1
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Tang R, Pan L, Bai Q, Li C, Ma S, Ou J, Shen Y. Biobased Tannic Acid-Chitosan Composite Membranes as Reusable Adsorbents for Effective Enrichment of Phosphopeptides. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2024; 40:927-937. [PMID: 38134293 DOI: 10.1021/acs.langmuir.3c03115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2023]
Abstract
High-performance reusable materials from renewable resources are rare and urgently required in bioseparation. Herein, a series of tannic acid-chitosan composite membranes for the enrichment of phosphopeptides were fabricated by the freeze casting method. First, a tannic acid-chitosan composite membrane was acquired via the multiple hydrogen bonds between tannic acid and chitosan, which had a long-range aligned three-dimensional microstructure. Second, a covalent-hydrogen bond hybrid composite was also fabricated, with stable and aligned honeycomb-like microstructures that formed by the synergy of covalence and hydrogen bonding. Besides, a ternary composite membrane was "one-pot" synthesized by the copolymerization of tannic acid, chitosan, and Ti4+ ions, indicating the feasibility of involving metal ions in the composition of the polymer skeleton in place of additional modification steps. The as-prepared chitosan composite membranes exhibited excellent performance in the enrichment of phosphopeptides from β-casein tryptic digest and human serum. Benefitting from the long-range aligned honeycomb-like structure coordinated by hydrogen bonds and covalent bonds, and a large number of pyrogallol functional groups provided by tannic acid, the covalent-hydrogen bond hybrid membrane showed excellent reusability and could be reused up to 16 times in phosphopeptide enrichment, as far as we know, which is the best reported result to date.
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Affiliation(s)
- Ruizhi Tang
- College of Chemistry and Materials Science, Northwest University, Xi'an 710127, China
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian 116023, China
| | - Lei Pan
- College of Chemistry and Materials Science, Northwest University, Xi'an 710127, China
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian 116023, China
| | - Quan Bai
- College of Chemistry and Materials Science, Northwest University, Xi'an 710127, China
| | - Cong Li
- College of Chemistry and Materials Science, Northwest University, Xi'an 710127, China
| | - Shujuan Ma
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian 116023, China
| | - Junjie Ou
- College of Chemistry and Materials Science, Northwest University, Xi'an 710127, China
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian 116023, China
| | - Yehua Shen
- College of Chemistry and Materials Science, Northwest University, Xi'an 710127, China
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2
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Wang J, Zhao X, Zhang H, Chen Y, Bie Z. In situ digestion-assisted multi-template imprinted nanoparticles for efficient analysis of protein phosphorylation. Mikrochim Acta 2023; 190:490. [PMID: 38030869 DOI: 10.1007/s00604-023-06081-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 10/29/2023] [Indexed: 12/01/2023]
Abstract
A new general approach called in situ digestion-assisted multi-template imprinting is proposed for preparation of phospho-specific molecularly imprinted nanoparticles. Through the novel templating strategy and controllable imprinting process, imprinted nanoparticles specific to the intact phosphoprotein and its phosphopeptides were synthesized. The prepared imprinted nanoparticles exhibited excellent specificity (cross reactivity < 10%), high affinity (10-6 M), high efficiency (47.5%), and good generality (both intact phosphoprotein and phosphopeptides). We also realized the fine tuning of the recognition at peptide level of the imprinted nanoparticles by adjusting the imprinting time. Based on the selective enrichment of the imprinted nanoparticles, the MS identification of both the intact phosphoprotein (Tau) and phosphopeptides (angiotensin II and peptides of Tau) in real complex samples could be achieved. Therefore, we believe that the in situ digestion-assisted multi-template imprinting strategy holds promising future in both phosphorylation analysis and proteomics applications.
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Affiliation(s)
- Jie Wang
- Department of Chemistry, Bengbu Medical University, 2600 Donghai Avenue, Bengbu, 233030, China
| | - Xiuling Zhao
- School of Pharmacy, Bengbu Medical University, 2600 Donghai Avenue, Bengbu, 233000, China
| | - Hui Zhang
- Department of Chemistry, Bengbu Medical University, 2600 Donghai Avenue, Bengbu, 233030, China
| | - Yang Chen
- Department of Chemistry, Bengbu Medical University, 2600 Donghai Avenue, Bengbu, 233030, China
- School of Pharmacy, Bengbu Medical University, 2600 Donghai Avenue, Bengbu, 233000, China
| | - Zijun Bie
- Department of Chemistry, Bengbu Medical University, 2600 Donghai Avenue, Bengbu, 233030, China.
- School of Pharmacy, Bengbu Medical University, 2600 Donghai Avenue, Bengbu, 233000, China.
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3
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Huynh CM, Arribas Díez I, Thi HKL, Jensen ON, Sellergren B, Irgum K. Terminally Phosphorylated Triblock Polyethers Acting Both as Templates and Pore-Forming Agents for Surface Molecular Imprinting of Monoliths Targeting Phosphopeptides. ACS OMEGA 2023; 8:8791-8803. [PMID: 36910939 PMCID: PMC9996590 DOI: 10.1021/acsomega.3c00007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 02/10/2023] [Indexed: 06/18/2023]
Abstract
The novel process reported here described the manufacture of monolithic molecularly imprinted polymers (MIPs) using a terminally functionalized block copolymer as the imprinting template and pore-forming agent. The MIPs were prepared through a step-growth polymerization process using a melamine-formaldehyde precondensate in a biphasic solvent system. Despite having a relatively low imprinting factor, the use of MIP monolith in liquid chromatography demonstrated the ability to selectively target desired analytes. An MIP capillary column was able to separate monophosphorylated peptides from a tryptic digest of bovine serum albumin. Multivariate data analysis and modeling of the phosphorylated and nonphosphorylated peptide retention times revealed that the number of phosphorylations was the strongest retention contributor for peptide retention on the monolithic MIP capillary column.
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Affiliation(s)
- Chau Minh Huynh
- Department
of Chemistry, Umeå University, S-901 87 Umeå, Sweden
| | - Ignacio Arribas Díez
- Department
of Biochemistry & Molecular Biology and VILLUM Center for Bioanalytical
Sciences, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark
| | - Hien Kim Le Thi
- Department
of Chemistry, Umeå University, S-901 87 Umeå, Sweden
| | - Ole N. Jensen
- Department
of Biochemistry & Molecular Biology and VILLUM Center for Bioanalytical
Sciences, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark
| | - Börje Sellergren
- Faculty
of Health and Society, Department of Biomedical Science, Malmö University, S-205 06 Malmö, Sweden
| | - Knut Irgum
- Department
of Chemistry, Umeå University, S-901 87 Umeå, Sweden
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4
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Halvorsen TG, Reubsaet L. The utility of molecularly imprinted polymers for mass spectrometric protein and proteomics analysis. Proteomics 2022; 22:e2100395. [PMID: 36217925 DOI: 10.1002/pmic.202100395] [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: 05/20/2022] [Revised: 09/30/2022] [Accepted: 10/04/2022] [Indexed: 11/08/2022]
Abstract
Selective and efficient sample clean-up is important in mass spectrometric protein- and proteomics analyses from biological matrices. Molecularly imprinted polymers (MIPs), polymers prepared to have tailor-made cavities for capture of target analytes may by such represent an interesting alternative for selective clean-up. The present review aims to give an overview of the utility of MIPs for protein capture from biological matrices prior to mass spectrometry (MS) analysis. The application of MIPs in depletion of abundant proteins, in protein and proteotypic peptide capture as well as in capture of post-translational modifications (PTMs) is described and discussed. In addition, an overview of available MIP formats and their advantages and challenges is given, together with an overview of the mass spectrometric techniques used in protein analysis after MIP capture. Overall, the present literature demonstrates that for many applications MIPs for sample clean-up in mass spectrometric protein and proteomics analysis from biological matrices is still not fully matured. MIPs for proteotypic peptide capture is the most mature approach and a method for routine use may be available within the next few years.
