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Materials, workflows and applications of IMAC for phosphoproteome profiling in the recent decade: A review. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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2
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Zhao J, Zhuang M, Liu J, Zhang M, Zeng C, Jiang B, Wu J, Song X. pHisPred: a tool for the identification of histidine phosphorylation sites by integrating amino acid patterns and properties. BMC Bioinformatics 2022; 23:399. [PMID: 36171552 PMCID: PMC9520798 DOI: 10.1186/s12859-022-04938-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 09/16/2022] [Indexed: 11/17/2022] Open
Abstract
Background Protein histidine phosphorylation (pHis) plays critical roles in prokaryotic signal transduction pathways and various eukaryotic cellular processes. It is estimated to account for 6–10% of the phosphoproteome, however only hundreds of pHis sites have been discovered to date. Due to the inherent disadvantages of experimental methods, it is an urgent task for developing efficient computational approaches to identify pHis sites. Results Here, we present a novel tool, pHisPred, for accurately identifying pHis sites from protein sequences. We manually collected the largest number of experimental validated pHis sites to build benchmark datasets. Using randomized tenfold CV, the weighted SVM-RBF model shows the best performance than other four commonly used classification models (LR, KNN, RF, and MLP). From ten thousands of features, 140 and 150 most informative features were individually selected out for eukaryotic and prokaryotic models. The average AUC and F1-score values of pHisPred were (0.81, 0.40) and (0.78, 0.46) for tenfold CV on the eukaryotic and prokaryotic training datasets, respectively. In addition, pHisPred significantly outperforms other tools on testing datasets, in particular on the eukaryotic one. Conclusion We implemented a python program of pHisPred, which is freely available for non-commercial use at https://github.com/xiaofengsong/pHisPred. Moreover, users can use it to train new models with their own data. Supplementary Information The online version contains supplementary material available at 10.1186/s12859-022-04938-x.
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Affiliation(s)
- Jian Zhao
- Department of Biomedical Engineering, Nanjing University of Aeronautics and Astronautics, Nanjing, 210016, China
| | - Minhui Zhuang
- Department of Biomedical Engineering, Nanjing University of Aeronautics and Astronautics, Nanjing, 210016, China
| | - Jingjing Liu
- Department of Biomedical Engineering, Nanjing University of Aeronautics and Astronautics, Nanjing, 210016, China
| | - Meng Zhang
- Department of Biomedical Engineering, Nanjing University of Aeronautics and Astronautics, Nanjing, 210016, China
| | - Cong Zeng
- Department of Biomedical Engineering, Nanjing University of Aeronautics and Astronautics, Nanjing, 210016, China
| | - Bin Jiang
- College of Automation Engineering, Nanjing University of Aeronautics and Astronautics, Nanjing, 211106, China
| | - Jing Wu
- School of Biomedical Engineering and Informatics, Nanjing Medical University, Nanjing, 211166, China.
| | - Xiaofeng Song
- Department of Biomedical Engineering, Nanjing University of Aeronautics and Astronautics, Nanjing, 210016, China.
