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Peng M, Zhou Y, Wan C. Identification of phosphorylated small ORF-encoded peptides in Hep3B cells by LC/MS/MS. J Proteomics 2024; 303:105214. [PMID: 38823442 DOI: 10.1016/j.jprot.2024.105214] [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: 02/20/2024] [Revised: 04/30/2024] [Accepted: 05/29/2024] [Indexed: 06/03/2024]
Abstract
Small ORF-encoded peptides (SEPs) are a class of low molecular weight proteins and peptides comprising <100 amino acids with important functions in various life activities. Although the sequence length is short, SEPs might also have post-translational modification (PTM). Phosphorylation is one of the most essential PTMs of proteins. In this work, we enriched phosphopeptides with IMAC and TiO2 materials and analyzed the phosphorylated SEPs in Hep3B cells. A total of 24 phosphorylated SEPs were identified, and 11 SEPs were coded by ncRNA. For the sequence analysis, we found that the general characteristics of phosphorylated SEPs are roughly the same as canonical proteins. Besides, two phosphorylation SEPs have the Stathmin family signature 2 motif, which can regulate the microtubule cytoskeleton. Some SEPs have domains or signal peptides, indicating their specific functions and subcellular locations. Kinase network analysis found a small number of kinases that may be a clue to the specific functions of some SEPs. However, only one-fifth of the predicted phosphorylation sites were identified by LC/MS/MS, indicating that many SEP PTMs are hidden in the dark, waiting to be uncovered and verified. This study helps expand our understanding of SEP and provides information for further SEP function investigation. SIGNIFICANCE: Small ORF-encoded peptides (SEPs) are important in various life activities. Although the sequence length is short (<100AA), SEPs might also have post-translational modification (PTM). Phosphorylation is one of the most essential PTMs of proteins. We enriched phosphopeptides and analyzed the phosphorylated SEPs in Hep3B cells. That is the first time to explore the PTM of SPEs systematically. Kinase network analysis found a small number of kinases that may be a clue to the specific functions of SEPs. More SEP PTMs are hidden in the dark and waiting to be uncovered and verified. This study helps expand our understanding of SEP and provides information for further SEP function investigation.
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Affiliation(s)
- Mingbo Peng
- School of Life Sciences, and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, Hubei 430079, People's Republic of China
| | - Yutian Zhou
- School of Life Sciences, and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, Hubei 430079, People's Republic of China
| | - Cuihong Wan
- School of Life Sciences, and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, Hubei 430079, People's Republic of China.
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2
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Wang Z, Zhang D, Wu J, Zhang W, Xia Y. Illuminating the dark space of neutral glycosphingolipidome by selective enrichment and profiling at multi-structural levels. Nat Commun 2024; 15:5627. [PMID: 38965283 PMCID: PMC11224418 DOI: 10.1038/s41467-024-50014-8] [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: 01/07/2024] [Accepted: 06/27/2024] [Indexed: 07/06/2024] Open
Abstract
Glycosphingolipids (GSLs) are essential components of cell membranes, particularly enriched in the nervous system. Altered molecular distributions of GSLs are increasingly associated with human diseases, emphasizing the significance of lipidomic profiling. Traditional GSL analysis methods are hampered by matrix effect from phospholipids and the difficulty in distinguishing structural isomers. Herein, we introduce a highly sensitive workflow that harnesses magnetic TiO2 nanoparticle-based selective enrichment, charge-tagging Paternò-Büchi reaction, and liquid chromatography-tandem mass spectrometry. This approach enables mapping over 300 distinct GSLs in brain tissues by defining sugar types, long chain bases, N-acyl chains, and the locations of desaturation and hydroxylation. Relative quantitation of GSLs across multiple structural levels provides evidence of dysregulated gene and protein expressions of FA2H and CerS2 in human glioma tissue. Based on the structural features of GSLs, our method accurately differentiates human glioma with/without isocitrate dehydrogenase genetic mutation, and normal brain tissue.
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Affiliation(s)
- Zidan Wang
- MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Department of Chemistry, Tsinghua University, Beijing, 100084, China
| | - Donghui Zhang
- State Key Laboratory of Precision Measurement Technology and Instruments, Tsinghua University, Department of Precision Instrument, Beijing, 100084, China
| | - Junhan Wu
- State Key Laboratory of Precision Measurement Technology and Instruments, Tsinghua University, Department of Precision Instrument, Beijing, 100084, China
| | - Wenpeng Zhang
- State Key Laboratory of Precision Measurement Technology and Instruments, Tsinghua University, Department of Precision Instrument, Beijing, 100084, China
| | - Yu Xia
- MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Department of Chemistry, Tsinghua University, Beijing, 100084, China.
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3
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Daly LA, Clarke CJ, Po A, Oswald SO, Eyers CE. Considerations for defining +80 Da mass shifts in mass spectrometry-based proteomics: phosphorylation and beyond. Chem Commun (Camb) 2023; 59:11484-11499. [PMID: 37681662 PMCID: PMC10521633 DOI: 10.1039/d3cc02909c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 08/21/2023] [Indexed: 09/09/2023]
Abstract
Post-translational modifications (PTMs) are ubiquitous and key to regulating protein function. Understanding the dynamics of individual PTMs and their biological roles requires robust characterisation. Mass spectrometry (MS) is the method of choice for the identification and quantification of protein modifications. This article focusses on the MS-based analysis of those covalent modifications that induce a mass shift of +80 Da, notably phosphorylation and sulfation, given the challenges associated with their discrimination and pinpointing the sites of modification on a polypeptide chain. Phosphorylation in particular is highly abundant, dynamic and can occur on numerous residues to invoke specific functions, hence robust characterisation is crucial to understanding biological relevance. Showcasing our work in the context of other developments in the field, we highlight approaches for enrichment and site localisation of phosphorylated (canonical and non-canonical) and sulfated peptides, as well as modification analysis in the context of intact proteins (top down proteomics) to explore combinatorial roles. Finally, we discuss the application of native ion-mobility MS to explore the effect of these PTMs on protein structure and ligand binding.
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Affiliation(s)
- Leonard A Daly
- Centre for Proteome Research, Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK.
| | - Christopher J Clarke
- Centre for Proteome Research, Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK.
| | - Allen Po
- Centre for Proteome Research, Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK.
| | - Sally O Oswald
- Centre for Proteome Research, Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK.
| | - Claire E Eyers
- Centre for Proteome Research, Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK.
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4
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Gao W, Zhang F, Zhang S, Li JY, Lian HZ. Ti(IV) immobilized bisphosphate fructose-modified magnetic Zr metal organic framework (MOF) for specific enrichment of phosphopeptides. Sep Purif Technol 2023. [DOI: 10.1016/j.seppur.2022.122426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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5
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Recent advances in metal oxide affinity chromatography materials for phosphoproteomics. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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6
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Zeng X, Lan Y, Xiao J, Hu L, Tan L, Liang M, Wang X, Lu S, Peng T, Long F. Advances in phosphoproteomics and its application to COPD. Expert Rev Proteomics 2022; 19:311-324. [PMID: 36730079 DOI: 10.1080/14789450.2023.2176756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
INTRODUCTION Chronic obstructive pulmonary disease (COPD) was the third leading cause of global death in 2019, causing a huge economic burden to society. Therefore, it is urgent to identify specific phenotypes of COPD patients through early detection, and to promptly treat exacerbations. The field of phosphoproteomics has been a massive advancement, compelled by the developments in mass spectrometry, enrichment strategies, algorithms, and tools. Modern mass spectrometry-based phosphoproteomics allows understanding of disease pathobiology, biomarker discovery, and predicting new therapeutic modalities. AREAS COVERED In this article, we present an overview of phosphoproteomic research and strategies for enrichment and fractionation of phosphopeptides, identification of phosphorylation sites, chromatographic separation and mass spectrometry detection strategies, and the potential application of phosphorylated proteomic analysis in the diagnosis, treatment, and prognosis of COPD disease. EXPERT OPINION The role of phosphoproteomics in COPD is critical for understanding disease pathobiology, identifying potential biomarkers, and predicting new therapeutic approaches. However, the complexity of COPD requires the more comprehensive understanding that can be achieved through integrated multi-omics studies. Phosphoproteomics, as a part of these multi-omics approaches, can provide valuable insights into the underlying mechanisms of COPD.