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Affiliation(s)
| | - Léon Reubsaet
- Department of Pharmacy, University of Oslo, Oslo, Norway
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5
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Wu W, Tang R, Li Z, Shen Y, Ma S, Ou J. Fabrication of hydrophilic titanium (IV)-immobilized polydispersed microspheres via inverse suspension polymerization for enrichment of phosphopeptides in milk. Food Chem 2022; 395:133608. [DOI: 10.1016/j.foodchem.2022.133608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 05/29/2022] [Accepted: 06/28/2022] [Indexed: 11/17/2022]
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6
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Zhang X, Wang Y, Wei ZH, An DY, Pu WR, Liu ZS, Huang YP. Improving the Identification of Lysine-Acetylated Peptides Using a Molecularly Imprinted Monolith Prepared by a Deep Eutectic Solvent Monomer. J Proteome Res 2022; 21:325-338. [PMID: 35050640 DOI: 10.1021/acs.jproteome.1c00553] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
To overcome the identification challenge of low-abundance lysine acetylation (Kac), a novel approach based on a molecularly imprinted polymer (MIP) was developed to improve the extraction capacity of Kac peptides in real samples. Green deep eutectic solvents (DESs) were introduced and used as one of the synergistic functional monomers with zinc acrylate (ZnA). Glycine-glycine-alanine-lysine(ac)-arginine (GGAKacR) was chosen as a template and N,N'-methylenbisacrylamide (MBAA) was used as a cross-linker. The obtained GGAKacR-MIP had excellent selectivity for the template with an imprinting factor (IF) of up to 21.4. The histone digest addition experiment demonstrated that GGAKacR-MIP could successfully extract GGAKacR from a complex sample. Finally, the application to the extraction of Kac peptides from mouse liver protein digestion was studied in detail. The number of Kac peptides and Kac proteins identified was 130 and 110, which were 3.71-fold and 3.93-fold higher than those of the untreated sample. In addition, the number of peptides and proteins identified after treatment increased from 5535 and 1092 to 17 149 and 4037 (3.10-fold and 3.70-fold, respectively). The results showed that the obtained MIP may provide an effective technical tool for the identification of Kac-modification and peptide fractionation, as well as a potential approach for simultaneously identifying post-translational-modified proteomic and proteomic information.
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Affiliation(s)
- Xue Zhang
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin 300070, China
| | - Yang Wang
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin 300070, China
| | - Ze-Hui Wei
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin 300070, China
| | - Dong-Yu An
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin 300070, China
| | - Wan-Rong Pu
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin 300070, China
| | - Zhao-Sheng Liu
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin 300070, China
| | - Yan-Ping Huang
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin 300070, China
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7
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Pasquardini L, Bossi AM. Molecularly imprinted polymers by epitope imprinting: a journey from molecular interactions to the available bioinformatics resources to scout for epitope templates. Anal Bioanal Chem 2021; 413:6101-6115. [PMID: 34018035 PMCID: PMC8440283 DOI: 10.1007/s00216-021-03409-1] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 04/26/2021] [Accepted: 05/11/2021] [Indexed: 01/07/2023]
Abstract
The molecular imprinting of proteins is the process of forming biomimetics with entailed protein-recognition by means of a template-assisted synthesis. Protein-imprinted polymers (pMIPs) have been successfully employed in separations, assays, sensors, and imaging. From a technical point of view, imprinting a protein is both costly, for protein expression and purification, and challenging, for the preservation of the protein's structural properties. In fact, the imprinting process needs to guarantee the preservation of the same protein three-dimensional conformation that later would be recognized. So far, the captivating idea to imprint just a portion of the protein, i.e., an epitope, instead of the whole, proved successful, offering reduced costs, compatibility with many synthetic conditions (solvents, pH, temperatures), and fine-tuning of the peptide sequence so to target specific physiological and functional conditions of the protein, such as post-translational modifications. Here, protein-protein interactions and the biochemical features of the epitopes are inspected, deriving lessons to prepare more effective pMIPs. Epitopes are categorized in linear or structured, immunogenic or not, located at the protein's surface or buried in its core and the imprinting strategies are discussed. Moreover, attention is given to freely available online bioinformatics resources that might offer key tools to gain further rationale amid the selection process of suitable epitopes templates.
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Affiliation(s)
| | - Alessandra Maria Bossi
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134, Verona, Italy.
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8
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Nicholls IA, Golker K, Olsson GD, Suriyanarayanan S, Wiklander JG. The Use of Computational Methods for the Development of Molecularly Imprinted Polymers. Polymers (Basel) 2021; 13:2841. [PMID: 34502881 PMCID: PMC8434026 DOI: 10.3390/polym13172841] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 08/16/2021] [Accepted: 08/19/2021] [Indexed: 12/29/2022] Open
Abstract
Recent years have witnessed a dramatic increase in the use of theoretical and computational approaches in the study and development of molecular imprinting systems. These tools are being used to either improve understanding of the mechanisms underlying the function of molecular imprinting systems or for the design of new systems. Here, we present an overview of the literature describing the application of theoretical and computational techniques to the different stages of the molecular imprinting process (pre-polymerization mixture, polymerization process and ligand-molecularly imprinted polymer rebinding), along with an analysis of trends within and the current status of this aspect of the molecular imprinting field.
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Affiliation(s)
- Ian A. Nicholls
- Bioorganic & Biophysical Chemistry Laboratory, Linnaeus University Centre for Biomaterials Chemistry, Department of Chemistry & Biomedical Sciences, Linnaeus University, SE-391 82 Kalmar, Sweden; (K.G.); (G.D.O.); (S.S.); (J.G.W.)
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9
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Low TY, Mohtar MA, Lee PY, Omar N, Zhou H, Ye M. WIDENING THE BOTTLENECK OF PHOSPHOPROTEOMICS: EVOLVING STRATEGIES FOR PHOSPHOPEPTIDE ENRICHMENT. MASS SPECTROMETRY REVIEWS 2021; 40:309-333. [PMID: 32491218 DOI: 10.1002/mas.21636] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 05/11/2020] [Accepted: 05/12/2020] [Indexed: 06/11/2023]
Abstract
Phosphorylation is a form of protein posttranslational modification (PTM) that regulates many biological processes. Whereas phosphoproteomics is a scientific discipline that identifies and quantifies the phosphorylated proteome using mass spectrometry (MS). This task is extremely challenging as ~30% of the human proteome is phosphorylated; and each phosphoprotein may exist as multiple phospho-isoforms that are present in low abundance and stoichiometry. Hence, phosphopeptide enrichment techniques are indispensable to (phospho)proteomics laboratories. These enrichment methods encompass widely-adopted techniques such as (i) affinity-based chromatography; (ii) ion exchange and mixed-mode chromatography (iii) enrichment with phospho-specific antibodies and protein domains, and (iv) functionalized polymers and other less common but emerging technologies such as hydroxyapatite chromatography and precipitation with inorganic ions. Here, we review these techniques, their history, continuous development and evaluation. Besides, we outline associating challenges of phosphoproteomics that are linked to experimental design, sample preparation, and proteolytic digestion. In addition, we also discuss about the future outlooks in phosphoproteomics, focusing on elucidating the noncanonical phosphoproteome and deciphering the "dark phosphoproteome". © 2020 John Wiley & Sons Ltd.
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Affiliation(s)
- Teck Yew Low
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, 56000, Kuala Lumpur, Malaysia
| | - M Aiman Mohtar
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, 56000, Kuala Lumpur, Malaysia
| | - Pey Yee Lee
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, 56000, Kuala Lumpur, Malaysia
| | - Nursyazwani Omar
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, 56000, Kuala Lumpur, Malaysia
| | - Houjiang Zhou
- Medical Research Council (MRC) Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH, United Kingdom
| | - Mingliang Ye
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Centre, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
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10
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Application of SILAC Labeling in Phosphoproteomics Analysis. Methods Mol Biol 2021. [PMID: 33950491 DOI: 10.1007/978-1-0716-1024-4_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
The analysis of disease-related changes in the phosphorylation status of cellular signal transduction networks is of major interest to biomedical researchers. Mass spectrometry-based proteomics allows the analysis of phosphorylation in a global manner. However, several technical challenges need to be addressed when the phosphorylation of proteins is analyzed. Low-abundant phosphopeptides need to be enriched before analysis, thereby introducing additional steps in sample preparation. Consequently, the applied quantification strategies should be robust towards elaborate sampling handling, rendering label-based quantification strategies the methods of choice in many experiments. Here, we present a protocol for SILAC labeling and the subsequent isolation of phosphopeptides using TiO2 affinity chromatography. We outline the corresponding LC-MS/MS analysis and the essential steps of data processing.
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11
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Tu X, Shi X, Zhao M, Zhang H. Molecularly imprinted dispersive solid-phase microextraction sorbents for direct and selective drug capture from the undiluted bovine serum. Talanta 2021; 226:122142. [PMID: 33676693 DOI: 10.1016/j.talanta.2021.122142] [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: 10/31/2020] [Revised: 01/18/2021] [Accepted: 01/21/2021] [Indexed: 11/26/2022]
Abstract
The preparation of well-defined new hydrophilic molecularly imprinted polymer (MIP) microspheres and their use as the dispersive solid-phase microextraction (dSPME) sorbents for direct and selective drug (i.e., propranolol) capture from the undiluted bovine serum are described. These MIPs have surface-grafted dense poly(2-hydroxyethyl methacrylate) (PHEMA) brushes with different molecular weights and grafting densities. They were readily prepared via the facile reversible addition-fragmentation chain transfer (RAFT) coupling chemistry. Both the molecular weights and grafting densities of PHEMA brushes showed significant influence on their complex biological sample-compatibility, and only those MIPs bearing PHEMA brushes with high enough molecular weights and grafting densities could selectively recognize propranolol in the undiluted pure milk and bovine serum. In particular, they have proven to be highly versatile dSPME sorbents for directly and selectively capturing propranolol from the undiluted bovine serum with satisfactory recoveries (85.2-97.4%) and high accuracy (RSD = 2.3-3.7%), even in the presence of one analogue of propranolol. The limit of detection was 0.002 μM with a linear correlation coefficient of 0.9994 in the range of 0.01-100 μM. Excellent precision was verified by both the intraday and interday analytical results. Their good reusability was also confirmed. This work demonstrates the high potential of such hydrophilic MIP-based dSPME sorbents for rapid, accurate, and reliable drug determination in complex biological samples.