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Ma ZQ, Wang YH, Peng Y, Guo X, Meng Z. A Novel Molybdenum Disulfide Nanosheet Loaded Titanium/Zirconium Bimetal Oxide Affinity Probe for Efficient Enrichment of Phosphopeptides in A549 Cells. J Chromatogr B Analyt Technol Biomed Life Sci 2022; 1199:123235. [DOI: 10.1016/j.jchromb.2022.123235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 03/17/2022] [Accepted: 03/28/2022] [Indexed: 10/18/2022]
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Zn(II)-DPA functionalized graphene oxide two-dimensional nanocomposites for N-phosphoproteins enrichment. Talanta 2022; 243:123384. [DOI: 10.1016/j.talanta.2022.123384] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 03/07/2022] [Accepted: 03/11/2022] [Indexed: 11/15/2022]
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5
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A novel graphene oxide/chitosan foam incorporated with metal–organic framework stationary phase for simultaneous enrichment of glycopeptide and phosphopeptide with high efficiency. Anal Bioanal Chem 2022; 414:2251-2263. [DOI: 10.1007/s00216-021-03861-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 12/07/2021] [Accepted: 12/20/2021] [Indexed: 01/07/2023]
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6
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Zhao Y, Li Z, Ma J, Jia Q. Design of a Spiropyran-Based Smart Adsorbent with Dual Response: Focusing on Highly Efficient Enrichment of Phosphopeptides. ACS APPLIED MATERIALS & INTERFACES 2021; 13:55806-55814. [PMID: 34786943 DOI: 10.1021/acsami.1c14739] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Smart responsive materials have attractive application prospects due to their tunable behaviors. In this work, we design novel spiropyran (SP)-based magnetic nanoparticles (MNP-SP) with dual response to ultraviolet light and pH and apply them to the enrichment of phosphopeptides. SP is modified on the surface of magnetic nanoparticles through a simple esterification reaction, based on which an MNP-SP-MS phosphopeptide identification platform is established. The capture and release of phosphopeptides are facilely adjusted by changing external light and the pH of the solution. The smart responsive MNP-SP has fast magnetic response performance, high sensitivity (detection limit of 0.4 fmol), and good reusability (6 cycles). In addition, MNP-SP is used for the enrichment of phosphopeptides in skimmed milk, human saliva, and human serum samples, indicating that it is an ideal adsorbent for enriching low-abundance phosphopeptides in complex biological environments.
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Affiliation(s)
- Yanqing Zhao
- College of Chemistry, Jilin University, Changchun 130012, China
| | - Zheng Li
- College of Chemistry, Jilin University, Changchun 130012, China
| | - Jiutong Ma
- College of Chemistry, Jilin University, Changchun 130012, China
| | - Qiong Jia
- College of Chemistry, Jilin University, Changchun 130012, China
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, College of Life Sciences, Jilin University, Changchun 130012, China
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7
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Cui F, Qian X, Ying W. Integrated Strategy for Unbiased Profiling of the Histidine Phosphoproteome. Anal Chem 2021; 93:15584-15589. [PMID: 34787389 DOI: 10.1021/acs.analchem.1c03374] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Histidine phosphorylation (pHis), which plays a key role in signal transduction in bacteria and lower eukaryotes, has been shown to be involved in tumorigenesis. Due to its chemical instability, substoichiometric properties, and lack of specific enrichment reagents, there is a lack of approaches for specific and unbiased enrichment of pHis-proteins/peptides. In this study, an integrated strategy was established and evaluated as an unbiased tool for exploring the histidine phosphoproteome. First, taking advantage of the lower charge states of pHis-peptides versus the non-modified naked peptides at weak acid solution (∼pH 2.7), strong cation exchange (SCX) chromatography was used to differentiate modified and non-modified naked peptides. Furthermore, selective enrichment of the pHis-peptide was performed by applying Cu-IDA beads enrichment. Finally, stable isotope dimethyl labeling was introduced to guarantee high-confidence assignment of pHis-peptides. Using this integrated strategy, 563 different pHis-peptides (H = 1) in 385 proteins were identified from HeLa lysates. Motif analysis revealed that pHis prefers hydrophobic amino acids and has the consensus motif-HxxK, which covered the reports from different approaches. Thus, our method may provide an unbiased and effective tool to reveal histidine phosphoproteome and to study the biological process and function of histidine phosphorylation.
