytical Science for Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, College of Chemistry, Fuzhou University, Fuzhou, Fujian, 350108, China
| | - Shasha Zhang
- Ministry of Education Key Laboratory of Analytical Science for Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, College of Chemistry, Fuzhou University, Fuzhou, Fujian, 350108, China
| | - Chao Zhong
- Ministry of Education Key Laboratory of Analytical Science for Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, College of Chemistry, Fuzhou University, Fuzhou, Fujian, 350108, China
| | - Yixin Yang
- Ministry of Education Key Laboratory of Analytical Science for Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, College of Chemistry, Fuzhou University, Fuzhou, Fujian, 350108, China
| | - Guorong Li
- Ministry of Education Key Laboratory of Analytical Science for Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, College of Chemistry, Fuzhou University, Fuzhou, Fujian, 350108, China
| | - Yin Ji
- Ministry of Education Key Laboratory of Analytical Science for Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, College of Chemistry, Fuzhou University, Fuzhou, Fujian, 350108, China
| | - Zian Lin
- Ministry of Education Key Laboratory of Analytical Science for Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, College of Chemistry, Fuzhou University, Fuzhou, Fujian, 350108, China.
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Yang F, Wang C. Profiling of post-translational modifications by chemical and computational proteomics. Chem Commun (Camb) 2020; 56:13506-13519. [PMID: 33084662 DOI: 10.1039/d0cc05447j] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Post-translational modifications (PTMs) diversify the molecular structures of proteins and play essential roles in regulating their functions. Abnormal PTM status has been linked to a variety of developmental disorders and human diseases, highlighting the importance of studying PTMs in understanding physiological processes and discovering novel nodes and links with therapeutic intervention potential. Classical biochemical methods are suitable for studying PTMs on individual proteins; however, global profiling of PTMs in proteomes remains a challenging task. In this feature article, we start with a brief review of the traditional affinity-based strategies and shift the emphasis to summarizing recent progress in the development and application of chemical and computational proteomic strategies to delineate the global landscapes of functional PTMs. Finally, we discuss current challenges in PTM detection and provide future perspectives on how the field can be further advanced.
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Affiliation(s)
- Fan Yang
- Synthetic and Functional Biomolecules Center, 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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Metal–organic framework-based affinity materials in proteomics. Anal Bioanal Chem 2019; 411:1745-1759. [DOI: 10.1007/s00216-019-01610-x] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Revised: 12/31/2018] [Accepted: 01/14/2019] [Indexed: 01/17/2023]
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Jiang J, Sun X, She X, Li J, Li Y, Deng C, Duan G. Magnetic microspheres modified with Ti(IV) and Nb(V) for enrichment of phosphopeptides. Mikrochim Acta 2018; 185:309. [PMID: 29802452 DOI: 10.1007/s00604-018-2837-z] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 05/06/2018] [Indexed: 01/04/2023]
Abstract
Magnetic microspheres (Fe3O4) were coated with polydopamine (PDA) and loaded with the metal ions Ti(IV) and Nb(V) to give a material of type Fe3O4@PDA-Ti/Nb. It is shown to be useful for affinity chromatography and for enrichment of phosphopeptides from both standard protein solutions and real samples. For comparison, such microspheres loaded with single metal ions only (Fe3O4@PDA-Ti and Fe3O4@PDA-Nb) and their physical mixtures were also investigated under identical conditions. The binary metal ion-loaded magnetic microspheres display better enrichment efficiency than the single metal ion-loaded microspheres and their physical mixture. Both multiphosphopeptides and monophosphopeptides can be extracted. The Fe3O4@PDA-Ti/Nb microspheres exhibit ultra-high sensitivity (the lowest detection amount being 2 fmol) and selectivity at a low mass ratio such as in case of β-casein/BSA (1:1000). Graphical abstract Magnetic microspheres (Fe3O4) were coated with polydopamine (PDA) and loaded with the metal ions Ti(IV) and Nb(V) to give a material of type Fe3O4@PDA-Ti/Nb. Results showed its great potential as an affinity probe in phosphoproteome research due to rapid magnetic separation of phosphopeptides, ultrahigh sensitivity and selectivity, and remarkable reusability.
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Affiliation(s)
- Jiebing Jiang
- Fudan University Affiliated Pudong Medical Center & 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
| | - Xiaojian She
- Fudan University Affiliated Pudong Medical Center & Pharmaceutical Analysis Department, School of Pharmacy, Fudan University, Shanghai, 201203, China
| | - Jiajia Li
- Fudan University Affiliated Pudong Medical Center & Pharmaceutical Analysis Department, School of Pharmacy, Fudan University, Shanghai, 201203, China
| | - Yan Li
- Fudan University Affiliated Pudong Medical Center & 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
- Fudan University Affiliated Pudong Medical Center & Pharmaceutical Analysis Department, School of Pharmacy, Fudan University, Shanghai, 201203, China
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Hayashi Y, Ohara K, Taki R, Saeki T, Yamaguchi K. Combined analysis of 1,3-benzodioxoles by crystalline sponge X-ray crystallography and laser desorption ionization mass spectrometry. Analyst 2018; 143:1475-1481. [DOI: 10.1039/c7an01906h] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The combination of X-ray analysis and laser desorption ionization by using crystalline sponge will be a promising method to determine guest structures.
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Affiliation(s)
- Yukako Hayashi
- Faculty of Pharmaceutical Sciences at Kagawa Campus
- Tokushima Bunri University
- Sanuki
- Japan
| | - Kazuaki Ohara
- Faculty of Pharmaceutical Sciences at Kagawa Campus
- Tokushima Bunri University
- Sanuki
- Japan
| | - Rika Taki
- Faculty of Pharmaceutical Sciences at Kagawa Campus
- Tokushima Bunri University
- Sanuki
- Japan
| | - Tomomi Saeki
- Faculty of Pharmaceutical Sciences at Kagawa Campus
- Tokushima Bunri University
- Sanuki
- Japan
| | - Kentaro Yamaguchi
- Faculty of Pharmaceutical Sciences at Kagawa Campus
- Tokushima Bunri University
- Sanuki
- Japan
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Huang W, Zhang Y, Li D. Adsorptive removal of phosphate from water using mesoporous materials: A review. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2017; 193:470-482. [PMID: 28249762 DOI: 10.1016/j.jenvman.2017.02.030] [Citation(s) in RCA: 115] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Revised: 02/08/2017] [Accepted: 02/12/2017] [Indexed: 05/20/2023]
Abstract
Mesoporous materials have significant potential for use as adsorbents for removal of phosphate from water. The chemical and structural properties of materials greatly affect their capacity and rate in the phosphate adsorption process. This paper reviews recent activities in the development of mesoporous materials as phosphate adsorbents. In particular, it mainly focuses on the synthesis, properties and phosphate removal efficiency of various materials with mesoporosity, including metal-coordinated amino-functionalized silicas, ammonium-functionalized silicas, metal-doped mesoporous silicas, metal oxides, metal sulfate and carbon.