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Affiliation(s)
- Xiaozheng Tu
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Functional Polymer Materials (Ministry of Education), Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), and College of Chemistry, Nankai University, Tianjin, 300071, China
| | - Xiaohui Shi
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Functional Polymer Materials (Ministry of Education), Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), and College of Chemistry, Nankai University, Tianjin, 300071, China
| | - Man Zhao
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Functional Polymer Materials (Ministry of Education), Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), and College of Chemistry, Nankai University, Tianjin, 300071, China
| | - Huiqi Zhang
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Functional Polymer Materials (Ministry of Education), Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), and College of Chemistry, Nankai University, Tianjin, 300071, China.
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12
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Fang X, Wang Z, Sun N, Deng C. Magnetic metal oxide affinity chromatography-based molecularly imprinted approach for effective separation of serous and urinary phosphoprotein biomarker. Talanta 2021; 226:122143. [DOI: 10.1016/j.talanta.2021.122143] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 01/18/2021] [Accepted: 01/21/2021] [Indexed: 02/06/2023]
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13
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Incel A, Arribas Díez I, Wierzbicka C, Gajoch K, Jensen ON, Sellergren B. Selective Enrichment of Histidine Phosphorylated Peptides Using Molecularly Imprinted Polymers. Anal Chem 2021; 93:3857-3866. [PMID: 33591162 PMCID: PMC8023515 DOI: 10.1021/acs.analchem.0c04474] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
![]()
Protein histidine
phosphorylation
(pHis) is involved in molecular signaling networks in bacteria, fungi,
plants, and higher eukaryotes including mammals and is implicated
in human diseases such as cancer. Detailed investigations of the pHis
modification are hampered due to its acid-labile nature and consequent
lack of tools to study this post-translational modification (PTM).
We here demonstrate three molecularly imprinted polymer (MIP)-based
reagents, MIP1–MIP3, for enrichment of pHis peptides and subsequent
characterization by chromatography and mass spectrometry (LC–MS).
The combination of MIP1 and β-elimination provided some selectivity
for improved detection of pHis peptides. MIP2 was amenable to larger
pHis peptides, although with poor selectivity. Microsphere-based MIP3
exhibited improved selectivity and was amenable to enrichment and
detection by LC–MS of pHis peptides in tryptic digests of protein
mixtures. These MIP protocols do not involve any acidic solvents during
sample preparation and enrichment, thus preserving the pHis modification.
The presented proof-of-concept results will lead to new protocols
for highly selective enrichment of labile protein phosphorylations
using molecularly imprinted materials.
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Affiliation(s)
- Anıl Incel
- Department of Biomedical Science, Faculty of Health and Society, Malmö University, 205 06 Malmö, Sweden
| | - Ignacio Arribas Díez
- Department of Biochemistry & Molecular Biology and VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, DK-5230 Odense M, Denmark
| | - Celina Wierzbicka
- Department of Biomedical Science, Faculty of Health and Society, Malmö University, 205 06 Malmö, Sweden
| | - Katarzyna Gajoch
- Department of Biomedical Science, Faculty of Health and Society, Malmö University, 205 06 Malmö, Sweden
| | - Ole N Jensen
- Department of Biochemistry & Molecular Biology and VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, DK-5230 Odense M, Denmark
| | - Börje Sellergren
- Department of Biomedical Science, Faculty of Health and Society, Malmö University, 205 06 Malmö, Sweden
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14
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Hauser A, Poulou E, Müller F, Schmieder P, Hackenberger CPR. Synthesis and Evaluation of Non-Hydrolyzable Phospho-Lysine Peptide Mimics. Chemistry 2021; 27:2326-2331. [PMID: 32986895 PMCID: PMC7898648 DOI: 10.1002/chem.202003947] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 09/25/2020] [Indexed: 01/16/2023]
Abstract
The intrinsic lability of the phosphoramidate P-N bond in phosphorylated histidine (pHis), arginine (pHis) and lysine (pLys) residues is a significant challenge for the investigation of these post-translational modifications (PTMs), which gained attention rather recently. While stable mimics of pHis and pArg have contributed to study protein substrate interactions or to generate antibodies for enrichment as well as detection, no such analogue has been reported yet for pLys. This work reports the synthesis and evaluation of two pLys mimics, a phosphonate and a phosphate derivative, which can easily be incorporated into peptides using standard fluorenyl-methyloxycarbonyl- (Fmoc-)based solid-phase peptide synthesis (SPPS). In order to compare the biophysical properties of natural pLys with our synthetic mimics, the pKa values of pLys and analogues were determined in titration experiments applying nuclear magnetic resonance (NMR) spectroscopy in small model peptides. These results were used to compute electrostatic potential (ESP) surfaces obtained after molecular geometry optimization. These findings indicate the potential of the designed non-hydrolyzable, phosphonate-based mimic for pLys in various proteomic approaches.
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Affiliation(s)
- Anett Hauser
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP)Robert-Rössle-Strasse 1013125BerlinGermany
- Department of ChemistryHumboldt-Universität zu BerlinBrook-Taylor-Strasse 212489BerlinGermany
| | - Eleftheria Poulou
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP)Robert-Rössle-Strasse 1013125BerlinGermany
| | - Fabian Müller
- Department of ChemistryHumboldt-Universität zu BerlinBrook-Taylor-Strasse 212489BerlinGermany
| | - Peter Schmieder
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP)Robert-Rössle-Strasse 1013125BerlinGermany
| | - Christian P. R. Hackenberger
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP)Robert-Rössle-Strasse 1013125BerlinGermany
- Department of ChemistryHumboldt-Universität zu BerlinBrook-Taylor-Strasse 212489BerlinGermany
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15
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Tang R, Yu Y, Dong J, Yao Y, Ma S, Ou J, Ye M. Facile preparation of bifunctional adsorbents for efficiently enriching N-glycopeptides and phosphopeptides. Anal Chim Acta 2020; 1144:111-120. [PMID: 33453787 DOI: 10.1016/j.aca.2020.12.015] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 12/03/2020] [Accepted: 12/08/2020] [Indexed: 01/23/2023]
Abstract
In bottom-up strategy, specific enrichment of glycopeptides and phosphopeptides from complicated biological samples is a prerequisite for efficient identifying glycosylation and phosphorylation by mass spectrometry. Although there were a plethora of materials used as either hydrophilic interaction liquid chromatography (HILIC) or immobilized metal affinity chromatography (IMAC) adsorbents, even several bifunctional materials for simultaneous enrichment of glycopeptides and phosphopeptides, most of them are not easily commercialized as many other well-performing adsorbents due to the complicated preparation process. In our case, a one-step modification strategy was developed to prepare bifunctional adsorbents for HILIC and IMAC, employing O-phospho-l-serine as the modifier and poly(GMA-co-EDMA) microspheres, a kind of macroporous adsorption resin (MAR) with epoxy groups, as the matrix. The MARs were directly modified with O-phospho-l-serine under facile condition for HILIC strategy and further chelated with Ti4+ for IMAC strategy. A total of 522 unique N-glycopeptides and 442 unique N-glycosylation sites mapped to 275 N-glycoproteins was identified from HeLa cell proteins, showing excellent enrichment efficiency in HILIC. Additionally, 3141 unique phosphopeptides were unambiguously identified from 200 μg of digest of HeLa cell proteins, demonstrating great enrichment efficiency in IMAC. Moreover, these materials have been successfully applied in the analysis of multiple biological samples including human serum and milk, demonstrating their feasibility for real sample applications and potential business value.
