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Driver R, Mishra S. Organ-On-A-Chip Technology: An In-depth Review of Recent Advancements and Future of Whole Body-on-chip. BIOCHIP JOURNAL 2022. [DOI: 10.1007/s13206-022-00087-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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2
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Barasinski M, Garnweitner G. Aufreinigung von Nano‐ und Submikronpartikeln durch präparative Gelelektrophorese. CHEM-ING-TECH 2022. [DOI: 10.1002/cite.202200134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Matthäus Barasinski
- Technische Universität Braunschweig Institut für Partikeltechnik und Laboratory for Emerging Nanometrology 38104 Braunschweig Deutschland
| | - Georg Garnweitner
- Technische Universität Braunschweig Institut für Partikeltechnik und Laboratory for Emerging Nanometrology 38104 Braunschweig Deutschland
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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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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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Mikšík I. Capillary electrochromatography of proteins and peptides (2006-2015). J Sep Sci 2016; 40:251-271. [DOI: 10.1002/jssc.201600908] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Revised: 10/01/2016] [Accepted: 10/01/2016] [Indexed: 01/14/2023]
Affiliation(s)
- Ivan Mikšík
- Institute of Physiology; Academy of Sciences of the Czech Republic; Prague Czech Republic
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7
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Kler PA, Sydes D, Huhn C. Column–coupling strategies for multidimensional electrophoretic separation techniques. Anal Bioanal Chem 2014; 407:119-38. [DOI: 10.1007/s00216-014-8099-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Revised: 08/06/2014] [Accepted: 08/08/2014] [Indexed: 10/24/2022]
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8
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Ciogli A, Pierri G, Kotoni D, Cavazzini A, Botta L, Villani C, Kocergin J, Gasparrini F. Toward enantioselective nano ultrahigh-performance liquid chromatography with Whelk-O1 chiral stationary phase. Electrophoresis 2014; 35:2819-23. [DOI: 10.1002/elps.201400240] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2014] [Revised: 06/25/2014] [Accepted: 06/30/2014] [Indexed: 12/23/2022]
Affiliation(s)
- Alessia Ciogli
- Department of Drug Chemistry and Technology; “Sapienza” University of Rome; Rome Italy
| | - Giuseppe Pierri
- Department of Drug Chemistry and Technology; “Sapienza” University of Rome; Rome Italy
| | - Dorina Kotoni
- Department of Drug Chemistry and Technology; “Sapienza” University of Rome; Rome Italy
| | - Alberto Cavazzini
- Department of Chemistry and Pharmaceutical Sciences; University of Ferrara; Ferrara Italy
| | - Lorenzo Botta
- Department of Pharmacy; University of Naples Federico II; Naples Italy
| | - Claudio Villani
- Department of Drug Chemistry and Technology; “Sapienza” University of Rome; Rome Italy
| | | | - Francesco Gasparrini
- Department of Drug Chemistry and Technology; “Sapienza” University of Rome; Rome Italy
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Wheelock AM, Goto S. Effects of post-electrophoretic analysis on variance in gel-based proteomics. Expert Rev Proteomics 2014; 3:129-42. [PMID: 16445357 DOI: 10.1586/14789450.3.1.129] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
2D electrophoresis (2DE) is a prominent separation method for complex proteomes. Although recent advances have increased the utility of this method in quantitative proteomics studies, many sources of variance still exist. This review discusses the post-electrophoretic sources of variance in current 2DE analysis. The essential improvements in protein visualization and software algorithms that have made 2DE a leading quantitative proteomics method are briefly reviewed. A number of shortcomings in the post-electrophoretic analysis of 2DE data that require further attention are highlighted. Topics discussed include protein visualization and image acquisition, internal standards and normalization methods, background subtraction algorithms, normality of distribution, and the need for standardized tests for the evaluation of 2DE analysis software packages.
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Affiliation(s)
- Asa M Wheelock
- Kyoto University, Bioinformatics Center, Institute for Chemical Research, Uji, Kyoto, 611-0011, Japan.
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Gama MR, Collins CH, Bottoli CBG. Nano-Liquid Chromatography in Pharmaceutical and Biomedical Research. J Chromatogr Sci 2013; 51:694-703. [DOI: 10.1093/chromsci/bmt023] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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11
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Bahnasy MF, Lucy CA. A versatile semi-permanent sequential bilayer/diblock polymer coating for capillary isoelectric focusing. J Chromatogr A 2012; 1267:89-95. [DOI: 10.1016/j.chroma.2012.07.016] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2012] [Revised: 07/03/2012] [Accepted: 07/06/2012] [Indexed: 12/30/2022]
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Abstract
Microscale 2D separation systems have been implemented in capillaries and microfabricated channels. They offer advantages of faster analysis, higher separation efficiency and less sample consumption than the conventional methods, such as liquid chromatography (LC) in a column and slab gel electrophoresis. In this article, we review their recent advancement, focusing on three types of platforms, including 2D capillary electrophoresis (CE), CE coupling with capillary LC, and microfluidic devices. A variety of CE and LC modes have been employed to construct 2D separation systems via sophistically designed interfaces. Coupling of different separation modes has also been realized in a number of microfluidic devices. These separation systems have been applied for the proteomic analysis of various biological samples, ranging from a single cell to tumor tissues.
