1
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Li J, Zhan X. Mass spectrometry analysis of phosphotyrosine-containing proteins. MASS SPECTROMETRY REVIEWS 2024; 43:857-887. [PMID: 36789499 DOI: 10.1002/mas.21836] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Revised: 12/19/2022] [Accepted: 01/24/2023] [Indexed: 06/18/2023]
Abstract
Tyrosine phosphorylation is a crucial posttranslational modification that is involved in various aspects of cell biology and often has functions in cancers. It is necessary not only to identify the specific phosphorylation sites but also to quantify their phosphorylation levels under specific pathophysiological conditions. Because of its high sensitivity and accuracy, mass spectrometry (MS) has been widely used to identify endogenous and synthetic phosphotyrosine proteins/peptides across a range of biological systems. However, phosphotyrosine-containing proteins occur in extremely low abundance and they degrade easily, severely challenging the application of MS. This review highlights the advances in both quantitative analysis procedures and enrichment approaches to tyrosine phosphorylation before MS analysis and reviews the differences among phosphorylation, sulfation, and nitration of tyrosine residues in proteins. In-depth insights into tyrosine phosphorylation in a wide variety of biological systems will offer a deep understanding of how signal transduction regulates cellular physiology and the development of tyrosine phosphorylation-related drugs as cancer therapeutics.
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Affiliation(s)
- Jiajia Li
- Medical Science and Technology Innovation Center, Shandong Key Laboratory of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University & Shandong Academy of Medical Sciences, Shandong, Jinan, People's Republic of China
- Key Laboratory of Cancer Proteomics of Chinese Ministry of Health, Central South University, Changsha, Hunan, People's Republic of China
| | - Xianquan Zhan
- Medical Science and Technology Innovation Center, Shandong Key Laboratory of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University & Shandong Academy of Medical Sciences, Shandong, Jinan, People's Republic of China
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2
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Chamrád I, Simerský R, Lenobel R, Novák O. Exploring affinity chromatography in proteomics: A comprehensive review. Anal Chim Acta 2024; 1306:342513. [PMID: 38692783 DOI: 10.1016/j.aca.2024.342513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 03/19/2024] [Accepted: 03/20/2024] [Indexed: 05/03/2024]
Abstract
Over the past decades, the proteomics field has undergone rapid growth. Progress in mass spectrometry and bioinformatics, together with separation methods, has brought many innovative approaches to the study of the molecular biology of the cell. The potential of affinity chromatography was recognized immediately after its first application in proteomics, and since that time, it has become one of the cornerstones of many proteomic protocols. Indeed, this chromatographic technique exploiting the specific binding between two molecules has been employed for numerous purposes, from selective removal of interfering (over)abundant proteins or enrichment of scarce biomarkers in complex biological samples to mapping the post-translational modifications and protein interactions with other proteins, nucleic acids or biologically active small molecules. This review presents a comprehensive survey of this versatile analytical tool in current proteomics. To navigate the reader, the haphazard space of affinity separations is classified according to the experiment's aims and the separated molecule's nature. Different types of available ligands and experimental strategies are discussed in further detail for each of the mentioned procedures.
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Affiliation(s)
- Ivo Chamrád
- Laboratory of Growth Regulators, Faculty of Science, Palacký University and Institute of Experimental Botany of the Czech Academy of Sciences, Šlechtitelů 241/27, CZ-77900, Olomouc, Holice, Czech Republic.
| | - Radim Simerský
- Department of Chemical Biology, Faculty of Science, Palacký University, Šlechtitelů 241/27, CZ-77900, Olomouc, Holice, Czech Republic
| | - René Lenobel
- Laboratory of Growth Regulators, Faculty of Science, Palacký University and Institute of Experimental Botany of the Czech Academy of Sciences, Šlechtitelů 241/27, CZ-77900, Olomouc, Holice, Czech Republic
| | - Ondřej Novák
- Laboratory of Growth Regulators, Faculty of Science, Palacký University and Institute of Experimental Botany of the Czech Academy of Sciences, Šlechtitelů 241/27, CZ-77900, Olomouc, Holice, Czech Republic
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3
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Zhou J, Mujahid Ali M, Yu W, Cheng X, Gao Y, Hu L. Oriented docking of the template for improved imprinting efficiency toward peptide with modifications. Anal Chim Acta 2024; 1301:342450. [PMID: 38553121 DOI: 10.1016/j.aca.2024.342450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2024] [Accepted: 03/04/2024] [Indexed: 04/02/2024]
Abstract
Molecular imprinting polymers (MIPs) are synthetic receptors as biomimetic materials for various applications ranging from sensing to separation and catalysis. However, currently existing MIPs are stuck to some of the issues including the longer preparation steps and poor performance. In this report, a facile and one-pot strategy by integrating the in-situ growth of magnetic nanoparticles and reversed phase microemulsion oriented molecularly imprinting strategy to develop magnetic molecular imprinted nanocomposites was proposed. Through self-assembling of the template, it brought up highly ordered and uniform arrangement of the imprinting structure, which offered faster adsorption kinetic as adsorption equilibrium was achived within 15 min, higher adsorption capacity (Qmax = 48.78 ± 1.54 μmol/g) and high affinity (Kd = 127.63 ± 9.66 μM) toward paradigm molecule-adenosine monophosphate (AMP) compared to the conventional bulk imprinting. The developed MIPs offered better affinity and superior specificity which allowed the specific enrichment toward targeted phosphorylated peptides from complex samples containing 100-fold more abundant interfering peptides. Interestingly, different types of MIPs can be developed which could targetly enrich the specific phosphorylated peptides for mass spectrometry analysis by simply switching the templates, and this strategy also successfully achieved imprinting of macromolecular peptides. Collectively, the approach showed broad applicability to target specific enrichment from metabolites to phosphorylated peptides and providing an alternative choice for selective recognition and analysis from complex biological systems.
