51
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Mirza MR, Rainer M, Messner CB, Güzel Y, Schemeth D, Stasyk T, Choudhary MI, Huber LA, Rode BM, Bonn GK. A new type of metal chelate affinity chromatography using trivalent lanthanide ions for phosphopeptide enrichment. Analyst 2013; 138:2995-3004. [DOI: 10.1039/c3an36853j] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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52
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Fischnaller M, Bakry R, Vallant RM, Huber LA, Bonn GK. C60-fullerene bound silica for the preconcentration and the fractionation of multiphosphorylated peptides. Anal Chim Acta 2013; 761:92-101. [DOI: 10.1016/j.aca.2012.11.019] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2012] [Revised: 11/05/2012] [Accepted: 11/10/2012] [Indexed: 12/20/2022]
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53
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Güzel Y, Rainer M, Mirza MR, Messner CB, Bonn GK. Highly selective recovery of phosphopeptides using trypsin-assisted digestion of precipitated lanthanide–phosphoprotein complexes. Analyst 2013; 138:2897-905. [DOI: 10.1039/c3an00066d] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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54
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Li Y, Zhang X, Deng C. Functionalized magnetic nanoparticles for sample preparation in proteomics and peptidomics analysis. Chem Soc Rev 2013; 42:8517-39. [DOI: 10.1039/c3cs60156k] [Citation(s) in RCA: 139] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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55
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Shen F, Hu Y, Guan P, Ren X. Facile preparation of titanium phosphate-modified chitosan for selective capture of phosphopeptides. J Sep Sci 2012; 36:540-7. [DOI: 10.1002/jssc.201200821] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2012] [Revised: 09/29/2012] [Accepted: 10/12/2012] [Indexed: 11/11/2022]
Affiliation(s)
- Feng Shen
- Department of Plant Nutrition, College of Resources and Environmental Sciences; China Agricultural University; Beijing P. R. China
| | - Yufeng Hu
- Department of Environmental Sciences and Engineering, College of Resources and Environmental Sciences; China Agricultural University; Beijing P. R. China
| | - Ping Guan
- Department of Plant Nutrition, College of Resources and Environmental Sciences; China Agricultural University; Beijing P. R. China
| | - Xueqin Ren
- Department of Environmental Sciences and Engineering, College of Resources and Environmental Sciences; China Agricultural University; Beijing P. R. China
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56
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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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57
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Stolowitz ML. On-target and nanoparticle-facilitated selective enrichment of peptides and proteins for analysis by MALDI-MS. Proteomics 2012; 12:3438-50. [DOI: 10.1002/pmic.201200252] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2012] [Revised: 08/27/2012] [Accepted: 09/20/2012] [Indexed: 01/09/2023]
Affiliation(s)
- Mark L. Stolowitz
- Canary Center at Stanford for Cancer Early Detection; Department of Radiology; Stanford University School of Medicine; Palo Alto CA USA
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58
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Cheung RCF, Wong JH, Ng TB. Immobilized metal ion affinity chromatography: a review on its applications. Appl Microbiol Biotechnol 2012; 96:1411-20. [PMID: 23099912 DOI: 10.1007/s00253-012-4507-0] [Citation(s) in RCA: 151] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2012] [Revised: 10/10/2012] [Accepted: 10/10/2012] [Indexed: 01/14/2023]
Abstract
After 35 years of development, immobilized metal ion affinity chromatography (IMAC) has evolved into a popular protein purification technique. This review starts with a discussion of its mechanism and advantages. It continues with its applications which include the purification of histidine-tagged proteins, natural metal-binding proteins, and antibodies. IMAC used in conjunction with mass spectroscopy for phosphoprotein fractionation and proteomics is also covered. Finally, this review addresses the developments, limitations, and considerations of IMAC in the biopharmaceutical industry.
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Affiliation(s)
- Randy Chi Fai Cheung
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, China
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59
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Najam-ul-Haq M, Jabeen F, Hussain D, Saeed A, Musharraf SG, Huck CW, Bonn GK. Versatile nanocomposites in phosphoproteomics: A review. Anal Chim Acta 2012; 747:7-18. [DOI: 10.1016/j.aca.2012.08.004] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2012] [Revised: 08/01/2012] [Accepted: 08/02/2012] [Indexed: 10/28/2022]
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60
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Ti4+-phosphate functionalized cellulose for phosphopeptides enrichment and its application in rice phosphoproteome analysis. J Chromatogr B Analyt Technol Biomed Life Sci 2012; 902:108-15. [DOI: 10.1016/j.jchromb.2012.06.033] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2012] [Revised: 05/17/2012] [Accepted: 06/13/2012] [Indexed: 11/23/2022]
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61
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Queffélec C, Petit M, Janvier P, Knight DA, Bujoli B. Surface modification using phosphonic acids and esters. Chem Rev 2012; 112:3777-807. [PMID: 22530923 DOI: 10.1021/cr2004212] [Citation(s) in RCA: 551] [Impact Index Per Article: 45.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Clémence Queffélec
- LUNAM Université, CNRS, UMR, Chimie Et Interdisciplinarité: Synthèse Analyse Modélisation, UFR Sciences et Techniques, Nantes, France
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62
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Chang IF, Hsu JL, Hsu PH, Sheng WA, Lai SJ, Lee C, Chen CW, Hsu JC, Wang SY, Wang LY, Chen CC. Comparative phosphoproteomic analysis of microsomal fractions of Arabidopsis thaliana and Oryza sativa subjected to high salinity. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2012; 185-186:131-42. [PMID: 22325874 DOI: 10.1016/j.plantsci.2011.09.009] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2011] [Revised: 09/26/2011] [Accepted: 09/28/2011] [Indexed: 05/20/2023]
Abstract
Plants respond to salt stress by initiating phosphorylation cascades in their cells. Many key phosphorylation events take place at membranes. Microsomal fractions from 400 mM salt-treated Arabidopsis suspension plants were isolated, followed by trypsin shaving, enrichment using Zirconium ion-charged or TiO(2) magnetic beads, and tandem mass spectrometry analyses for site mapping. A total of 27 phosphorylation sites from 20 Arabidopsis proteins including photosystem II reaction center protein H PsbH were identified. In addition to Arabidopsis, microsomal fractions from shoots of 200 mM salt-treated rice was carried out, followed by trypsin digestion using shaving or tube-gel, and enrichment using Zirconium ion-charged or TiO(2) magnetic beads. This yielded identification of 13 phosphorylation sites from 8 proteins including photosystem II reaction center protein H PsbH. Label-free quantitative analysis suggests that the phosphorylation sites of PsbH were regulated by salt stress in Arabidopsis and rice. Sequence alignment of PsbH phosphorylation sites indicates that Thr-2 and Thr-4 are evolutionarily conserved in plants. Four conserved phosphorylation motifs were predicted, and these suggest that a specific unknown kinase or phosphatase is involved in high-salt stress responses in plants.