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Affiliation(s)
- Fangfang Cui
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, No. 38, Life Park Road, Changping District, Beijing, 102206, China
| | - Xiaohong Qian
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, No. 38, Life Park Road, Changping District, Beijing, 102206, China
| | - Wantao Ying
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, No. 38, Life Park Road, Changping District, Beijing, 102206, China
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8
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Zhang K, Hao Y, Hu D, Deng S, Jin Y, Wang X, Liu H, Liu Y, Xie M. Development of dual-ligand titanium (IV) hydrophilic network sorbent for highly selective enrichment of phosphopeptides. J Chromatogr A 2021; 1659:462648. [PMID: 34739963 DOI: 10.1016/j.chroma.2021.462648] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 10/20/2021] [Accepted: 10/21/2021] [Indexed: 10/20/2022]
Abstract
A hydrophilic metal-organic network based on Ti4+ and dual natural ligand, tannic acid (TA) and phytic acid (PA), has been developed to enrich phosphopeptides from complex bio-samples prior to liquid chromatography-mass spectrometric analysis. Due to the strong chelation ability of TA and PA, abundant Ti4+ can be immobilized in the material, forming hydrophilic network by one-step coordination-driven self-assembly approach. The sorbent, TA-Ti-PA@Fe3O4, exhibited satisfactory selectivity for the phosphopeptides in the tryptic digest of β-casein, and can eliminate the interference components in 1000-fold excess of bovine serum albumin. The adsorption capacity of the sorbents for phosphopeptides was up to 35.2 mg g-1 and the adsorbing equilibrium can be reached in 5 min. The adsorbing mechanism has been investigated and the results indicated that the Ti4+ in forms of [Ti(f-TA)(H2O)4]2+, [Ti(f-PA)(H2O)4]2+ and Ti(f-PA)2(H2O)2 may play an important role in the adsorption process. The sorbent of the TA-Ti-PA@Fe3O4 has been applied to enrichment of the phosphopeptides in tryptic digest of rat liver lysate, and 3408 phosphopeptides have been identified, while the numbers of the identified phosphopeptides were 2730 and 1217 when the sample was enriched by the commercial TiO2 and Fe3+-IMAC kit, respectively. This work provides a strategy to enrich phosphopeptides from complex samples and shows great potential application in phosphoproteome research.
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Affiliation(s)
- Kaina Zhang
- Analytical and Testing Center of Beijing Normal University, Beijing 100875, China
| | - Yun Hao
- Analytical and Testing Center of Beijing Normal University, Beijing 100875, China
| | - Dehua Hu
- Analytical and Testing Center of Beijing Normal University, Beijing 100875, China
| | - Suimin Deng
- Analytical and Testing Center of Beijing Normal University, Beijing 100875, China
| | - Yuhao Jin
- Analytical and Testing Center of Beijing Normal University, Beijing 100875, China
| | - Xiangfeng Wang
- Analytical and Testing Center of Beijing Normal University, Beijing 100875, China
| | - Hailing Liu
- Analytical and Testing Center of Beijing Normal University, Beijing 100875, China
| | - Yuan Liu
- Analytical and Testing Center of Beijing Normal University, Beijing 100875, China
| | - Mengxia Xie
- Analytical and Testing Center of Beijing Normal University, Beijing 100875, China.
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He Y, Hao Y, Shen J, Wang C, Wei Y. Removal of adsorption sites on the external surface of mesoporous adsorbent for eliminating the interference of proteins in enrichment of phosphopeptides/nucleotides. Anal Chim Acta 2021; 1178:338849. [PMID: 34482875 DOI: 10.1016/j.aca.2021.338849] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 07/07/2021] [Accepted: 07/09/2021] [Indexed: 01/19/2023]
Abstract
Various mesoporous adsorbents are of great promise for enriching small molecules from biological samples based on the size-exclusion effect. At present, the mesoporous adsorbents have adsorption sites distributed uniformly on the internal and external surfaces of mesopores. However, the adsorption sites on the external surface can adsorb proteins, interfering with the enrichment of small molecules. Herein, a novel immobilized-Ti4+ magnetic mesoporous adsorbent removing the adsorption sites on the external surface was facile prepared via the coupling chemistry of isocyanate with amine and consequent hydrolysis of urea linkage by urease. The adsorbent enables fast and selective enrichment of phosphopeptides and nucleotides from biological samples. In addition, sensitive detection methods for phosphopeptides and nucleotides in human serum are developed by coupling the magnetic solid-phase extraction with matrix-assisted laser desorption/ionization time of flight mass spectrometry and liquid chromatography-mass spectrometer, respectively. Under optimal conditions, response is linear (R2 ≥ 0.9923), limits of detection are low (0.41-9.48 ng mL-1), and reproducibility is acceptable (inter- and intra-day assay RSDs of≤15.0%) for six nucleotides. The developed strategy offers an effective method to eliminate the interference of proteins in the enrichment of small molecules from real biological samples.