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Affiliation(s)
- Juntao Zhou
- Center for Supramolecular Chemical Biology, State Key Laboratory of Supramolecular Structure and Materials, School of Life Sciences, Jilin University, Changchun, 130012, China
| | - Muhammad Mujahid Ali
- State Key Laboratory of Bioelectronics, National Demonstration Center for Experimental Biomedical Engineering Education, Southeast University, Nanjing, 210096, China.
| | - Wenjing Yu
- Center for Supramolecular Chemical Biology, State Key Laboratory of Supramolecular Structure and Materials, School of Life Sciences, Jilin University, Changchun, 130012, China
| | - Xianhui Cheng
- Center for Supramolecular Chemical Biology, State Key Laboratory of Supramolecular Structure and Materials, School of Life Sciences, Jilin University, Changchun, 130012, China
| | - Yujun Gao
- Center for Supramolecular Chemical Biology, State Key Laboratory of Supramolecular Structure and Materials, School of Life Sciences, Jilin University, Changchun, 130012, China
| | - Lianghai Hu
- Center for Supramolecular Chemical Biology, State Key Laboratory of Supramolecular Structure and Materials, School of Life Sciences, Jilin University, Changchun, 130012, China.
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4
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Xiong F, Zhang T, Ma J, Jia Q. Dual-ligand hydrogen-bonded organic framework: Tailored for mono-phosphopeptides and glycopeptides analysis. Talanta 2024; 266:125068. [PMID: 37574607 DOI: 10.1016/j.talanta.2023.125068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 08/06/2023] [Accepted: 08/08/2023] [Indexed: 08/15/2023]
Abstract
Hydrogen-bonded organic frameworks (HOFs) have emerged as a promising class of materials for applications of separation and enrichment. Utilizing multiple-ligands to construct HOFs is a promising avenue towards the development of structurally stable and functionally diverse frameworks, offering opportunities to create customized binding sites for selective recognition of biomolecules. In recent years, due to the crucial role that protein post-translational modifications (PTMs) play in maintaining protein function and regulating signaling pathways, and the growing recognition of the extensive cross-talk that can occur between PTMs, simultaneous analysis of different types of PTMs represents a requirement of a new generation of enrichment materials. Here, for the first attempt, we report a dual-ligand HOF constructed from borate anion and guanidinium cation for the simultaneous identification of glycopeptides and phosphopeptides, especially mono-phosphopeptides. According to theoretical calculations, the HOF functional sites display a synergistic "matching" effect with mono-phosphopeptides, resulting in a stronger enrichment effect for mono-phosphopeptides as compared to multi-phosphopeptides. Also, due to its high hydrophilicity and boronate affinity, this material can efficiently capture glycoproteins. HOF is set to become an active research direction in the development of highly efficient simultaneous protein enrichment materials, and offers a new approach for comprehensive PTMs analysis.
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Affiliation(s)
- Fangfang Xiong
- College of Chemistry, Jilin University, Changchun 130012, China
| | - Te Zhang
- China-Japan Union Hospital of Jilin University, Changchun 130033, China
| | - Jiutong Ma
- College of Chemistry, Jilin University, Changchun 130012, China
| | - Qiong Jia
- College of Chemistry, Jilin University, Changchun 130012, China; Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, College of Life Sciences, Jilin University, Changchun 130012, China.
