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Rebak AS, Hendriks IA, Nielsen ML. Characterizing citrullination by mass spectrometry-based proteomics. Philos Trans R Soc Lond B Biol Sci 2023; 378:20220237. [PMID: 37778389 PMCID: PMC10542455 DOI: 10.1098/rstb.2022.0237] [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: 03/15/2023] [Accepted: 05/25/2023] [Indexed: 10/03/2023] Open
Abstract
Citrullination is an important post-translational modification (PTM) of arginine, known to play a role in autoimmune disorders, innate immunity response and maintenance of stem cell potency. However, citrullination remains poorly characterized and not as comprehensively understood compared to other PTMs, such as phosphorylation and ubiquitylation. High-resolution mass spectrometry (MS)-based proteomics offers a valuable approach for studying citrullination in an unbiased manner, allowing confident identification of citrullination modification sites and distinction from deamidation events on asparagine and glutamine. MS efforts have already provided valuable insights into peptidyl arginine deaminase targeting along with site-specific information of citrullination in for example synovial fluids derived from rheumatoid arthritis patients. Still, there is unrealized potential for the wider citrullination field by applying MS-based mass spectrometry approaches for proteome-wide investigations. Here we will outline contemporary methods and current challenges for studying citrullination by MS, and discuss how the development of neoteric citrullination-specific proteomics approaches still may improve our understanding of citrullination networks. This article is part of the Theo Murphy meeting issue 'The virtues and vices of protein citrullination'.
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Affiliation(s)
- A. S. Rebak
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - I. A. Hendriks
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - M. L. Nielsen
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
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2
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Majuta SN, DeBastiani A, Li P, Valentine SJ. Combining Field-Enabled Capillary Vibrating Sharp-Edge Spray Ionization with Microflow Liquid Chromatography and Mass Spectrometry to Enhance 'Omics Analyses. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:473-485. [PMID: 33417454 PMCID: PMC8132193 DOI: 10.1021/jasms.0c00376] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Field-enabled capillary vibrating sharp-edge spray ionization (cVSSI) has been combined with high-flow liquid chromatography (LC) and mass spectrometry (MS) to establish current ionization capabilities for metabolomics and proteomics investigations. Comparisons are made between experiments employing cVSSI and a heated electrospray ionization probe representing the state-of-the-art in microflow LC-MS methods for 'omics studies. For metabolomics standards, cVSSI is shown to provide an ionization enhancement by factors of 4 ± 2 for both negative and positive ion mode analyses. For chymotryptic peptides, cVSSI is shown to provide an ionization enhancement by factors of 5 ± 2 and 2 ± 1 for negative and positive ion mode analyses, respectively. Slightly broader high-performance liquid chromatography peaks are observed in the cVSSI datasets, and several studies suggest that this results from a slightly decreased post-split flow rate. This may result from partial obstruction of the pulled-tip emitter over time. Such a challenge can be remedied with the use of LC pumps that operate in the 10 to 100 μL·min-1 flow regime. At this early stage, the proof-of-principle studies already show ion signal advantages over state-of-the-art electrospray ionization (ESI) for a wide variety of analytes in both positive and negative ion mode. Overall, this represents a ∼20-50-fold improvement over the first demonstration of LC-MS analyses by voltage-free cVSSI. Separate comparisons of the ion abundances of compounds eluting under identical solvent conditions reveal ionization efficiency differences between cVSSI and ESI and may suggest varied contributions to ionization from different physicochemical properties of the compounds. Future investigations of parameters that could further increase ionization gains in negative and positive ion mode analyses with the use of cVSSI are briefly presented.
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Affiliation(s)
- Sandra N. Majuta
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown WV 26501
| | - Anthony DeBastiani
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown WV 26501
| | - Peng Li
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown WV 26501
| | - Stephen J. Valentine
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown WV 26501
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3
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Pandeswari PB, Sabareesh V. Middle-down approach: a choice to sequence and characterize proteins/proteomes by mass spectrometry. RSC Adv 2018; 9:313-344. [PMID: 35521579 PMCID: PMC9059502 DOI: 10.1039/c8ra07200k] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Accepted: 12/11/2018] [Indexed: 12/27/2022] Open
Abstract
Owing to rapid growth in the elucidation of genome sequences of various organisms, deducing proteome sequences has become imperative, in order to have an improved understanding of biological processes. Since the traditional Edman method was unsuitable for high-throughput sequencing and also for N-terminus modified proteins, mass spectrometry (MS) based methods, mainly based on soft ionization modes: electrospray ionization and matrix-assisted laser desorption/ionization, began to gain significance. MS based methods were adaptable for high-throughput studies and applicable for sequencing N-terminus blocked proteins/peptides too. Consequently, over the last decade a new discipline called 'proteomics' has emerged, which encompasses the attributes necessary for high-throughput identification of proteins. 'Proteomics' may also be regarded as an offshoot of the classic field, 'biochemistry'. Many protein sequencing and proteomic investigations were successfully accomplished through MS dependent sequence elucidation of 'short proteolytic peptides (typically: 7-20 amino acid residues), which is called the 'shotgun' or 'bottom-up (BU)' approach. While the BU approach continues as a workhorse for proteomics/protein sequencing, attempts to sequence intact proteins without proteolysis, called the 'top-down (TD)' approach started, due to ambiguities in the BU approach, e.g., protein inference problem, identification of proteoforms and the discovery of posttranslational modifications (PTMs). The high-throughput TD approach (TD proteomics) is yet in its infancy. Nevertheless, TD characterization of purified intact proteins has been useful for detecting PTMs. With the hope to overcome the pitfalls of BU and TD strategies, another concept called the 'middle-down (MD)' approach was put forward. Similar to BU, the MD approach also involves proteolysis, but in a restricted manner, to produce 'longer' proteolytic peptides than the ones usually obtained in BU studies, thereby providing better sequence coverage. In this regard, special proteases (OmpT, Sap9, IdeS) have been used, which can cleave proteins to produce longer proteolytic peptides. By reviewing ample evidences currently existing in the literature that is predominantly on PTM characterization of histones and antibodies, herein we highlight salient features of the MD approach. Consequently, we are inclined to claim that the MD concept might have widespread applications in future for various research areas, such as clinical, biopharmaceuticals (including PTM analysis) and even for general/routine characterization of proteins including therapeutic proteins, but not just limited to analysis of histones or antibodies.