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Affiliation(s)
- Yijia He
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, College of Chemistry & Materials Science, Northwest University, Xi'an, 710127, China
| | - Yirui Hao
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, College of Chemistry & Materials Science, Northwest University, Xi'an, 710127, China
| | - Jiwei Shen
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, College of Chemistry & Materials Science, Northwest University, Xi'an, 710127, China
| | - Chaozhan Wang
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, College of Chemistry & Materials Science, Northwest University, Xi'an, 710127, China
| | - Yinmao Wei
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, College of Chemistry & Materials Science, Northwest University, Xi'an, 710127, China.
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10
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Wang L, Li B, You Z, Wang A, Chen X, Song G, Yang L, Chen D, Yu X, Liu J, Chen C. Heterojunction of Vertically Arrayed MoS 2 Nanosheet/N-Doped Reduced Graphene Oxide Enabling a Nanozyme for Sensitive Biomolecule Monitoring. Anal Chem 2021; 93:11123-11132. [PMID: 34342969 DOI: 10.1021/acs.analchem.1c01550] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Enzymes are still indispensable for bio-assaying methods in biomolecule detection by far. The unsatisfied long-term instability, high cost, and susceptibility to the physical environment of natural enzymes are obvious weak points. Here, we developed peroxidase-like heterostructured nanozyme, vertically arraying molybdenum disulfide nanosheets on a substrate layer of nitrogen-doped reduced graphene oxide (MoS2/N-rGO), with a well-pleasing stability that is characterized by the retained enzymatic activity and maintained structure after 2 years of casual storage at ambient temperatures or 80 cycles of catalytic reaction. The catalytic kinetics of the as-prepared heterostructured nanozyme was superior to some reported nanozymes and even horse radish peroxidase, which was demonstrated due to the defect-rich MoS2 with Mo and S vacancies and nitrogen-doped rGO experimentally and theoretically. The vertically heterostructured nanozyme exhibited adequate analytical performance in sensitive and quantitative detection of glucose and glutathione (GSH), with a large dynamic sensing range and extremely low limit of detection (0.02 and 0.12 μM (3σ/slope) for glucose and GSH, respectively). We hope this inspired artificial nanozyme will contribute to the future development in sensitive detection of other biomolecules in physiological conditions.