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5
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He JY, Li Q, Xu HX, Zheng QY, Zhang QH, Zhou LD, Wang CZ, Yuan CS. Recognition and analysis of biomarkers in tumor microenvironments based on promising molecular imprinting strategies with high selectivity. Trends Analyt Chem 2023. [DOI: 10.1016/j.trac.2023.117033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
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6
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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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7
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Peng C, Li S, Wang Y, Ge L, Zhang S, Cai Q, Zhen D, Chen P. Preparation of Er-Nd-TiO2 nanocomposite for the highly selective enrichment of phosphotyrosine peptides. Microchem J 2023. [DOI: 10.1016/j.microc.2023.108597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/09/2023]
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8
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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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9
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Xie Z, Feng Q, Zhang S, Yan Y, Deng C, Ding CF. Advances in proteomics sample preparation and enrichment for phosphorylation and glycosylation analysis. Proteomics 2022; 22:e2200070. [PMID: 36100958 DOI: 10.1002/pmic.202200070] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 08/06/2022] [Accepted: 08/15/2022] [Indexed: 11/08/2022]
Abstract
As the common and significant chemical modifications, post-translational modifications (PTMs) play a key role in the functional proteome. Affected by the signal interference, low concentration, and insufficient ionization efficiency of impurities, the direct detection of PTMs by mass spectrometry (MS) still faces many challenges. Therefore, sample preparation and enrichment are an indispensable link before MS analysis of PTMs in proteomics. The rapid development of functionalized materials with diverse morphologies and compositions provides an avenue for sample preparation and enrichment for PTMs analysis. In this review, we summarize recent advances in the application of novel functionalized materials in sample preparation for phosphoproteomes and glycoproteomes analysis. In addition, this review specifically discusses the design and preparation of functionalized materials based on different enrichment mechanisms, and proposes research directions and potential challenges for proteomic PTMs research.
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Affiliation(s)
- Zehu Xie
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang, China
| | - Quanshou Feng
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang, China
| | - Shun Zhang
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang, China
| | - Yinghua Yan
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang, China.,Department of Experimental Medical Science, HwaMei Hospital, University of Chinese Academy of Sciences, Ningbo, Zhejiang, China
| | - Chunhui Deng
- Department of Chemistry, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Chuan-Fan Ding
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang, China.,Department of Experimental Medical Science, HwaMei Hospital, University of Chinese Academy of Sciences, Ningbo, Zhejiang, China
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10
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Materials, workflows and applications of IMAC for phosphoproteome profiling in the recent decade: A review. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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11
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Xia C, Wang Q, Liang W, Wang B, Feng Q, Zhou C, Xie Y, Yan Y, Zhao L, Jiang B, Cui W, Liang H. Superhydrophilic nanocomposite adsorbents modified via nitrogen-rich phosphonate-functionalized ionic liquid linkers: enhanced phosphopeptide enrichment and phosphoproteome analysis of tau phosphorylation in the hippocampal lysate of Alzheimer's transgenic mice. J Mater Chem B 2022; 10:7967-7978. [PMID: 36124862 DOI: 10.1039/d2tb01508k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this study, new graphene-based IMAC nanocomposites for phosphopeptide enrichment were prepared according to the guideline of our new design strategy. Superhydrophilic polyethyleneimine (PEI) was introduced, to which a phosphonate-functionalized ionic liquid (PFIL) was covalently bound, to form superhydrophilic and cationic surface layers with high densities of nitrogen atoms, phosphonate functional groups, and high-loading metal ions. Due to the combined features of superhydrophilicity, flexibility, highly dense metal binding sites, large surface area and excellent size-exclusion effect, the fabricated nanocomposite G@mSiO2@PEI-PFIL-Ti4+ exhibits superior detection sensitivity to enrich phosphopeptides (tryptic β-casein digest, 0.1 fmol), and extraordinary enrichment specificity to enrich phosphopeptides from a digest mixture of β-casein and bovine serum albumin (BSA) (molar ratio, 1 : 12 000). The excellent size-exclusion effect was also observed, and 27 endogenous phosphopeptides were identified in human saliva. All these results could be attributed to the unique superhydrophilic nanocomposite structure with a high density of a cationic linker modified with phosphonate functionality. Moreover, G@mSiO2@PEI-PFIL-Ti4+ adsorbents were used to extract phosphopeptides from the tryptic digests of hippocampal lysates for quantitative phosphoproteome analysis. The preliminary results indicate that 1649 phosphoproteins, 3286 phosphopeptides and 4075 phosphorylation sites were identified. A total of 13 Alzheimer's disease (AD)-related phosphopeptides within tau proteins were detected with a wide coverage from p-Thr111 to p-Ser404, in which the amounts of some phoshopeptides at certain sites in AD transgenic mice were found statistically higher than those in wild type littermates. Besides, phosphorylated neurofilament heavy chains, a potential biomarker for amyotrophic lateral sclerosis and traumatic brain injury, were also identified. Finally, the adsorbent was applied to human cerebrospinal fluid (CSF) and blood samples. 5 unique phosphopeptides of neuroendocrine specific VGF were identified in the CSF, while many phosphopeptides originated from the nervous system were found in the blood sample. All these results suggest that our new IMAC materials exhibit unbiased enrichment ability with superior detection sensitivity and specificity, allowing the global phosphoproteome analysis of complicated biological samples more convincible and indicating the potential use in disease diagnosis.