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Affiliation(s)
- P Boomathi Pandeswari
- Advanced Centre for Bio Separation Technology (CBST), Vellore Institute of Technology (VIT) Vellore Tamil Nadu 632014 India
| | - Varatharajan Sabareesh
- Advanced Centre for Bio Separation Technology (CBST), Vellore Institute of Technology (VIT) Vellore Tamil Nadu 632014 India
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4
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Guo S, Zhu X, Jańczewski D, Lee SSC, He T, Teo SLM, Vancso GJ. Measuring protein isoelectric points by AFM-based force spectroscopy using trace amounts of sample. NATURE NANOTECHNOLOGY 2016; 11:817-23. [PMID: 27454881 DOI: 10.1038/nnano.2016.118] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2016] [Accepted: 06/03/2016] [Indexed: 05/14/2023]
Abstract
Protein charge at various pH and isoelectric point (pI) values is important in understanding protein function. However, often only trace amounts of unknown proteins are available and pI measurements cannot be obtained using conventional methods. Here, we show a method based on the atomic force microscope (AFM) to determine pI using minute quantities of proteins. The protein of interest is immobilized on AFM colloidal probes and the adhesion force of the protein is measured against a positively and a negatively charged substrate made by layer-by-layer deposition of polyelectrolytes. From the AFM force-distance curves, pI values with an estimated accuracy of ±0.25 were obtained for bovine serum albumin, myoglobin, fibrinogen and ribonuclease A over a range of 4.7-9.8. Using this method, we show that the pI of the 'footprint' of the temporary adhesive proteins secreted by the barnacle cyprid larvae of Amphibalanus amphitrite is in the range 9.6-9.7.
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Affiliation(s)
- Shifeng Guo
- Institute of Materials Research and Engineering, A*STAR (Agency for Science, Technology and Research), 2 Fusionopolis Way, Innovis, No. 08-03, Singapore 138634, Singapore
| | - Xiaoying Zhu
- Institute of Materials Research and Engineering, A*STAR (Agency for Science, Technology and Research), 2 Fusionopolis Way, Innovis, No. 08-03, Singapore 138634, Singapore
| | - Dominik Jańczewski
- Institute of Materials Research and Engineering, A*STAR (Agency for Science, Technology and Research), 2 Fusionopolis Way, Innovis, No. 08-03, Singapore 138634, Singapore
- Laboratory of Technological Processes, Faculty of Chemistry, Warsaw University of Technology, Noakowskiego 3, 00-664 Warsaw, Poland
| | - Serina Siew Chen Lee
- Tropical Marine Science Institute, National University of Singapore, 18 Kent Ridge Road, 119227 Singapore, Singapore
| | - Tao He
- Institute of Materials Research and Engineering, A*STAR (Agency for Science, Technology and Research), 2 Fusionopolis Way, Innovis, No. 08-03, Singapore 138634, Singapore
| | - Serena Lay Ming Teo
- Tropical Marine Science Institute, National University of Singapore, 18 Kent Ridge Road, 119227 Singapore, Singapore
| | - G Julius Vancso
- Institute of Chemical and Engineering Sciences A*STAR, 1 Pesek Road, Jurong Island, 627833 Singapore, Singapore
- MESA+ Institute for Nanotechnology, Materials Science and Technology of Polymers, University of Twente, PO Box 217, 7500 AE Enschede, The Netherlands
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5
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Walker GC. Nanobiotechnology: Net charge of trace proteins. NATURE NANOTECHNOLOGY 2016; 11:739-740. [PMID: 27454877 DOI: 10.1038/nnano.2016.143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Affiliation(s)
- Gilbert C Walker
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario M5S 3H6, Canada
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6
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Xu J, Gao J, Yu C, He H, Yang Y, Figeys D, Zhou H. Development of Online pH Gradient-Eluted Strong Cation Exchange Nanoelectrospray-Tandem Mass Spectrometry for Proteomic Analysis Facilitating Basic and Histidine-Containing Peptides Identification. Anal Chem 2015; 88:583-91. [DOI: 10.1021/acs.analchem.5b04000] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Jingjing Xu
- Department
of Analytical Chemistry, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- CAS
Key Laboratory of Receptor Research, Shanghai Institute of Materia
Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, China
- University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100049, China
| | - Jing Gao
- Department
of Analytical Chemistry, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- CAS
Key Laboratory of Receptor Research, Shanghai Institute of Materia
Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, China
- SIMMUOMICS
Laboratory, Joint Research Laboratory of Translational “OMICS” between Shanghai Institute of Materia Medica, Chinese Academy of Sciences, China and University of Ottawa, Canada, 555 Zuchongzhi Road, Shanghai, 201203, China
| | - Chengli Yu
- Department
of Analytical Chemistry, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- CAS
Key Laboratory of Receptor Research, Shanghai Institute of Materia
Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, China
- University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100049, China
| | - Han He
- Department
of Analytical Chemistry, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- CAS
Key Laboratory of Receptor Research, Shanghai Institute of Materia
Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, China
| | - Yiming Yang
- Department
of Analytical Chemistry, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Daniel Figeys
- Department
of Biochemistry, Microbiology and Immunology, and Department of Chemistry
and Biomolecular Sciences, University of Ottawa, 451 Smyth Road, Ottawa, Ontario K1H 8M5, Canada
- SIMMUOMICS
Laboratory, Joint Research Laboratory of Translational “OMICS” between Shanghai Institute of Materia Medica, Chinese Academy of Sciences, China and University of Ottawa, Canada, 555 Zuchongzhi Road, Shanghai, 201203, China
| | - Hu Zhou
- Department
of Analytical Chemistry, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- CAS
Key Laboratory of Receptor Research, Shanghai Institute of Materia
Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, China
- SIMMUOMICS
Laboratory, Joint Research Laboratory of Translational “OMICS” between Shanghai Institute of Materia Medica, Chinese Academy of Sciences, China and University of Ottawa, Canada, 555 Zuchongzhi Road, Shanghai, 201203, China
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7
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Hattan SJ, Du J, Parker KC. Bifunctional Glass Membrane Designed to Interface SDS-PAGE Separations of Proteins with the Detection of Peptides by Mass Spectrometry. Anal Chem 2015; 87:3685-93. [DOI: 10.1021/ac503980x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Stephen J. Hattan
- SimulTOF Systems, 60 Union Avenue, Sudbury, Massachusetts 01776, United States
| | - Jie Du
- Toxikon Corporation, 15 Wiggins Avenue, Bedford, Massachusetts 01730, United States
| | - Kenneth C. Parker
- SimulTOF Systems, 60 Union Avenue, Sudbury, Massachusetts 01776, United States
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8
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Poehler E, Herzog C, Lotter C, Pfeiffer SA, Aigner D, Mayr T, Nagl S. Label-free microfluidic free-flow isoelectric focusing, pH gradient sensing and near real-time isoelectric point determination of biomolecules and blood plasma fractions. Analyst 2015; 140:7496-502. [DOI: 10.1039/c5an01345c] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Continuous biomolecular separation and pH gradient observation using UV and NIR fluorescence.