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Affiliation(s)
- Longwei Wang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, School of Medicine, Northwest University, Xi'an 710069, China.,CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety and CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China, University of Chinese Academy of Sciences, Beijing 100190, China
| | - Bo Li
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, School of Medicine, Northwest University, Xi'an 710069, China
| | - Zhen You
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, School of Medicine, Northwest University, Xi'an 710069, China
| | - Aizhu Wang
- Institute for Advanced Interdisciplinary Research, University of Jinan, Jinan 250022, China
| | - Xuanyu Chen
- Institute for Advanced Interdisciplinary Research, University of Jinan, Jinan 250022, China
| | - Gaojing Song
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, School of Medicine, Northwest University, Xi'an 710069, China
| | - Ling Yang
- Sichuan Academy of Medical Sciences, Sichuan Provincial People's Hospital, Sichuan 610072, China
| | - Dan Chen
- Sichuan Academy of Medical Sciences, Sichuan Provincial People's Hospital, Sichuan 610072, China
| | - Xin Yu
- Institute for Advanced Interdisciplinary Research, University of Jinan, Jinan 250022, China
| | - Jing Liu
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, School of Medicine, Northwest University, Xi'an 710069, China.,CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety and CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China, University of Chinese Academy of Sciences, Beijing 100190, China
| | - Chunying Chen
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety and CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China, University of Chinese Academy of Sciences, Beijing 100190, China
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Smythers AL, Hicks LM. Mapping the plant proteome: tools for surveying coordinating pathways. Emerg Top Life Sci 2021; 5:203-220. [PMID: 33620075 PMCID: PMC8166341 DOI: 10.1042/etls20200270] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 02/07/2021] [Accepted: 02/09/2021] [Indexed: 12/14/2022]
Abstract
Plants rapidly respond to environmental fluctuations through coordinated, multi-scalar regulation, enabling complex reactions despite their inherently sessile nature. In particular, protein post-translational signaling and protein-protein interactions combine to manipulate cellular responses and regulate plant homeostasis with precise temporal and spatial control. Understanding these proteomic networks are essential to addressing ongoing global crises, including those of food security, rising global temperatures, and the need for renewable materials and fuels. Technological advances in mass spectrometry-based proteomics are enabling investigations of unprecedented depth, and are increasingly being optimized for and applied to plant systems. This review highlights recent advances in plant proteomics, with an emphasis on spatially and temporally resolved analysis of post-translational modifications and protein interactions. It also details the necessity for generation of a comprehensive plant cell atlas while highlighting recent accomplishments within the field.
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Affiliation(s)
- Amanda L Smythers
- Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, U.S.A
| | - Leslie M Hicks
- Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, U.S.A
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Qi H, Li Z, Zheng H, Jia Q. Carnosine functionalized magnetic metal-organic framework nanocomposites for synergistic enrichment of phosphopeptides. Anal Chim Acta 2021; 1157:338383. [PMID: 33832591 DOI: 10.1016/j.aca.2021.338383] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 02/25/2021] [Accepted: 02/27/2021] [Indexed: 10/21/2022]
Abstract
Protein phosphorylation regulates the conformations and function of proteins, which plays an important part in organisms. However, systematic and in-depth analysis of phosphorylation often hinders on account of the low abundance and suppressed ionization of phosphopeptides. Various materials based on single enrichment mechanism show potential in phosphopeptides enrichment, but the enrichment performance is typically not satisfactory. Herein, we developed a carnosine (Car) functionalized magnetic metal organic framework designed as Fe3O4@NH2@ZIF-90@Car. Benefiting from the multiple recognition groups of Car and massive metal ions site of ZIF-90, the as-fabricated Fe3O4@NH2@ZIF-90@Car was utilized as a multifunctional material with synergistic effect for phosphopeptides enrichment. On the basis of combined immobilized metal ion affinity chromatography (IMAC) and amine-based affinity enrichment mechanism, Fe3O4@NH2@ZIF-90@Car exhibited higher enrichment performance of phosphopeptides compared with Fe3O4@NH2@ZIF-90 (single IMAC mechanism). Besides, the feasibility of Fe3O4@NH2@ZIF-90@Car nanocomposites in complicated samples was further verified by enriching phosphopeptides from nonfat milk, human fluids such as serum and saliva, demonstrating its bright application prospects in phosphoproteomics analysis.
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Affiliation(s)
- He Qi
- College of Chemistry, Jilin University, Changchun, 130012, China
| | - Zheng Li
- College of Chemistry, Jilin University, Changchun, 130012, China
| | - Haijiao Zheng
- College of Chemistry, Jilin University, Changchun, 130012, China.
| | - Qiong Jia
- College of Chemistry, Jilin University, Changchun, 130012, China; Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, College of Life Sciences, Jilin University, Changchun, 130012, China.
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