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Affiliation(s)
- Chenglong Xia
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, School of Materials Science and Chemical Engineering, Ningbo University, Ningbo 315211, China.
| | - Qiyao Wang
- Ningbo Key Laboratory of Behavior Neuroscience, Zhejiang Province Key Laboratory of Pathophysiology, School of Medicine, Ningbo University, Ningbo 315211, China.
| | - Weida Liang
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, School of Materials Science and Chemical Engineering, Ningbo University, Ningbo 315211, China.
| | - Binbin Wang
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, School of Materials Science and Chemical Engineering, Ningbo University, Ningbo 315211, China.
| | - Quanshou Feng
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, School of Materials Science and Chemical Engineering, Ningbo University, Ningbo 315211, China.
| | - Chenyang Zhou
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, School of Materials Science and Chemical Engineering, Ningbo University, Ningbo 315211, China.
| | - Yishan Xie
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, School of Materials Science and Chemical Engineering, Ningbo University, Ningbo 315211, China.
| | - Yinghua Yan
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, School of Materials Science and Chemical Engineering, Ningbo University, Ningbo 315211, China.
| | - Lingling Zhao
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, School of Materials Science and Chemical Engineering, Ningbo University, Ningbo 315211, China.
| | - Bo Jiang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian, Liaoning, 116023, P. R. China
| | - Wei Cui
- Ningbo Key Laboratory of Behavior Neuroscience, Zhejiang Province Key Laboratory of Pathophysiology, School of Medicine, Ningbo University, Ningbo 315211, China.
| | - Hongze Liang
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, School of Materials Science and Chemical Engineering, Ningbo University, Ningbo 315211, China.
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Ren Y, Zhou J, Ali MM, Zhang X, Hu L. Isoform-specific recognition of phosphopeptides by molecular imprinting nanoparticles with double-binding mode. Anal Chim Acta 2022; 1219:340034. [PMID: 35715134 DOI: 10.1016/j.aca.2022.340034] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 05/29/2022] [Accepted: 06/02/2022] [Indexed: 11/17/2022]
Abstract
Phosphorylation is one of the most important post-translational modifications of proteins, but due to the low abundance of phosphopeptides, enrichment is an essential step before mass spectrometric analysis. Although there are a number of enrichment methods developed targeting different forms of proteins phosphorylations, there are few reports on specific recognition and capture of single phosphopeptide. Herein, based on the advantages of dual affinity of TiO2 and urea to a phosphate group and molecular imprinting towards the peptide sequence, the precise recognition of intact phosphorylated peptides was successfully achieved. The same peptide sequence with different phosphorylation forms (c.a. Ser, Thr and Tyr) were used as templates for proof-of-principle study, and the imprinted particles were successfully synthesized, characterized, and have the capacity to specifically recognize the targeted unique phosphorylation excluding even its isoforms. In addition, the produced molecularly imprinted nanoparticles have numerous important advantages, including strong affinity, high specificity toward single phosphopeptides, tolerance to interferences, fast binding kinetics, substantial binding capacity, excellent stability and reusability, making them an ideal sorbent for specific enrichment of unique phosphopeptides. Finally, different phosphorylation forms were specifically enriched from both standard peptides' mixture and casein/milk digests.
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Affiliation(s)
- Yujuan Ren
- Center for Supramolecular Chemical Biology, State Key Laboratory of Supramolecular Structure and Materials, School of Life Sciences, Jilin University, Changchun, 130012, China
| | - Juntao Zhou
- Center for Supramolecular Chemical Biology, State Key Laboratory of Supramolecular Structure and Materials, School of Life Sciences, Jilin University, Changchun, 130012, China
| | - Muhammad Mujahid Ali
- State Key Laboratory of Bioelectronics, National Demonstration Center for Experimental Biomedical Engineering Education, Southeast University, Nanjing, China
| | - Xue Zhang
- Center for Supramolecular Chemical Biology, State Key Laboratory of Supramolecular Structure and Materials, School of Life Sciences, Jilin University, Changchun, 130012, China
| | - Lianghai Hu
- Center for Supramolecular Chemical Biology, State Key Laboratory of Supramolecular Structure and Materials, School of Life Sciences, Jilin University, Changchun, 130012, China.