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Affiliation(s)
- Elisabeth Poehler
- Institut für Analytische Chemie
- Universität Leipzig
- 04103 Leipzig
- Germany
| | - Christin Herzog
- Institut für Analytische Chemie
- Universität Leipzig
- 04103 Leipzig
- Germany
| | - Carsten Lotter
- Institut für Analytische Chemie
- Universität Leipzig
- 04103 Leipzig
- Germany
| | - Simon A. Pfeiffer
- Institut für Analytische Chemie
- Universität Leipzig
- 04103 Leipzig
- Germany
| | - Daniel Aigner
- Institut für Analytische Chemie und Lebensmittelchemie
- Technische Universität Graz
- 8010 Graz
- Austria
| | - Torsten Mayr
- Institut für Analytische Chemie und Lebensmittelchemie
- Technische Universität Graz
- 8010 Graz
- Austria
| | - Stefan Nagl
- Institut für Analytische Chemie
- Universität Leipzig
- 04103 Leipzig
- Germany
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9
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Lee JS, Yoo YH, Yoon CN. Small-molecule probes elucidate global enzyme activity in a proteomic context. BMB Rep 2014; 47:149-57. [PMID: 24499666 PMCID: PMC4163878 DOI: 10.5483/bmbrep.2014.47.3.264] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2013] [Revised: 12/19/2013] [Accepted: 12/20/2013] [Indexed: 12/05/2022] Open
Abstract
The recent dramatic improvements in high-resolution mass spectrometry (MS) have revolutionized the speed and scope of proteomic studies. Conventional MS-based proteomics methodologies allow global protein profiling based on expression levels. Although these techniques are promising, there are numerous biological activities yet to be unveiled, such as the dynamic regulation of enzyme activity. Chemical proteomics is an emerging field that extends these types proteomic profiling. In particular, activity-based protein profiling (ABPP) utilizes small-molecule probes to monitor enzyme activity directly in living intact subjects. In this mini-review, we summarize the unique roles of smallmolecule probes in proteomics studies and highlight some recent examples in which this principle has been applied. [BMB Reports 2014; 47(3): 149-157]
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Affiliation(s)
- Jun-Seok Lee
- Molecular Recognition Research Center, Korea Institute of Science and Technology (KIST), Seoul 136-791; University of Science and Technology, Daejeon 305-333, Korea
| | - Young-Hwa Yoo
- Molecular Recognition Research Center, Korea Institute of Science and Technology (KIST), Seoul 136-791, Korea
| | - Chang No Yoon
- Molecular Recognition Research Center, Korea Institute of Science and Technology (KIST), Seoul 136-791, Korea
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10
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Proteomics meets genetics: SILAC labeling of Drosophila melanogaster larvae and cells for in vivo functional studies. Methods Mol Biol 2014; 1188:293-311. [PMID: 25059620 DOI: 10.1007/978-1-4939-1142-4_21] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Stable isotope labeling by amino acids in cell culture (SILAC) is an established and potent method for quantitative proteomics. When combined with high-resolution mass spectrometry (MS) and efficient algorithms for the analysis of quantitative MS data, SILAC has proven to be the strategy of choice for the in-depth characterization of functional states at the protein level. The fruit fly Drosophila melanogaster is one of the most widely used model systems for studies of genetics and developmental biology. Despite this, a global proteomic approach in Drosophila is rarely considered. Here, we describe an adaptation of SILAC for functional investigation of fruit flies by proteomics: We illustrate how to perform efficient SILAC labeling of cells in culture and whole fly larvae. The combination of SILAC, a highly accurate global protein quantification method, and of the fruit fly, the prime genetics and developmental model, represents a unique opportunity for quantitative proteomic studies in vivo.
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11
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Wöhlbrand L, Trautwein K, Rabus R. Proteomic tools for environmental microbiology-A roadmap from sample preparation to protein identification and quantification. Proteomics 2013; 13:2700-30. [DOI: 10.1002/pmic.201300175] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2013] [Revised: 06/07/2013] [Accepted: 06/28/2013] [Indexed: 02/03/2023]
Affiliation(s)
- Lars Wöhlbrand
- Institute for Chemistry and Biology of the Marine Environment (ICBM); Carl von Ossietzky University Oldenburg; Oldenburg Germany
| | - Kathleen Trautwein
- Institute for Chemistry and Biology of the Marine Environment (ICBM); Carl von Ossietzky University Oldenburg; Oldenburg Germany
| | - Ralf Rabus
- Institute for Chemistry and Biology of the Marine Environment (ICBM); Carl von Ossietzky University Oldenburg; Oldenburg Germany
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12
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13
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Righetti PG, Sebastiano R, Citterio A. Capillary electrophoresis and isoelectric focusing in peptide and protein analysis. Proteomics 2012. [DOI: 10.1002/pmic.201200378] [Citation(s) in RCA: 134] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
| | - Roberto Sebastiano
- Department of Chemistry, Materials and Chemical Engineering “Giulio Natta”; Politecnico di Milano; Milano; Italy
| | - Attilio Citterio
- Department of Chemistry, Materials and Chemical Engineering “Giulio Natta”; Politecnico di Milano; Milano; Italy
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14
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Wagner M, Reiche K, Blume A, Garidel P. The electrokinetic potential of therapeutic proteins and its modulation: Impact on protein stability. Colloids Surf A Physicochem Eng Asp 2012. [DOI: 10.1016/j.colsurfa.2012.09.024] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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15
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Duncombe TA, Herr AE. Use of Polyacrylamide Gel Moving Boundary Electrophoresis to Enable Low-Power Protein Analysis in a Compact Microdevice. Anal Chem 2012; 84:8740-7. [DOI: 10.1021/ac301875e] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Todd A. Duncombe
- University of California, Berkeley−University of California, San Francisco
Graduate Program
in Bioengineering, 342 Stanley Hall, Berkeley, California 94720, United
States
| | - Amy E. Herr
- University of California, Berkeley−University of California, San Francisco
Graduate Program
in Bioengineering, 342 Stanley Hall, Berkeley, California 94720, United
States
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16
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Pihlasalo S, Auranen L, Hänninen P, Härmä H. Method for estimation of protein isoelectric point. Anal Chem 2012; 84:8253-8. [PMID: 22946671 DOI: 10.1021/ac301569b] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Adsorption of sample protein to Eu(3+) chelate-labeled nanoparticles is the basis of the developed noncompetitive and homogeneous method for the estimation of the protein isoelectric point (pI). The lanthanide ion of the nanoparticle surface-conjugated Eu(3+) chelate is dissociated at a low pH, therefore decreasing the luminescence signal. A nanoparticle-adsorbed sample protein prevents the dissociation of the chelate, leading to a high luminescence signal. The adsorption efficiency of the sample protein is reduced above the isoelectric point due to the decreased electrostatic attraction between the negatively charged protein and the negatively charged particle. Four proteins with isoelectric points ranging from ~5 to 9 were tested to show the performance of the method. These pI values measured with the developed method were close to the theoretical and experimental literature values. The method is sensitive and requires a low analyte concentration of submilligrams per liter, which is nearly 10000 times lower than the concentration required for the traditional isoelectric focusing. Moreover, the method is significantly faster and simpler than the existing methods, as a ready-to-go assay was prepared for the microtiter plate format. This mix-and-measure concept is a highly attractive alternative for routine laboratory work.