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Affiliation(s)
- Xiaoyin Zeng
- Sino-French Hoffmann Institute, School of Basic Medical Science, State Key Laboratory of Respiratory Disease, Guangzhou Medical University, Guangzhou, China
| | - Yanting Lan
- Sino-French Hoffmann Institute, School of Basic Medical Science, State Key Laboratory of Respiratory Disease, Guangzhou Medical University, Guangzhou, China
| | - Jing Xiao
- Sino-French Hoffmann Institute, School of Basic Medical Science, State Key Laboratory of Respiratory Disease, Guangzhou Medical University, Guangzhou, China
| | - Longbo Hu
- Sino-French Hoffmann Institute, School of Basic Medical Science, State Key Laboratory of Respiratory Disease, Guangzhou Medical University, Guangzhou, China
| | - Long Tan
- Sino-French Hoffmann Institute, School of Basic Medical Science, State Key Laboratory of Respiratory Disease, Guangzhou Medical University, Guangzhou, China
| | - Mengdi Liang
- Sino-French Hoffmann Institute, School of Basic Medical Science, State Key Laboratory of Respiratory Disease, Guangzhou Medical University, Guangzhou, China
| | - Xufei Wang
- Sino-French Hoffmann Institute, School of Basic Medical Science, State Key Laboratory of Respiratory Disease, Guangzhou Medical University, Guangzhou, China
| | - Shaohua Lu
- Sino-French Hoffmann Institute, School of Basic Medical Science, State Key Laboratory of Respiratory Disease, Guangzhou Medical University, Guangzhou, China
| | - Tao Peng
- Sino-French Hoffmann Institute, School of Basic Medical Science, State Key Laboratory of Respiratory Disease, Guangzhou Medical University, Guangzhou, China.,Guangdong South China Vaccine Co. Ltd, Guangzhou, China
| | - Fei Long
- Sino-French Hoffmann Institute, School of Basic Medical Science, State Key Laboratory of Respiratory Disease, Guangzhou Medical University, Guangzhou, China
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7
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Pan Y, Zhang C, Xiao R, Zhang L, Zhang W. Dual-functionalized magnetic bimetallic metal-organic framework composite for highly specific enrichments of phosphopeptides and glycopeptides. Anal Chim Acta 2021; 1158:338412. [DOI: 10.1016/j.aca.2021.338412] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 03/05/2021] [Accepted: 03/12/2021] [Indexed: 01/15/2023]
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8
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Xiao J, Yang SS, Wu JX, Wu N, Yu X, Shang W, Gu ZY. Sn-based metal-organic framework for highly selective capture of monophosphopeptides. Talanta 2021; 224:121812. [PMID: 33379037 DOI: 10.1016/j.talanta.2020.121812] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Revised: 10/19/2020] [Accepted: 10/23/2020] [Indexed: 11/28/2022]
Abstract
Sn-based metal-organic framework (MOF) was utilized to effectively capture monophosphopeptides due to the unique affinity. The Sn-based MOF demonstrated the good sensitivity and selectivity in the model phosphoproteins enrichment and was successfully applied in the biological fluids.
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Affiliation(s)
- Jing Xiao
- Jiangsu Key Laboratory of Biofunctional Materials, Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, College of Chemistry and Materials Science, Nanjing Normal University, Nanjing, 210023, China
| | - Shi-Shu Yang
- Jiangsu Key Laboratory of Biofunctional Materials, Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, College of Chemistry and Materials Science, Nanjing Normal University, Nanjing, 210023, China
| | - Jian-Xiang Wu
- Jiangsu Key Laboratory of Biofunctional Materials, Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, College of Chemistry and Materials Science, Nanjing Normal University, Nanjing, 210023, China
| | - Nan Wu
- Jiangsu Key Laboratory of Biofunctional Materials, Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, College of Chemistry and Materials Science, Nanjing Normal University, Nanjing, 210023, China
| | - Xizhong Yu
- Key Laboratory for Metabolic Diseases in Chinese Medicine, First College of Clinical Medicine, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Wenbin Shang
- Key Laboratory for Metabolic Diseases in Chinese Medicine, First College of Clinical Medicine, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Zhi-Yuan Gu
- Jiangsu Key Laboratory of Biofunctional Materials, Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, College of Chemistry and Materials Science, Nanjing Normal University, Nanjing, 210023, China.
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9
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Yan S, Luo B, He J, Lan F, Wu Y. Phytic acid functionalized magnetic bimetallic metal-organic frameworks for phosphopeptide enrichment. J Mater Chem B 2021; 9:1811-1820. [PMID: 33503098 DOI: 10.1039/d0tb02517h] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Highly specific enrichment of phosphopeptides from complex biological samples was a precondition for further studying its physiological and pathological processes due to the important and trace amounts of phosphopeptides. In this work, phytic acid (PA) functionalized magnetic cerium and zirconium bimetallic metal-organic framework nanocomposites (denoted as Fe3O4@SiO2@Ce-Zr-MOF@PA) were fabricated by a facile yet efficient method. The as-prepared nanomaterial exhibited high sensitivity (0.1 fmol μL-1), high selectivity toward phosphopeptides from β-casein tryptic digests/BSA (1 : 800), and good reusability of five cycles for enriching phosphopeptides. This affinity probe was applied to biological samples, and 19, 4 and 15 phosphopeptides were identified from non-fat milk, human serum and human saliva, respectively. The above marked advantages are attributed to the strong affinity of the abundant Ce-O and Zr-O nanoclusters on the surface of the MOF shell with the improved hydrophilicity from a great number of phosphate groups. Therefore, the novel Fe3O4@SiO2@Ce-Zr-MOF@PA nanospheres could not only enrich phosphopeptides effectively, but also reduce the adsorption of phosphopeptides, manifesting great potential in the identification and further analysis of low abundance phosphopeptides in complex biological samples.
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Affiliation(s)
- Shuang Yan
- National Engineering Research Center for Biomaterials, Sichuan University, Chengdu 610064, P. R. China.
| | - Bin Luo
- National Engineering Research Center for Biomaterials, Sichuan University, Chengdu 610064, P. R. China.
| | - Jia He
- National Engineering Research Center for Biomaterials, Sichuan University, Chengdu 610064, P. R. China.
| | - Fang Lan
- National Engineering Research Center for Biomaterials, Sichuan University, Chengdu 610064, P. R. China.
| | - Yao Wu
- National Engineering Research Center for Biomaterials, Sichuan University, Chengdu 610064, P. R. China.
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10
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Mehnert M, Ciuffa R, Frommelt F, Uliana F, van Drogen A, Ruminski K, Gstaiger M, Aebersold R. Multi-layered proteomic analyses decode compositional and functional effects of cancer mutations on kinase complexes. Nat Commun 2020; 11:3563. [PMID: 32678104 PMCID: PMC7366679 DOI: 10.1038/s41467-020-17387-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 06/26/2020] [Indexed: 01/09/2023] Open
Abstract
Rapidly increasing availability of genomic data and ensuing identification of disease associated mutations allows for an unbiased insight into genetic drivers of disease development. However, determination of molecular mechanisms by which individual genomic changes affect biochemical processes remains a major challenge. Here, we develop a multilayered proteomic workflow to explore how genetic lesions modulate the proteome and are translated into molecular phenotypes. Using this workflow we determine how expression of a panel of disease-associated mutations in the Dyrk2 protein kinase alter the composition, topology and activity of this kinase complex as well as the phosphoproteomic state of the cell. The data show that altered protein-protein interactions caused by the mutations are associated with topological changes and affected phosphorylation of known cancer driver proteins, thus linking Dyrk2 mutations with cancer-related biochemical processes. Overall, we discover multiple mutation-specific functionally relevant changes, thus highlighting the extensive plasticity of molecular responses to genetic lesions.