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13
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Li X, Ma S, Tang R, Ou J. Interface-Engineered Hollow Nanospheres with Titanium(IV) Binding Sites and Microwindows as Affinity Probes for Ultrafast and Enhanced Phosphopeptides Enrichment. Anal Chem 2022; 94:5159-5166. [PMID: 35300494 DOI: 10.1021/acs.analchem.2c00164] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Enrichment and identification of phosphopeptides in real biological samples are of great significance in many aspects. Herein, Ti4+-immobilized silica hollow nanospheres were tailored via chelating with phosphonic acid groups produced from dealkylation of phosphonate ester functionalized silica hollow nanospheres, which were synthesized through a single micelle templated method with diethylphosphatoethyltriethoxysilane (DPTES) and tetramethoxysilane (TMOS) as silane precursors under neutral conditions. The characterization results of transmission electron microscopy (TEM), nitrogen sorption isotherms, FT-IR, and energy-dispersive X-ray (EDX) spectroscopy confirmed the successful preparation of Ti4+-immobilized silica hollow nanospheres (SHS-Ti; approximately 17 nm particle size), which possessed a 10 nm hollow cavity with 1.6 nm micropores on the thin shell (about 3.5 nm). Attributed to the immobilized Ti4+ and high specific area (396 m2/g), SHS-Ti was applied as a Ti4+-immobilized metal affinity chromatography (Ti-IMAC) material and showed good specificity, a low limit of detection (5 fmol), high selectivity (tryptic digestion mixture of bovine serum albumin/β-casein, 1000:1 molar ratio), high binding capacity (120 mg/g for pyridoxal 5'-phosphate), and a high binding constant (1.30 × 103 L/mg). Particularly, benefiting from the unique hollow structure with microwindows on the thin shell, a short transport path, and small mass transfer resistance, SHS-Ti exhibited excellent enrichment speed in which both phosphopeptide loading and elution could be completed in 1 min. The 5298 unique phosphopeptides from 1618 unique phosphoproteins were identified after enrichment by SHS-Ti from 100 μg Jurkat cell lysates within three independent replicates. The results showed that SHS-Ti could be utilized as a novel and promising enrichment probe for phosphopeptide characterization in MS-based phosphoproteomics and related fields.
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Affiliation(s)
- Xiaowei Li
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian 116023, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shujuan Ma
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian 116023, China
| | - Ruizhi Tang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian 116023, China
| | - Junjie Ou
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian 116023, China.,University of Chinese Academy of Sciences, Beijing 100049, China
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14
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Urban J. A review on recent trends in the phosphoproteomics workflow. From sample preparation to data analysis. Anal Chim Acta 2022; 1199:338857. [DOI: 10.1016/j.aca.2021.338857] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Revised: 07/14/2021] [Accepted: 07/15/2021] [Indexed: 12/12/2022]
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15
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Teixeira SPB, Reis RL, Peppas NA, Gomes ME, Domingues RMA. Epitope-imprinted polymers: Design principles of synthetic binding partners for natural biomacromolecules. SCIENCE ADVANCES 2021; 7:eabi9884. [PMID: 34714673 PMCID: PMC8555893 DOI: 10.1126/sciadv.abi9884] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Accepted: 09/07/2021] [Indexed: 05/27/2023]
Abstract
Molecular imprinting (MI) has been explored as an increasingly viable tool for molecular recognition in various fields. However, imprinting of biologically relevant molecules like proteins is severely hampered by several problems. Inspired by natural antibodies, the use of epitopes as imprinting templates has been explored to circumvent those limitations, offering lower costs and greater versatility. Here, we review the latest innovations in this technology, as well as different applications where MI polymers (MIPs) have been used to target biomolecules of interest. We discuss the several steps in MI, from the choice of epitope and functional monomers to the different production methods and possible applications. We also critically explore how MIP performance can be assessed by various parameters. Last, we present perspectives on future breakthroughs and advances, offering insights into how MI techniques can be expanded to new fields such as tissue engineering.
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Affiliation(s)
- Simão P. B. Teixeira
- 3B’s Research Group, I3Bs—Research Institute on Biomaterials, Biodegradables and Biomimetics, University of Minho, Headquarters of the European Institute of Excellence on Tissue Engineering and Regenerative Medicine, AvePark—Parque de Ciência e Tecnologia, Zona Industrial da Gandra, 4805-017 Barco, Guimarães, Portugal
- ICVS/3B’s—PT Government Associate Laboratory, Braga, Guimarães, Portugal
| | - Rui L. Reis
- 3B’s Research Group, I3Bs—Research Institute on Biomaterials, Biodegradables and Biomimetics, University of Minho, Headquarters of the European Institute of Excellence on Tissue Engineering and Regenerative Medicine, AvePark—Parque de Ciência e Tecnologia, Zona Industrial da Gandra, 4805-017 Barco, Guimarães, Portugal