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Affiliation(s)
- Ing-Feng Chang
- Institute of Plant Biology, National Taiwan University, Taipei, Taiwan.
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63
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Hennrich ML, van den Toorn HWP, Groenewold V, Heck AJR, Mohammed S. Ultra Acidic Strong Cation Exchange Enabling the Efficient Enrichment of Basic Phosphopeptides. Anal Chem 2012; 84:1804-8. [DOI: 10.1021/ac203303t] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Marco L. Hennrich
- Biomolecular Mass Spectrometry and Proteomics
Group, Bijvoet Center for Biomolecular Research and Utrecht Institute
for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
- Netherlands Proteomics Centre, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Henk W. P. van den Toorn
- Biomolecular Mass Spectrometry and Proteomics
Group, Bijvoet Center for Biomolecular Research and Utrecht Institute
for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
- Netherlands Proteomics Centre, Padualaan 8, 3584 CH Utrecht, The Netherlands
- Netherlands Bioinformatics Centre, Geert Grooteplein 28, 6525 GA Nijmegen, The Netherlands
| | - Vincent Groenewold
- Molecular Cancer Research and Cancer
Genomics Centre, University Medical Center Utrecht, Universiteitsweg 100, 3584 CG Utrecht, The Netherlands
| | - Albert J. R. Heck
- Biomolecular Mass Spectrometry and Proteomics
Group, Bijvoet Center for Biomolecular Research and Utrecht Institute
for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
- Netherlands Proteomics Centre, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Shabaz Mohammed
- Biomolecular Mass Spectrometry and Proteomics
Group, Bijvoet Center for Biomolecular Research and Utrecht Institute
for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
- Netherlands Proteomics Centre, Padualaan 8, 3584 CH Utrecht, The Netherlands
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64
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Batalha IL, Lowe CR, Roque AC. Platforms for enrichment of phosphorylated proteins and peptides in proteomics. Trends Biotechnol 2012; 30:100-10. [DOI: 10.1016/j.tibtech.2011.07.004] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2011] [Revised: 07/21/2011] [Accepted: 07/21/2011] [Indexed: 01/17/2023]
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65
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Li XS, Xu LD, Zhu GT, Yuan BF, Feng YQ. Zirconium arsenate-modified magnetic nanoparticles: preparation, characterization and application to the enrichment of phosphopeptides. Analyst 2012; 137:959-67. [DOI: 10.1039/c2an15985f] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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66
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Galezowska J, Gumienna-Kontecka E. Phosphonates, their complexes and bio-applications: A spectrum of surprising diversity. Coord Chem Rev 2012. [DOI: 10.1016/j.ccr.2011.07.002] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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67
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Engineering of a phosphorylatable tag for specific protein binding on zirconium phosphonate based microarrays. J Biol Inorg Chem 2011; 17:399-407. [DOI: 10.1007/s00775-011-0863-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2011] [Accepted: 11/15/2011] [Indexed: 10/14/2022]
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68
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Zirconium arsenate-modified silica nanoparticles for specific capture of phosphopeptides and direct analysis by matrix-assisted laser desorption/ionization mass spectrometry. Anal Bioanal Chem 2011; 402:1041-56. [DOI: 10.1007/s00216-011-5547-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2011] [Revised: 10/14/2011] [Accepted: 10/31/2011] [Indexed: 10/15/2022]
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69
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Tichy A, Salovska B, Rehulka P, Klimentova J, Vavrova J, Stulik J, Hernychova L. Phosphoproteomics: Searching for a needle in a haystack. J Proteomics 2011; 74:2786-97. [DOI: 10.1016/j.jprot.2011.07.018] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2011] [Revised: 07/13/2011] [Accepted: 07/22/2011] [Indexed: 11/27/2022]
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70
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Wang F, Song C, Cheng K, Jiang X, Ye M, Zou H. Perspectives of Comprehensive Phosphoproteome Analysis Using Shotgun Strategy. Anal Chem 2011; 83:8078-85. [DOI: 10.1021/ac201833j] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Fangjun Wang
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Chunxia Song
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Kai Cheng
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Xinning Jiang
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Mingliang Ye
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Hanfa Zou
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
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71
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Tsougeni K, Zerefos P, Tserepi A, Vlahou A, Garbis SD, Gogolides E. TiO2-ZrO2 affinity chromatography polymeric microchip for phosphopeptide enrichment and separation. LAB ON A CHIP 2011; 11:3113-3120. [PMID: 21796280 DOI: 10.1039/c1lc20133f] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
We fabricated a TiO(2)-ZrO(2) affinity chromatography micro-column on 2 mm PMMA plates, and demonstrated the enrichment and separation of (a) a standard mono- and tetra-phosphopeptide, and (b) phosphopeptides contained in a tryptic digest of β-Casein. The chromatography column consisted of 32 parallel microchannels with common input and output ports and was fabricated by lithography directly on the polymeric substrate followed by plasma etching (i.e. standard MEMS processing) and sealed with lamination. The liquid deposited TiO(2)-ZrO(2) stationary phase was characterized by X-ray diffraction and was found to be mostly TiO(2) and ZrO(2) in crystalline phases. Off-chip UV detection and MALDI MS identification of the separated effluents were used. The chip had a capacity of >1.4 μg (0.7 nmol) of a prototype mono-phosphopeptide and a recovery of 94 ± 3%, and can be used with small samples (less than 0.1 μL depending on the syringe pump used). The chip design allows an expansion of its capacity by means of increasing the number of parallel microchannels at a constant sample volume. Our approach provided an alternative to off-line extraction tips (with typical capacities of 1-2 μg and sample volumes of 1-10 μL), and to on-chip efforts based on packed bed and frit formats.