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Affiliation(s)
- Martin Mehnert
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Switzerland.
| | - Rodolfo Ciuffa
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Switzerland
| | - Fabian Frommelt
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Switzerland
| | - Federico Uliana
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Switzerland
| | - Audrey van Drogen
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Switzerland
| | - Kilian Ruminski
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Switzerland
- Centre d'Immunologie de Marseille-Luminy, Aix Marseille Université, INSERM, CNRS, Marseille, France
| | - Matthias Gstaiger
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Switzerland.
| | - Ruedi Aebersold
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Switzerland.
- Faculty of Science, University of Zurich, Zurich, Switzerland.
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11
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Leitner A, Dorn G, Allain FHT. Combining Mass Spectrometry (MS) and Nuclear Magnetic Resonance (NMR) Spectroscopy for Integrative Structural Biology of Protein-RNA Complexes. Cold Spring Harb Perspect Biol 2019; 11:a032359. [PMID: 31262947 PMCID: PMC6601463 DOI: 10.1101/cshperspect.a032359] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Deciphering complex RNA-protein interactions on a (near-)atomic level is a hurdle that hinders advancing our understanding of fundamental processes in RNA metabolism and RNA-based gene regulation. To overcome challenges associated with individual structure determination methods, structural information derived from complementary biophysical methods can be combined in integrative structural biology approaches. Here, we review recent advances in such hybrid structural approaches with a focus on combining mass spectrometric analysis of cross-linked protein-RNA complexes and nuclear magnetic resonance (NMR) spectroscopy.
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Affiliation(s)
- Alexander Leitner
- Institute of Molecular Systems Biology, Department of Biology, Eidgenössische Technische Hochschule (ETH) Zürich, 8093 Zürich, Switzerland
| | - Georg Dorn
- Institute of Molecular Biology and Biophysics, Department of Biology, ETH Zürich, 8093 Zürich, Switzerland
| | - Frédéric H-T Allain
- Institute of Molecular Biology and Biophysics, Department of Biology, ETH Zürich, 8093 Zürich, Switzerland
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12
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Xiao J, Yang SS, Wu JX, Wang H, Yu X, Shang W, Chen GQ, Gu ZY. Highly Selective Capture of Monophosphopeptides by Two-Dimensional Metal–Organic Framework Nanosheets. Anal Chem 2019; 91:9093-9101. [DOI: 10.1021/acs.analchem.9b01581] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Jing Xiao
- Jiangsu Key Laboratory of Biofunctional Materials, Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, College of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210023, China
| | - Shi-Shu Yang
- Jiangsu Key Laboratory of Biofunctional Materials, Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, College of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210023, China
| | - Jian-Xiang Wu
- Jiangsu Key Laboratory of Biofunctional Materials, Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, College of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210023, China
| | - He Wang
- State Key Laboratory of Pharmaceutical Biotechnology, MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Nanjing University, 12 Xuefu Avenue, Nanjing, 210061, China
| | - Xizhong Yu
- Key Laboratory for Metabolic Diseases in Chinese Medicine, First College of Clinical Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Wenbin Shang
- Key Laboratory for Metabolic Diseases in Chinese Medicine, First College of Clinical Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Gui-Quan Chen
- State Key Laboratory of Pharmaceutical Biotechnology, MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Nanjing University, 12 Xuefu Avenue, Nanjing, 210061, China
| | - Zhi-Yuan Gu
- Jiangsu Key Laboratory of Biofunctional Materials, Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, College of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210023, China
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13
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Yang SS, Chang YJ, Zhang H, Yu X, Shang W, Chen GQ, Chen DDY, Gu ZY. Enrichment of Phosphorylated Peptides with Metal–Organic Framework Nanosheets for Serum Profiling of Diabetes and Phosphoproteomics Analysis. Anal Chem 2018; 90:13796-13805. [DOI: 10.1021/acs.analchem.8b04417] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Shi-Shu Yang
- Jiangsu Key Laboratory of Biofunctional Materials, Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, College of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210023, China
| | - Yu-Jie Chang
- Jiangsu Key Laboratory of Biofunctional Materials, Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, College of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210023, China
| | - Hao Zhang
- Key Laboratory for Metabolic Diseases in Chinese Medicine, First College of Clinical Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Xizhong Yu
- Key Laboratory for Metabolic Diseases in Chinese Medicine, First College of Clinical Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Wenbin Shang
- Key Laboratory for Metabolic Diseases in Chinese Medicine, First College of Clinical Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Gui-Quan Chen
- State Key Laboratory of Pharmaceutical Biotechnology, MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Nanjing University, 12 Xuefu Avenue, Nanjing 210061, China
| | - David Da Yong Chen
- Jiangsu Key Laboratory of Biofunctional Materials, Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, College of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210023, China
- Department of Chemistry, University of British Columbia, Vancouver, BC V6T 1Z1, Canada
| | - Zhi-Yuan Gu
- Jiangsu Key Laboratory of Biofunctional Materials, Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, College of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210023, China
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14
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Jiang J, Sun X, She X, Li J, Li Y, Deng C, Duan G. Magnetic microspheres modified with Ti(IV) and Nb(V) for enrichment of phosphopeptides. Mikrochim Acta 2018; 185:309. [PMID: 29802452 DOI: 10.1007/s00604-018-2837-z] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 05/06/2018] [Indexed: 01/04/2023]
Abstract
Magnetic microspheres (Fe3O4) were coated with polydopamine (PDA) and loaded with the metal ions Ti(IV) and Nb(V) to give a material of type Fe3O4@PDA-Ti/Nb. It is shown to be useful for affinity chromatography and for enrichment of phosphopeptides from both standard protein solutions and real samples. For comparison, such microspheres loaded with single metal ions only (Fe3O4@PDA-Ti and Fe3O4@PDA-Nb) and their physical mixtures were also investigated under identical conditions. The binary metal ion-loaded magnetic microspheres display better enrichment efficiency than the single metal ion-loaded microspheres and their physical mixture. Both multiphosphopeptides and monophosphopeptides can be extracted. The Fe3O4@PDA-Ti/Nb microspheres exhibit ultra-high sensitivity (the lowest detection amount being 2 fmol) and selectivity at a low mass ratio such as in case of β-casein/BSA (1:1000). Graphical abstract Magnetic microspheres (Fe3O4) were coated with polydopamine (PDA) and loaded with the metal ions Ti(IV) and Nb(V) to give a material of type Fe3O4@PDA-Ti/Nb. Results showed its great potential as an affinity probe in phosphoproteome research due to rapid magnetic separation of phosphopeptides, ultrahigh sensitivity and selectivity, and remarkable reusability.