- ICVS/3B’s—PT Government Associate Laboratory, Braga, Guimarães, Portugal
| | - Nicholas A. Peppas
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, TX 78712-1801, USA
- Institute for Biomaterials, Drug Delivery, and Regenerative Medicine, University of Texas at Austin, Austin, TX 78712-1801, USA
- Department of Biomedical Engineering, University of Texas at Austin, Austin, TX 78712-1801, USA
- Department of Pediatrics, Dell Medical School, University of Texas at Austin, Austin, TX 78712-1801, USA
- Department of Surgery and Perioperative Care, Dell Medical School, University of Texas at Austin, Austin, TX 78712-1801, USA
- Division of Molecular Pharmaceutics and Drug Delivery, College of Pharmacy, University of Texas at Austin, Austin, TX 78712-1801, USA
| | - Manuela E. Gomes
- 3B’s Research Group, I3Bs—Research Institute on Biomaterials, Biodegradables and Biomimetics, University of Minho, Headquarters of the European Institute of Excellence on Tissue Engineering and Regenerative Medicine, AvePark—Parque de Ciência e Tecnologia, Zona Industrial da Gandra, 4805-017 Barco, Guimarães, Portugal
- ICVS/3B’s—PT Government Associate Laboratory, Braga, Guimarães, Portugal
| | - Rui M. A. Domingues
- 3B’s Research Group, I3Bs—Research Institute on Biomaterials, Biodegradables and Biomimetics, University of Minho, Headquarters of the European Institute of Excellence on Tissue Engineering and Regenerative Medicine, AvePark—Parque de Ciência e Tecnologia, Zona Industrial da Gandra, 4805-017 Barco, Guimarães, Portugal
- ICVS/3B’s—PT Government Associate Laboratory, Braga, Guimarães, Portugal
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16
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Affinity capture in bottom-up protein analysis - Overview of current status of proteolytic peptide capture using antibodies and molecularly imprinted polymers. Anal Chim Acta 2021; 1182:338714. [PMID: 34602193 DOI: 10.1016/j.aca.2021.338714] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 05/27/2021] [Accepted: 05/28/2021] [Indexed: 12/17/2022]
Abstract
Antibody-based affinity capture has become the gold standard in sample preparation for determination of low-abundance protein biomarkers in biological matrices prior to liquid chromatography-mass spectrometry (LC-MS) determination. This comprises both capture of intact proteins prior to the digestion step and capture of proteolytic peptides after digestion of the sample. The latter can be performed both using antibodies specifically developed to capture target proteolytic peptides, as well as by the less explored use of anti-protein antibodies to capture the proteolytic epitope peptide. Molecularly imprinted polymers (MIPs), also called plastic antibodies are another affinity-based approach emerging as sample preparation technique in LC-MS based protein biomarker analysis. The current review gives a critical and comprehensive overview of proteolytic peptide capture using antibodies and MIPs in LC-MS based protein biomarker determination during the last five years. The main emphasis is on capture of non-modified peptides, while a brief overview of affinity capture of peptides containing post-translational modifications (PTMs) is provided.
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17
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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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18
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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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19
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Arribas Diez I, Govender I, Naicker P, Stoychev S, Jordaan J, Jensen ON. Zirconium(IV)-IMAC Revisited: Improved Performance and Phosphoproteome Coverage by Magnetic Microparticles for Phosphopeptide Affinity Enrichment. J Proteome Res 2020; 20:453-462. [PMID: 33226818 DOI: 10.1021/acs.jproteome.0c00508] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Phosphopeptide enrichment is an essential step in large-scale, quantitative phosphoproteomics by mass spectrometry. Several phosphopeptide affinity enrichment techniques exist, such as immobilized metal-ion affinity chromatography (IMAC) and metal oxide affinity chromatography (MOAC). We compared zirconium(IV) IMAC (Zr-IMAC) magnetic microparticles to more commonly used titanium(IV) IMAC (Ti-IMAC) and TiO2 magnetic microparticles for phosphopeptide enrichment from simple and complex protein samples prior to phosphopeptide sequencing and characterization by mass spectrometry (liquid chromatography-tandem mass spectrometry, LC-MS/MS). We optimized sample-loading conditions to increase phosphopeptide recovery for Zr-IMAC-, Ti-IMAC-, and TiO2-based workflows by 22, 24, and 35%, respectively. The optimized protocol resulted in improved performance of Zr-IMAC over Ti-IMAC and TiO2 as well as high-performance liquid chromatography-based Fe(III)-IMAC with up to 23% more identified phosphopeptides. The different enrichment chemistries showed a high degree of overlap but also differences in phosphopeptide selectivity and complementarity. We conclude that Zr-IMAC improves phosphoproteome coverage and recommend that this complementary and scalable affinity enrichment method is more widely used in biological and biomedical studies of cell signaling and the search for biomarkers. Data are available via ProteomeXchange with identifier PXD018273.