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Affiliation(s)
- Ruizhi Tang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Yang Yu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jing Dong
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Yating Yao
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Shujuan Ma
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China.
| | - Junjie Ou
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Mingliang Ye
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China; University of Chinese Academy of Sciences, Beijing, 100049, China
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16
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Schuld J, Orfanos Z, Chevessier F, Eggers B, Heil L, Uszkoreit J, Unger A, Kirfel G, van der Ven PFM, Marcus K, Linke WA, Clemen CS, Schröder R, Fürst DO. Homozygous expression of the myofibrillar myopathy-associated p.W2710X filamin C variant reveals major pathomechanisms of sarcomeric lesion formation. Acta Neuropathol Commun 2020; 8:154. [PMID: 32887649 PMCID: PMC7650280 DOI: 10.1186/s40478-020-01001-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 07/22/2020] [Indexed: 01/06/2023] Open
Abstract
Filamin C (FLNc) is mainly expressed in striated muscle cells where it localizes to Z-discs, myotendinous junctions and intercalated discs. Recent studies have revealed numerous mutations in the FLNC gene causing familial and sporadic myopathies and cardiomyopathies with marked clinical variability. The most frequent myopathic mutation, p.W2710X, which is associated with myofibrillar myopathy, deletes the carboxy-terminal 16 amino acids from FLNc and abolishes the dimerization property of Ig-like domain 24. We previously characterized "knock-in" mice heterozygous for this mutation (p.W2711X), and have now investigated homozygous mice using protein and mRNA expression analyses, mass spectrometry, and extensive immunolocalization and ultrastructural studies. Although the latter mice display a relatively mild myopathy under normal conditions, our analyses identified major mechanisms causing the pathophysiology of this disease: in comparison to wildtype animals (i) the expression level of FLNc protein is drastically reduced; (ii) mutant FLNc is relocalized from Z-discs to particularly mechanically strained parts of muscle cells, i.e. myotendinous junctions and myofibrillar lesions; (iii) the number of lesions is greatly increased and these lesions lack Bcl2-associated athanogene 3 (BAG3) protein; (iv) the expression of heat shock protein beta-7 (HSPB7) is almost completely abolished. These findings indicate grave disturbances of BAG3-dependent and -independent autophagy pathways that are required for efficient lesion repair. In addition, our studies reveal general mechanisms of lesion formation and demonstrate that defective FLNc dimerization via its carboxy-terminal domain does not disturb assembly and basic function of myofibrils. An alternative, more amino-terminally located dimerization site might compensate for that loss. Since filamins function as stress sensors, our data further substantiate that FLNc is important for mechanosensing in the context of Z-disc stabilization and maintenance.
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17
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Eggers B, Pacharra S, Eisenacher M, Marcus K, Uszkoreit J. Let me infuse this for you - A way to solve the first YPIC challenge. EUPA OPEN PROTEOMICS 2020; 22-23:19-21. [PMID: 31890549 PMCID: PMC6924283 DOI: 10.1016/j.euprot.2019.07.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Accepted: 07/17/2019] [Indexed: 11/30/2022]
Abstract
In a common proteomics analysis today, the origins of our sample in the vial are known and therefore a database dependent approach to identify the containing peptides can be used. The first YPIC challenge though provided us with 19 synthetic peptides, which together formed an English sentence. For the identification of these peptides, a de-novo approach was used, which brought us together with an internet search engine to the hidden sentence. But only having the sentence was not sufficient for us, we also wanted to identify as many as possible of the spectra in our data. Therefore, we created and refined a database approach from the de-novo method and finally could identify the peptide-sentence with a good overlap.
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Affiliation(s)
- Britta Eggers
- Ruhr University Bochum, Faculty of Medicine, Medizinisches Proteom-Center, Gesundheitscampus 4, D-44801, Bochum, Germany
| | - Sandra Pacharra
- Ruhr University Bochum, Faculty of Medicine, Medizinisches Proteom-Center, Gesundheitscampus 4, D-44801, Bochum, Germany
| | - Martin Eisenacher
- Ruhr University Bochum, Faculty of Medicine, Medizinisches Proteom-Center, Gesundheitscampus 4, D-44801, Bochum, Germany
| | - Katrin Marcus
- Ruhr University Bochum, Faculty of Medicine, Medizinisches Proteom-Center, Gesundheitscampus 4, D-44801, Bochum, Germany
| | - Julian Uszkoreit
- Ruhr University Bochum, Faculty of Medicine, Medizinisches Proteom-Center, Gesundheitscampus 4, D-44801, Bochum, Germany
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18
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Yang K, Li S, Liu L, Chen Y, Zhou W, Pei J, Liang Z, Zhang L, Zhang Y. Epitope Imprinting Technology: Progress, Applications, and Perspectives toward Artificial Antibodies. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2019; 31:e1902048. [PMID: 31423663 DOI: 10.1002/adma.201902048] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2019] [Revised: 06/17/2019] [Indexed: 06/10/2023]
Abstract
Epitope imprinting is a promising tool to generate antibody-like specific recognition sites. Recently, because of the ease of obtaining templates, the flexibility in selecting monomers, their resistance to harsh environments, and the high specificity toward targets, epitope-imprinted materials have attracted much attention in various fields, such as bioanalysis, clinical therapy, and pharmacy. Here, the discussion is focused on the current representative epitope imprinting technologies, including epitope bulk imprinting and epitope surface imprinting. Moreover, the application of epitope-imprinted materials to the recognition of peptides, proteins, and cells is reviewed. Finally, the remaining challenges arising from the intrinsic properties of epitope imprinting are discussed, and future development in the field is prospected.
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Affiliation(s)
- Kaiguang Yang
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Senwu Li
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Lukuan Liu
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Yuwan Chen
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Wen Zhou
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Jiaqi Pei
- Zhang Dayu School of Chemistry, Dalian University of Technology, Dalian, 116024, China
| | - Zhen Liang
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Lihua Zhang
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Yukui Zhang
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
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19
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Zhou T, Che G, Ding L, Sun D, Li Y. Recent progress of selective adsorbents: From preparation to complex sample pretreatment. Trends Analyt Chem 2019. [DOI: 10.1016/j.trac.2019.115678] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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20
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Hussain D, Musharraf SG, Fatima B, Saeed A, Jabeen F, Ashiq MN, Najam-ul-Haq M. Magnetite nanoparticles coated with chitosan and polyethylenimine as anion exchanger for sorptive enrichment of phosphopeptides. Mikrochim Acta 2019; 186:852. [DOI: 10.1007/s00604-019-3971-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Accepted: 10/25/2019] [Indexed: 11/28/2022]
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21
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Yan Y, Deng C. Recent advances in nanomaterials for sample pre-treatment in phosphoproteomics research. Trends Analyt Chem 2019. [DOI: 10.1016/j.trac.2019.115655] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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22
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Capriotti AL, Antonelli M, Antonioli D, Cavaliere C, Chiarcos R, Gianotti V, Piovesana S, Sparnacci K, Laus M, Laganà A. Effect of shell structure of Ti-immobilized metal ion affinity chromatography core-shell magnetic particles for phosphopeptide enrichment. Sci Rep 2019; 9:15782. [PMID: 31673007 PMCID: PMC6823385 DOI: 10.1038/s41598-019-51995-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 09/28/2019] [Indexed: 11/09/2022] Open
Abstract
Magnetic materials in sample preparation for shotgun phosphoproteomics offer several advantages over conventional systems, as the enrichment can be achieved directly in solution, but they still suffer from some drawbacks, due to limited stability and selectivity, which is supposed to be affected by the hydrophilicity of the polymeric supports used for cation immobilization. The paper describes the development of an improved magnetic material with increased stability, thanks to a two-step covering of the magnetic core, for the enrichment of phosphopeptides in biological samples. Four materials were prepared featuring a polymeric shell with tunable hydrophilicity, obtained by "grafting from" polymerization of glycidyl methacrylate with 0-8.3% of polyethylene glycol methacrylate (PEGMA), the latter used to modulate the hydrophilicity of the material surface. Finally, the materials were functionalized with iminodiacetic acid for Ti4+ ion immobilization. The materials were analyzed for their composition by a combination of CHN elemental analysis and thermogravimetric analysis, also hyphenated to gas chromatography and mass spectrometric detection. Surface characteristics were evaluated by water contact angle measurements, scanning electron microscopy and energy dispersive X-ray spectrometry. These materials were applied to the enrichment of phosphopeptides from yeast protein digests. Peptides were identified by proteomics techniques using nano-high performance liquid chromatography coupled to mass spectrometry and bioinformatics. Qualitatively the peptides identified by the four systems were comparable, with 1606-1693 phosphopeptide identifications and a selectivity of 47-54% for all materials. The physico-chemical features of the identified peptides were also the same for the four materials. In particular, the grand average of hydropathy index values indicated that the enriched phosphopeptides were hydrophilic (ca. 90%), and only some co-enriched non-phosphorylated peptides were hydrophobic (21-28%), regardless of the material used for enrichment. Peptides had a pI ≤ 7, which indicated a well-known bias for acidic peptides binding, attributed to the interaction with the metal center itself. The results indicated that the enrichment of phosphopeptides and the co-enrichment of non-phosphorylated peptides is mainly driven by interactions with Ti4+ and does not depend on the amount of PEGMA chains in the polymer shell.