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Affiliation(s)
- Jiebing Jiang
- Fudan University Affiliated Pudong Medical Center & Pharmaceutical Analysis Department, School of Pharmacy, Fudan University, Shanghai, 201203, China
| | - Xueni Sun
- Institute of Functional Genomics, University of Regensburg, Am BioPark 9, 93053, Regensburg, Germany
| | - Xiaojian She
- Fudan University Affiliated Pudong Medical Center & Pharmaceutical Analysis Department, School of Pharmacy, Fudan University, Shanghai, 201203, China
| | - Jiajia Li
- Fudan University Affiliated Pudong Medical Center & Pharmaceutical Analysis Department, School of Pharmacy, Fudan University, Shanghai, 201203, China
| | - Yan Li
- Fudan University Affiliated Pudong Medical Center & Pharmaceutical Analysis Department, School of Pharmacy, Fudan University, Shanghai, 201203, China.
| | - Chunhui Deng
- Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200433, China
| | - Gengli Duan
- Fudan University Affiliated Pudong Medical Center & Pharmaceutical Analysis Department, School of Pharmacy, Fudan University, Shanghai, 201203, China
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15
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Yang SS, Yu HX, Wang ZZ, Liu HL, Zhang H, Yu X, Shang W, Chen GQ, Gu ZY. An Exfoliated 2D Egyptian Blue Nanosheet for Highly Selective Enrichment of Multi-phosphorylated Peptides in Mass Spectrometric Analysis. Chemistry 2017; 24:2109-2116. [DOI: 10.1002/chem.201704138] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2017] [Indexed: 01/19/2023]
Affiliation(s)
- Shi-Shu Yang
- Jiangsu Key Laboratory of Biofunctional Materials, Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, College of Chemistry and Materials Science, College of Life Sciences; Nanjing Normal University; Nanjing 210023 China
| | - Hai-Xia Yu
- Jiangsu Key Laboratory of Biofunctional Materials, Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, College of Chemistry and Materials Science, College of Life Sciences; Nanjing Normal University; Nanjing 210023 China
| | - Zi-Zhen Wang
- Jiangsu Key Laboratory of Biofunctional Materials, Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, College of Chemistry and Materials Science, College of Life Sciences; Nanjing Normal University; Nanjing 210023 China
| | - Hai-Long Liu
- Jiangsu Key Laboratory of Biofunctional Materials, Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, College of Chemistry and Materials Science, College of Life Sciences; Nanjing Normal University; Nanjing 210023 China
| | - Hao Zhang
- Key Laboratory for Metabolic Diseases in Chinese Medicine, First College of Clinical Medicine; Nanjing University of, Chinese Medicine; Nanjing 210023 China
| | - Xizhong Yu
- Key Laboratory for Metabolic Diseases in Chinese Medicine, First College of Clinical Medicine; Nanjing University of, Chinese Medicine; Nanjing 210023 China
| | - Wenbin Shang
- Key Laboratory for Metabolic Diseases in Chinese Medicine, First College of Clinical Medicine; Nanjing University of, Chinese Medicine; Nanjing 210023 China
| | - Gui-Quan Chen
- State Key Laboratory of Pharmaceutical Biotechnology, MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center; Nanjing University; 12 Xuefu Avenue Nanjing 210061 China
| | - Zhi-Yuan Gu
- Jiangsu Key Laboratory of Biofunctional Materials, Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, College of Chemistry and Materials Science, College of Life Sciences; Nanjing Normal University; Nanjing 210023 China
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16
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Dorn G, Leitner A, Boudet J, Campagne S, von Schroetter C, Moursy A, Aebersold R, Allain FHT. Structural modeling of protein-RNA complexes using crosslinking of segmentally isotope-labeled RNA and MS/MS. Nat Methods 2017; 14:487-490. [PMID: 28346450 PMCID: PMC5505470 DOI: 10.1038/nmeth.4235] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 02/22/2017] [Indexed: 11/09/2022]
Abstract
Ribonucleoproteins (RNPs) are key regulators of cellular function. We established an efficient approach that combines segmental isotope labeling of RNA with photo-crosslinking and tandem mass spectrometry to localize protein-RNA interactions simultaneously at amino acid and nucleotide resolution. The approach was tested on Polypyrimidine Tract Binding Protein 1 and U1 small nuclear RNP and the results support integrative atomic-scale structural modeling thus providing mechanistic insights into RNP regulated processes.
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Affiliation(s)
- G Dorn
- Department of Biology, Institute for Molecular Biology and Biophysics, ETH Zürich, 8093 Zürich, Switzerland
| | - A Leitner
- Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, 8093 Zürich, Switzerland
| | - J Boudet
- Department of Biology, Institute for Molecular Biology and Biophysics, ETH Zürich, 8093 Zürich, Switzerland
| | - S Campagne
- Department of Biology, Institute for Molecular Biology and Biophysics, ETH Zürich, 8093 Zürich, Switzerland
| | - C von Schroetter
- Department of Biology, Institute for Molecular Biology and Biophysics, ETH Zürich, 8093 Zürich, Switzerland
| | - A Moursy
- Department of Biology, Institute for Molecular Biology and Biophysics, ETH Zürich, 8093 Zürich, Switzerland
| | - R Aebersold
- Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, 8093 Zürich, Switzerland.,Faculty of Science, University of Zurich, Zürich, Switzerland
| | - F H-T Allain
- Department of Biology, Institute for Molecular Biology and Biophysics, ETH Zürich, 8093 Zürich, Switzerland
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17
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Leitner A, Sakeye M, Zimmerli CE, Smått JH. Insights into chemoselectivity principles in metal oxide affinity chromatography using tailored nanocast metal oxide microspheres and mass spectrometry-based phosphoproteomics. Analyst 2017; 142:1993-2003. [DOI: 10.1039/c7an00570a] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Custom-made nanocast metal oxide materials provide new insights into the mechanisms of metal oxide affinity chromatography, a method widely used to study proteome-wide protein phosphorylation.
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Affiliation(s)
- Alexander Leitner
- Department of Biology
- Institute of Molecular Systems Biology
- ETH Zurich
- 8093 Zurich
- Switzerland
| | - Motolani Sakeye
- Laboratory of Physical Chemistry and Center of Functional Materials
- Åbo Akademi University
- 20500 Turku
- Finland
| | | | - Jan-Henrik Smått
- Laboratory of Physical Chemistry and Center of Functional Materials
- Åbo Akademi University
- 20500 Turku
- Finland
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18
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Xu D, Yan G, Gao M, Deng C, Zhang X. Highly selective SiO2–NH2@TiO2 hollow microspheres for simultaneous enrichment of phosphopeptides and glycopeptides. Anal Bioanal Chem 2016; 409:1607-1614. [DOI: 10.1007/s00216-016-0101-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2016] [Revised: 10/30/2016] [Accepted: 11/14/2016] [Indexed: 01/01/2023]
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19
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Yang X, Xia Y. Urea-modified metal-organic framework of type MIL-101(Cr) for the preconcentration of phosphorylated peptides. Mikrochim Acta 2016. [DOI: 10.1007/s00604-016-1860-1] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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20
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Li XS, Yuan BF, Feng YQ. Recent advances in phosphopeptide enrichment: Strategies and techniques. Trends Analyt Chem 2016. [DOI: 10.1016/j.trac.2015.11.001] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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21
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Krenkova J, Moravkova J, Buk J, Foret F. Phosphopeptide enrichment with inorganic nanofibers prepared by forcespinning technology. J Chromatogr A 2016; 1427:8-15. [DOI: 10.1016/j.chroma.2015.12.022] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Revised: 12/04/2015] [Accepted: 12/08/2015] [Indexed: 10/22/2022]
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22
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DePuccio DP, Landry CC. Photocatalytic oxidation of methanol using porous Au/WO3 and visible light. Catal Sci Technol 2016. [DOI: 10.1039/c6cy01449f] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Porous WO3 and Au/WO3 were used as new visible light photocatalysts for the oxidation of MeOH.
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23
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Lei C, Zhou L, Xu C, Sun X, Nouwens A, Yu C. Binder-Free TiO2 Monolith-Packed Pipette Tips for the Enrichment of Phosphorylated Peptides. Aust J Chem 2016. [DOI: 10.1071/ch16443] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
A macroporous TiO2 monolith-entrapped pipette-tip was developed through a binder-free packing method for convenient phosphorylated peptide enrichment. A detection limit of 1 ng mL–1 for phosphorylated peptide is achieved, showing a better enrichment efficiency compared with the commercial pure TiO2-embedded NuTip.