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Affiliation(s)
- Weiya Huang
- School of Metallurgy and Chemical Engineering, Jiangxi University of Science and Technology, Ganzhou, 341000, China; Department of Materials Science and Engineering, Taizhou University, Linhai, 317000, China
| | - Yuanming Zhang
- Department of Chemistry, Jinan University, Guangzhou, 510632, China.
| | - Dan Li
- School of Engineering and Information Technology, Murdoch University, Murdoch, Western Australia, 6150, Australia.
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Li D, Yin D, Chen Y, Liu Z. Coupling of metal-organic frameworks-containing monolithic capillary-based selective enrichment with matrix-assisted laser desorption ionization-time-of-flight mass spectrometry for efficient analysis of protein phosphorylation. J Chromatogr A 2017; 1498:56-63. [DOI: 10.1016/j.chroma.2016.10.054] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Revised: 09/29/2016] [Accepted: 10/24/2016] [Indexed: 12/19/2022]
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9
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Li D, Bie Z. Metal–organic framework incorporated monolithic capillary for selective enrichment of phosphopeptides. RSC Adv 2017. [DOI: 10.1039/c7ra00263g] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Protein phosphorylation is a major post-translational modification, which plays a central role in the cellular signaling of numerous biological processes.
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Affiliation(s)
- Daojin Li
- College of Chemistry and Chemical Engineering
- Henan Key Laboratory of Fuction-Oriented Porous Materials
- Luoyang Normal University
- Luoyang 471022
- P. R. China
| | - Zijun Bie
- Department of Chemistry
- Bengbu Medical College
- China
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10
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Hayama T, Kiyokawa E, Yoshida H, Imakyure O, Yamaguchi M, Nohta H. Fluorous-assisted metal chelate affinity extraction technique for analysis of protein kinase activity. Talanta 2016; 156-157:1-5. [DOI: 10.1016/j.talanta.2016.04.058] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Revised: 04/25/2016] [Accepted: 04/26/2016] [Indexed: 02/07/2023]
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11
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Nawaz MI, Hasan N, Wu HF. CoFe2 O4 -ZnO nanoparticles for rapid microwave-assisted tryptic digestion of phosphoprotein and phosphopeptide analysis by matrix-assisted laser desorption/ionization mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2016; 30:1443-1453. [PMID: 27321831 DOI: 10.1002/rcm.7559] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/25/2015] [Revised: 03/08/2016] [Accepted: 03/10/2016] [Indexed: 06/06/2023]
Abstract
RATIONALE Phosphorylation is a post-translational modification of proteins that plays very important role in a large number of biological processes. However, despite recent advancements in phosphoproteome research, large-scale detection and characterization of phosphopeptides by mass spectrometry (MS) is still a challenging task due to the low abundance of phosphopeptides and sub-stoichiometric nature of phosphorylation sites. On-particle microwave-assisted trypsin digestion of phosphoproteins and enrichment of phosphopeptides is an effective method for identification/characterization of phosphopeptides. Magnetic nanoparticles typically can absorb microwave radiation and generate heat in order to resolve complex phosphproteins and to enhance the digestion rate and capture the phosphopeptides on their modified surfaces. METHODS In this study, we used a cheap and efficient method for rapid microwave-assisted tryptic digestion of phosphoproteins and simultaneous enrichment of phosphopeptides using CoFe2 O4 -ZnO magnetic nanoparticles. Using this technique, the digestion time of phosphoproteins can be reduced and the phosphopeptides can be quickly analyzed by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOFMS). For the first time, we have applied CoFe2 O4 -ZnO magnetic nanoparticles for enrichment of phosphopeptides from standard phosphoproteins (β-casein and ovalbumin), complex samples (human serum and egg white) and a protein mixture of β-casein and BSA (1:100). RESULTS Our results demonstrate that the capture efficiency of CoFe2 O4 -ZnO nanoparticles for β-casein and ovalbumin in MALDI-TOFMS is very high (detection limits 0.2 fmol and 20 fmol, respectively). The CoFe2 O4 -ZnO nanoparticles have high affinity for phosphopeptide enrichment for β-casein in complex mixtures with BSA at 1:10 and 1:100 molar ratios in the microwave within 30 s. CONCLUSIONS Compared with other reported magnetic nanoparticles, the CoFe2 O4 -ZnO nanoparticles are easy to prepare and handle, and can save time in the phosphopeptide enrichment procedure, making these nanoparticle a good choice for highly sensitive phosphopeptide enrichment. Copyright © 2016 John Wiley & Sons, Ltd.
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Affiliation(s)
- Mohd Imtiaz Nawaz
- Department of Chemistry and Center for Nanoscience and Nanotechnology, National Sun Yat-Sen University, Kaohsiung, 70 Lien-Hai Road, Kaohsiung, 80424, Taiwan
| | - Nazim Hasan
- Department of Chemistry and Center for Nanoscience and Nanotechnology, National Sun Yat-Sen University, Kaohsiung, 70 Lien-Hai Road, Kaohsiung, 80424, Taiwan
- Department of Chemistry, Faculty of Medicine, Jazan University, Jazan, 82621, KSA
| | - Hui-Fen Wu
- Department of Chemistry and Center for Nanoscience and Nanotechnology, National Sun Yat-Sen University, Kaohsiung, 70 Lien-Hai Road, Kaohsiung, 80424, Taiwan
- School of Pharmacy, College of Pharmacy, Kaohsiung Medical University, Kaohsiung, 807, Taiwan
- Doctoral Degree Program in Marine Biotechnology, National Sun Yat - Sen University and Academia Sinica, Kaohsiung, 80424, Taiwan
- Institute of Medical Science and Technology, National Sun Yat-Sen University, Kaohsiung, 80424, Taiwan
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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: 131] [Impact Index Per Article: 14.6] [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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Long XY, Song Q, Lian HZ. Development of magnetic LuPO4 microspheres for highly selective enrichment and identification of phosphopeptides for MALDI-TOF MS analysis. J Mater Chem B 2015; 3:9330-9339. [DOI: 10.1039/c5tb01378j] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Lichee-like core–shell structured magnetic lutetium phosphate (Fe3O4@LuPO4) affinity microspheres were synthesized, characterized and successfully applied to enrich phosphopeptides.