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Affiliation(s)
- Katerina Tsougeni
- Institute of Microelectronics, NCSR Demokritos, P.O. BOX 60228, 153 10, Aghia Paraskevi, Greece
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72
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Chen SY, Juang YM, Chien MW, Li KI, Yu CS, Lai CC. Magnetic iron oxide nanoparticle enrichment of phosphopeptides on a radiate microstructure MALDI chip. Analyst 2011; 136:4454-9. [PMID: 21897971 DOI: 10.1039/c1an15334j] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Several methods can be used to improve the enrichment of phosphorylated proteins. In this paper, phosphopeptides were enriched using magnetic iron(II,III) oxide (magnetite, Fe(3)O(4)) nanoparticles (NPs) on a radiate microstructure silicon chip and then analyzed using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOFMS) without further purification processes. We have developed a radiate microstructure chip on which samples can be concentrated for analysis by MALDI-TOFMS. The phosphoprotein digests and magnetic iron oxide NPs aqueous solution were deposited onto the central zone of the radiate microstructure silicon chip and enabled the on-chip enrichment of phosphopeptides. Microscopic analysis confirmed that the applied samples were confined to the central zone. Sample spots focused on the chip were much smaller than those on an unmodified plate with the same total volume. Different additives were used and optimized processes were performed to minimize non-phosphopeptides interference. These data collectively demonstrate that our on-chip phosphopeptide enrichment protocol is a rapid and easy-to-use method for phosphoproteome analysis.
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Affiliation(s)
- Shun-Yuan Chen
- Institute of Molecular Biology, National Chung Hsing University, Taichung, Taiwan
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73
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Hennrich ML, Groenewold V, Kops GJPL, Heck AJR, Mohammed S. Improving Depth in Phosphoproteomics by Using a Strong Cation Exchange-Weak Anion Exchange-Reversed Phase Multidimensional Separation Approach. Anal Chem 2011; 83:7137-43. [DOI: 10.1021/ac2015068] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Marco L. Hennrich
- Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
- Netherlands Proteomics Centre, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Vincent Groenewold
- Molecular Cancer Research and Cancer Genomics Centre, University Medical Center Utrecht, Universiteitsweg 100, 3584 CG Utrecht, The Netherlands
| | - Geert J. P. L. Kops
- Netherlands Proteomics Centre, Padualaan 8, 3584 CH Utrecht, The Netherlands
- Molecular Cancer Research and Cancer Genomics Centre, University Medical Center Utrecht, Universiteitsweg 100, 3584 CG Utrecht, The Netherlands
| | - Albert J. R. Heck
- Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
- Netherlands Proteomics Centre, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Shabaz Mohammed
- Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
- Netherlands Proteomics Centre, Padualaan 8, 3584 CH Utrecht, The Netherlands
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74
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Zhou H, Low TY, Hennrich ML, van der Toorn H, Schwend T, Zou H, Mohammed S, Heck AJR. Enhancing the identification of phosphopeptides from putative basophilic kinase substrates using Ti (IV) based IMAC enrichment. Mol Cell Proteomics 2011; 10:M110.006452. [PMID: 21715320 DOI: 10.1074/mcp.m110.006452] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Metal and metal oxide chelating-based phosphopeptide enrichment technologies provide powerful tools for the in-depth profiling of phosphoproteomes. One weakness inherent to current enrichment strategies is poor binding of phosphopeptides containing multiple basic residues. The problem is exacerbated when strong cation exchange (SCX) is used for pre-fractionation, as under low pH SCX conditions phosphorylated peptides with multiple basic residues elute with the bulk of the tryptic digest and therefore require more stringent enrichment. Here, we report a systematic evaluation of the characteristics of a novel phosphopeptide enrichment approach based on a combination of low pH SCX and Ti(4+)-immobilized metal ion affinity chromatography (IMAC) comparing it one-to-one with the well established low pH SCX-TiO(2) enrichment method. We also examined the effect of 1,1,1,3,3,3-hexafluoroisopropanol (HFP), trifluoroacetic acid (TFA), or 2,5-dihydroxybenzoic acid (DHB) in the loading buffer, as it has been hypothesized that high levels of TFA and the perfluorinated solvent HFP improve the enrichment of phosphopeptides containing multiple basic residues. We found that Ti(4+)-IMAC in combination with TFA in the loading buffer, outperformed all other methods tested, enabling the identification of around 5000 unique phosphopeptides containing multiple basic residues from 400 μg of a HeLa cell lysate digest. In comparison, ∼ 2000 unique phosphopeptides could be identified by Ti(4+)-IMAC with HFP and close to 3000 by TiO(2). We confirmed, by motif analysis, the basic phosphopeptides enrich the number of putative basophilic kinases substrates. In addition, we performed an experiment using the SCX/Ti(4+)-IMAC methodology alongside the use of collision-induced dissociation (CID), higher energy collision induced dissociation (HCD) and electron transfer dissociation with supplementary activation (ETD) on considerably more complex sample, consisting of a total of 400 μg of triple dimethyl labeled MCF-7 digest. This analysis led to the identification of over 9,000 unique phosphorylation sites. The use of three peptide activation methods confirmed that ETD is best capable of sequencing multiply charged peptides. Collectively, our data show that the combination of SCX and Ti(4+)-IMAC is particularly advantageous for phosphopeptides with multiple basic residues.