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Affiliation(s)
- Anna Laura Capriotti
- Department of Chemistry, Sapienza Università di Roma, Piazzale Aldo Moro 5, 00185, Rome, Italy
| | - Michela Antonelli
- Department of Chemistry, Sapienza Università di Roma, Piazzale Aldo Moro 5, 00185, Rome, Italy
| | - Diego Antonioli
- Department of Science and Technological Innovation, Università degli Studi del Piemonte Orientale, Alessandria, Italy
- INSTM, UdR Alessandria, Viale Teresa Michel 11, 15121, Alessandria, Italy
| | - Chiara Cavaliere
- Department of Chemistry, Sapienza Università di Roma, Piazzale Aldo Moro 5, 00185, Rome, Italy
| | - Riccardo Chiarcos
- Department of Science and Technological Innovation, Università degli Studi del Piemonte Orientale, Alessandria, Italy
| | - Valentina Gianotti
- Department of Science and Technological Innovation, Università degli Studi del Piemonte Orientale, Alessandria, Italy
- INSTM, UdR Alessandria, Viale Teresa Michel 11, 15121, Alessandria, Italy
| | - Susy Piovesana
- Department of Chemistry, Sapienza Università di Roma, Piazzale Aldo Moro 5, 00185, Rome, Italy.
| | - Katia Sparnacci
- Department of Science and Technological Innovation, Università degli Studi del Piemonte Orientale, Alessandria, Italy
- INSTM, UdR Alessandria, Viale Teresa Michel 11, 15121, Alessandria, Italy
| | - Michele Laus
- Department of Science and Technological Innovation, Università degli Studi del Piemonte Orientale, Alessandria, Italy
- INSTM, UdR Alessandria, Viale Teresa Michel 11, 15121, Alessandria, Italy
| | - Aldo Laganà
- Department of Chemistry, Sapienza Università di Roma, Piazzale Aldo Moro 5, 00185, Rome, Italy
- CNR NANOTEC, Campus Ecotekne, University of Salento, Via Monteroni, 73100, Lecce, Italy
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23
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Liu M, Torsetnes SB, Wierzbicka C, Jensen ON, Sellergren B, Irgum K. Selective Enrichment of Phosphorylated Peptides by Monolithic Polymers Surface Imprinted with bis-Imidazolium Moieties by UV-Initiated Cryopolymerization. Anal Chem 2019; 91:10188-10196. [DOI: 10.1021/acs.analchem.9b02211] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Mingquan Liu
- Umeå University, Department of Chemistry, S-901 87 Umeå, Sweden
| | - Silje Bøen Torsetnes
- University of Southern Denmark, Department of Biochemistry and Molecular Biology and VILLUM Center for Bioanalytical Sciences, Campusvej 55, DK-5230 Odense M, Denmark
| | - Celina Wierzbicka
- Malmö University, Department of Biomedical Sciences, Faculty of Health and Society, S-205 06 Malmö, Sweden
| | - Ole Nørregaard Jensen
- University of Southern Denmark, Department of Biochemistry and Molecular Biology and VILLUM Center for Bioanalytical Sciences, Campusvej 55, DK-5230 Odense M, Denmark
| | - Börje Sellergren
- Malmö University, Department of Biomedical Sciences, Faculty of Health and Society, S-205 06 Malmö, Sweden
| | - Knut Irgum
- Umeå University, Department of Chemistry, S-901 87 Umeå, Sweden
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24
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Oertzen-Hagemann V, Kirmse M, Eggers B, Pfeiffer K, Marcus K, de Marées M, Platen P. Effects of 12 Weeks of Hypertrophy Resistance Exercise Training Combined with Collagen Peptide Supplementation on the Skeletal Muscle Proteome in Recreationally Active Men. Nutrients 2019; 11:E1072. [PMID: 31091754 PMCID: PMC6566884 DOI: 10.3390/nu11051072] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 05/07/2019] [Accepted: 05/10/2019] [Indexed: 01/08/2023] Open
Abstract
Evidence has shown that protein supplementation following resistance exercise training (RET) helps to further enhance muscle mass and strength. Studies have demonstrated that collagen peptides containing mostly non-essential amino acids increase fat-free mass (FFM) and strength in sarcopenic men. The aim of this study was to investigate whether collagen peptide supplementation in combination with RET influences the protein composition of skeletal muscle. Twenty-five young men (age: 24.2 ± 2.6 years, body mass (BM): 79.6 ± 5.6 kg, height: 185.0 ± 5.0 cm, fat mass (FM): 11.5% ± 3.4%) completed body composition and strength measurements and vastus lateralis biopsies were taken before and after a 12-week training intervention. In a double-blind, randomized design, subjects consumed either 15 g of specific collagen peptides (COL) or a non-caloric placebo (PLA) every day within 60 min after their training session. A full-body hypertrophy workout was completed three times per week and included four exercises using barbells. Muscle proteome analysis was performed by liquid chromatography tandem mass spectrometry (LC-MS/MS). BM and FFM increased significantly in COL compared with PLA, whereas no differences in FM were detected between the two groups. Both groups improved in strength levels, with a slightly higher increase in COL compared with PLA. In COL, 221 higher abundant proteins were identified. In contrast, only 44 proteins were of higher abundance in PLA. In contrast to PLA, the upregulated proteins in COL were mostly associated with the protein metabolism of the contractile fibers. In conclusion, the use of RET in combination with collagen peptide supplementation results in a more pronounced increase in BM, FFM, and muscle strength than RET alone. More proteins were upregulated in the COL intervention most of which were associated with contractile fibers.
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Affiliation(s)
- Vanessa Oertzen-Hagemann
- Department of Sports Medicine and Sports Nutrition, Ruhr University Bochum, 44801 Bochum, Germany.
| | - Marius Kirmse
- Department of Sports Medicine and Sports Nutrition, Ruhr University Bochum, 44801 Bochum, Germany.
| | - Britta Eggers
- Medizinisches Proteom-Center, Medical Faculty, Ruhr University Bochum, 44801 Bochum, Germany.
| | - Kathy Pfeiffer
- Medizinisches Proteom-Center, Medical Faculty, Ruhr University Bochum, 44801 Bochum, Germany.
| | - Katrin Marcus
- Medizinisches Proteom-Center, Medical Faculty, Ruhr University Bochum, 44801 Bochum, Germany.
| | - Markus de Marées
- Department of Sports Medicine and Sports Nutrition, Ruhr University Bochum, 44801 Bochum, Germany.
| | - Petra Platen
- Department of Sports Medicine and Sports Nutrition, Ruhr University Bochum, 44801 Bochum, Germany.
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25
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Xing R, Wen Y, He H, Guo Z, Liu Z. Recent progress in the combination of molecularly imprinted polymer-based affinity extraction and mass spectrometry for targeted proteomic analysis. Trends Analyt Chem 2019. [DOI: 10.1016/j.trac.2018.11.033] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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26
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Sathe G, Na CH, Renuse S, Madugundu A, Albert M, Moghekar A, Pandey A. Phosphotyrosine profiling of human cerebrospinal fluid. Clin Proteomics 2018; 15:29. [PMID: 30220890 PMCID: PMC6136184 DOI: 10.1186/s12014-018-9205-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Accepted: 09/04/2018] [Indexed: 12/21/2022] Open
Abstract
Background Cerebrospinal fluid (CSF) is an important source of potential biomarkers that affect the brain. Biomarkers for neurodegenerative disorders are needed to assist in diagnosis, monitoring disease progression and evaluating efficacy of therapies. Recent studies have demonstrated the involvement of tyrosine kinases in neuronal cell death. Thus, neurodegeneration in the brain is related to altered tyrosine phosphorylation of proteins in the brain and identification of abnormally phosphorylated tyrosine peptides in CSF has the potential to ascertain candidate biomarkers for neurodegenerative disorders. Methods In this study, we used an antibody-based tyrosine phosphopeptide enrichment method coupled with high resolution Orbitrap Fusion Tribrid Lumos Fourier transform mass spectrometer to catalog tyrosine phosphorylated peptides from cerebrospinal fluid. The subset of identified tyrosine phosphorylated peptides was also validated using parallel reaction monitoring (PRM)-based targeted approach. Results To date, there are no published studies on global profiling of phosphotyrosine modifications of CSF proteins. We carried out phosphotyrosine profiling of CSF using an anti-phosphotyrosine antibody-based enrichment and analysis using high resolution Orbitrap Fusion Lumos mass spectrometer. We identified 111 phosphotyrosine peptides mapping to 66 proteins, which included 24 proteins which have not been identified in CSF previously. We then validated a set of 5 tyrosine phosphorylated peptides in an independent set of CSF samples from cognitively normal subjects, using a PRM-based targeted approach. Conclusions The findings from this deep phosphotyrosine profiling of CSF samples have the potential to identify novel disease-related phosphotyrosine-containing peptides in CSF. Electronic supplementary material The online version of this article (10.1186/s12014-018-9205-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Gajanan Sathe
- 1Center for Molecular Medicine, National Institute of Mental Health and Neurosciences (NIMHANS), Hosur Road, Bangalore, 560029 India.,Institute of Bioinformatics, International Technology Park, Bangalore, 560 066 India.,7Manipal Academy of Higher Education (MAHE), Manipal, Karnataka 576104 India
| | - Chan Hyun Na
- 3McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA.,4Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA.,6Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
| | - Santosh Renuse
- Institute of Bioinformatics, International Technology Park, Bangalore, 560 066 India.,3McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
| | - Anil Madugundu
- 1Center for Molecular Medicine, National Institute of Mental Health and Neurosciences (NIMHANS), Hosur Road, Bangalore, 560029 India.,Institute of Bioinformatics, International Technology Park, Bangalore, 560 066 India.,7Manipal Academy of Higher Education (MAHE), Manipal, Karnataka 576104 India
| | - Marilyn Albert
- 4Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
| | - Abhay Moghekar
- 4Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
| | - Akhilesh Pandey
- 1Center for Molecular Medicine, National Institute of Mental Health and Neurosciences (NIMHANS), Hosur Road, Bangalore, 560029 India.,3McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA.,5Departments of Biological Chemistry, Pathology and Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
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27
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Capriotti AL, Cavaliere C, Ferraris F, Gianotti V, Laus M, Piovesana S, Sparnacci K, Zenezini Chiozzi R, Laganà A. New Ti-IMAC magnetic polymeric nanoparticles for phosphopeptide enrichment from complex real samples. Talanta 2018; 178:274-281. [DOI: 10.1016/j.talanta.2017.09.010] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Revised: 08/30/2017] [Accepted: 09/04/2017] [Indexed: 12/22/2022]
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28
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Shinde S, Selvalatchmanan J, Incel A, Akhoundian M, Bendt AK, Torta F. Mesoporous polymeric microspheres with high affinity for phosphorylated biomolecules. NEW J CHEM 2018. [DOI: 10.1039/c8nj01114a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Bis-imidazolium functionalized mesoporous microspheres selectively extract phosphorylated peptides/lipids from biofluids.