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Affiliation(s)
- Xing-yu Long
- State Key Laboratory of Analytical Chemistry for Life Science
- Collaborative Innovation Center of Chemistry for Life Sciences
- School of Chemistry & Chemical Engineering and Center of Materials Analysis
- Nanjing University
- Nanjing 210093
| | - Qun Song
- State Key Laboratory of Analytical Chemistry for Life Science
- Collaborative Innovation Center of Chemistry for Life Sciences
- School of Chemistry & Chemical Engineering and Center of Materials Analysis
- Nanjing University
- Nanjing 210093
| | - Hong-zhen Lian
- State Key Laboratory of Analytical Chemistry for Life Science
- Collaborative Innovation Center of Chemistry for Life Sciences
- School of Chemistry & Chemical Engineering and Center of Materials Analysis
- Nanjing University
- Nanjing 210093
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14
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Huang X, Wang J, Liu C, Guo T, Wang S. A novel rGR–TiO2–ZrO2 composite nanosheet for capturing phosphopeptides from biosamples. J Mater Chem B 2015; 3:2505-2515. [DOI: 10.1039/c4tb01899k] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A novel rGR–TiO2–ZrO2 composite nanosheet was synthesized and applied to selectively capture phosphopeptides from complex biosamples.
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Affiliation(s)
- Xuan Huang
- Key Laboratory of Food Nutrition and Safety
- Ministry of Education
- Tianjin Key Laboratory of Food Nutrition and Safety
- Tianjin University of Science and Technology
- Tianjin 300457
| | - Junping Wang
- Key Laboratory of Food Nutrition and Safety
- Ministry of Education
- Tianjin Key Laboratory of Food Nutrition and Safety
- Tianjin University of Science and Technology
- Tianjin 300457
| | - Cuicui Liu
- Key Laboratory of Food Nutrition and Safety
- Ministry of Education
- Tianjin Key Laboratory of Food Nutrition and Safety
- Tianjin University of Science and Technology
- Tianjin 300457
| | - Ting Guo
- Key Laboratory of Food Nutrition and Safety
- Ministry of Education
- Tianjin Key Laboratory of Food Nutrition and Safety
- Tianjin University of Science and Technology
- Tianjin 300457
| | - Shuo Wang
- Key Laboratory of Food Nutrition and Safety
- Ministry of Education
- Tianjin Key Laboratory of Food Nutrition and Safety
- Tianjin University of Science and Technology
- Tianjin 300457
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Ohara K, Nakai A, Yamaguchi K. Laser desorption ionization of stilbenes in crystalline sponge. EUROPEAN JOURNAL OF MASS SPECTROMETRY (CHICHESTER, ENGLAND) 2015; 21:413-421. [PMID: 26307722 DOI: 10.1255/ejms.1319] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The laser desorption (LD) ionization of three stilbenes in the nano porous metal-organic frameworks called "crystalline sponge" is demonstrated. The analyte position in the pore and the interaction between the analyte and the framework that functions as a matrix are discussed based on the results of single- crystal X-ray analysis. It is confirmed that the analyte/ligand ratio of 1:2 is sufficient for the analyte ionization. This method makes it possible to visualize hot spots on a target plate to be irradiated. That the sample requirement is dramatically reduced to the order of femtomoles is also an advantage. The relationship between laser interaction, analyte position in the pore, and analyte/ligand ratio is discussed as a new ionization field to elucidate the molecular structure of the analyte by LD ionization mass spectrometry.
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Affiliation(s)
- Kazuaki Ohara
- Faculty of Pharmaceutical Sciences at Kagawa Campus, Tokushima Bunri University, 1314-1 Shido, Sanuki, Kagawa 769-2193, Japan.
| | - Ayaka Nakai
- Faculty of Pharmaceutical Sciences at Kagawa Campus, Tokushima Bunri University, 1314-1 Shido, Sanuki, Kagawa 769-2193, Japan.
| | - Kentaro Yamaguchi
- Faculty of Pharmaceutical Sciences at Kagawa Campus, Tokushima Bunri University, 1314-1 Shido, Sanuki, Kagawa 769- 2193, Japan.
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Yang X, Hu L, Ye M, Zou H. Analysis of the human urine endogenous peptides by nanoparticle extraction and mass spectrometry identification. Anal Chim Acta 2014; 829:40-7. [DOI: 10.1016/j.aca.2014.04.040] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Revised: 04/13/2014] [Accepted: 04/21/2014] [Indexed: 02/04/2023]
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Yan Y, Zheng Z, Li Y, Deng C, Zhang X. Titanium(IV)‐Immobilized Hydrophilic Hierarchically Ordered Macro‐/Mesoporous Silica for Fast Enrichment of Phosphopeptides. Chempluschem 2014. [DOI: 10.1002/cplu.201300411] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Yinghua Yan
- Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai 200433 (P. R. China)
| | - Zhifang Zheng
- Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai 200433 (P. R. China)
| | - Yan Li
- Pharmaceutical Analysis Department, School of Pharmacy, Fudan University, Shanghai 201203 (P. R. China)
| | - Chunhui Deng
- Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai 200433 (P. R. China)
| | - Xiangmin Zhang
- Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai 200433 (P. R. China)
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18
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Gao M, Deng C, Zhang X. Magnetic nanoparticles-based digestion and enrichment methods in proteomics analysis. Expert Rev Proteomics 2014; 8:379-90. [DOI: 10.1586/epr.11.25] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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19
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Cheng G, Yu X, Zhou M, Zheng S. Preparation of magnetic graphene composites with hierarchical structure for selective capture of phosphopeptides. J Mater Chem B 2014; 2:4711-4719. [PMID: 25264490 PMCID: PMC4174403 DOI: 10.1039/c4tb00509k] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
A novel graphene composite affinity material consisting of graphene scaffold, Fe3O4 nanoparticles for actuation and fully covered porous titania nanostructures as affinity coating has been designed and constructed. The obtained magnetic graphene composites have a saturation magnetization (Ms) value of 7.3 emu g-1, a BET specific surface area of 111.8 m2 g-1 and an average pore size of 15.1 nm for the porous affinity coating. The multifunctional graphene composites can realize the selective capture and convenient magnetic separation of target phosphopeptides by taking advantage of the decorated magnetic nanoparticles, highly pure and well crystallized affinity coating, and unique porous structure. Sensitivity and selectivity of the affinity graphene composites were evaluated using digests of standard proteins and complex biosamples as well as by comparison with the widely used TiO2 affinity microspheres. The results show that the affinity graphene composites can realize selective capture and rapid separation of low-abundance phosphopeptides from complex biological samples. Thus, this work will contribute to future applications in the purification and separation of specific biomolecules, in particular, low-abundance phosphopeptide biomarkers.