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24
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Yang X, Xia Y. Selective enrichment and separation of phosphotyrosine peptides by thermosensitive molecularly imprinted polymers. J Sep Sci 2015; 39:419-26. [DOI: 10.1002/jssc.201501063] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Revised: 11/01/2015] [Accepted: 11/02/2015] [Indexed: 11/09/2022]
Affiliation(s)
- Xiaoqing Yang
- Research Center for Analytical Sciences, College of Chemistry; Nankai University; Tianjin China
| | - Yan Xia
- Research Center for Analytical Sciences, College of Chemistry; Nankai University; Tianjin China
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25
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Wang J, Wang Y, Gao M, Zhang X, Yang P. Facile synthesis of hydrophilic polyamidoxime polymers as a novel solid-phase extraction matrix for sequential characterization of glyco- and phosphoproteomes. Anal Chim Acta 2015; 907:69-76. [PMID: 26803004 DOI: 10.1016/j.aca.2015.12.015] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Revised: 11/02/2015] [Accepted: 12/01/2015] [Indexed: 11/15/2022]
Abstract
Selective enrichment of glycopeptides or phosphopeptides with great biological significance is essential for high-throughput mass spectrometry analysis. However, most previously reported methods only focused on enriching either glycopeptides or phosphopeptides rather than enriching them both. In this work, for the first time, a facile route was developed for the synthesis of polyamidoxime polymers with intrinsic hydrophilic skeletons and attractive long chain structure. The polyamidoxime materials (co-PAN) were synthesized from polyacrylonitrile (PAN) precursor and were successfully used for selective enrichment of glycopeptides. After that, co-PAN as a matrix functionalized with titanium ions (co-PAN@Ti(4+)) could efficiently enrich phosphopeptides. The performances of the polymers for sequential selective and effective enrichment of glycopeptides and phosphopeptides were evaluated with standard peptide mixtures and human serum. Moreover, the efficiency of enrichment of the material was still retained after being used repeatedly. These results demonstrated that the polymers showed great potential in the practical application of proteomics.
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Affiliation(s)
- Jiaxi Wang
- Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai 200433, China
| | - Yanan Wang
- Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai 200433, China
| | - Mingxia Gao
- Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai 200433, China.
| | - Xiangmin Zhang
- Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai 200433, China
| | - Pengyuan Yang
- Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai 200433, China
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26
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Sfakianaki A, Stalikas C. Selective microextraction of mononucleotides from milk using alumina and stannia hollow fibers prior to their determination by hydrophilic interaction liquid chromatography–diode array detection. Food Chem 2015; 184:188-95. [DOI: 10.1016/j.foodchem.2015.03.074] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2014] [Revised: 01/29/2015] [Accepted: 03/21/2015] [Indexed: 11/26/2022]
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27
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Jabeen F, Najam-ul-Haq M, Rainer M, Güzel Y, Huck CW, Bonn GK. Newly Fabricated Magnetic Lanthanide Oxides Core–Shell Nanoparticles in Phosphoproteomics. Anal Chem 2015; 87:4726-32. [DOI: 10.1021/ac504818s] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Fahmida Jabeen
- Division
of Analytical Chemistry, Institute of Chemical Sciences, Bahauddin Zakariya University, Multan 60800, Pakistan
- Institute
of Analytical Chemistry and Radiochemistry, Leopold-Franzens University, Innrain 80-82, Innsbruck 6020, Austria
| | - Muhammad Najam-ul-Haq
- Division
of Analytical Chemistry, Institute of Chemical Sciences, Bahauddin Zakariya University, Multan 60800, Pakistan
- Institute
of Analytical Chemistry and Radiochemistry, Leopold-Franzens University, Innrain 80-82, Innsbruck 6020, Austria
| | - Matthias Rainer
- Institute
of Analytical Chemistry and Radiochemistry, Leopold-Franzens University, Innrain 80-82, Innsbruck 6020, Austria
| | - Yüksel Güzel
- Institute
of Analytical Chemistry and Radiochemistry, Leopold-Franzens University, Innrain 80-82, Innsbruck 6020, Austria
| | - Christian W. Huck
- Institute
of Analytical Chemistry and Radiochemistry, Leopold-Franzens University, Innrain 80-82, Innsbruck 6020, Austria
| | - Guenther K. Bonn
- Institute
of Analytical Chemistry and Radiochemistry, Leopold-Franzens University, Innrain 80-82, Innsbruck 6020, Austria
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28
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Lee DCH, Jones AR, Hubbard SJ. Computational phosphoproteomics: from identification to localization. Proteomics 2015; 15:950-63. [PMID: 25475148 PMCID: PMC4384807 DOI: 10.1002/pmic.201400372] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2014] [Revised: 10/31/2014] [Accepted: 11/26/2014] [Indexed: 01/08/2023]
Abstract
Analysis of the phosphoproteome by MS has become a key technology for the characterization of dynamic regulatory processes in the cell, since kinase and phosphatase action underlie many major biological functions. However, the addition of a phosphate group to a suitable side chain often confounds informatic analysis by generating product ion spectra that are more difficult to interpret (and consequently identify) relative to unmodified peptides. Collectively, these challenges have motivated bioinformaticians to create novel software tools and pipelines to assist in the identification of phosphopeptides in proteomic mixtures, and help pinpoint or "localize" the most likely site of modification in cases where there is ambiguity. Here we review the challenges to be met and the informatics solutions available to address them for phosphoproteomic analysis, as well as highlighting the difficulties associated with using them and the implications for data standards.
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Affiliation(s)
- Dave C H Lee
- Faculty of Life Sciences, University of ManchesterManchester, UK
| | - Andrew R Jones
- Institute of Integrative Biology, University of LiverpoolLiverpool, UK
| | - Simon J Hubbard
- Faculty of Life Sciences, University of ManchesterManchester, UK
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29
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Li XS, Chen X, Yuan BF, Feng YQ. Phosphonate-modified metal oxides for the highly selective enrichment of phosphopeptides. RSC Adv 2015. [DOI: 10.1039/c4ra13878c] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Phosphonate-modified metal oxides display higher selectivity than unmodified ones for the effective enrichment of phosphopeptides.
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Affiliation(s)
- Xiao-Shui Li
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education)
- Department of Chemistry
- Wuhan University
- Wuhan 430072
- China
| | - Xi Chen
- Wuhan Institute of Biotechnology
- Wuhan 430072
- China
| | - Bi-Feng Yuan
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education)
- Department of Chemistry
- Wuhan University
- Wuhan 430072
- China
| | - Yu-Qi Feng
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education)
- Department of Chemistry
- Wuhan University
- Wuhan 430072
- China
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30
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Zhao Y, Gong X, Si X, Wei Z, Yang C, Zhang S, Zhang X. Coupling a solid phase microextraction (SPME) probe with ambient MS for rapid enrichment and detection of phosphopeptides in biological samples. Analyst 2015; 140:2599-602. [DOI: 10.1039/c4an02156h] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
A simple method of excellent selectivity and sensitivity for enrichment of phosphopeptides in complex biological samples.