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Affiliation(s)
- Houjiang Zhou
- Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands
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75
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Preparation of magnetic polymer material with phosphate group and its application to the enrichment of phosphopeptides. J Chromatogr A 2011; 1218:3845-53. [DOI: 10.1016/j.chroma.2011.04.044] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2010] [Revised: 04/15/2011] [Accepted: 04/18/2011] [Indexed: 11/18/2022]
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76
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Krenkova J, Foret F. Iron oxide nanoparticle coating of organic polymer-based monolithic columns for phosphopeptide enrichment. J Sep Sci 2011; 34:2106-12. [PMID: 21560247 DOI: 10.1002/jssc.201100256] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2011] [Revised: 04/01/2011] [Accepted: 04/01/2011] [Indexed: 11/06/2022]
Abstract
A new monolithic capillary column with an iron oxide nanoparticle coating has been developed for selective and efficient enrichment of phosphopeptides. Iron oxide nanoparticles were prepared by a co-precipitation method and stabilized by citrate ions. A stable coating of nanoparticles was obtained via multivalent electrostatic interactions of citrate ions on the surface of iron oxide nanoparticles with a quaternary amine functionalized poly(glycidyl methacrylate-co-ethylene dimethacrylate) monolith. A high dynamic binding capacity of 86 μmol/mL column volume was measured with an adenosine-5'-triphosphate. Performance of the monolithic column was demonstrated with the efficient and selective enrichment of phosphopeptides from peptide mixtures of α-casein and β-casein digests and their MALDI/MS characterization in off-line mode.
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Affiliation(s)
- Jana Krenkova
- Institute of Analytical Chemistry of the ASCR, v. v. i., Veveri, Brno, Czech Republic.
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77
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Kouvonen P, Rainio EM, Suni V, Koskinen P, Corthals GL. Enrichment and sequencing of phosphopeptides on indium tin oxide coated glass slides. MOLECULAR BIOSYSTEMS 2011; 7:1828-37. [PMID: 21523302 DOI: 10.1039/c0mb00269k] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Unambiguous identification of phosphorylation sites is of premier importance to biologists, who seek to understand the role of phosphorylation from the perspective of site-specific control of biological phenomena. Despite this widely asked and highly specific information, many methods developed are aimed at analysis of complete proteomes, indeed even phospho-proteomes, surpassing the basic requests of many biologists. We have therefore further developed a simple method that specifically deals with the analysis of multiple phosphorylation sites on singular proteins or small collections of proteins. With this method, the whole purification process, from sample application to MALDI-MS analysis, can be performed on commercially available indium tin oxide (ITO) coated glass slides. We show that fifteen (15) samples can be purified within one hour, and that low femtomole sensitivity can be achieved. This limit of identification is demonstrated by the successful MS/MS-based identification of 6 fmol of monophosphopeptide from β-casein. We demonstrate that the method can be applied for identifying phosphorylation sites from recombinant and cell-derived biological protein samples. Since ITO-coated glass slides are inexpensive and available from several suppliers the method is readily and inexpensively available to other researchers. Taken together, the presented protocols and materials render this method as an extremely fast and sensitive phosphopeptide identification protocol that should aid biologists in discovery and validation of phosphorylation sites.
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Affiliation(s)
- Petri Kouvonen
- University of Turku, Centre for Biotechnology, Turku, Finland
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78
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Wang H, Duan J, Cheng Q. Photocatalytically patterned TiO2 arrays for on-plate selective enrichment of phosphopeptides and direct MALDI MS analysis. Anal Chem 2011; 83:1624-31. [PMID: 21306131 PMCID: PMC7360113 DOI: 10.1021/ac1024232] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
We report the development of photocatalytically patterned TiO(2) arrays for selective on-plate enrichment and direct matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) analysis of phosphopeptides. A thin TiO(2) nanofilm with controlled porosity is prepared on gold-covered glass slides by a layer-by-layer (LbL) deposition/calcination process. The highly porous and rough nanostructure offers high surface area for selective binding of phosphorylated species. The patterned arrays are generated using an octadecyltrichlorosilane (OTS) coating in combination of UV irradiation with a photomask, followed by NaOH etching. The resulting hydrophilic TiO(2) spots are thus surrounded by a hydrophobic OTS layer, which can facilitate the enrichment of low-abundance components by confining a large volume sample into a small area. The TiO(2) arrays exhibit high specificity toward phosphopeptides in complex samples including phosphoprotein digests and human serum, and the detection can be made in the fmole range. Additional advantages of the arrays include excellent stability, reusability/reproducibility, and low cost. This method has been successfully applied to the analysis of phosphopeptides in nonfat milk. The patterned TiO(2) arrays provide an attractive interface for performing on-plate reactions, including selective capture of target species for MALDI-MS analysis, and can serve as a versatile lab-on-a-chip platform for high throughput analysis in phosphoproteome research.
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Affiliation(s)
| | | | - Quan Cheng
- Department of Chemistry, University of California, Riverside, California 92521
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79
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Lu J, Li Y, Deng C. Facile synthesis of zirconium phosphonate-functionalized magnetic mesoporous silica microspheres designed for highly selective enrichment of phosphopeptides. NANOSCALE 2011; 3:1225-1233. [PMID: 21264407 DOI: 10.1039/c0nr00896f] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
In this work, we present a facile approach for the synthesis of zirconium phosphate (ZrP)-functionalized magnetic silica mesoporous microspheres for the selective enrichment of phosphopeptides. At first, magnetic mesoporous silica microspheres were prepared by directly coating mesoporous silica onto Fe3O4 magnetic microspheres, and then addition of phosphate onto the magnetic mesoporous silica microspheres was performed using 3-(trihydroxysilyl)propyl methylphosphate. The obtained phosphate-modified magnetic mesoporous microspheres were monodispersed with a mean diameter of 350 nm, and had an obvious mesoporous silica shell (∼65 nm). Finally, the resultant phosphate-functionalized magnetic mesoporous microspheres were incubated in ZrOCl2 solution with gentle stirring overnight for the loading of Zr4+ cations. The obtained Zr4+-functionalized materials were applied to the selective enrichment of phosphopeptides from both standard protein digestion and real samples. The enriched peptides were analyzed by MALDI-TOF MS and LC-ESI MS. Experimental results demonstrated that zirconium phosphonate-modified magnetic mesoporous silica microspheres show excellent potential for the selective enrichment of phosphopeptides.