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Affiliation(s)
- Sari Pihlasalo
- Laboratory of Biophysics and Medicity Research Laboratory, University of Turku, Tykistökatu 6A, FI-20520 Turku, Finland.
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17
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Di Palma S, Hennrich ML, Heck AJ, Mohammed S. Recent advances in peptide separation by multidimensional liquid chromatography for proteome analysis. J Proteomics 2012; 75:3791-813. [DOI: 10.1016/j.jprot.2012.04.033] [Citation(s) in RCA: 104] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2012] [Revised: 04/19/2012] [Accepted: 04/23/2012] [Indexed: 10/28/2022]
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18
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García-Cañas V, Simó C, León C, Ibáñez E, Cifuentes A. MS-based analytical methodologies to characterize genetically modified crops. MASS SPECTROMETRY REVIEWS 2011; 30:396-416. [PMID: 21500243 DOI: 10.1002/mas.20286] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2009] [Revised: 11/18/2009] [Accepted: 11/18/2009] [Indexed: 05/09/2023]
Abstract
The development of genetically modified crops has had a great impact on the agriculture and food industries. However, the development of any genetically modified organism (GMO) requires the application of analytical procedures to confirm the equivalence of the GMO compared to its isogenic non-transgenic counterpart. Moreover, the use of GMOs in foods and agriculture faces numerous criticisms from consumers and ecological organizations that have led some countries to regulate their production, growth, and commercialization. These regulations have brought about the need of new and more powerful analytical methods to face the complexity of this topic. In this regard, MS-based technologies are increasingly used for GMOs analysis to provide very useful information on GMO composition (e.g., metabolites, proteins). This review focuses on the MS-based analytical methodologies used to characterize genetically modified crops (also called transgenic crops). First, an overview on genetically modified crops development is provided, together with the main difficulties of their analysis. Next, the different MS-based analytical approaches applied to characterize GM crops are critically discussed, and include "-omics" approaches and target-based approaches. These methodologies allow the study of intended and unintended effects that result from the genetic transformation. This information is considered to be essential to corroborate (or not) the equivalence of the GM crop with its isogenic non-transgenic counterpart.
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Affiliation(s)
- Virginia García-Cañas
- Institute of Industrial Fermentations (CSIC), Juan de la Cierva 3, 28006 Madrid, Spain
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19
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Balch WE, Yates JR. Application of mass spectrometry to study proteomics and interactomics in cystic fibrosis. Methods Mol Biol 2011; 742:227-247. [PMID: 21547736 DOI: 10.1007/978-1-61779-120-8_14] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
The cystic fibrosis transmembrane conductance regulator (CFTR) does not function in isolation, but rather in a complex network of protein-protein interactions that dictate the physiology of a healthy cell and tissue and, when defective, the pathophysiology characteristic of cystic fibrosis (CF) disease. To begin to address the organization and operation of the extensive cystic fibrosis protein network dictated by simultaneous and sequential interactions, it will be necessary to understand the global protein environment (the proteome) in which CFTR functions in the cell and the local network that dictates CFTR folding, trafficking, and function at the cell surface. Emerging mass spectrometry (MS) technologies and methodologies offer an unprecedented opportunity to fully characterize both the proteome and the protein interactions directing normal CFTR function and to define what goes wrong in disease. Below we provide the CF investigator with a general introduction to the capabilities of modern mass spectrometry technologies and methodologies with the goal of inspiring further application of these technologies for development of a basic understanding of the disease and for the identification of novel pathways that may be amenable to therapeutic intervention in the clinic.
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Affiliation(s)
- William E Balch
- Department of Cell Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.
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20
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Ek P, Stjernström M, Emmer A, Roeraade J. Electrospray ionization mass spectrometry from discrete nanoliter-sized sample volumes. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2010; 24:2561-2568. [PMID: 20740531 DOI: 10.1002/rcm.4674] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
We describe a method for nanoelectrospray ionization mass spectrometry (nESI-MS) of very small sample volumes. Nanoliter-sized sample droplets were taken up by suction into a nanoelectrospray needle from a silicon microchip prior to ESI. To avoid a rapid evaporation of the small sample volumes, all manipulation steps were performed under a cover of fluorocarbon liquid. Sample volumes down to 1.5 nL were successfully analyzed, and an absolute limit of detection of 105 attomole of insulin (chain B, oxidized) was obtained. The open access to the sample droplets on the silicon chip provides the possibility to add reagents to the sample droplets and perform chemical reactions under an extended period of time. This was demonstrated in an example where we performed a tryptic digestion of cytochrome C in a nanoliter-sized sample volume for 2.5 h, followed by monitoring the outcome of the reaction with nESI-MS. The technology was also utilized for tandem mass spectrometry (MS/MS) sequencing analysis of a 2 nL solution of angiotensin I.
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Affiliation(s)
- Patrik Ek
- Division of Analytical Chemistry, Royal Institute of Technology, SE-100 44 Stockholm, Sweden
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Staňová A, Marák J, Maier V, Ranc V, Znaleziona J, Ševčík J, Kaniansky D. Analysis of buserelin in urine by online combination of capillary zone electrophoresis with electrospray mass spectrometry. Electrophoresis 2010; 31:1234-1240. [DOI: 10.1002/elps.200900422] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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22
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Ali I, Aboul-Enein HY, Singh P, Singh R, Sharma B. Separation of biological proteins by liquid chromatography. Saudi Pharm J 2010; 18:59-73. [PMID: 23960722 DOI: 10.1016/j.jsps.2010.02.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2009] [Accepted: 11/03/2009] [Indexed: 01/11/2023] Open
Abstract
After the success of human genome project, proteome is a new emerging field of biochemistry as it provides the knowledge of enzymes (proteins) interactions with different body organs and medicines administrated into human body. Therefore, the study of proteomics is very important for the development of new and effective drugs to control many lethal diseases. In proteomics study, analyses of proteome is essential and significant from the pathological point of views, i.e., in several serious diseases such as cancer, Alzheimer's disease and aging, heart diseases and also for plant biology. The separation and identification of proteomics is a challenging job due to their complex structures and closely related physico-chemical behaviors. However, the recent advances in liquid chromatography make this job easy. Various kinds of liquid chromatography, along with different detectors and optimization strategies, have been discussed in this article. Besides, attempts have been made to include chirality concept in proteomics for understanding mechanism and medication of various disease controlled by different body proteins.