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Affiliation(s)
- Gong Cheng
- Department of Bioengineering, The Pennsylvania State University, University Park, PA 16802, (USA)
| | - Xu Yu
- Department of Bioengineering, The Pennsylvania State University, University Park, PA 16802, (USA)
| | - Mingda Zhou
- Department of Bioengineering, The Pennsylvania State University, University Park, PA 16802, (USA)
| | - Siyang Zheng
- Department of Bioengineering, The Pennsylvania State University, University Park, PA 16802, (USA)
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20
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Wang ZG, Cheng G, Liu YL, Zhang JL, Sun DH, Ni JZ. Novel core-shell cerium(IV)-immobilized magnetic polymeric microspheres for selective enrichment and rapid separation of phosphopeptides. J Colloid Interface Sci 2013; 417:217-26. [PMID: 24407680 DOI: 10.1016/j.jcis.2013.11.004] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2013] [Revised: 11/05/2013] [Accepted: 11/07/2013] [Indexed: 01/31/2023]
Abstract
In this work, novel magnetic polymeric core-shell structured microspheres with immobilized Ce(IV), Fe3O4@SiO2@PVPA-Ce(IV), were designed rationally and synthesized successfully via a facile route for the first time. Magnetic Fe3O4@SiO2 microspheres were first prepared by directly coating a thin layer of silica onto Fe3O4 magnetic particles using a sol-gel method, a poly(vinylphosphonic acid) (PVPA) shell was then coated on the Fe3O4@SiO2 microspheres to form Fe3O4@SiO2@PVPA microspheres through a radical polymerization reaction, and finally Ce(IV) ions were robustly immobilized onto the Fe3O4@SiO2@PVPA microspheres through strong chelation between Ce(IV) ions and phosphate moieties in the PVPA. The applicability of the Fe3O4@SiO2@PVPA-Ce(IV) microspheres for selective enrichment and rapid separation of phosphopeptides from proteolytic digests of standard and real protein samples was investigated. The results demonstrated that the core-shell structured Fe3O4@SiO2@PVPA-Ce(IV) microspheres with abundant Ce(IV) affinity sites and excellent magnetic responsiveness can effectively purify phosphopeptides from complex biosamples for MS detection taking advantage of the rapid magnetic separation and the selective affinity between Ce(IV) ions and phosphate moieties of the phosphopeptides. Furthermore, they can be effectively recycled and show good reusability, and have better performance than commercial TiO2 beads and homemade Fe3O4@PMAA-Ce(IV) microspheres. Thus the Fe3O4@SiO2@PVPA-Ce(IV) microspheres can benefit greatly the mass spectrometric qualitative analysis of phosphopeptides in phosphoproteome research.
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Affiliation(s)
- Zhi-Gang Wang
- State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Changchun 130022, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Gong Cheng
- State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Changchun 130022, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yan-Lin Liu
- State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Changchun 130022, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ji-Lin Zhang
- State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Changchun 130022, China.
| | - De-Hui Sun
- Changchun Institute Technology, Changchun 130012, China
| | - Jia-Zuan Ni
- State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Changchun 130022, China; College of Life Science, Shenzhen University, Shenzhen 518060, China
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21
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Novel nanomaterials used for sample preparation for protein analysis. Anal Bioanal Chem 2013; 406:35-47. [DOI: 10.1007/s00216-013-7392-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2013] [Revised: 09/09/2013] [Accepted: 09/20/2013] [Indexed: 11/26/2022]
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22
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Gan J, Qian K, Wan J, Qiao L, Guo W, Yang P, Girault HH, Liu B. Amino-functionalized macroporous silica for efficient tryptic digestion in acidic solutions. Proteomics 2013; 13:3117-23. [DOI: 10.1002/pmic.201300108] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2013] [Revised: 06/23/2013] [Accepted: 08/28/2013] [Indexed: 01/04/2023]
Affiliation(s)
- Jinrui Gan
- Department of Chemistry; Institute of Biomedical Sciences and State Key Lab of Molecular Engineering of Polymers; Fudan University; Shanghai China
| | - Kun Qian
- Department of Chemistry; Institute of Biomedical Sciences and State Key Lab of Molecular Engineering of Polymers; Fudan University; Shanghai China
| | - Jingjing Wan
- Department of Chemistry; Institute of Biomedical Sciences and State Key Lab of Molecular Engineering of Polymers; Fudan University; Shanghai China
| | - Liang Qiao
- Laboratoire d'Electrochimie Physique et Analytique; Ecole Polytechnique Fédérale de Lausanne; Lausanne Switzerland
| | - Weichao Guo
- Department of Chemistry; Institute of Biomedical Sciences and State Key Lab of Molecular Engineering of Polymers; Fudan University; Shanghai China
| | - Pengyuan Yang
- Department of Chemistry; Institute of Biomedical Sciences and State Key Lab of Molecular Engineering of Polymers; Fudan University; Shanghai China
| | - Hubert H. Girault
- Laboratoire d'Electrochimie Physique et Analytique; Ecole Polytechnique Fédérale de Lausanne; Lausanne Switzerland
| | - Baohong Liu
- Department of Chemistry; Institute of Biomedical Sciences and State Key Lab of Molecular Engineering of Polymers; Fudan University; Shanghai China
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23
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Zheng L, Dong H, Hu L. Zirconium-Cation-Immobilized Core/Shell (Fe3O4@Polymer) Microspheres as an IMAC Material for the Selective Enrichment of Phosphopeptides. Ind Eng Chem Res 2013. [DOI: 10.1021/ie4003377] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Leyou Zheng
- NHU Co. Ltd. of Zhejiang, 4 Jiangbei Road,
Xinchang, Zhejiang 312500, P. R. China
| | - Huaping Dong
- College of Chemistry and Chemical Engineering, Shaoxing University, 508 Huancheng West Road, Shaoxing,
Zhejiang 312000, P. R. China
| | - Liujiang Hu
- College of Chemistry and Chemical Engineering, Shaoxing University, 508 Huancheng West Road, Shaoxing,
Zhejiang 312000, P. R. China
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24
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Yan Y, Zheng Z, Deng C, Zhang X, Yang P. Facile synthesis of Ti(4+)-immobilized Fe3O4@polydopamine core-shell microspheres for highly selective enrichment of phosphopeptides. Chem Commun (Camb) 2013; 49:5055-7. [PMID: 23625148 DOI: 10.1039/c3cc41330f] [Citation(s) in RCA: 108] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
In this work, for the first time, Ti(4+)-Fe3O4@polydopamine microspheres were designed and synthesized for efficient and selective enrichment of phosphopeptides in biological samples.