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Affiliation(s)
- Jin Lu
- Department of Chemistry & Institutes of Biomedical Sciences, Fudan University, Shanghai, 200433, China
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80
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Hu Y, Peng Y, Lin K, Shen H, Brousseau LC, Sakamoto J, Sun T, Ferrari M. Surface engineering on mesoporous silica chips for enriching low molecular weight phosphorylated proteins. NANOSCALE 2011; 3:421-8. [PMID: 21135976 PMCID: PMC3397147 DOI: 10.1039/c0nr00720j] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Phosphorylated peptides and proteins play an important role in normal cellular activities, e.g., gene expression, mitosis, differentiation, proliferation, and apoptosis, as well as tumor initiation, progression and metastasis. However, technical hurdles hinder the use of common fractionation methods to capture phosphopeptides from complex biological fluids such as human sera. Herein, we present the development of a dual strategy material that offers enhanced capture of low molecular weight phosphoproteins: mesoporous silica thin films with precisely engineered pore sizes that sterically select for molecular size combined with chemically selective surface modifications (i.e. Ga3+, Ti4+ and Zr4+) that target phosphoroproteins. These materials provide high reproducibility (CV=18%) and increase the stability of the captured proteins by excluding degrading enzymes, such as trypsin. The chemical and physical properties of the composite mesoporous thin films were characterized by X-ray diffraction, transmission electron microscopy, X-ray photoelectron spectroscopy, energy dispersive X-ray spectroscopy and ellipsometry. Using mass spectroscopy and biostatistics analysis, the enrichment efficiency of different metal ions immobilized on mesoporous silica chips was investigated. The novel technology reported provides a platform capable of efficiently profiling the serum proteome for biomarker discovery, forensic sampling, and routine diagnostic applications.
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Affiliation(s)
- Ye Hu
- Department of Nanomedicine and Biomedical Engineering, the University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Yang Peng
- Department of Nanomedicine and Biomedical Engineering, the University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Kevin Lin
- Department of Biomedical Engineering, the University of Texas at Austin, Austin, TX, USA
| | - Haifa Shen
- Department of Nanomedicine and Biomedical Engineering, the University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Louis C. Brousseau
- Department of Nanomedicine and Biomedical Engineering, the University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Jason Sakamoto
- Department of Nanomedicine and Biomedical Engineering, the University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Tong Sun
- Department of Nanomedicine and Biomedical Engineering, the University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Mauro Ferrari
- Department of Nanomedicine and Biomedical Engineering, the University of Texas Health Science Center at Houston, Houston, TX, USA
- Department of Biomedical Engineering, the University of Texas at Austin, Austin, TX, USA
- The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Bioengineering, Rice University, Houston, TX, USA
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81
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Chen H, Liu S, Li Y, Deng C, Zhang X, Yang P. Development of oleic acid-functionalized magnetite nanoparticles as hydrophobic probes for concentrating peptides with MALDI-TOF-MS analysis. Proteomics 2011; 11:890-7. [DOI: 10.1002/pmic.201000509] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2010] [Revised: 11/22/2010] [Accepted: 11/29/2010] [Indexed: 11/09/2022]
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82
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Zhao L, Wu R, Zou H. Selective capture of phosphopeptides by zirconium phosphonate-magnetic nanoparticles. Methods Mol Biol 2011; 790:215-222. [PMID: 21948418 DOI: 10.1007/978-1-61779-319-6_17] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Immobilized metal affinity chromatography is a widely used method for the enrichment of phosphopeptides from proteolytic digests prior to mass spectrometric analysis. Here, we describe the selective enrichment of phosphopeptides from tryptic digests of proteins (α- and β-caseins) by zirconium phosphonate-magnetic Fe(3)O(4)/SiO(2) (core/shell) nanoparticles for phosphoproteome analysis with MALDI-TOF mass spectrometry.
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Affiliation(s)
- Liang Zhao
- National Chromatographic R & A Center, CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
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83
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An optimized magnetite microparticle-based phosphopeptide enrichment strategy for identifying multiple phosphorylation sites in an immunoprecipitated protein. Anal Biochem 2011; 408:19-31. [DOI: 10.1016/j.ab.2010.08.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2010] [Revised: 06/26/2010] [Accepted: 08/02/2010] [Indexed: 11/22/2022]
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84
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Chen SY, Li KI, Yu CS, Wang JS, Hu YC, Lai CC. A radiate microstructure MALDI chip for sample concentration and detection. Anal Chem 2010; 82:5951-7. [PMID: 20553036 DOI: 10.1021/ac101426n] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Although matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOFMS) analysis is an important tool for analyzing and characterizing biomolecules of varying complexity, the sensitivity of MALDI-TOFMS is dependent on proper preparation of the sample, a process that is oftentimes problematic and requires considerable expertise. In this study, we have developed a radiate microstructure chip on which samples can be concentrated for analysis by MALDI-TOFMS. The sample/matrix mixture was deposited onto the central space of the well on the chip and allowed to dry. Microscopic analysis confirmed that the applied samples were confined to the central zone. Sample spots focused on the chip were much smaller than those on an unmodified plate with the same total volume. Optimizing processes of several preparation factors were also performed to ensure matrix homogeneity in our chip. Analysis of the samples with MALDI-TOFMS showed that the signals from samples on our chip were significantly greater than those on the unmodified plate. The feasibility of using this chip to detect peptides and phosphopeptides was also demonstrated.