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Key Words
- 2D-nano LC, two-dimensional nano liquid chromatography quadrupole
- ACN, acetonitrile
- AIEC, anion exchange chromatography
- CEC, capillary electro-chromatography
- CIEF, capillary isoelectric focusing
- CSF, cerebrospinal fluid
- Chirality
- EC, electro-chromatography
- ESI-LC–MS, electrospray ionization liquid chromatography–mass spectrometry
- FA, formic acid
- FLP, FMRF amide-like peptide
- FT-ICR-MS, ion cyclotron resonance-mass spectrometry
- GPI-APs, glycosylphosphadylinositol anchored proteins
- GSH, glutathione stimulating hormone
- GSTs, glutathione-S-transferase isoenzyme
- Gene
- HFBA, heptafluorobutyric acid
- HPLC, high performance liquid chromatography
- ICAT, isotope coded affinity tag
- IEF-SEC, isoelectrofocussing size-exclusion chromatography
- IMCD, inner medullary collecting duct
- LC-Q-TOF, liquid chromatography-quadrupole time-of-flight tandem mass
- LC-dual ESI, liquid chromatography dual electrospray ionization-Fourier transform
- LC–MS, liquid chromatography–mass spectrometry
- Liquid chromatography
- MALDI-TOF, matrix-assisted laser desorption/ionization-time-of flight
- MFGM, milk fat globule membranes
- MMA, mass measurement accuracy
- MPC, mesenchymal progenitor cell
- MS/MS, spectrometry
- NLFs, Nasal lavage fluids
- NLP, neuropeptide like protein
- Nano detection
- PC2, prohormone convertase-2
- PS II, photosystem II
- Preparation
- Proteomics
- Q-TOFMS/MS, time-of-flight tandem-mass spectrometry
- RPLC, reversed phase liquid chromatography
- SCX, strong cation exchange
- SEC, size-exclusion chromatography
- TFA, trifluoroacetic acid
- TIC, total ion current
- TRAF, tumor necrosis factor receptor
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Affiliation(s)
- Imran Ali
- Department of Chemistry, Jamia Millia Islamia (Central University), New Delhi 110 025, India
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Gibson GTT, Marecak DM, Oleschuk RD. Reversed phase capillary HPLC using polymer-entrapped C18 particles. J Sep Sci 2009; 32:4025-32. [DOI: 10.1002/jssc.200900447] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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24
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Petyuk VA, Qian WJ, Smith RD, Smith DJ. Mapping protein abundance patterns in the brain using voxelation combined with liquid chromatography and mass spectrometry. Methods 2009; 50:77-84. [PMID: 19654045 DOI: 10.1016/j.ymeth.2009.07.009] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2008] [Revised: 07/27/2009] [Accepted: 07/30/2009] [Indexed: 10/20/2022] Open
Abstract
Voxelation creates expression atlases by high-throughput analysis of spatially registered cubes or voxels harvested from the brain. The modality independence of voxelation allows a variety of bioanalytical techniques to be used to map abundance. Protein expression patterns in the brain can be obtained using liquid chromatography (LC) combined with mass spectrometry (MS). Here we describe the methodology of voxelation as it pertains particularly to LC-MS proteomic analysis: sample preparation, instrumental set up and analysis, peptide identification and protein relative abundance quantitation. We also briefly describe some of the advantages, limitations and insights into the brain that can be obtained using combined proteomic and transcriptomic maps.
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Affiliation(s)
- Vladislav A Petyuk
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99352, USA
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Yates JR, Ruse CI, Nakorchevsky A. Proteomics by Mass Spectrometry: Approaches, Advances, and Applications. Annu Rev Biomed Eng 2009; 11:49-79. [DOI: 10.1146/annurev-bioeng-061008-124934] [Citation(s) in RCA: 798] [Impact Index Per Article: 53.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- John R. Yates
- Department of Chemical Physiology and Cell Biology, The Scripps Research Institute, La Jolla, California 92037;
| | - Cristian I. Ruse
- Department of Chemical Physiology and Cell Biology, The Scripps Research Institute, La Jolla, California 92037;
| | - Aleksey Nakorchevsky
- Department of Chemical Physiology and Cell Biology, The Scripps Research Institute, La Jolla, California 92037;
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26
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Hesse H, Hoefgen R. On the way to understand biological complexity in plants: S-nutrition as a case study for systems biology. Cell Mol Biol Lett 2009; 11:37-56. [PMID: 16847747 PMCID: PMC6275866 DOI: 10.2478/s11658-006-0004-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2005] [Accepted: 11/17/2005] [Indexed: 11/20/2022] Open
Abstract
The establishment of technologies for high-throughput DNA sequencing (genomics), gene expression (transcriptomics), metabolite and ion analysis (metabolomics/ionomics) and protein analysis (proteomics) carries with it the challenge of processing and interpreting the accumulating data sets. Publicly accessible databases and newly development and adapted bioinformatic tools are employed to mine this data in order to filter relevant correlations and create models describing physiological states. These data allow the reconstruction of networks of interactions of the various cellular components as enzyme activities and complexes, gene expression, metabolite pools or pathway flux modes. Especially when merging information from transcriptomics, metabolomics and proteomics into consistent models, it will be possible to describe and predict the behaviour of biological systems, for example with respect to endogenous or environmental changes. However, to capture the interactions of network elements requires measurements under a variety of conditions to generate or refine existing models. The ultimate goal of systems biology is to understand the molecular principles governing plant responses and consistently explain plant physiology.
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Affiliation(s)
- Holger Hesse
- Max-Planck-Institute fuer Molekulare Pflanzenphysiologie, Golm, Germany.