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Affiliation(s)
- Sudhirkumar Shinde
- Department of Biomedical Sciences
- Faculty of Health and Society
- Malmö University
- SE 205 06 Malmö
- Sweden
| | - Jayashree Selvalatchmanan
- Singapore Lipidomics Incubator (SLING)
- Life Sciences Institute
- National University of Singapore
- Singapore 117456
- Singapore
| | - Anil Incel
- Department of Biomedical Sciences
- Faculty of Health and Society
- Malmö University
- SE 205 06 Malmö
- Sweden
| | - Maedeh Akhoundian
- Department of Biomedical Sciences
- Faculty of Health and Society
- Malmö University
- SE 205 06 Malmö
- Sweden
| | - Anne K. Bendt
- Singapore Lipidomics Incubator (SLING)
- Life Sciences Institute
- National University of Singapore
- Singapore 117456
- Singapore
| | - Federico Torta
- Singapore Lipidomics Incubator (SLING)
- Department of Biochemistry
- YLL School of Medicine
- National University of Singapore
- Singapore 11745
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29
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Bllaci L, Torsetnes SB, Wierzbicka C, Shinde S, Sellergren B, Rogowska-Wrzesinska A, Jensen ON. Phosphotyrosine Biased Enrichment of Tryptic Peptides from Cancer Cells by Combining pY-MIP and TiO2 Affinity Resins. Anal Chem 2017; 89:11332-11340. [DOI: 10.1021/acs.analchem.7b02091] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Loreta Bllaci
- Department
of Biochemistry and Molecular Biology and VILLUM Center for Bioanalytical
Sciences, University of Southern Denmark, DK-5230 Odense
M, Denmark
| | - Silje B. Torsetnes
- Department
of Biochemistry and Molecular Biology and VILLUM Center for Bioanalytical
Sciences, University of Southern Denmark, DK-5230 Odense
M, Denmark
| | - Celina Wierzbicka
- Department
of Biomedical Sciences, Malmö University, S-20506 Malmö, Sweden
| | - Sudhirkumar Shinde
- Department
of Biomedical Sciences, Malmö University, S-20506 Malmö, Sweden
| | - Börje Sellergren
- Department
of Biomedical Sciences, Malmö University, S-20506 Malmö, Sweden
| | - Adelina Rogowska-Wrzesinska
- Department
of Biochemistry and Molecular Biology and VILLUM Center for Bioanalytical
Sciences, University of Southern Denmark, DK-5230 Odense
M, Denmark
| | - Ole N. Jensen
- Department
of Biochemistry and Molecular Biology and VILLUM Center for Bioanalytical
Sciences, University of Southern Denmark, DK-5230 Odense
M, Denmark
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30
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Duarte M, Subedi P, Yilmaz E, Marcus K, Laurell T, Ekström S. Molecularly imprinted polymers synthesizedviatemplate immobilization on fumed silica nanoparticles for the enrichment of phosphopeptides. J Mol Recognit 2017; 31. [DOI: 10.1002/jmr.2677] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Revised: 08/27/2017] [Accepted: 09/08/2017] [Indexed: 01/14/2023]
Affiliation(s)
- Mariana Duarte
- Department of Biomedical Engineering; Lund University; Lund Sweden
- MIP Technologies AB, a subsidiary of Biotage AB; Lund Sweden
| | - Prabal Subedi
- Medizinisches Proteom-Center; Ruhr-University Bochum; Bochum Germany
| | - Ecevit Yilmaz
- MIP Technologies AB, a subsidiary of Biotage AB; Lund Sweden
| | - Katrin Marcus
- Medizinisches Proteom-Center; Ruhr-University Bochum; Bochum Germany
| | - Thomas Laurell
- Department of Biomedical Engineering; Lund University; Lund Sweden
| | - Simon Ekström
- Department of Biomedical Engineering; Lund University; Lund Sweden
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31
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Jabeen F, Najam-ul-Haq M, Rainer M, Huck CW, Bonn GK. In-Tip Lanthanum Oxide Monolith for the Enrichment of Phosphorylated Biomolecules. Anal Chem 2017; 89:10232-10238. [DOI: 10.1021/acs.analchem.7b01573] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Fahmida Jabeen
- Division
of Analytical Chemistry, Institute of Chemical Sciences, Bahauddin Zakariya University, Multan, Punjab 60800, Pakistan
- Institute
of Analytical Chemistry and Radiochemistry, Leopold-Franzens University, Innrain 80-82, Innsbruck, Tyrol 6020, Austria
| | - Muhammad Najam-ul-Haq
- Division
of Analytical Chemistry, Institute of Chemical Sciences, Bahauddin Zakariya University, Multan, Punjab 60800, Pakistan
- Institute
of Analytical Chemistry and Radiochemistry, Leopold-Franzens University, Innrain 80-82, Innsbruck, Tyrol 6020, Austria
| | - Matthias Rainer
- Institute
of Analytical Chemistry and Radiochemistry, Leopold-Franzens University, Innrain 80-82, Innsbruck, Tyrol 6020, Austria
| | - Christian W. Huck
- Institute
of Analytical Chemistry and Radiochemistry, Leopold-Franzens University, Innrain 80-82, Innsbruck, Tyrol 6020, Austria
| | - Guenther K. Bonn
- Institute
of Analytical Chemistry and Radiochemistry, Leopold-Franzens University, Innrain 80-82, Innsbruck, Tyrol 6020, Austria
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32
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Cenci L, Bertolla M, Anesi A, Ambrosi E, Guella G, Bossi AM. Micro- versus nano-sized molecularly imprinted polymers in MALDI-TOF mass spectrometry analysis of peptides. Anal Bioanal Chem 2017; 409:6253-6261. [DOI: 10.1007/s00216-017-0569-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Revised: 07/12/2017] [Accepted: 08/04/2017] [Indexed: 11/24/2022]
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33
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Rossetti C, Ore OG, Sellergren B, Halvorsen TG, Reubsaet L. Exploring the peptide retention mechanism in molecularly imprinted polymers. Anal Bioanal Chem 2017; 409:5631-5643. [PMID: 28752338 DOI: 10.1007/s00216-017-0520-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Revised: 07/09/2017] [Accepted: 07/12/2017] [Indexed: 12/18/2022]
Abstract
Molecularly imprinted polymers (MIPs) have been used as useful sorbents in solid-phase extraction for a wide range of molecules and sample matrices. Their unique selectivity can be fine-tuned in the imprinting process and is crucial for the extraction of macromolecules from complex matrices such as serum. A relevant example of this is the application of MIPs to peptides in diagnostic assays. In this article the selectivity of MIPs, previously implemented in a quantitative mass-spectrometric assay for the biomarker pro-gastrin-releasing peptide, is investigated. Partial least squares regression was used to generate models for the evaluation and prediction of the retention mechanism of MIPs. A hypothesis on interactions of MIPs with the target peptide was verified by ad hoc experiments considering the relevant peptide physicochemical properties highlighted from the multivariate analysis. Novel insights into and knowledge of the driving forces responsible for the MIP selectivity have been obtained and can be directly used for further optimization of MIP imprinting strategies. Graphical Abstract Applied analytical strategy: the Solid Phase Extraction (SPE) of digested Bovin Serum Albumin (BSA), using Molecularly Imprinted Polymers (MIP), is followed by the liquid chromatography-mass spectrometry (LC-MS) analysis for the identification of the retained peptides. The further application of multivariate analysis allows setting up a Partial Least Square (PLS) model, which describes the peptide retention into the MIP and gives additional knowledge to be used in the optimization of the MIP and the whole SPE method.