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Affiliation(s)
- Yinghua Yan
- Department of Chemistry & Institutes of Biomedical Science, Fudan University, Shanghai 200433, China
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25
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Zhang Y, Wang H, Lu H. Sequential selective enrichment of phosphopeptides and glycopeptides using amine-functionalized magnetic nanoparticles. MOLECULAR BIOSYSTEMS 2013; 9:492-500. [PMID: 23361475 DOI: 10.1039/c2mb25288k] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
As two of the most common and important post-translational modifications (PTMs) of proteins, glycosylation and phosphorylation play critical roles in biological processes. Because of the low abundance of phosphopeptides/glycopeptides, specific and sensitive strategies are especially indispensable for the identification of protein phosphorylation and glycosylation by mass spectrometry (MS). However, most of those previously reported methods only focused on enriching either phosphopeptides or glycopeptides rather than enriching both of them. In the present study, amine-functionalized magnetic nanoparticles were synthesized in a one-pot procedure and successfully used for selective enrichment of both phosphopeptides and glycopeptides. The selectivity of this method was demonstrated by analyzing the mixture of peptides/phosphopeptides/glycopeptides at molar ratio of 10:1:1; the post-enrichment recovery was 88% and 76% for phosphopeptides and glycopeptides respectively. The sensitivity was at the fmol level for both of the phosphopeptides and glycopeptides. In addition, sequence coverage was increased from 25.6% to 51.8% corresponding to a 102% increase for a model protein asialofetuin. These newly identified phosphopeptides or glycopeptides provided additional sequence information, which was beneficial to the protein identification.
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Affiliation(s)
- Ying Zhang
- Shanghai Cancer Center, Fudan University, Shanghai 200032, P. R. China
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26
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Recent advances of mesoporous materials in sample preparation. J Chromatogr A 2012; 1228:193-204. [DOI: 10.1016/j.chroma.2011.09.051] [Citation(s) in RCA: 103] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2011] [Revised: 09/14/2011] [Accepted: 09/19/2011] [Indexed: 11/19/2022]
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27
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Zhao L, Qin H, Hu Z, Zhang Y, Wu R, Zou H. A poly(ethylene glycol)-brush decorated magnetic polymer for highly specific enrichment of phosphopeptides. Chem Sci 2012. [DOI: 10.1039/c2sc20363d] [Citation(s) in RCA: 89] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
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28
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Zirconium arsenate-modified silica nanoparticles for specific capture of phosphopeptides and direct analysis by matrix-assisted laser desorption/ionization mass spectrometry. Anal Bioanal Chem 2011; 402:1041-56. [DOI: 10.1007/s00216-011-5547-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2011] [Revised: 10/14/2011] [Accepted: 10/31/2011] [Indexed: 10/15/2022]
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29
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Highly selective and sensitive enrichment of phosphopeptides via NiO nanoparticles using a microwave-assisted centrifugation on-particle ionization/enrichment approach in MALDI-MS. Anal Bioanal Chem 2011; 400:3451-62. [PMID: 21533801 DOI: 10.1007/s00216-011-5016-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2011] [Revised: 04/12/2011] [Accepted: 04/12/2011] [Indexed: 10/18/2022]
Abstract
The strategy to concentrate phosphopeptides has become a critical issue for mapping protein phosphorylation sites, which are well known as posttranslational modifications in proteomics. In this study, we propose a simple and highly sensitive method for phosphopeptide enrichment on NiO nanoparticles (NPs) from a trypsin predigested phosphoprotein complex solution in a microwave oven. Furthermore, this technique was combined with centrifugation on-particle ionization/enrichment of phosphopeptides and phosphopeptides were analyzed by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Weak magnetism of these NPs and a positive surface charge effect at low pH accomplished rapid and selective phosphopeptide enrichment within 30s. Trypsin-digested products of phosphoproteins such as α-casein and β-casein, human blood serum, nonfat milk, and egg white were also investigated to explore their phosphopeptide enrichment from complex samples by this approach. The results demonstrate that NiO NPs exhibit good affinity to trace the phosphopeptides even in the presence of 30 times higher molar concentration of complex solution of non-phosphopeptide proteolytic predigested bovine serum albumin. The detection limits of NiO NPs for α-casein and β-casein were 2.0 × 10(-9) M, with good signal-to-noise ratio in the mass spectrum. NiO NPs were found to be effective and selective for enrichment of singly and multiply phosphorylated peptides at a trace level in complex samples in a microwave oven. The cost of preparing NiO NPs is low, the NiO NPs are thermally stable, and therefore, they hold great promise for use in phosphopeptide enrichment.
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30
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Hu Y, Peng Y, Lin K, Shen H, Brousseau LC, Sakamoto J, Sun T, Ferrari M. Surface engineering on mesoporous silica chips for enriching low molecular weight phosphorylated proteins. NANOSCALE 2011; 3:421-8. [PMID: 21135976 PMCID: PMC3397147 DOI: 10.1039/c0nr00720j] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Phosphorylated peptides and proteins play an important role in normal cellular activities, e.g., gene expression, mitosis, differentiation, proliferation, and apoptosis, as well as tumor initiation, progression and metastasis. However, technical hurdles hinder the use of common fractionation methods to capture phosphopeptides from complex biological fluids such as human sera. Herein, we present the development of a dual strategy material that offers enhanced capture of low molecular weight phosphoproteins: mesoporous silica thin films with precisely engineered pore sizes that sterically select for molecular size combined with chemically selective surface modifications (i.e. Ga3+, Ti4+ and Zr4+) that target phosphoroproteins. These materials provide high reproducibility (CV=18%) and increase the stability of the captured proteins by excluding degrading enzymes, such as trypsin. The chemical and physical properties of the composite mesoporous thin films were characterized by X-ray diffraction, transmission electron microscopy, X-ray photoelectron spectroscopy, energy dispersive X-ray spectroscopy and ellipsometry. Using mass spectroscopy and biostatistics analysis, the enrichment efficiency of different metal ions immobilized on mesoporous silica chips was investigated. The novel technology reported provides a platform capable of efficiently profiling the serum proteome for biomarker discovery, forensic sampling, and routine diagnostic applications.