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Affiliation(s)
- Shun-Yuan Chen
- Institute of Molecular Biology, National Chung Hsing University, Taichung, Taiwan
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85
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Qin W, Zhang W, Song L, Zhang Y, Qian X. Surface Initiated Atom Transfer Radical Polymerization: Access to Three Dimensional Wavelike Polymer Structure Modified Capillary Columns for Online Phosphopeptide Enrichment. Anal Chem 2010; 82:9461-8. [DOI: 10.1021/ac1021437] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Weijie Qin
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, No. 33 Life Science Park Road, Changping District, Beijing 102206, PR China
| | - Wanjun Zhang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, No. 33 Life Science Park Road, Changping District, Beijing 102206, PR China
| | - Lina Song
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, No. 33 Life Science Park Road, Changping District, Beijing 102206, PR China
| | - Yangjun Zhang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, No. 33 Life Science Park Road, Changping District, Beijing 102206, PR China
| | - Xiaohong Qian
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, No. 33 Life Science Park Road, Changping District, Beijing 102206, PR China
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86
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Tiseanu C, Parvulescu V, Parvulescu V, Cotoi E, Gessner A, Kumke M, Simon S, Vasiliu F. Structural and photoluminescence characterization of mesoporous silicon-phosphates. J Photochem Photobiol A Chem 2010. [DOI: 10.1016/j.jphotochem.2010.07.015] [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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87
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Lu Z, Duan J, He L, Hu Y, Yin Y. Mesoporous TiO2 Nanocrystal Clusters for Selective Enrichment of Phosphopeptides. Anal Chem 2010; 82:7249-58. [DOI: 10.1021/ac1011206] [Citation(s) in RCA: 109] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Zhenda Lu
- Department of Chemistry, Unversity of California, Riverside, California 92521
| | - Jicheng Duan
- Department of Chemistry, Unversity of California, Riverside, California 92521
| | - Le He
- Department of Chemistry, Unversity of California, Riverside, California 92521
| | - Yongxing Hu
- Department of Chemistry, Unversity of California, Riverside, California 92521
| | - Yadong Yin
- Department of Chemistry, Unversity of California, Riverside, California 92521
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88
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Bürgel SC, Guillaume-Gentil O, Zheng L, Vörös J, Bally M. Zirconium ion mediated formation of liposome multilayers. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2010; 26:10995-11002. [PMID: 20507172 DOI: 10.1021/la9047566] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Phospholipid vesicles have attracted considerable interest as a platform for a variety of biomolecular binding assays, especially in the area of membrane protein sensing. The development of liposome-based biosensors widely relies on the availability of simple and efficient protocols for their surface immobilization. We present a novel approach toward the creation of three-dimensional phospholipid vesicle constructs using multivalent zirconium ions as linkers between the liposomes. Such three-dimensional sensing platforms are likely to play a key role in the development of biosensing devices with increased loading capacity and sensitivity. After demonstrating the affinity of Zr(4+) toward the phospholipids, we formed vesicle multilayers by sequential injections of solutions containing either liposomes or ZrOCl(2). In situ adlayer characterization was carried out by optical waveguide lightmode spectroscopy (OWLS) and quartz crystal microbalance with dissipation (QCM-D) measurements while imaging was performed by atomic force microscopy (AFM) and fluorescence microscopy. Multilayers were successfully constructed, and as demonstrated in a model fluorescence-based biomolecular binding assay, the sensor's loading capacity was increased. Furthermore, we observed that lipid exchange between the vesicles is promoted in the presence of Zr(4+) and that addition of a phosphate-containing buffer leads to adlayer loosening and creation of lipidic tubular structures. The approach presented here could be applied to the study of membrane proteins in a highly sensitive manner due to the increased surface area or to produce functional coatings for controlled drug release and host response.
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Affiliation(s)
- Sebastian C Bürgel
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH and University Zurich, 8092 Zurich, Switzerland
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89
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Iliuk AB, Martin VA, Alicie BM, Geahlen RL, Tao WA. In-depth analyses of kinase-dependent tyrosine phosphoproteomes based on metal ion-functionalized soluble nanopolymers. Mol Cell Proteomics 2010; 9:2162-72. [PMID: 20562096 DOI: 10.1074/mcp.m110.000091] [Citation(s) in RCA: 130] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The ability to obtain in-depth understanding of signaling networks in cells is a key objective of systems biology research. Such ability depends largely on unbiased and reproducible analysis of phosphoproteomes. We present here a novel proteomics tool, polymer-based metal ion affinity capture (PolyMAC), for the highly efficient isolation of phosphopeptides to facilitate comprehensive phosphoproteome analyses. This approach uses polyamidoamine dendrimers multifunctionalized with titanium ions and aldehyde groups to allow the chelation and subsequent isolation of phosphopeptides in a homogeneous environment. Compared with current strategies based on solid phase micro- and nanoparticles, PolyMAC demonstrated outstanding reproducibility, exceptional selectivity, fast chelation times, and high phosphopeptide recovery from complex mixtures. Using the PolyMAC method combined with antibody enrichment, we identified 794 unique sites of tyrosine phosphorylation in malignant breast cancer cells, 514 of which are dependent on the expression of Syk, a protein-tyrosine kinase with unusual properties of a tumor suppressor. The superior sensitivity of PolyMAC allowed us to identify novel components in a variety of major signaling networks, including cell migration and apoptosis. PolyMAC offers a powerful and widely applicable tool for phosphoproteomics and molecular signaling.