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Affiliation(s)
- Yaoyao Zhao
- Beijing Key Laboratory for Microanalytical Methods and Instrumentation
- Department of Chemistry
- Tsinghua University
- Beijing 10084
- China
| | - Xiaoyun Gong
- Beijing Key Laboratory for Microanalytical Methods and Instrumentation
- Department of Chemistry
- Tsinghua University
- Beijing 10084
- China
| | - Xingyu Si
- Beijing Key Laboratory for Microanalytical Methods and Instrumentation
- Department of Chemistry
- Tsinghua University
- Beijing 10084
- China
| | - Zhenwei Wei
- Beijing Key Laboratory for Microanalytical Methods and Instrumentation
- Department of Chemistry
- Tsinghua University
- Beijing 10084
- China
| | - Chengdui Yang
- Beijing Key Laboratory for Microanalytical Methods and Instrumentation
- Department of Chemistry
- Tsinghua University
- Beijing 10084
- China
| | - Sichun Zhang
- Beijing Key Laboratory for Microanalytical Methods and Instrumentation
- Department of Chemistry
- Tsinghua University
- Beijing 10084
- China
| | - Xinrong Zhang
- Beijing Key Laboratory for Microanalytical Methods and Instrumentation
- Department of Chemistry
- Tsinghua University
- Beijing 10084
- China
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31
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Perovskite for the highly selective enrichment of phosphopeptides. J Chromatogr A 2015; 1376:143-8. [DOI: 10.1016/j.chroma.2014.12.036] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2014] [Revised: 12/08/2014] [Accepted: 12/10/2014] [Indexed: 11/17/2022]
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32
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Iliuk AB, Arrington JV, Tao WA. Analytical challenges translating mass spectrometry-based phosphoproteomics from discovery to clinical applications. Electrophoresis 2014; 35:3430-40. [PMID: 24890697 PMCID: PMC4250476 DOI: 10.1002/elps.201400153] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2014] [Revised: 04/29/2014] [Accepted: 05/12/2014] [Indexed: 12/21/2022]
Abstract
Phosphoproteomics is the systematic study of one of the most common protein modifications in high throughput with the aim of providing detailed information of the control, response, and communication of biological systems in health and disease. Advances in analytical technologies and strategies, in particular the contributions of high-resolution mass spectrometers, efficient enrichments of phosphopeptides, and fast data acquisition and annotation, have catalyzed dramatic expansion of signaling landscapes in multiple systems during the past decade. While phosphoproteomics is an essential inquiry to map high-resolution signaling networks and to find relevant events among the apparently ubiquitous and widespread modifications of proteome, it presents tremendous challenges in separation sciences to translate it from discovery to clinical practice. In this mini-review, we summarize the analytical tools currently utilized for phosphoproteomic analysis (with focus on MS), progresses made on deciphering clinically relevant kinase-substrate networks, MS uses for biomarker discovery and validation, and the potential of phosphoproteomics for disease diagnostics and personalized medicine.
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Affiliation(s)
- Anton B. Iliuk
- Department of Biochemistry, Purdue University, West Lafayette, IN, USA
| | | | - Weiguo Andy Tao
- Department of Biochemistry, Purdue University, West Lafayette, IN, USA
- Department of Chemistry, Purdue University, West Lafayette, IN, USA
- Purdue Center for Cancer Research, Purdue University, West Lafayette, IN, USA
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33
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Wang M, Deng C, Li Y, Zhang X. Magnetic binary metal oxides affinity probe for highly selective enrichment of phosphopeptides. ACS APPLIED MATERIALS & INTERFACES 2014; 6:11775-11782. [PMID: 24911384 DOI: 10.1021/am502530c] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
In this work, for the first time, binary metal oxides ((Ti-Sn)O4) were integrated into one entity on an atomic scale on magnetic graphene as affinity probe for highly selective enrichment of phosphopeptides. The newly prepared Fe3O4/graphene/(Ti-Sn)O4 (magG/(Ti-Sn)O4) composites gathered the advantages of large specific surface area of graphene, superparamagnetism, and biocompatibility of iron oxide, and enhanced affinity properties of binary metal oxides. The phosphopeptide enrichment efficiency of the magG/(Ti-Sn)O4 composite was investigated, and the results indicated an ultralow detection limit (1 pg/μL or 4.0 × 10(-11) M) and an ultrahigh selectivity (weight ratio of β-casein and BSA reached up to 1:1500). Compared with magnetic affinity probes with single metal oxide (magG/TiO2, magG/SnO2) or the simple physical mixture of magG/TiO2 and magG/SnO2, the magG/(Ti-Sn)O4 composite possessed stronger specificity, higher selectivity and better efficiency; and more importantly, it possessed the ability to enrich both the mono- and multi- phosophorylated peptides, demonstrating the notable features of the novel binary metal oxides affinity probe in the specific and selective enrichment of phosphopeptides. Additionally, by utilizing the magG/(Ti-Sn)O4 composites, a total number of 349 phosphorylation sites on 170 phosphopeptides including 66 monophosphopeptides and 104 multiphosphopeptides were captured and identified from mouse brain, indicating the great potential for their application in phosphoproteomics analysis in the future.
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Affiliation(s)
- Mengyi Wang
- Department of Chemistry and Institutes of Biomedical Sciences, Fudan University , Shanghai 200433, China
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34
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Comparison of a novel TiO2/diatomite composite and pure TiO2 for the purification of phosvitin phosphopeptides. J Chromatogr B Analyt Technol Biomed Life Sci 2014; 960:52-8. [DOI: 10.1016/j.jchromb.2014.03.038] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2013] [Revised: 03/26/2014] [Accepted: 03/31/2014] [Indexed: 11/22/2022]
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35
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Yan Y, Zhang X, Deng C. Designed synthesis of titania nanoparticles coated hierarchially ordered macro/mesoporous silica for selective enrichment of phosphopeptides. ACS APPLIED MATERIALS & INTERFACES 2014; 6:5467-5471. [PMID: 24666404 DOI: 10.1021/am500412v] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Metal oxide affinity chromatography (MOAC) is a powerful technique in phosphoproteome research. However, the achievement of highly specific enrichment and sensitive detection of phosphopeptide by MOAC remains a big challenge since the lack of high specificity and large binding capacity of conventional MOAC materials. In this work, a new MOAC material, TiO2-coated hierarchically ordered macro/mesoporous silica (denoted as HOMMS@TiO2) composites, was prepared via a facile process. The HOMMS@TiO2 composites were demonstrated to have low limit of detection (8 fmol) and great specificity with a very rapid enrichment speed (within 1 min). These experimental results have demonstrated that the HOMMS@TiO2 exhibit great potential in phosphoproteome research.
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Affiliation(s)
- Yinghua Yan
- Department of Chemistry, Fudan University , Shanghai 200433, China
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36
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Yan Y, Sun X, Deng C, Li Y, Zhang X. Metal Oxide Affinity Chromatography Platform–Polydopamine Coupled Functional Two-Dimensional Titania Graphene Nanohybrid for Phosphoproteome Research. Anal Chem 2014; 86:4327-32. [DOI: 10.1021/ac500047p] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Yinghua Yan
- Department
of Chemistry, Fudan University, Shanghai 200433, China
| | - Xueni Sun
- Pharmaceutical
Analysis Department, School of Pharmacy, Fudan University, Shanghai 201203, China
| | - Chunhui Deng
- Department
of Chemistry, Fudan University, Shanghai 200433, China
| | - Yan Li
- Pharmaceutical
Analysis Department, School of Pharmacy, Fudan University, Shanghai 201203, China
| | - Xiangmin Zhang
- Department
of Chemistry, Fudan University, Shanghai 200433, China
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37
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Li L, Chen S, Xu L, Bai Y, Nie Z, Liu H, Qi L. Template-free synthesis of uniform mesoporous SnO2 nanospheres for efficient phosphopeptide enrichment. J Mater Chem B 2014; 2:1121-1124. [DOI: 10.1039/c3tb21617a] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Mesoporous SnO2 nanospheres were prepared via a one-step and template-free method and excellent enrichment performance was achieved in their applications for phosphopeptide enrichment.