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Affiliation(s)
- Ye Hu
- Department of Nanomedicine and Biomedical Engineering, the University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Yang Peng
- Department of Nanomedicine and Biomedical Engineering, the University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Kevin Lin
- Department of Biomedical Engineering, the University of Texas at Austin, Austin, TX, USA
| | - Haifa Shen
- Department of Nanomedicine and Biomedical Engineering, the University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Louis C. Brousseau
- Department of Nanomedicine and Biomedical Engineering, the University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Jason Sakamoto
- Department of Nanomedicine and Biomedical Engineering, the University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Tong Sun
- Department of Nanomedicine and Biomedical Engineering, the University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Mauro Ferrari
- Department of Nanomedicine and Biomedical Engineering, the University of Texas Health Science Center at Houston, Houston, TX, USA
- Department of Biomedical Engineering, the University of Texas at Austin, Austin, TX, USA
- The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Bioengineering, Rice University, Houston, TX, USA
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31
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An optimized magnetite microparticle-based phosphopeptide enrichment strategy for identifying multiple phosphorylation sites in an immunoprecipitated protein. Anal Biochem 2011; 408:19-31. [DOI: 10.1016/j.ab.2010.08.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2010] [Revised: 06/26/2010] [Accepted: 08/02/2010] [Indexed: 11/22/2022]
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32
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Wang F, Han G, Yu Z, Jiang X, Sun S, Chen R, Ye M, Zou H. Fractionation of phosphopeptides on strong anion-exchange capillary trap column for large-scale phosphoproteome analysis of microgram samples. J Sep Sci 2010; 33:1879-87. [PMID: 20533337 DOI: 10.1002/jssc.200900718] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
It is one of the key issues to develop powerful fractionating method to increase the identification of the low-abundance phosphopeptides. In this study, a semi-online 2-D LC separation strategy based on three-step fractionation of the enriched peptides on strong anion-exchange trap column was developed. It was demonstrated that the sensitivity and phosphoproteome coverage obtained by this fractionating method with strong anion-exchange trap column is much higher than those by the conventional methods based on C18 trap column. In addition, when the same amount of sample was loaded, the number of identified phosphopeptides had increased 108%. Combination of this three-step fractionation method with RPLC-MS/MS analysis by 300 min RP-gradient separation was applied to phosphoproteome analysis of human liver proteins, and 853 unique phosphopeptides was positively identified from 500 microg tryptic digest of human liver proteins. After three cycles' consecutive analyses, 1554 unique phosphopeptides and 1566 phosphorylated sites were totally identified from 735 phosphorylated proteins at a false discovery rate of <1% in about 54 h of analysis time.
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Affiliation(s)
- Fangjun Wang
- CAS Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, P. R. China
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33
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Liu S, Chen H, Lu X, Deng C, Zhang X, Yang P. Facile Synthesis of Copper(II)Immobilized on Magnetic Mesoporous Silica Microspheres for Selective Enrichment of Peptides for Mass Spectrometry Analysis. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.201003602] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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34
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Liu S, Chen H, Lu X, Deng C, Zhang X, Yang P. Facile Synthesis of Copper(II)Immobilized on Magnetic Mesoporous Silica Microspheres for Selective Enrichment of Peptides for Mass Spectrometry Analysis. Angew Chem Int Ed Engl 2010; 49:7557-61. [PMID: 20806305 DOI: 10.1002/anie.201003602] [Citation(s) in RCA: 132] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Shasha Liu
- Department of Chemistry & Institutes of Biomedical Sciences, Fudan University, Shanghai 200433, China
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35
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Lu Z, Duan J, He L, Hu Y, Yin Y. Mesoporous TiO2 Nanocrystal Clusters for Selective Enrichment of Phosphopeptides. Anal Chem 2010; 82:7249-58. [DOI: 10.1021/ac1011206] [Citation(s) in RCA: 109] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Zhenda Lu
- Department of Chemistry, Unversity of California, Riverside, California 92521
| | - Jicheng Duan
- Department of Chemistry, Unversity of California, Riverside, California 92521
| | - Le He
- Department of Chemistry, Unversity of California, Riverside, California 92521
| | - Yongxing Hu
- Department of Chemistry, Unversity of California, Riverside, California 92521
| | - Yadong Yin
- Department of Chemistry, Unversity of California, Riverside, California 92521
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36
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Kim J, Kim BC, Lopez-Ferrer D, Petritis K, Smith RD. Nanobiocatalysis for protein digestion in proteomic analysis. Proteomics 2010; 10:687-99. [PMID: 19953546 DOI: 10.1002/pmic.200900519] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The process of protein digestion is a critical step for successful protein identification in bottom-up proteomic analyses. To substitute the present practice of in-solution protein digestion, which is long, tedious, and difficult to automate, many efforts have been dedicated for the development of a rapid, recyclable and automated digestion system. Recent advances of nanobiocatalytic approaches have improved the performance of protein digestion by using various nanomaterials such as nanoporous materials, magnetic nanoparticles, and polymer nanofibers. Especially, the unprecedented success of trypsin stabilization in the form of trypsin-coated nanofibers, showing no activity decrease under repeated uses for 1 year and retaining good resistance to proteolysis, has demonstrated its great potential to be employed in the development of automated, high-throughput, and on-line digestion systems. This review discusses recent developments of nanobiocatalytic approaches for the improved performance of protein digestion in speed, detection sensitivity, recyclability, and trypsin stability. In addition, we also introduce approaches for protein digestion under unconventional energy input for protein denaturation and the development of microfluidic enzyme reactors that can benefit from recent successes of these nanobiocatalytic approaches.
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Affiliation(s)
- Jungbae Kim
- Department of Chemical and Biological Engineering, Korea University, Anam-dong, Seongbuk-gu, Seoul, Republic of Korea.
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37
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Wu Z, Webley PA, Zhao D. Comprehensive study of pore evolution, mesostructural stability, and simultaneous surface functionalization of ordered mesoporous carbon (FDU-15) by wet oxidation as a promising adsorbent. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2010; 26:10277-10286. [PMID: 20392120 DOI: 10.1021/la100455w] [Citation(s) in RCA: 87] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Fuctionalization of porous carbon materials through chemical methods orientates the development of new hybrid materials with specific functions. In this paper, a comprehensive study of pore evolution, mesostructural oxidation resistance, and simultaneous surface functionalization of ordered mesoporous carbon FDU-15 under various oxidation conditions is presented for the first time. The mesostructure and pore evolution with increasing oxidative strength are retrieved from XRD, TEM, and N(2) sorption techniques. The textural properties can be conveniently manipulated by changing the oxidation parameters, including different oxidative solution, temperature, and duration. It is revealed that the mesoporous carbon FDU-15 shows excellent structural stability under severe oxidation treatments by acidic (NH(4))(2)S(2)O(8), HNO(3), and H(2)O(2) solutions, much more stable than the mesostructural analogue CMK-3 carbon prepared by the nanocasting method. The surface area and porosity deteriorate to a large extent compared to the pristine carbon, with the micropores/small mesopores as the major contribution to the deterioration. The micropore/small mesopore can be blocked by the attached surface oxides under mild oxidation, while reopened with more carbon layer dissolution under more severe conditions. Simultaneously, high densities of surface oxygen complexes, especially carboxylic groups, can be generated. The contents and properties of the surface oxygen-containing groups are extensively studied by FTIR, TG, elemental analyses, and water and ammonia adsorption techniques. Such surface-functionalized mesoporous carbons can be used as a highly efficient adsorbent for immobilization of heavy metal ions as well as functional organic and biomolecules, with high capacities and excellent binding capabilities. Thus, we believe that the functionalized mesoporous carbon materials can be utilized as a promising solid and stable support for water treatment and organic/biomolecules immobilization and may be applicable in drug delivery, separation, adsorption technology, and columns for GC and HPLC systems in the near future.