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Affiliation(s)
- Anton B Iliuk
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907, USA
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90
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The use of liquid phase deposition prepared phosphonate grafted silica nanoparticle-deposited capillaries in the enrichment of phosphopeptides. J Sep Sci 2010; 33:1806-15. [DOI: 10.1002/jssc.201000029] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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91
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Qi D, Mao Y, Lu J, Deng C, Zhang X. Phosphate-functionalized magnetic microspheres for immobilization of Zr4+ ions for selective enrichment of the phosphopeptides. J Chromatogr A 2010; 1217:2606-17. [DOI: 10.1016/j.chroma.2009.10.084] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2009] [Revised: 10/27/2009] [Accepted: 10/29/2009] [Indexed: 11/27/2022]
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92
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Patti GJ, Woo HK, Yanes O, Shriver L, Thomas D, Uritboonthai W, Apon JV, Steenwyk R, Manchester M, Siuzdak G. Detection of carbohydrates and steroids by cation-enhanced nanostructure-initiator mass spectrometry (NIMS) for biofluid analysis and tissue imaging. Anal Chem 2010; 82:121-8. [PMID: 19961200 DOI: 10.1021/ac9014353] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Nanostructure-initiator mass spectrometry (NIMS) is a highly sensitive, matrix-free technique that is well suited for biofluid analysis and imaging of biological tissues. Here we provide a new technical variation of NIMS to analyze carbohydrates and steroids, molecules that are challenging to detect with traditional mass spectrometric approaches. Analysis of carbohydrates and steroids was accomplished by spray depositing NaCl or AgNO(3) on the NIMS porous silicon surface to provide a uniform environment rich with cationization agents prior to desorption of the fluorinated polymer initiator. Laser desorption/ionization of the ion-coated NIMS surface allowed for Na(+) cationization of carbohydrates and Ag(+) cationization of steroids. The reliability of the approach is quantitatively demonstrated with a calibration curve over the physiological range of glucose and cholesterol concentrations in human serum (1-200 microM). Additionally, we illustrate the sensitivity of the method by showing its ability to detect carbohydrates and steroids down to the 800-amol and 100-fmol levels, respectively. The technique developed is well suited for tissue imaging of biologically significant metabolites such as sucrose and cholesterol. To highlight its applicability, we used cation-enhanced NIMS to image the distribution of sucrose in a Gerbera jamesonii flower stem and the distribution of cholesterol in a mouse brain. The flower stem and brain sections were placed directly on the ion-coated NIMS surface without further preparation and analyzed directly. The overall results reported underscore the potential of NIMS to analyze and image chemically diverse compounds that have been traditionally challenging to observe with mass spectrometry-based techniques.
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Affiliation(s)
- Gary J Patti
- Department of Molecular Biology, Scripps Center for Mass Spectrometry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA
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93
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Hoang T, Roth U, Kowalewski K, Belisle C, Steinert K, Karas M. Highly specific capture and direct MALDI MS analysis of phosphopeptides by zirconium phosphonate on self-assembled monolayers. Anal Chem 2010; 82:219-28. [PMID: 19968246 DOI: 10.1021/ac9017583] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
The dynamic range and low stoichiometry of protein phosphorylation frequently demands the enrichment of phosphorylated peptides from protein digests prior to mass spectrometry. Several techniques have been reported in literature for phosphopeptide enrichment, including metal oxides such as TiO(2) and ion metal affinity chromatography (IMAC). While the metal oxides have been used with reasonable success, IMAC has suffered from reduced selectivity and poor reproducibility. In this report, we present the first demonstration of the use of immobilized zirconium on a phosphonate-terminated self-assembled monolayer (SAM) for specific phosphopeptide capture and direct analysis by MALDI MS. By using the herein described functionalized-surface-based technology, efficient enrichment of phosphopeptides in different standard test systems such as alpha- or beta-casein digests or synthetic phosphopeptides spiked in nonphosphorylated protein digest has been demonstrated. The limit of detection for a beta-casein phosphopeptide was assessed to be at the low femtomole level. Compared to other state-of the-art technologies, like use of TiO(2) and Fe-IMAC, the presented technique demonstrated a superior performance with respect to specificity and bias with respect to singly or multiply phosphorylated peptides. Additionally, this platform was also successfully applied for ESI sample preparation, providing detailed sequence information of the investigated phosphopeptide. This technology was also proven to be applicable for real life samples such as phosphorylation site analysis of recombinant human MAPK1 and HSP B1 isolated from a 2D-gel spot by phosphopeptide enrichment and direct MALDI MS/MS.
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Affiliation(s)
- Tri Hoang
- Institute of Pharmaceutical Chemistry, Goethe-University Frankfurt/Main, Max-von-Laue-Str. 9, D-60438 Frankfurt, Germany
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94
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Enhanced MALDI-TOF MS analysis of phosphopeptides using an optimized DHAP/DAHC matrix. J Biomed Biotechnol 2010; 2010:759690. [PMID: 20339515 PMCID: PMC2842900 DOI: 10.1155/2010/759690] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2009] [Revised: 09/11/2009] [Accepted: 12/31/2009] [Indexed: 11/17/2022] Open
Abstract
Selecting an appropriate matrix solution is one of the most effective means of increasing the ionization efficiency of phosphopeptides in matrix-assisted laser-desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS). In this study, we systematically assessed matrix combinations of 2, 6-dihydroxyacetophenone (DHAP) and diammonium hydrogen citrate (DAHC), and demonstrated that the low ratio DHAP/DAHC matrix was more effective in enhancing the ionization of phosphopeptides. Low femtomole level of phosphopeptides from the tryptic digests of α-casein and β-casein was readily detected by MALDI-TOF-MS in both positive and negative ion mode without desalination or phosphopeptide enrichment. Compared with the DHB/PA matrix, the optimized DHAP/DAHC matrix yielded superior sample homogeneity and higher phosphopeptide measurement sensitivity, particularly when multiple phosphorylated peptides were assessed. Finally, the DHAP/DAHC matrix was applied to identify phosphorylation sites from α-casein and β-casein and to characterize two phosphorylation sites from the human histone H1 treated with Cyclin-Dependent Kinase-1 (CDK1) by MALDI-TOF/TOF MS.