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Affiliation(s)
- Liping Li
- Beijing National Laboratory for Molecular Sciences
- Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education
- College of Chemistry
- Peking University
- Beijing 100871, China
| | - Shuai Chen
- Beijing National Laboratory for Molecular Sciences
- State Key Laboratory for Structural Chemistry of Stable and Unstable Species
- College of Chemistry
- Peking University
- Beijing 100871, China
| | - Linnan Xu
- Beijing National Laboratory for Molecular Sciences
- Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education
- College of Chemistry
- Peking University
- Beijing 100871, China
| | - Yu Bai
- Beijing National Laboratory for Molecular Sciences
- Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education
- College of Chemistry
- Peking University
- Beijing 100871, China
| | - Zongxiu Nie
- Key Laboratory of Analytical Chemistry for Living Biosystems
- Institute of Chemistry
- The Chinese Academy of Sciences
- Beijing 100190, China
| | - Huwei Liu
- Beijing National Laboratory for Molecular Sciences
- Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education
- College of Chemistry
- Peking University
- Beijing 100871, China
| | - Limin Qi
- Beijing National Laboratory for Molecular Sciences
- State Key Laboratory for Structural Chemistry of Stable and Unstable Species
- College of Chemistry
- Peking University
- Beijing 100871, China
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38
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Highly selective enrichment of phosphopeptides with high-index facets exposed octahedral tin dioxide nanoparticles for mass spectrometric analysis. Talanta 2013; 119:452-7. [PMID: 24401440 DOI: 10.1016/j.talanta.2013.11.049] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2013] [Revised: 11/14/2013] [Accepted: 11/16/2013] [Indexed: 11/22/2022]
Abstract
High-index facets exposed octahedral tin dioxide (SnO2) nanoparticles were successfully synthesized and applied to selectively enrich phosphopeptides for mass spectrometric analysis. The high selectivity and capacity of the octahedral SnO2 nanoparticles were demonstrated by effectively enriching phosphopeptides from digests of phosphoprotein (α- or β-casein), protein mixtures of β-casein and bovine serum albumin, milk, and human serum samples. The unique octahedral SnO2 with abundant unsaturated coordination Sn atoms exhibited enhanced affinity and selective coordination ability with phosphopeptides due to their high chemical activity. The strong affinity led to highly selective capture and enrichment of phosphopeptides for sensitive detection through the bidentate bonds formed between surface atoms and phosphate. The phosphopeptides could be detected in β-casein down to 4 × 10(-9)M or in the mixture of β-casein and BSA with a molar ratio of even 1:100. The performance in selective enrichment of phosphopeptides from drinking milk and human serum showed powerful evidence of high selectivity and efficiency in identifying the low-abundant phosphopeptides from complicated biological samples. This work provided a way to improve the physical and chemical properties of materials by tailoring their exposed facets for selective enrichment of phosphopeptides.
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39
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Vilasi A, Fiume I, Pace P, Rossi M, Pocsfalvi G. Enrichment specificity of micro and nano-sized titanium and zirconium dioxides particles in phosphopeptide mapping. JOURNAL OF MASS SPECTROMETRY : JMS 2013; 48:1188-1198. [PMID: 24259207 DOI: 10.1002/jms.3254] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2013] [Revised: 06/18/2013] [Accepted: 07/11/2013] [Indexed: 06/02/2023]
Abstract
Owning to their anion-exchange properties, titanium and zirconium dioxides are widely used in phosphopeptide enrichment and purification protocols. The physical and chemical characteristics of the particles can significantly influence the loading capacity, the capture efficiency and phosphopeptide specificity and thus the outcome of the analyses. Although there are a number of protocols and commercial kits available for phosphopeptide purification, little data are found in the literature on the choice of the enrichment media. Here, we studied the influence of particle size on the affinity capture of phosphopeptides by TiO2 and ZrO2. Bovine milk casein derived phosphopeptides were enriched by micro and nanoparticles using a single-tube in-solution protocol at different peptide-to-beads ratio ranging from 1 : 1 to 1 : 200. Unsupervised hierarchical cluster analysis based on the whole set of Matrix Assisted Laser Desorption/Ionization time-of-flight mass spectra of the phosphopeptide enriched samples revealed 62 clustered peptide peaks and shows that nanoparticles have considerably higher enrichment capacity than bulk microparticles. Moreover, ZrO2 particles have higher enrichment capacity than TiO2. The selectivity and specificity of the enrichment was studied by monitoring the ion abundances of monophosphorylated, multiphosphorylated and non-phosphorylated casein-derived peptide peaks at different peptide-to-beads ratios. Comparison of the resulting plots enabled the determination of the optimal peptide-to-beads ratios for the different beads studied and showed that nano-TiO2 have higher selectivity for phosphopeptides than nano-ZrO2 particles.
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Affiliation(s)
- Annalisa Vilasi
- Mass Spectrometry and Proteomics, Institute of Protein Biochemistry, National Research Council of Italy, Napoli, Italy
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Novel nanomaterials used for sample preparation for protein analysis. Anal Bioanal Chem 2013; 406:35-47. [DOI: 10.1007/s00216-013-7392-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2013] [Revised: 09/09/2013] [Accepted: 09/20/2013] [Indexed: 11/26/2022]
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Sun Z, Hamilton KL, Reardon KF. Evaluation of quantitative performance of sequential immobilized metal affinity chromatographic enrichment for phosphopeptides. Anal Biochem 2013; 445:30-7. [PMID: 24096195 DOI: 10.1016/j.ab.2013.09.025] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2013] [Revised: 08/28/2013] [Accepted: 09/24/2013] [Indexed: 11/30/2022]
Abstract
We evaluated a sequential elution protocol from immobilized metal affinity chromatography (SIMAC) employing gallium-based immobilized metal affinity chromatography (IMAC) in conjunction with titanium dioxide-based metal oxide affinity chromatography (MOAC). The quantitative performance of this SIMAC enrichment approach, assessed in terms of repeatability, dynamic range, and linearity, was evaluated using a mixture composed of tryptic peptides from caseins, bovine serum albumin, and phosphopeptide standards. Although our data demonstrate the overall consistent performance of the SIMAC approach under various loading conditions, the results also revealed that the method had limited repeatability and linearity for most phosphopeptides tested, and different phosphopeptides were found to have different linear ranges. These data suggest that, unless additional strategies are used, SIMAC should be regarded as a semiquantitative method when used in large-scale phosphoproteomics studies in complex backgrounds.
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Affiliation(s)
- Zeyu Sun
- Department of Chemical and Biological Engineering, Colorado State University, Fort Collins, CO 80523, USA
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Li LP, Zheng T, Xu LN, Li Z, Sun LD, Nie ZX, Bai Y, Liu HW. SnO2–ZnSn(OH)6: a novel binary affinity probe for global phosphopeptide detection. Chem Commun (Camb) 2013; 49:1762-4. [DOI: 10.1039/c3cc38909j] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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Zhou H, Di Palma S, Preisinger C, Peng M, Polat AN, Heck AJR, Mohammed S. Toward a comprehensive characterization of a human cancer cell phosphoproteome. J Proteome Res 2012. [PMID: 23186163 DOI: 10.1021/pr300630k] [Citation(s) in RCA: 320] [Impact Index Per Article: 26.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Mass spectrometry (MS)-based phosphoproteomics has achieved extraordinary success in qualitative and quantitative analysis of cellular protein phosphorylation. Considering that an estimated level of phosphorylation in a cell is placed at well above 100,000 sites, there is still much room for improvement. Here, we attempt to extend the depth of phosphoproteome coverage while maintaining realistic aspirations in terms of available material, robustness, and instrument running time. We developed three strategies, where each provided a different balance between these three key parameters. The first strategy simply used enrichment by Ti(4+)-IMAC followed by reversed chromatography LC-MS (termed 1D). The second strategy incorporated an additional fractionation step through the use of HILIC (2D). Finally, a third strategy was designed employing first an SCX fractionation, followed by Ti(4+)-IMAC enrichment and additional fractionation by HILIC (3D). A preliminary evaluation was performed on the HeLa cell line. Detecting 3700 phosphopeptides in about 2 h, the 1D strategy was found to be the most sensitive but limited in comprehensivity, mainly due to issues with complexity and dynamic range. Overall, the best balance was achieved using the 2D based strategy, identifying close to 17,000 phosphopeptides with less than 1 mg of material in about 48 h. Subsequently, we confirmed the findings with the K562 cell sample. When sufficient material was available, the 3D strategy increased phosphoproteome allowing over 22,000 unique phosphopeptides to be identified. Unfortunately, the 3D strategy required more time and over 1 mg of material before it started to outperform 2D. Ultimately, combining all strategies, we were able to identify over 16,000 and nearly 24,000 unique phosphorylation sites from the cancer cell lines HeLa and K562, respectively. In summary, we demonstrate the need to carry out extensive fractionation for deep mining of the phosphoproteome and provide a guide for appropriate strategies depending on sample amount and/or analysis time.