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Affiliation(s)
- Zhangxiong Wu
- Department of Chemistry, Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Fudan University, Shanghai 200433, PR China
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38
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Zhang L, Lu H, Yang P. Recent developments of nanoparticle-based enrichment methods for mass spectrometric analysis in proteomics. Sci China Chem 2010. [DOI: 10.1007/s11426-010-0112-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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39
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Tang J, Yin P, Lu X, Qi D, Mao Y, Deng C, Yang P, Zhang X. Development of mesoporous TiO2 microspheres with high specific surface area for selective enrichment of phosphopeptides by mass spectrometric analysis. J Chromatogr A 2010; 1217:2197-205. [DOI: 10.1016/j.chroma.2010.02.008] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2009] [Revised: 01/30/2010] [Accepted: 02/02/2010] [Indexed: 10/19/2022]
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40
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Wei LM, Shen Q, Lu HJ, Yang PY. Pretreatment of low-abundance peptides on detonation nanodiamond for direct analysis by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. J Chromatogr B Analyt Technol Biomed Life Sci 2009; 877:3631-7. [DOI: 10.1016/j.jchromb.2009.09.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2008] [Revised: 08/31/2009] [Accepted: 09/02/2009] [Indexed: 10/20/2022]
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41
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Kim JS, Cui E, Kim HJ. Picolinamidination of phosphopeptides for MALDI-TOF-TOF mass spectrometric sequencing with enhanced sensitivity. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2009; 20:1751-1758. [PMID: 19586781 DOI: 10.1016/j.jasms.2009.05.016] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2009] [Revised: 05/25/2009] [Accepted: 05/26/2009] [Indexed: 05/28/2023]
Abstract
Two orders of magnitude matrix-assisted laser desorption/ionization (MALDI) signal enhancement of phosphopeptides has been achieved by picolinamidination of N-terminal amine group and epsilon-amine group of lysine residues. Due to the presence of picolinamidination tag at the N-terminal amine of peptides, MS/MS spectra with a strong b-ion series was obtained, which greatly facilitated sequencing and identification of the phosphorylation site. Phosphorylation site of a phosphopeptide could be identified from MALDI TOF/TOF spectrum obtained from a tryptic or a chymotryptic phosphopeptide, which was not even detected in the positive ion mode, without signal enhancement by picolinamidination, due to the negative charge of the phosphate group in the presence of other peptides.
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Affiliation(s)
- Jong-Seo Kim
- Department of Chemistry, Seoul National University, Seoul, Korea
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42
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Xue Y, Wei J, Han H, Zhao L, Cao D, Wang J, Yang X, Zhang Y, Qian X. Application of open tubular capillary columns coated with zirconium phosphonate for enrichment of phosphopeptides. J Chromatogr B Analyt Technol Biomed Life Sci 2009; 877:757-64. [DOI: 10.1016/j.jchromb.2009.02.020] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2008] [Revised: 02/05/2009] [Accepted: 02/05/2009] [Indexed: 11/17/2022]
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43
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Dong X, Wu R, Dong J, Wu M, Zhu Y, Zou H. Recent progress of polar stationary phases in CEC and capillary liquid chromatography. Electrophoresis 2009; 30:141-54. [DOI: 10.1002/elps.200800412] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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44
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Hu L, Zhou H, Li Y, Sun S, Guo L, Ye M, Tian X, Gu J, Yang S, Zou H. Profiling of Endogenous Serum Phosphorylated Peptides by Titanium (IV) Immobilized Mesoporous Silica Particles Enrichment and MALDI-TOFMS Detection. Anal Chem 2008; 81:94-104. [DOI: 10.1021/ac801974f] [Citation(s) in RCA: 143] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Lianghai Hu
- Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China, The Second Affiliated Hospital of Dalian Medical University, Dalian 116023, China, State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Shanghai Jiao Tong University, Shanghai 200032, China, Shanghai Research Center of Biotechnology, Chinese Academy of Sciences, Shanghai
| | - Houjiang Zhou
- Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China, The Second Affiliated Hospital of Dalian Medical University, Dalian 116023, China, State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Shanghai Jiao Tong University, Shanghai 200032, China, Shanghai Research Center of Biotechnology, Chinese Academy of Sciences, Shanghai
| | - Yinghua Li
- Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China, The Second Affiliated Hospital of Dalian Medical University, Dalian 116023, China, State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Shanghai Jiao Tong University, Shanghai 200032, China, Shanghai Research Center of Biotechnology, Chinese Academy of Sciences, Shanghai
| | - Shutao Sun
- Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China, The Second Affiliated Hospital of Dalian Medical University, Dalian 116023, China, State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Shanghai Jiao Tong University, Shanghai 200032, China, Shanghai Research Center of Biotechnology, Chinese Academy of Sciences, Shanghai
| | - Lihai Guo
- Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China, The Second Affiliated Hospital of Dalian Medical University, Dalian 116023, China, State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Shanghai Jiao Tong University, Shanghai 200032, China, Shanghai Research Center of Biotechnology, Chinese Academy of Sciences, Shanghai
| | - Mingliang Ye
- Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China, The Second Affiliated Hospital of Dalian Medical University, Dalian 116023, China, State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Shanghai Jiao Tong University, Shanghai 200032, China, Shanghai Research Center of Biotechnology, Chinese Academy of Sciences, Shanghai
| | - Xiaofeng Tian
- Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China, The Second Affiliated Hospital of Dalian Medical University, Dalian 116023, China, State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Shanghai Jiao Tong University, Shanghai 200032, China, Shanghai Research Center of Biotechnology, Chinese Academy of Sciences, Shanghai
| | - Jianren Gu
- Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China, The Second Affiliated Hospital of Dalian Medical University, Dalian 116023, China, State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Shanghai Jiao Tong University, Shanghai 200032, China, Shanghai Research Center of Biotechnology, Chinese Academy of Sciences, Shanghai
| | - Shengli Yang
- Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China, The Second Affiliated Hospital of Dalian Medical University, Dalian 116023, China, State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Shanghai Jiao Tong University, Shanghai 200032, China, Shanghai Research Center of Biotechnology, Chinese Academy of Sciences, Shanghai
| | - Hanfa Zou
- Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China, The Second Affiliated Hospital of Dalian Medical University, Dalian 116023, China, State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Shanghai Jiao Tong University, Shanghai 200032, China, Shanghai Research Center of Biotechnology, Chinese Academy of Sciences, Shanghai
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45