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27
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Zeisbergerová M, Adámková A, Glatz Z. Integration of on-line protein digestion by trypsin in CZE by means of electrophoretically mediated microanalysis. Electrophoresis 2009; 30:2378-84. [DOI: 10.1002/elps.200800757] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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28
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Stutz H. Protein attachment onto silica surfaces - a survey of molecular fundamentals, resulting effects and novel preventive strategies in CE. Electrophoresis 2009; 30:2032-61. [DOI: 10.1002/elps.200900015] [Citation(s) in RCA: 114] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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29
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Knjazeva T, Kulp M, Kaljurand M. CE separation of various analytes of biological origin using polyether ether ketone capillaries and contactless conductivity detection. Electrophoresis 2009; 30:424-30. [DOI: 10.1002/elps.200800252] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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30
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31
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Ali I, Aboul-Enein HY, Gupta VK. Microchip-Based Nano Chromatography and Nano Capillary Electrophoresis in Genomics and Proteomics. Chromatographia 2008. [DOI: 10.1365/s10337-008-0813-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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32
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Seo J, Suh MS, Thangadurai TD, Kim J, Rhee YH, Yoon HJ, Shin SK. Mass-Balanced 1H/2H Isotope Dipeptide Tag for Simultaneous Protein Quantitation and Identification. Anal Chem 2008; 80:6145-53. [DOI: 10.1021/ac801007y] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jongcheol Seo
- Bio-Nanotechnology Center, Department of Chemistry, Pohang University of Science and Technology, San31 Hyojadong Namgu, Pohang, Korea 790-784
| | - Min-Soo Suh
- Bio-Nanotechnology Center, Department of Chemistry, Pohang University of Science and Technology, San31 Hyojadong Namgu, Pohang, Korea 790-784
| | - T. Daniel Thangadurai
- Bio-Nanotechnology Center, Department of Chemistry, Pohang University of Science and Technology, San31 Hyojadong Namgu, Pohang, Korea 790-784
| | - Jinhee Kim
- Bio-Nanotechnology Center, Department of Chemistry, Pohang University of Science and Technology, San31 Hyojadong Namgu, Pohang, Korea 790-784
| | - Young Ho Rhee
- Bio-Nanotechnology Center, Department of Chemistry, Pohang University of Science and Technology, San31 Hyojadong Namgu, Pohang, Korea 790-784
| | - Hye-Joo Yoon
- Bio-Nanotechnology Center, Department of Chemistry, Pohang University of Science and Technology, San31 Hyojadong Namgu, Pohang, Korea 790-784
| | - Seung Koo Shin
- Bio-Nanotechnology Center, Department of Chemistry, Pohang University of Science and Technology, San31 Hyojadong Namgu, Pohang, Korea 790-784
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33
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Gutstein HB, Morris JS, Annangudi SP, Sweedler JV. Microproteomics: analysis of protein diversity in small samples. MASS SPECTROMETRY REVIEWS 2008; 27:316-30. [PMID: 18271009 PMCID: PMC2743962 DOI: 10.1002/mas.20161] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Proteomics, the large-scale study of protein expression in organisms, offers the potential to evaluate global changes in protein expression and their post-translational modifications that take place in response to normal or pathological stimuli. One challenge has been the requirement for substantial amounts of tissue in order to perform comprehensive proteomic characterization. In heterogeneous tissues, such as brain, this has limited the application of proteomic methodologies. Efforts to adapt standard methods of tissue sampling, protein extraction, arraying, and identification are reviewed, with an emphasis on those appropriate to smaller samples ranging in size from several microliters down to single cells. The effects of miniaturization on these analyses are highlighted using neuroscience-related examples, as are statistical issues unique to the high-dimensional datasets generated by proteomic experiments.
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Affiliation(s)
- Howard B Gutstein
- Department of Anesthesiology, University of Texas-MD Anderson Cancer Center, 1515 Holcombe Blvd., Box 110, Houston, TX 77030-4009, USA.
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34
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Herrero M, Ibañez E, Cifuentes A. Capillary electrophoresis-electrospray-mass spectrometry in peptide analysis and peptidomics. Electrophoresis 2008; 29:2148-60. [DOI: 10.1002/elps.200700404] [Citation(s) in RCA: 107] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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35
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Silvertand LHH, Toraño JS, de Jong GJ, van Bennekom WP. Improved repeatability and matrix-assisted desorption/ionization – time of flight mass spectrometry compatibility in capillary isoelectric focusing. Electrophoresis 2008; 29:1985-96. [DOI: 10.1002/elps.200700434] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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36
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Boonen K, Landuyt B, Baggerman G, Husson SJ, Huybrechts J, Schoofs L. Peptidomics: The integrated approach of MS, hyphenated techniques and bioinformatics for neuropeptide analysis. J Sep Sci 2008; 31:427-45. [DOI: 10.1002/jssc.200700450] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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37
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Kim KH, Kang D, Koo HM, Moon MH. Molecular mass sorting of proteome using hollow fiber flow field-flow fractionation for proteomics. J Proteomics 2008; 71:123-31. [PMID: 18541480 DOI: 10.1016/j.jprot.2008.02.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2007] [Revised: 02/04/2008] [Accepted: 02/04/2008] [Indexed: 10/22/2022]
Abstract
Hollow fiber flow field-flow fractionation (HF FlFFF) has been demonstrated as a tool for pre-fractionating proteomes by differences in molecular mass (Mr), where the resulting protein fractions are subsequently digested and analyzed by shotgun proteomics using two-dimensional liquid chromatography-electrospray ionization-tandem mass spectrometry (2D-LC-ESI-MS/MS). HF FlFFF is a separation device capable of fractionating proteins or cells by hydrodynamic radius, and protein fraction can be readily collected as intact conditions in aqueous buffer solutions. In this study, HF FlFFF was applied to fractionate the proteome of Corynebacterium glutamicum, a well known soil bacterium that has been widely used in bioindustry due to its remarkable ability to secrete high amounts of glutamic acid. The collected HF FlFFF fractions of different MW intervals were enzymatically digested for protein identification by 2D-LC-ESI-MS/MS. Experiments showed improvements in protein identification when HF FlFFF pre-fractionation was applied, due to decreases in the ionization suppression effect and the MS exclusion effect by spectral congestion. Pre-fractionation of C. glutamicum proteome allowed us to find 90 additional proteins by 2D-LC-ESI-MS/MS that were not found by a direct shotgun analysis without pre-fractionation. A total of 415 proteins were found overall with 203 proteins commonly found from experiments with and without pre-fractionation.
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Affiliation(s)
- Ki Hun Kim
- Department of Chemistry, Yonsei University, Seoul, 120-749, South Korea
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38
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Recent development of multi-dimensional chromatography strategies in proteome research. J Chromatogr B Analyt Technol Biomed Life Sci 2008; 866:123-32. [PMID: 18289947 PMCID: PMC7185551 DOI: 10.1016/j.jchromb.2008.01.029] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2007] [Revised: 01/15/2008] [Accepted: 01/18/2008] [Indexed: 11/23/2022]
Abstract
As a complementary approach to two-dimensional polyacrylamide gel electrophoresis (2D-PAGE), multi-dimensional chromatography separation methods have been widely applied in all kinds of biological sample investigations. Multi-dimensional liquid chromatography (MDLC) coupled with bio-mass spectrometry (MS) is playing important roles in proteome research due to its high speed, high resolution and high sensitivity. Proteome analysis strategies mainly include bottom-up and top-down approaches which carry out biological sample separation based on peptide and protein levels, respectively. Electrophoretic methods combined with liquid chromatography like IEF-HPLC and HPLC-SDS-PAGE have been successful applied for protein separations. As for MDLC strategy, ion-exchange chromatography (IEX) together with reversed phase liquid chromatography (RPLC) is still a most widely used chromatography in proteome analysis, other chromatographic methods are also frequently used in protein pre-fractionations, while affinity chromatography is usually adopted for specific functional protein analysis. Recent MDLC technologies and applications to variety of proteome analysis have been achieved great development. A digest peptide-based approach as so-called “bottom-up” and intact protein-based approach “top-down” analysis of proteome samples were briefly reviewed in this paper. The diversity of combinations of different chromatography modes to set up MDLC systems was demonstrated and discussed. Novel developments of MDLC techniques such as high-abundance protein depletion and chromatography array were also included in this review.