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Affiliation(s)
- Houjiang Zhou
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
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Sakeye M, Smått JH. Comparison of different amino-functionalization procedures on a selection of metal oxide microparticles: degree of modification and hydrolytic stability. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2012; 28:16941-16950. [PMID: 23153336 DOI: 10.1021/la303925x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Amino-modified metal oxide materials are essential in a wide range of applications, including chromatography, ion adsorption, and as biomaterials. The aim of this study is to compare different functionalization techniques on a selection of metal oxides (SiO(2), TiO(2), ZrO(2), and SnO(2)) in order to determine which combination has the optimal properties for a certain application. We have used the nanocasting approach to synthesize micrometer-sized TiO(2), ZrO(2), and SnO(2) particles, which have similar morphologies and porosities as the starting mesoporous SiO(2) microparticles (Lichroprep Si 60). These metal oxides were subsequently functionalized by four different approaches, (a) covalent bonding of 3-aminopropyltriethoxysilane (APTES), (b) adsorption of 2-aminoethyl dihydrogen phosphate (AEDP), (c) surface polymerization of aziridine (AZ), and (d) electrostatic interaction of poly(ethylenimine) (PEI), to produce a high surface coverage of amino groups on their surfaces. Scanning electron microscopy, nitrogen physisorption, and X-ray diffraction were used to characterize the unmodified metal oxide particles, while thermogravimetric analysis, ninhydrin adsorption, and ζ potential titrations were applied to gain insight into the successfulness of the various surface modifications. Finally, the hydrolytic stability at pH 2 and 10 was investigated by ζ potential measurements. Unfortunately, the AEDP approach was not able to produce efficient amino-modification on any of the tested metal oxide surfaces. On the other hand, modifications with APTES, aziridine, and PEI appeared to give fairly stable amino-functionalizations at high pH values for all metal oxides, while these modifications were easily detached at pH 2, with the exception of SnO(2), where the AZ and PEI samples were stable up to 40 h. The results are expected to give valuable insights into the possibility of replacing amino-modified silica with more hydrolytically stable metal oxides in various application fields, for example, chromatography and drug delivery.
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Affiliation(s)
- Motolani Sakeye
- Center for Functional Materials and Laboratory of Physical Chemistry, Department of Natural Sciences, Åbo Akademi University, Porthansgatan 3, 20500 Turku, Finland
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Sun Z, Hamilton KL, Reardon KF. Phosphoproteomics and molecular cardiology: Techniques, applications and challenges. J Mol Cell Cardiol 2012; 53:354-68. [DOI: 10.1016/j.yjmcc.2012.06.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/02/2011] [Revised: 05/26/2012] [Accepted: 06/03/2012] [Indexed: 12/16/2022]
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Wang ST, Wang MY, Su X, Yuan BF, Feng YQ. Facile Preparation of SiO2/TiO2 Composite Monolithic Capillary Column and Its Application in Enrichment of Phosphopeptides. Anal Chem 2012; 84:7763-70. [DOI: 10.1021/ac301258q] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Shao-Ting Wang
- Key Laboratory of Analytical Chemistry for Biology and Medicine
(Ministry of Education), Department of Chemistry, Wuhan University, Wuhan 430072, P.R. China
| | - Meng-Ya Wang
- Key Laboratory of Analytical Chemistry for Biology and Medicine
(Ministry of Education), Department of Chemistry, Wuhan University, Wuhan 430072, P.R. China
| | - Xin Su
- Key Laboratory of Analytical Chemistry for Biology and Medicine
(Ministry of Education), Department of Chemistry, Wuhan University, Wuhan 430072, P.R. China
| | - Bi-Feng Yuan
- Key Laboratory of Analytical Chemistry for Biology and Medicine
(Ministry of Education), Department of Chemistry, Wuhan University, Wuhan 430072, P.R. China
| | - Yu-Qi Feng
- Key Laboratory of Analytical Chemistry for Biology and Medicine
(Ministry of Education), Department of Chemistry, Wuhan University, Wuhan 430072, P.R. China
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Tang LAL, Wang J, Lim TK, Bi X, Lee WC, Lin Q, Chang YT, Lim CT, Loh KP. High-performance graphene-titania platform for detection of phosphopeptides in cancer cells. Anal Chem 2012; 84:6693-700. [PMID: 22839352 DOI: 10.1021/ac301119r] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Phosphopeptides play a crucial role in many biological processes and constitute some of the most powerful biomarkers in disease detection. However they are often present in very low concentration, which makes their detection highly challenging. Here, we demonstrate the use of a solution-dispersible graphene-titania platform for the selective extraction of phosphopeptides from peptide mixtures. This is followed by direct analysis by surface-enhanced laser desorption/ionization time-of-flight mass spectrometry (SELDI-TOF MS). The efficient charge and energy exchange between graphene and TiO(2) during laser irradiation in SELDI-TOF MS promotes the soft ionization of analytes and affords a detection limit in the attomole range, which is 10(2)-10(5) more sensitive than conventional platforms. The graphene-titania platform can also be used for detecting phosphopeptides in cancer cells (HeLa cells), where it shows high specificity (94%). An expanded library of 967 unique phosphopeptides is detected using significantly reduced loading of extraction matrixes compared to conventional TiO(2) bead-based assays.
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Affiliation(s)
- Lena Ai Ling Tang
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, 117543, Singapore
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Zeng YY, Chen HJ, Shiau KJ, Hung SU, Wang YS, Wu CC. Efficient enrichment of phosphopeptides by magnetic TiO₂-coated carbon-encapsulated iron nanoparticles. Proteomics 2012; 12:380-90. [PMID: 22144111 DOI: 10.1002/pmic.201000726] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2011] [Revised: 10/31/2011] [Accepted: 11/14/2011] [Indexed: 01/17/2023]
Abstract
Titanium dioxide (TiO₂) has been widely used for phosphopeptide enrichment. Several approaches have been reported to produce magnetic TiO₂ affinity probes. In this report, we present a facile approach to immobilize TiO₂ onto poly(acrylic acid)-functionalized magnetic carbon-encapsulated iron nanoparticles as affinity probes for efficient enrichment of phosphopeptides. By using the new magnetic TiO₂ affinity probes, denoted as TiO₂-coated Fe@CNPs, rapid and effective MALDI-TOF MS profiling of phosphopeptides was demonstrated in different model systems such as tryptic digests of β-casein, and complex β-casein/BSA mixture. The TiO₂-coated Fe@CNPs out-performed the commercial TiO₂-coated magnetic beads for detection of phosphopeptides from tryptic digests of β-casein/BSA mixture with a molar ratio of 1:100. The new TiO₂-coated magnetic probes were also proven to be applicable for real life samples. The magnetic TiO₂-coated Fe@CNPs were employed to selectively isolate phosphopeptides from tryptic digests of HeLa cell lysates and out-performed the commercial magnetic TiO₂ beads in the number of identified phosphopeptides and phosphorylation sites. In a 200-μg equivalent of HeLa cell lysates, we identified 1415 unique phosphopeptides and 1093 phosphorylation sites, indicating the good performance of the new approach.
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Affiliation(s)
- Yi Y Zeng
- Department of Applied Chemistry, National Chi Nan University, Puli, Nantou, Taiwan
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49
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Zhao L, Qin H, Hu Z, Zhang Y, Wu R, Zou H. A poly(ethylene glycol)-brush decorated magnetic polymer for highly specific enrichment of phosphopeptides. Chem Sci 2012. [DOI: 10.1039/c2sc20363d] [Citation(s) in RCA: 89] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
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50
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Li X, Guo Z, Sheng Q, Xue X, Liang X. Sequential elution of multiply and singly phosphorylated peptides with polar-copolymerized mixed-mode RP18/SCX material. Analyst 2012; 137:2774-6. [DOI: 10.1039/c2an35247h] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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