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95
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Zhao Y, Jensen ON. Modification-specific proteomics: strategies for characterization of post-translational modifications using enrichment techniques. Proteomics 2010; 9:4632-41. [PMID: 19743430 DOI: 10.1002/pmic.200900398] [Citation(s) in RCA: 261] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
More than 300 different types of protein post-translational modifications (PTMs) have been described, many of which are known to have pivotal roles in cellular physiology and disease. Nevertheless, only a handful of PTMs have been extensively investigated at the proteome level. Knowledge of protein substrates and their PTM sites is key to dissection of PTM-mediated cellular processes. The past several years have seen a tremendous progress in developing MS-based proteomics technologies for global PTM analysis, including numerous studies of yeast and other microbes. Modification-specific enrichment techniques combined with advanced MS/MS methods and computational data analysis have revealed a surprisingly large extent of PTMs in proteins, including multi-site, cooperative modifications in individual proteins. We review some of the current strategies employed for enrichment and detection of PTMs in modification-specific proteomics.
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Affiliation(s)
- Yingming Zhao
- The Ben May Department for Cancer Research, The University of Chicago, Chicago, IL, USA.
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96
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97
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Dunn JD, Reid GE, Bruening ML. Techniques for phosphopeptide enrichment prior to analysis by mass spectrometry. MASS SPECTROMETRY REVIEWS 2010; 29:29-54. [PMID: 19263479 DOI: 10.1002/mas.20219] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Mass spectrometry is the tool of choice to investigate protein phosphorylation, which plays a vital role in cell regulation and diseases such as cancer. However, low abundances of phosphopeptides and low degrees of phosphorylation typically necessitate isolation and concentration of phosphopeptides prior to MS analysis. This review discusses the enrichment of phosphopeptides with immobilized metal affinity chromatography, reversible covalent binding, and metal oxide affinity chromatography. Capture of phosphopeptides on TiO(2) seems especially promising in terms of selectivity and recovery, but the success of all methods depends on careful selection of binding, washing, and elution solutions. Enrichment techniques are complementary, such that a combination of methods greatly enhances the number of phosphopeptides isolated from complex samples. Development of a standard series of phosphopeptides in a highly complex mixture of digested proteins would greatly aid the comparison of different enrichment methods. Phosphopeptide binding to magnetic beads and on-plate isolation prior to MALDI-MS are emerging as convenient methods for purification of small (microL) samples. On-plate enrichment can yield >70% recoveries of phosphopeptides in mixtures of a few digested proteins and can avoid sample-handling steps, but this technique is likely limited to relatively simple samples such as immunoprecipitates. With recent advances in enrichment techniques in hand, MS analysis should provide important insights into phosphorylation pathways.
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Affiliation(s)
- Jamie D Dunn
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, USA
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98
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Qiao L, Bi H, Busnel JM, Hojeij M, Mendez M, Liu B, Girault HH. Controlling the specific enrichment of multi-phosphorylated peptides on oxide materials: aluminium foil as a target plate for laser desorption ionization mass spectrometry. Chem Sci 2010. [DOI: 10.1039/c0sc00224k] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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99
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Kailasa SK, Wu HF. Multifunctional ZrO2 nanoparticles and ZrO2-SiO2 nanorods for improved MALDI-MS analysis of cyclodextrins, peptides, and phosphoproteins. Anal Bioanal Chem 2009; 396:1115-25. [DOI: 10.1007/s00216-009-3330-7] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2009] [Revised: 11/18/2009] [Accepted: 11/18/2009] [Indexed: 11/28/2022]
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Hsu JL, Wang LY, Wang SY, Lin CH, Ho KC, Shi FK, Chang IF. Functional phosphoproteomic profiling of phosphorylation sites in membrane fractions of salt-stressed Arabidopsis thaliana. Proteome Sci 2009; 7:42. [PMID: 19900291 PMCID: PMC2778640 DOI: 10.1186/1477-5956-7-42] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2009] [Accepted: 11/10/2009] [Indexed: 12/13/2022] Open
Abstract
Background Under conditions of salt stress, plants respond by initiating phosphorylation cascades. Many key phosphorylation events occur at the membrane. However, to date only limited sites have been identified that are phosphorylated in response to salt stress in plants. Results Membrane fractions from three-day and 200 mM salt-treated Arabidopsis suspension plants were isolated, followed by protease shaving and enrichment using Zirconium ion-charged magnetic beads, and tandem mass spectrometry analyses. From this isolation, 18 phosphorylation sites from 15 Arabidopsis proteins were identified. A unique phosphorylation site in 14-3-3-interacting protein AHA1 was predominately identified in 200 mM salt-treated plants. We also identified some phosphorylation sites in aquaporins. A doubly phosphorylated peptide of PIP2;1 as well as a phosphopeptide containing a single phosphorylation site (Ser-283) and a phosphopeptide containing another site (Ser-286) of aquaporin PIP2;4 were identified respectively. These two sites appeared to be novel of which were not reported before. In addition, quantitative analyses of protein phosphorylation with either label-free or stable-isotope labeling were also employed in this study. The results indicated that level of phosphopeptides on five membrane proteins such as AHA1, STP1, Patellin-2, probable inactive receptor kinase (At3g02880), and probable purine permease 18 showed at least two-fold increase in comparison to control in response to 200 mM salt-stress. Conclusion In this study, we successfully identified novel salt stress-responsive protein phosphorylation sites from membrane isolates of abiotic-stressed plants by membrane shaving followed by Zr4+-IMAC enrichment. The identified phosphorylation sites can be important in the salt stress response in plants.
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Affiliation(s)
- Jue-Liang Hsu
- Graduate Institute of Biotechnology, National Pingtung University of Science and Technology, Taiwan.
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