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Affiliation(s)
- Ignacio Arribas Diez
- Department of Biochemistry & Molecular Biology and VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, Odense M DK-5230, Denmark
| | - Ireshyn Govender
- NextGen Health, Council for Scientific and Industrial Research, Pretoria 0184, South Africa
| | - Previn Naicker
- NextGen Health, Council for Scientific and Industrial Research, Pretoria 0184, South Africa
| | - Stoyan Stoychev
- NextGen Health, Council for Scientific and Industrial Research, Pretoria 0184, South Africa.,ReSyn Biosciences, Pretoria 1610, Gauteng, South Africa
| | - Justin Jordaan
- ReSyn Biosciences, Pretoria 1610, Gauteng, South Africa.,Rhodes University, Grahamstown 6139, South Africa
| | - Ole N Jensen
- Department of Biochemistry & Molecular Biology and VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, Odense M DK-5230, Denmark
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20
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Qiu W, Evans CA, Landels A, Pham TK, Wright PC. Phosphopeptide enrichment for phosphoproteomic analysis - A tutorial and review of novel materials. Anal Chim Acta 2020; 1129:158-180. [PMID: 32891386 DOI: 10.1016/j.aca.2020.04.053] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Revised: 04/23/2020] [Accepted: 04/24/2020] [Indexed: 12/12/2022]
Abstract
Significant technical advancements in phosphopeptide enrichment have enabled the identification of thousands of p-peptides (mono and multiply phosphorylated) in a single experiment. However, it is still not possible to enrich all p-peptide species in a single step. A range of new techniques and materials has been developed, with the potential to provide a step-change in phosphopeptide enrichment. The first half of this review contains a tutorial for new potential phosphoproteomic researchers; discussing the key steps of a typical phosphoproteomic experiment used to investigate canonical phosphorylation sites (serine, threonine and tyrosine). The latter half then show-cases the latest developments in p-peptide enrichment including: i) Strategies to mitigate non-specific binding in immobilized metal ion affinity chromatography and metal oxide affinity chromatography protocols; ii) Techniques to separate multiply phosphorylated peptides from monophosphorylated peptides (including canonical from non-canonical phosphorylated peptides), or to simultaneously co-enrich other post-translational modifications; iii) New hybrid materials and methods directed towards enhanced selectivity and efficiency of metal-based enrichment; iv) Novel materials that hold promise for enhanced phosphotyrosine enrichment. A combination of well-understood techniques and materials is much more effective than any technique in isolation; but the field of phosphoproteomics currently requires benchmarking of novel materials against current methodologies to fully evaluate their utility in peptide based proteoform analysis.
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Affiliation(s)
- Wen Qiu
- State Key Laboratory of Rice Biology and Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, 310058, Hangzhou, China
| | - Caroline A Evans
- ChELSI Institute, Department of Chemical and Biological Engineering, The University of Sheffield, Mappin Street, Sheffield, S1 3JD, United Kingdom
| | - Andrew Landels
- ChELSI Institute, Department of Chemical and Biological Engineering, The University of Sheffield, Mappin Street, Sheffield, S1 3JD, United Kingdom
| | - Trong Khoa Pham
- ChELSI Institute, Department of Chemical and Biological Engineering, The University of Sheffield, Mappin Street, Sheffield, S1 3JD, United Kingdom
| | - Phillip C Wright
- School of Engineering, Faculty of Science, Agriculture and Engineering, Newcastle University, Newcastle Upon Tyne, NE1 7RU, United Kingdom.
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21
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A polymer monolith composed of a perovskite and cucurbit[6]uril hybrid for highly selective enrichment of phosphopeptides prior to mass spectrometric analysis. Mikrochim Acta 2019; 187:68. [PMID: 31853651 DOI: 10.1007/s00604-019-4054-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Accepted: 11/28/2019] [Indexed: 12/21/2022]
Abstract
A hybrid monolith was prepared from perovskite and cucurbit[6]uril [poly(hydroxyethyl methacrylate-pentaerythritol triacrylate) monolith] for the enrichment of phosphopeptides. By coupling with mass spectrometry, three goals were simultaneously realized, viz. (a) selective enrichment of phosphopeptides from non-phosphopeptides, (b) identification of mono- and multi-phosphopeptides, and (c) recognition of tyrosine phosphopeptides. The perovskite introduced into the monolith warrants high selectivity for phosphopeptides even at a high (10,000:1) ratio of non-phosphopeptides to phosphopeptides, and and enables identification of eight mono- and multi-phosphopeptides from standard β-casein tryptic digests. Tyrosine phosphopeptides were specifically detected via the recognition capability of cucurbit[6]uril integrated into the monolith. The method has remarkably specific enrichment capacity for phosphopeptides from samples including human serum, nonfat milk, and human acute myelocytic leukemia cell lysate. Graphical abstractSchematic representation of a monolith integrated with perovskite and cucurbit[6]uril. The monolithic column was coupled with mass spectrometry and applied to the enrichment of phosphopeptides. The method has remarkably specific enrichment capacity for phosphopeptides from complex biological samples.
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22
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Li K, Zhao S, Yan Y, Zhang D, Peng M, Wang Y, Guo G, Wang X. In-tube solid-phase microextraction capillary column packed with mesoporous TiO 2 nanoparticles for phosphopeptide analysis. Electrophoresis 2019; 40:2142-2148. [PMID: 31032959 DOI: 10.1002/elps.201900055] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Revised: 03/25/2019] [Accepted: 04/13/2019] [Indexed: 01/27/2023]
Abstract
In this study, an in-tube solid-phase microextraction column packed with mesoporous TiO2 nanoparticles, coupled with MALDI-TOF-MS, was applied to the selective enrichment and detection of phosphopeptides in complex biological samples. The mesoporous TiO2 nanoparticles with high specific surface areas, prepared by a sol-gel and solvothermal method, were injected into the capillary using a slurry packing method with in situ polymerized monolithic segments as frits. Compared with the traditional solid-phase extraction method, the TiO2 -packed column with an effective length of 1 cm exhibited excellent selectivity (α-casein/β-casein/BSA molar ratio of 1:1:100) and sensitivity (10 fmol of a β-casein enzymatic hydrolysis sample) for the enrichment of phosphopeptides. These performance characteristics make this system suitable for the detection of phosphorylated peptides in practical biosamples, such as nonfat milk.