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Affiliation(s)
- Cecilia Rossetti
- Department of Pharmaceutical Chemistry, School of Pharmacy, University of Oslo, P.O. Box 1068, Blindern, 0316, Oslo, Norway
| | - Odd Gøran Ore
- Department of Pharmaceutical Chemistry, School of Pharmacy, University of Oslo, P.O. Box 1068, Blindern, 0316, Oslo, Norway
| | - Börje Sellergren
- Department of Biomedical Sciences, Faculty of Health and Society, University of Malmö, 20506, Malmö, Sweden
| | - Trine Grønhaug Halvorsen
- Department of Pharmaceutical Chemistry, School of Pharmacy, University of Oslo, P.O. Box 1068, Blindern, 0316, Oslo, Norway
| | - Léon Reubsaet
- Department of Pharmaceutical Chemistry, School of Pharmacy, University of Oslo, P.O. Box 1068, Blindern, 0316, Oslo, Norway.
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34
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Qing G, Lu Q, Xiong Y, Zhang L, Wang H, Li X, Liang X, Sun T. New Opportunities and Challenges of Smart Polymers in Post-Translational Modification Proteomics. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2017; 29:1604670. [PMID: 28112833 DOI: 10.1002/adma.201604670] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Revised: 11/13/2016] [Indexed: 06/06/2023]
Abstract
Protein post-translational modifications (PTMs), which denote covalent additions of various functional groups (e.g., phosphate, glycan, methyl, or ubiquitin) to proteins, significantly increase protein complexity and diversity. PTMs play crucial roles in the regulation of protein functions and numerous cellular processes. However, in a living organism, native PTM proteins are typically present at substoichiometric levels, considerably impeding mass-spectrometry-based analyses and identification. Over the past decade, the demand for in-depth PTM proteomics studies has spawned a variety of selective affinity materials capable of capturing trace amounts of PTM peptides from highly complex biosamples. However, novel design ideas or strategies are urgently required for fulfilling the increasingly complex and accurate requirements of PTM proteomics analysis, which can hardly be met by using conventional enrichment materials. Considering two typical types of protein PTMs, phosphorylation and glycosylation, an overview of polymeric enrichment materials is provided here, with an emphasis on the superiority of smart-polymer-based materials that can function in intelligent modes. Moreover, some smart separation materials are introduced to demonstrate the enticing prospects and the challenges of smart polymers applied in PTM proteomics.
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Affiliation(s)
- Guangyan Qing
- State Key Laboratory of Advanced Technology for Materials Synthesis and Processing, Wuhan University of Technology, 122 Luoshi Road, Wuhan, 430070, P. R. China
| | - Qi Lu
- State Key Laboratory of Advanced Technology for Materials Synthesis and Processing, Wuhan University of Technology, 122 Luoshi Road, Wuhan, 430070, P. R. China
| | - Yuting Xiong
- State Key Laboratory of Advanced Technology for Materials Synthesis and Processing, Wuhan University of Technology, 122 Luoshi Road, Wuhan, 430070, P. R. China
| | - Lei Zhang
- Institute of Biomedical and Pharmaceutical Sciences, College of Bioengineering, Hubei University of Technology, 28 Nanli Road, Wuhan, 430068, P. R. China
| | - Hongxi Wang
- State Key Laboratory of Advanced Technology for Materials Synthesis and Processing, Wuhan University of Technology, 122 Luoshi Road, Wuhan, 430070, P. R. China
| | - Xiuling Li
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023, P. R. China
| | - Xinmiao Liang
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023, P. R. China
| | - Taolei Sun
- State Key Laboratory of Advanced Technology for Materials Synthesis and Processing, Wuhan University of Technology, 122 Luoshi Road, Wuhan, 430070, P. R. China
- International School of Materials Science and Engineering, Wuhan University of Technology, 122 Luoshi Road, Wuhan, 430070, P. R. China
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35
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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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36
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Bertolla M, Cenci L, Anesi A, Ambrosi E, Tagliaro F, Vanzetti L, Guella G, Bossi AM. Solvent-Responsive Molecularly Imprinted Nanogels for Targeted Protein Analysis in MALDI-TOF Mass Spectrometry. ACS APPLIED MATERIALS & INTERFACES 2017; 9:6908-6915. [PMID: 28151640 DOI: 10.1021/acsami.6b16291] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Molecular imprinted poly(acrylamido)-derivative nanogels have shown their selectivity to bind the protein human serum transferrin (HTR) and also showed their capability for instantaneous solvent-induced modification upon the addition of acetonitrile. Integrated to matrix-assisted laser desorption/ionization time-of-flight mass analysis the HTR-imprinted solvent-responsive nanogels permitted the determination of HTR straight from serum and offered novel perspectives in targeted protein analysis.
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Affiliation(s)
- Maddalena Bertolla
- Department of Physics, University of Trento , Via Sommarive 14, 38123 Trento, Italy
| | - Lucia Cenci
- Department of Biotechnology, University of Verona , Strada Le Grazie 15, 37134 Verona, Italy
| | - Andrea Anesi
- Department of Physics, University of Trento , Via Sommarive 14, 38123 Trento, Italy
| | - Emmanuele Ambrosi
- Department of Molecular Sciences and Nanosystems, University Cà Foscari Venezia , Via Torino 155/b, 30173 Venice, Italy
| | - Franco Tagliaro
- Department of Diagnostics and Public Health, Unit of Forensic Medicine, University of Verona , P.le L.A. Scuro 10, 37134 Verona, Italy
| | - Lia Vanzetti
- Fondazione Bruno Kessler CMM-MNF , Via Sommarive 18, 38123 Trento, Italy
| | - Graziano Guella
- Department of Physics, University of Trento , Via Sommarive 14, 38123 Trento, Italy
| | - Alessandra Maria Bossi
- Department of Biotechnology, University of Verona , Strada Le Grazie 15, 37134 Verona, Italy
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37
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Methionine residues around phosphorylation sites are preferentially oxidized in vivo under stress conditions. Sci Rep 2017; 7:40403. [PMID: 28079140 PMCID: PMC5227694 DOI: 10.1038/srep40403] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Accepted: 12/06/2016] [Indexed: 12/22/2022] Open
Abstract
Protein phosphorylation is one of the most prevalent and well-understood protein modifications. Oxidation of protein-bound methionine, which has been traditionally perceived as an inevitable damage derived from oxidative stress, is now emerging as another modification capable of regulating protein activity during stress conditions. However, the mechanism coupling oxidative signals to changes in protein function remains unknown. An appealing hypothesis is that methionine oxidation might serve as a rheostat to control phosphorylation. To investigate this potential crosstalk between phosphorylation and methionine oxidation, we have addressed the co-occurrence of these two types of modifications within the human proteome. Here, we show that nearly all (98%) proteins containing oxidized methionine were also phosphoproteins. Furthermore, phosphorylation sites were much closer to oxidized methionines when compared to non-oxidized methionines. This proximity between modification sites cannot be accounted for by their co-localization within unstructured clusters because it was faithfully reproduced in a smaller sample of structured proteins. We also provide evidence that the oxidation of methionine located within phosphorylation motifs is a highly selective process among stress-related proteins, which supports the hypothesis of crosstalk between methionine oxidation and phosphorylation as part of the cellular defence against oxidative stress.
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38
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Wierzbicka C, Torsetnes SB, Jensen ON, Shinde S, Sellergren B. Hierarchically templated beads with tailored pore structure for phosphopeptide capture and phosphoproteomics. RSC Adv 2017. [DOI: 10.1039/c7ra00385d] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Phosphotyrosine selective beads prepared by polymer templating at two length scales results in improved capture of larger sized peptide fragments from tryptic protein digests.
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Affiliation(s)
- Celina Wierzbicka
- Department of Biomedical Sciences
- Faculty of Health and Society
- Malmö University
- SE 205 06 Malmö
- Sweden
| | - Silje B. Torsetnes
- Department of Biochemistry and Molecular Biology and VILLUM Center for Bioanalytical Sciences
- University of Southern Denmark
- DK-5230 Odense M
- Denmark
| | - Ole N. Jensen
- Department of Biochemistry and Molecular Biology and VILLUM Center for Bioanalytical Sciences
- University of Southern Denmark
- DK-5230 Odense M
- Denmark
| | - Sudhirkumar Shinde
- Department of Biomedical Sciences
- Faculty of Health and Society
- Malmö University
- SE 205 06 Malmö
- Sweden
| | - Börje Sellergren
- Department of Biomedical Sciences
- Faculty of Health and Society
- Malmö University
- SE 205 06 Malmö
- Sweden
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39
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Wierzbicka C, Liu M, Bauer D, Irgum K, Sellergren B. Cationic pTyr/pSer imprinted polymers based on a bis-imidazolium host monomer: phosphopeptide recognition in aqueous buffers demonstrated by μ-liquid chromatography and monolithic columns. J Mater Chem B 2017; 5:953-960. [DOI: 10.1039/c6tb02864k] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Capillary monoliths featuring grafted molecularly imprinted polymer films incorporating on a bis-imidazolium host monomer, displayed a remarkable crossreactivity with phosphorylated peptides in buffered media.