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39
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15 Capillary electrophoresis and bioanalysis. ACTA ACUST UNITED AC 2008. [DOI: 10.1016/s0149-6395(07)00015-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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40
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Kubáň P, Hauser PC. High-performance liquid chromatography with contactless conductivity detection for the determination of peptides and proteins using a monolithic capillary column. J Chromatogr A 2007; 1176:185-91. [DOI: 10.1016/j.chroma.2007.10.109] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2007] [Revised: 10/26/2007] [Accepted: 10/31/2007] [Indexed: 01/16/2023]
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41
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Pennington JP, Schöneich C, Stobaugh JF. Selective Fluorogenic Derivatization with Isotopic Coding of Catechols and 2-Amino Phenols with Benzylamine: A Chemical Basis for the Relative Determination of 3-Hydroxy-tyrosine and 3-Nitro-tyrosine Peptides. Chromatographia 2007. [DOI: 10.1365/s10337-007-0410-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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42
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Simó C, Citterio A, Righetti PG. Mass distribution, polydispersity, and focusing properties of carrier ampholytes for IEF. Part V: pH 9-11 interval. Electrophoresis 2007; 28:3156-62. [PMID: 17854119 DOI: 10.1002/elps.200700123] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
As a last part of an investigation on all 2-pH-unit intervals of carrier ampholytes (CAs) for IEF (see Electrophoresis 2006, 27, 3919-3934; 2006, 27, 4849-4858; 2007, 28, 715-723) two different lots of Servalyt CAs, in the pH 9-11 range, have been analyzed by a 2-D technique based on preparative Rotofor fractionation followed by capillary electrophoresis mass-spectrometry of 10 out of 20 fractions harvested, in the second dimension. The findings: the two lots contain 65 and 69 different M(r) compounds, in the M(r) interval of 232-667 Da, for a total of 341-387 isoforms, respectively. Since this is a chaotic organic synthesis, the high reproducibility (here demonstrated for the first time during the 40 years of existence of CAs) of the synthetic process (for two batches produced at 6 years of distance) is remarkable, considering that a 94% agreement for the individual chemicals and 88% agreement for the total number of isoforms for the two lots is found. It is additionally demonstrated that the lower pI species are accompanied by considerably more isoforms than the high pI forms and that in all cases such isoforms consist of family of compounds clustered around the pI of the parental form, with a pI spread of ca. 0.1-0.2 pH units.
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Affiliation(s)
- Carolina Simó
- Department of Chemistry, Politecnico di Milano, Materials and Engineering Chemistry Giulio Natta, Milano, Italy
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43
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Eschelbach JW, Jorgenson JW. Improved protein recovery in reversed-phase liquid chromatography by the use of ultrahigh pressures. Anal Chem 2007; 78:1697-706. [PMID: 16503625 DOI: 10.1021/ac0518304] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The effect that elevated pressure used in ultrahigh-pressure liquid chromatography (UHPLC) has on protein recovery was investigated. Specifically, protein carryover ("ghosting") and recovery were examined. Four model proteins (ribonuclease A, ovalbumin, myoglobin, BSA) were separated by gradient RPLC at both conventional (160 bar) and ultrahigh pressures (>1500 bar). A custom gradient UHPLC system was used to generate conventional pressures on 5-microm diameter reversed-phase supports and ultrahigh pressures on identical 1.4-microm supports. The results indicate that, by increasing the pressure, protein carryover from run to run is reduced and in some cases eliminated above a certain threshold pressure for the model proteins studied. Further work indicates that recovery was enhanced for each of the proteins studied, even approaching 100% for certain proteins.
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Affiliation(s)
- John W Eschelbach
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599, USA
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44
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van de Meent MHM, de Jong GJ. Improvement of the liquid-chromatographic analysis of protein tryptic digests by the use of long-capillary monolithic columns with UV and MS detection. Anal Bioanal Chem 2007; 388:195-200. [PMID: 17393153 PMCID: PMC1914286 DOI: 10.1007/s00216-007-1215-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2006] [Revised: 01/29/2007] [Accepted: 02/16/2007] [Indexed: 11/09/2022]
Abstract
Optimisation of peak capacity is an important strategy in gradient liquid chromatography (LC). This can be achieved by using either long columns or columns packed with small particles. Monolithic columns allow the use of long columns at relatively low back-pressure. The gain in peak capacity using long columns was evaluated by the separation of a tryptic bovine serum albumin digest with an LC-UV-mass spectrometry (MS) system and monolithic columns of different length (150 and 750 mm). Peak capacities were determined from UV chromatograms and MS/MS data were used for Mascot database searching. Analyses with a similar gradient slope for the two columns produced ratios of the peak capacities that were close to the expected value of the square root of the column length ratio. Peak capacities of the short column were 12.6 and 25.0 with 3 and 15 min gradients, respectively, and 29.7 and 41.0 for the long column with 15 and 75 min gradients, respectively. Protein identification scores were also higher for the long column, 641 and 750 for the 3- and 15-min gradients with the short column and 1,376 and 993 for the 15- and 75-min gradients with the long column. Thus, the use of long monolithic columns provides improved peptide separation and increased reliability of protein identification.
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Affiliation(s)
- M H M van de Meent
- Division of Biomedical Analysis, Department of Pharmaceutical Sciences, Utrecht University, P.O. Box 80082, 3508 TB, Utrecht, The Netherlands.
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45
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Kang D, Moon MH. Development of non-gel-based two-dimensional separation of intact proteins by an on-line hyphenation of capillary isoelectric focusing and hollow fiber flow field-flow fractionation. Anal Chem 2007; 78:5789-98. [PMID: 16906725 DOI: 10.1021/ac0606958] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A rapid, non-gel-based, on-line, two-dimensional separation method is introduced for proteome analysis. Protein fractionation was carried out by first exploiting the differences in their respective isoelectric points (pI) in a Teflon capillary using isoelectric focusing (IEF), followed by a molecular weight (MW)-based separation in a hollow fiber by flow field-flow fractionation (FlFFF). The method developed here (CIEF-HFFlFFF) may be a powerful alternative to two-dimensional polyacrylamide gel electrophoresis, which is currently used for the separation and purification of proteins. In CIEF-HFFlFFF, proteins can be collected as a fraction of a certain pI and MW interval without being denatured. Additionally, the ampholyte solution is simultaneously removed during separation in the hollow fiber, and the overall process time is significantly reduced. This method was applied to a human urinary proteome sample, leading to the identification of 114 proteins with the subsequent off-line use of nanoflow liquid chromatography-tandem mass spectrometry after the tryptic digestion of each collected protein fraction.