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Affiliation(s)
- Ke Li
- Beijing Key Laboratory for Green Catalysis and Separation, Department of Chemistry and Chemical Engineering, Beijing University of Technology, Beijing, P. R. China
| | - Shuo Zhao
- Beijing Key Laboratory for Green Catalysis and Separation, Department of Chemistry and Chemical Engineering, Beijing University of Technology, Beijing, P. R. China
| | - Yong Yan
- Beijing Key Laboratory for Green Catalysis and Separation, Department of Chemistry and Chemical Engineering, Beijing University of Technology, Beijing, P. R. China
| | - Dongtang Zhang
- Beijing Key Laboratory for Green Catalysis and Separation, Department of Chemistry and Chemical Engineering, Beijing University of Technology, Beijing, P. R. China
| | - Manhua Peng
- Beijing Key Laboratory for Green Catalysis and Separation, Department of Chemistry and Chemical Engineering, Beijing University of Technology, Beijing, P. R. China
| | - Yanan Wang
- Beijing Key Laboratory for Green Catalysis and Separation, Department of Chemistry and Chemical Engineering, Beijing University of Technology, Beijing, P. R. China
| | - Guangsheng Guo
- Beijing Key Laboratory for Green Catalysis and Separation, Department of Chemistry and Chemical Engineering, Beijing University of Technology, Beijing, P. R. China
| | - Xiayan Wang
- Beijing Key Laboratory for Green Catalysis and Separation, Department of Chemistry and Chemical Engineering, Beijing University of Technology, Beijing, P. R. China
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23
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Yan Z, Deng P, Liu Y. Recent Advances in Protein Kinase Activity Analysis Based on Nanomaterials. Int J Mol Sci 2019; 20:ijms20061440. [PMID: 30901923 PMCID: PMC6471164 DOI: 10.3390/ijms20061440] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 03/10/2019] [Accepted: 03/12/2019] [Indexed: 12/20/2022] Open
Abstract
Protein phosphorylation regulated by protein kinases, as well as their dephosphorylation, is one of the most common post-translational modifications, and plays important roles in physiological activities, such as intracellular signal communications, gene transcription, cell proliferation and apoptosis. Over-expression of protein kinases is closely associated with various diseases. Consequently, accurate detection of protein kinases activities and their relevant inhibitors screening is critically important, not only to the biochemical research, but also to the clinical diagnosis and therapy. Nanomaterials, taking advantage of large surface areas, as well as excellent electrical, catalytic, magnetic and optical properties, have been utilized as target concentrators, recognition components, signal transducer or amplification elements in protein kinase related assays. This review summarizes the recent representative works to highlight the applications of nanomaterials in different biosensor technologies for protein kinases activities detection and their inhibitors screening. First, different nanomaterials developed for phosphoprotein/phosphopeptide enrichment and phosphate recognition are introduced. Next, representative works are selected that mainly focus on the utilization of nanomaterials as signal transducer or amplification elements in various protein kinases sensing platforms, such as electrochemical, colorimetric, fluorescent, and mass spectroscopy-based approaches. Finally, the major challenges and perspectives of nanomaterials being applied in protein kinases related assays are discussed.
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Affiliation(s)
- Zhiyong Yan
- Department of Chemistry, Beijing Key Laboratory for Analytical Methods and Instrumentation, Key Lab of Bioorganic Phosphorus Chemistry and Chemical Biology of Ministry of Education, Tsinghua University, Beijing 100084, China.
- Beijing Center for Physical and Chemical Analysis, Beijing 100089, China.
| | - Pingye Deng
- Beijing Center for Physical and Chemical Analysis, Beijing 100089, China.
| | - Yang Liu
- Department of Chemistry, Beijing Key Laboratory for Analytical Methods and Instrumentation, Key Lab of Bioorganic Phosphorus Chemistry and Chemical Biology of Ministry of Education, Tsinghua University, Beijing 100084, China.
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24
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Yuan H, Jiang B, Zhao B, Zhang L, Zhang Y. Recent Advances in Multidimensional Separation for Proteome Analysis. Anal Chem 2018; 91:264-276. [DOI: 10.1021/acs.analchem.8b04894] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Huiming Yuan
- Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian, Liaoning 116023, China
| | - Bo Jiang
- Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian, Liaoning 116023, China
| | - Baofeng Zhao
- Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian, Liaoning 116023, China
| | - Lihua Zhang
- Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian, Liaoning 116023, China
| | - Yukui Zhang
- Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian, Liaoning 116023, China
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