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Affiliation(s)
- Celina Wierzbicka
- Department of Biomedical Sciences
- Faculty of Health and Society
- Malmö University
- Malmö
- Sweden
| | - Mingquan Liu
- Department of Chemistry
- Umeå University
- 901 87 Umeå
- Sweden
| | - David Bauer
- Department of Biomedical Sciences
- Faculty of Health and Society
- Malmö University
- Malmö
- Sweden
| | - Knut Irgum
- Department of Chemistry
- Umeå University
- 901 87 Umeå
- Sweden
| | - Börje Sellergren
- Department of Biomedical Sciences
- Faculty of Health and Society
- Malmö University
- Malmö
- Sweden
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40
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Klement E, Medzihradszky KF. Extracellular Protein Phosphorylation, the Neglected Side of the Modification. Mol Cell Proteomics 2016; 16:1-7. [PMID: 27834735 DOI: 10.1074/mcp.o116.064188] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2016] [Revised: 11/10/2016] [Indexed: 12/18/2022] Open
Abstract
The very existence of extracellular phosphorylation has been questioned for a long time, although casein phosphorylation was discovered a century ago. In addition, several modification sites localized on secreted proteins or on extracellular or lumenal domains of transmembrane proteins have been catalogued in large scale phosphorylation analyses, though in most such studies this aspect of cellular localization was not considered. Our review presents examples when additional analyses were performed on already public data sets that revealed a wealth of information about this "neglected side" of the modification. We also sum up accumulated knowledge about extracellular phosphorylation, including the discovery of Golgi-residing kinases and the special difficulties encountered in targeted analyses. We hope future phosphorylation studies will not ignore the existence of phosphorylation outside of the cell, and further discoveries will shed more light on its biological role.
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Affiliation(s)
- Eva Klement
- From the ‡Laboratory of Proteomics Research, Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, Szeged, Hungary, and
| | - Katalin F Medzihradszky
- From the ‡Laboratory of Proteomics Research, Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, Szeged, Hungary, and .,the §Department of Pharmaceutical Chemistry, School of Pharmacy, University of California San Francisco, San Francisco, California
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41
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Chen J, Shinde S, Subedi P, Wierzbicka C, Sellergren B, Helling S, Marcus K. Validation of molecularly imprinted polymers for side chain selective phosphopeptide enrichment. J Chromatogr A 2016; 1471:45-50. [DOI: 10.1016/j.chroma.2016.10.018] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Revised: 09/12/2016] [Accepted: 10/08/2016] [Indexed: 01/13/2023]
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42
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Witzke KE, Rosowski K, Müller C, Ahrens M, Eisenacher M, Megger DA, Knobloch J, Koch A, Bracht T, Sitek B. Quantitative Secretome Analysis of Activated Jurkat Cells Using Click Chemistry-Based Enrichment of Secreted Glycoproteins. J Proteome Res 2016; 16:137-146. [DOI: 10.1021/acs.jproteome.6b00575] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Kathrin E. Witzke
- Medizinisches
Proteom-Center, Ruhr-Universität Bochum, 44801 Bochum, Germany
| | - Kristin Rosowski
- Medizinisches
Proteom-Center, Ruhr-Universität Bochum, 44801 Bochum, Germany
| | - Christian Müller
- Medizinisches
Proteom-Center, Ruhr-Universität Bochum, 44801 Bochum, Germany
| | - Maike Ahrens
- Medizinisches
Proteom-Center, Ruhr-Universität Bochum, 44801 Bochum, Germany
| | - Martin Eisenacher
- Medizinisches
Proteom-Center, Ruhr-Universität Bochum, 44801 Bochum, Germany
| | - Dominik A. Megger
- Medizinisches
Proteom-Center, Ruhr-Universität Bochum, 44801 Bochum, Germany
| | - Jürgen Knobloch
- Medical
Clinic III for Pneumology, Allergology, Sleep and Respiratory Medicine,
Bergmannsheil University Hospital, Ruhr-Universität Bochum, 44801 Bochum, Germany
| | - Andrea Koch
- Medical
Clinic III for Pneumology, Allergology, Sleep and Respiratory Medicine,
Bergmannsheil University Hospital, Ruhr-Universität Bochum, 44801 Bochum, Germany
| | - Thilo Bracht
- Medizinisches
Proteom-Center, Ruhr-Universität Bochum, 44801 Bochum, Germany
| | - Barbara Sitek
- Medizinisches
Proteom-Center, Ruhr-Universität Bochum, 44801 Bochum, Germany
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43
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Mutant desmin substantially perturbs mitochondrial morphology, function and maintenance in skeletal muscle tissue. Acta Neuropathol 2016; 132:453-73. [PMID: 27393313 PMCID: PMC4992032 DOI: 10.1007/s00401-016-1592-7] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Revised: 06/23/2016] [Accepted: 06/24/2016] [Indexed: 12/18/2022]
Abstract
Secondary mitochondrial dysfunction is a feature in a wide variety of human protein aggregate diseases caused by mutations in different proteins, both in the central nervous system and in striated muscle. The functional relationship between the expression of a mutated protein and mitochondrial dysfunction is largely unknown. In particular, the mechanism how this dysfunction drives the disease process is still elusive. To address this issue for protein aggregate myopathies, we performed a comprehensive, multi-level analysis of mitochondrial pathology in skeletal muscles of human patients with mutations in the intermediate filament protein desmin and in muscles of hetero- and homozygous knock-in mice carrying the R349P desmin mutation. We demonstrate that the expression of mutant desmin causes disruption of the extrasarcomeric desmin cytoskeleton and extensive mitochondrial abnormalities regarding subcellular distribution, number and shape. At the molecular level, we uncovered changes in the abundancy and assembly of the respiratory chain complexes and supercomplexes. In addition, we revealed a marked reduction of mtDNA- and nuclear DNA-encoded mitochondrial proteins in parallel with large-scale deletions in mtDNA and reduced mtDNA copy numbers. Hence, our data demonstrate that the expression of mutant desmin causes multi-level damage of mitochondria already in early stages of desminopathies.
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44
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Cenci L, Guella G, Andreetto E, Ambrosi E, Anesi A, Bossi AM. Guided folding takes a start from the molecular imprinting of structured epitopes. NANOSCALE 2016; 8:15665-70. [PMID: 27524659 DOI: 10.1039/c6nr03467e] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
A biomimetic route towards assisted folding was explored. Molecularly imprinted polymeric nanoparticles (MIP NPs), i.e. biomimetics with entailed molecular recognition properties made by a template assisted synthesis, were prepared to target a structured epitope: the cystine containing peptide CC9ox, which corresponds to the apical portion of the β-hairpin hormone Hepcidin-25. The structural selection was achieved by the MIP NPs; moreover, the MIP NPs demonstrated favouring the folding of the linear random peptide (CC9red) into the structured one (CC9ox), anticipating the future role of the MIP NPs as in situ nanomachines to counteract folding defects.
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Affiliation(s)
- L Cenci
- University of Verona, Dept. of Biotechnology, Strada Le Grazie 15, 37134 Verona, Italy.
| | - G Guella
- University of Trento, Dept. of Physics, Via Sommarive 14, 38123 Trento, Italy
| | - E Andreetto
- University of Verona, Dept. of Biotechnology, Strada Le Grazie 15, 37134 Verona, Italy.
| | - E Ambrosi
- University Cà Foscari Venezia, Dept. of Molecular Sciences and Nanosystems, Centro di Microscopia Elettronica "Giovanni Stevanato", Via Torino 155/b, 30173 Venice, Italy
| | - A Anesi
- University of Trento, Dept. of Physics, Via Sommarive 14, 38123 Trento, Italy
| | - A M Bossi
- University of Verona, Dept. of Biotechnology, Strada Le Grazie 15, 37134 Verona, Italy.
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45
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Magnetic graphitic carbon nitride anion exchanger for specific enrichment of phosphopeptides. J Chromatogr A 2016; 1437:137-144. [DOI: 10.1016/j.chroma.2016.01.080] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Revised: 01/26/2016] [Accepted: 01/30/2016] [Indexed: 11/19/2022]
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46
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Chen Y, Li D, Bie Z, He X, Liu Z. Coupling of Phosphate-Imprinted Mesoporous Silica Nanoparticles-Based Selective Enrichment with Matrix-Assisted Laser Desorption Ionization-Time-of-Flight Mass Spectrometry for Highly Efficient Analysis of Protein Phosphorylation. Anal Chem 2016; 88:1447-54. [DOI: 10.1021/acs.analchem.5b04343] [Citation(s) in RCA: 84] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Yang Chen
- State Key Laboratory
of Analytical
Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Daojin Li
- State Key Laboratory
of Analytical
Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Zijun Bie
- State Key Laboratory
of Analytical
Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Xinpei He
- State Key Laboratory
of Analytical
Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Zhen Liu
- State Key Laboratory
of Analytical
Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
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