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Affiliation(s)
- Dukjin Kang
- Department of Chemistry, Yonsei University, Seoul, 120-749, Korea
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46
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Abstract
A new method for displaying CE-MALDI-MS data for proteolytic digests is described. This data display mode yields distinct charge-based trends for plots of mass-to-charge (m/z) versus CE migration time. These trends arise owing to the in-solution charge state of the peptides, and this interpretation was confirmed by using empirical peptide electromigration models and peptide standards as charge-state markers. These charge-state specific trends exhibit analytical utility by providing additional chemical information about the peptides, which increases the confidence level of peptide identification and provides a rapid means for screening for posttranslationally modified peptides.
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Affiliation(s)
- Brad J Williams
- Laboratory for Biological Mass Spectrometry, Department of Chemistry, Texas A&M University, College Station, Texas 77843, USA
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47
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Gedela S, Medicherla NR. Chromatographic Techniques for the Separation of Peptides: Application to Proteomics. Chromatographia 2007. [DOI: 10.1365/s10337-007-0215-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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Armenta JM, Gu B, Thulin CD, Lee ML. Coupled affinity-hydrophobic monolithic column for on-line removal of immunoglobulin G, preconcentration of low abundance proteins and separation by capillary zone electrophoresis. J Chromatogr A 2007; 1148:115-22. [PMID: 17379232 DOI: 10.1016/j.chroma.2007.02.089] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2006] [Revised: 02/18/2007] [Accepted: 02/23/2007] [Indexed: 11/26/2022]
Abstract
A butyl methacrylate-co-ethylene dimethacrylate (BuMA-co-EDMA) monolith was synthesized by UV initiated polymerization at the inlet end of a 75 microm I.D. fused silica capillary that had been previously coated with a protein compatible polymer, poly(vinyl)alcohol. The monolith was used for on-line preconcentration of proteins followed by capillary electrophoresis (CE) separation. For the analysis of standard proteins (cytochrome c, lysozyme and trypsinogen A) this system proved reproducible. The run-to-run %RSD values for migration time and corrected peak area were less than 5%, which is typical of CE. As measured by frontal analysis using lysozyme as solute, saturation of a 1cm monolith was reached after loading 48 ng of protein. Finally, the BuMA-co-EDMA monolithic preconcentrator was coupled to a protein G monolithic column via a zero dead volume union. The coupled system was used for on-line removal of IgG, preconcentration of standard proteins and CE separation. This system could be a valuable sample preparation tool for the analysis of low abundance proteins in complex samples such as human serum, in which high abundance proteins, e.g., human serum albumin (HSA) and immunoglobulin G (IgG), hinder identification and quantification of low abundance proteins.
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Affiliation(s)
- Jenny M Armenta
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT 84602-5700, USA
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Ramasamy P, El-Maghrabi MR, Halada G, Miller LM, Rafailovich M. Examination of interactions of oppositely charged proteins in gels. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2007; 23:2021-9. [PMID: 17279690 DOI: 10.1021/la062365o] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Understanding the interactions of proteins with one another serves as an important step for developing faster protein separation methods. To examine protein-protein interactions of oppositely charged proteins, fluorescently labeled albumin and poly-l-lysine were subjected to electrophoresis in agarose gels, in which the cationic albumin and the anionic poly-L-lysine were allowed to migrate toward each other and interact. Fluorescence microscopy was used to image fluorescently tagged proteins in the gel. The secondary structure of the proteins in solution was studied using conventional FTIR spectroscopy. Results showed that sharp interfaces were formed where FITC tagged albumin met poly-L-lysine and that the interfaces did not migrate after they had been formed. The position of the interface in the gel was found to be linearly dependent upon the relative concentration of the proteins. The formation of the interface also depended upon the fluorescent tag attached to the protein. The size of the aggregates at the interface, the fluorescence intensity modifications, and the mobility of the interface for different pore sizes of the gel were investigated. It was observed that the interface was made up of aggregates of about 1 microm in size. Using dynamic light scattering, it was observed that the size of the aggregates that formed due to interactions of oppositely charged proteins depended upon the fluorescent tags attached to the proteins. The addition of small amounts of poly-L-lysine to solutions containing FITC albumin decreased the zeta potential drastically. For this, we propose a model suggesting that adding small amounts of poly-L-lysine to solutions containing FITC -albumin favors the formation of macromolecular complexes having FITC albumin molecules on its surface. Although oppositely charged FITC tagged poly-L-lysine and FITC tagged albumin influence each other's migration velocities by forming aggregates, there were no observable secondary structural modifications when the proteins were mixed in solution.
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Affiliation(s)
- Perumal Ramasamy
- Department of Materials Science and Engineering, SUNY Stony Brook, Stony Brook, New York 11794-2275, USA.
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Geiser L, Eeltink S, Svec F, Fréchet JM. Stability and repeatability of capillary columns based on porous monoliths of poly(butyl methacrylate-co-ethylene dimethacrylate). J Chromatogr A 2007; 1140:140-6. [PMID: 17182044 PMCID: PMC2680358 DOI: 10.1016/j.chroma.2006.11.079] [Citation(s) in RCA: 93] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2006] [Revised: 11/17/2006] [Accepted: 11/24/2006] [Indexed: 10/23/2022]
Abstract
Monolithic poly(butyl methacrylate-co-ethylene dimethacrylate) capillary columns have been prepared via either thermally or photochemically initiated polymerization of the corresponding monomers and the repeatability of their preparation has been explored. Three separate batches of 5 columns each were prepared using thermal and photochemical initiation for a total of 30 columns. All 30 capillary columns were tested in liquid chromatography-electrospray ionisation mass spectrometry mode for the separation of a model mixture of three proteins--ribonuclease A, cytochrome c and myoglobin. Excellent repeatability of retention times was observed for the proteins as evidenced by relative standard deviation (RSD) values of less than 1.5%. Somewhat broader variations with RSD values of up to 10% were observed for the pressure drop in the columns. The stability of retention times was also monitored using a single monolithic column and no significant shifts in either retention times or back pressure was observed in a series of almost 2200 consecutive protein separations.
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Affiliation(s)
- Laurent Geiser
- College of Chemistry, University of California, Berkeley, CA 94720-1460, USA, and The Molecular Foundry, E.O. Lawrence Berkeley National Laboratory, Berkeley, CA 94720-8139, USA
| | - Sebastiaan Eeltink
- College of Chemistry, University of California, Berkeley, CA 94720-1460, USA, and The Molecular Foundry, E.O. Lawrence Berkeley National Laboratory, Berkeley, CA 94720-8139, USA
| | - Frantisek Svec
- College of Chemistry, University of California, Berkeley, CA 94720-1460, USA, and The Molecular Foundry, E.O. Lawrence Berkeley National Laboratory, Berkeley, CA 94720-8139, USA
| | - Jean M.J. Fréchet
- College of Chemistry, University of California, Berkeley, CA 94720-1460, USA, and The Molecular Foundry, E.O. Lawrence Berkeley National Laboratory, Berkeley, CA 94720-8139, USA
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