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Dong X, Wu R, Dong J, Wu M, Zhu Y, Zou H. A mesoporous silica nanoparticles immobilized open‐tubular capillary column with a coating of cellulose tris(3,5‐dimethylphenyl‐carbamate) for enantioseparation in CEC. Electrophoresis 2008; 29:3933-40. [DOI: 10.1002/elps.200800025] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Xiaoli Dong
- National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, P. R. China
- Department of Chemistry, Xixi Campus, Zhejiang University, Hangzhou, P. R. China
| | - Ren'an Wu
- National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, P. R. China
| | - Jing Dong
- National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, P. R. China
| | - Minghuo Wu
- National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, P. R. China
| | - Yan Zhu
- Department of Chemistry, Xixi Campus, Zhejiang University, Hangzhou, P. R. China
| | - Hanfa Zou
- National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, P. R. China
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46
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Zhou H, Ye M, Dong J, Han G, Jiang X, Wu R, Zou H. Specific Phosphopeptide Enrichment with Immobilized Titanium Ion Affinity Chromatography Adsorbent for Phosphoproteome Analysis. J Proteome Res 2008; 7:3957-67. [DOI: 10.1021/pr800223m] [Citation(s) in RCA: 226] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Houjiang Zhou
- National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Mingliang Ye
- National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Jing Dong
- National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Guanghui Han
- National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Xinning Jiang
- National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Renan Wu
- National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Hanfa Zou
- National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
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47
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Chang CK, Wu CC, Wang YS, Chang HC. Selective Extraction and Enrichment of Multiphosphorylated Peptides Using Polyarginine-Coated Diamond Nanoparticles. Anal Chem 2008; 80:3791-7. [DOI: 10.1021/ac702618h] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Chia-Kai Chang
- Department of Applied Chemistry, National Chi Nan University, Puli, Nantou 545, Taiwan, Genomics Research Center, Academia Sinica, Nankang 115, Taiwan, and Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei 106, Taiwan
| | - Chih-Che Wu
- Department of Applied Chemistry, National Chi Nan University, Puli, Nantou 545, Taiwan, Genomics Research Center, Academia Sinica, Nankang 115, Taiwan, and Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei 106, Taiwan
| | - Yi-Sheng Wang
- Department of Applied Chemistry, National Chi Nan University, Puli, Nantou 545, Taiwan, Genomics Research Center, Academia Sinica, Nankang 115, Taiwan, and Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei 106, Taiwan
| | - Huan-Cheng Chang
- Department of Applied Chemistry, National Chi Nan University, Puli, Nantou 545, Taiwan, Genomics Research Center, Academia Sinica, Nankang 115, Taiwan, and Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei 106, Taiwan
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48
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Han G, Ye M, Zhou H, Jiang X, Feng S, Jiang X, Tian R, Wan D, Zou H, Gu J. Large-scale phosphoproteome analysis of human liver tissue by enrichment and fractionation of phosphopeptides with strong anion exchange chromatography. Proteomics 2008; 8:1346-61. [DOI: 10.1002/pmic.200700884] [Citation(s) in RCA: 171] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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49
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Wei J, Zhang Y, Wang J, Tan F, Liu J, Cai Y, Qian X. Highly efficient enrichment of phosphopeptides by magnetic nanoparticles coated with zirconium phosphonate for phosphoproteome analysis. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2008; 22:1069-1080. [PMID: 18327884 DOI: 10.1002/rcm.3485] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
The location of phosphorylation plays a vital role for the elucidation of biological processes. The challenge of low stoichiometry of phosphoproteins and signal suppression of phosphopeptides by nonphosphopeptides in mass spectrometry (MS) analysis makes the selective enrichment of phosphopeptides prior to MS analysis necessary. Besides the immobilized metal affinity chromatography (IMAC) method, some affinity methods based on nanoparticles displayed a higher enrichment efficiency for phosphopeptides such as Fe(3)O(4)/TiO2 and Fe(3)O(4)/ZrO(2) nanoparticles. To further improve the selectivity and compatibility of the affinity methods, a novel strategy based on magnetic nanoparticles coated with zirconium phosphonate for the enrichment of phosphopeptides has been developed in this study. Under optimized experimental conditions, 1 x 10(-9) M phosphopeptides in 50 microL tryptic digest of beta-casein could be enriched and identified successfully. Reliable results were also obtained for 1 x 10(-8) M phosphopeptides in 50 microL tryptic digest of beta-casein in the presence of nonphosphopeptides from a tryptic digest of bovine serum albumin (BSA) over 20 times in concentration. The performance of nanoparticles for use in a real sample was further demonstrated by employing the strong cation-exchange chromatography (SCX) fraction of a tryptic digest of a protein extract from Chang liver cells as a model sample. Experimental results show that the nanoparticles can be easily and effectively used for enrichment of phosphopeptides in low concentration. Most importantly, our approach is more compatible with commonly used SCX strategies than Fe(3+)-IMAC. The proposed method thus has great potential for future studies of large-scale phosphoproteomes.
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Affiliation(s)
- Junying Wei
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, No.33 Life Science Park Road, Changping District, Beijing 102206, PR China
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50
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Jiang X, Han G, Feng S, Jiang X, Ye M, Yao X, Zou H. Automatic validation of phosphopeptide identifications by the MS2/MS3 target-decoy search strategy. J Proteome Res 2008; 7:1640-9. [PMID: 18314942 DOI: 10.1021/pr700675j] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Manual checking is commonly employed to validate the phosphopeptide identifications from database searching of tandem mass spectra. It is very time-consuming and labor intensive as the number of phosphopeptide identifications increases greatly. In this study, a simple automatic validation approach was developed for phosphopeptide identification by combining consecutive stage mass spectrometry data and the target-decoy database searching strategy. Only phosphopeptides identified from both MS2 and its corresponding MS3 were accepted for further filtering, which greatly improved the reliability in phosphopeptide identification. Before database searching, the spectra were validated for charge state and neutral loss peak intensity, and then the invalid MS2/MS3 spectra were removed, which greatly reduced the database searching time. It was found that the sensitivity was significantly improved in MS2/MS3 strategy as the number of identified phosphopeptides was 2.5 times that obtained by the conventional filter-based MS2 approach. Because of the use of the target-decoy database, the false-discovery rate (FDR) of the identified phosphopeptides could be easily determined, and it was demonstrated that the determined FDR can precisely reflect the actual FDR without any manual validation stage.
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Affiliation(s)
- Xinning Jiang
- National Chromatographic R&A Center, Dalian Institute of Chemical Physics, The Chinese Academy of Sciences, Dalian 116023, China
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