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Affiliation(s)
- Xin Xu
- Interdisciplinary Microsystems Group, Department of Mechanical & Aerospace Engineering, University of Florida, Gainesville, FL 32611-6250, USA
| | - Ke Liu
- Interdisciplinary Microsystems Group, Department of Mechanical & Aerospace Engineering, University of Florida, Gainesville, FL 32611-6250, USA
| | - Z. Hugh Fan
- Interdisciplinary Microsystems Group, Department of Mechanical & Aerospace Engineering, University of Florida, Gainesville, FL 32611-6250, USA
- J Crayton Pruitt Family Department of Biomedical Engineering, University of Florida, Gainesville, FL 32611-6131, USA
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Fekete S, Veuthey JL, Guillarme D. New trends in reversed-phase liquid chromatographic separations of therapeutic peptides and proteins: theory and applications. J Pharm Biomed Anal 2012; 69:9-27. [PMID: 22475515 DOI: 10.1016/j.jpba.2012.03.024] [Citation(s) in RCA: 101] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2012] [Revised: 03/12/2012] [Accepted: 03/13/2012] [Indexed: 12/22/2022]
Abstract
In the pharmaceutical field, there is considerable interest in the use of peptides and proteins for therapeutic purposes. There are various ways to characterize such complex samples, but during the last few years, a significant number of technological developments have been brought to the field of RPLC and RPLC-MS. Thus, the present review focuses first on the basics of RPLC for peptides and proteins, including the inherent problems, some possible solutions and some directions for developing a new RPLC method that is dedicated to biomolecules. Then the latest advances in RPLC, such as wide-pore core-shell particles, fully porous sub-2 μm particles, organic monoliths, porous layer open tubular columns and elevated temperature, are described and critically discussed in terms of both kinetic efficiency and selectivity. Numerous applications with real samples are presented that confirm the relevance of these different strategies. Finally, one of the key advantages of RPLC for peptides and proteins over other historical approaches is its inherent compatibility with MS using both MALDI and ESI sources.
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Affiliation(s)
- Szabolcs Fekete
- School of Pharmaceutical Sciences, University of Geneva, University of Lausanne, Bd d'Yvoy 20, 1211 Geneva 4, Switzerland.
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Vannoy CH, Tavares AJ, Noor MO, Uddayasankar U, Krull UJ. Biosensing with quantum dots: a microfluidic approach. SENSORS (BASEL, SWITZERLAND) 2011; 11:9732-63. [PMID: 22163723 PMCID: PMC3231262 DOI: 10.3390/s111009732] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/01/2011] [Revised: 10/04/2011] [Accepted: 10/17/2011] [Indexed: 01/09/2023]
Abstract
Semiconductor quantum dots (QDs) have served as the basis for signal development in a variety of biosensing technologies and in applications using bioprobes. The use of QDs as physical platforms to develop biosensors and bioprobes has attracted considerable interest. This is largely due to the unique optical properties of QDs that make them excellent choices as donors in fluorescence resonance energy transfer (FRET) and well suited for optical multiplexing. The large majority of QD-based bioprobe and biosensing technologies that have been described operate in bulk solution environments, where selective binding events at the surface of QDs are often associated with relatively long periods to reach a steady-state signal. An alternative approach to the design of biosensor architectures may be provided by a microfluidic system (MFS). A MFS is able to integrate chemical and biological processes into a single platform and allows for manipulation of flow conditions to achieve, by sample transport and mixing, reaction rates that are not entirely diffusion controlled. Integrating assays in a MFS provides numerous additional advantages, which include the use of very small amounts of reagents and samples, possible sample processing before detection, ultra-high sensitivity, high throughput, short analysis time, and in situ monitoring. Herein, a comprehensive review is provided that addresses the key concepts and applications of QD-based microfluidic biosensors with an added emphasis on how this combination of technologies provides for innovations in bioassay designs. Examples from the literature are used to highlight the many advantages of biosensing in a MFS and illustrate the versatility that such a platform offers in the design strategy.
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Affiliation(s)
- Charles H. Vannoy
- Chemical Sensors Group, Department of Chemical and Physical Sciences, University of Toronto Mississauga, 3359 Mississauga Rd. North, Mississauga, Ontario L5L 1C6, Canada; E-Mails: (C.H.V.); (A.J.T.); (M.O.N.); (U.U.)
| | | | | | | | - Ulrich J. Krull
- Chemical Sensors Group, Department of Chemical and Physical Sciences, University of Toronto Mississauga, 3359 Mississauga Rd. North, Mississauga, Ontario L5L 1C6, Canada; E-Mails: (C.H.V.); (A.J.T.); (M.O.N.); (U.U.)
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Matros A, Kaspar S, Witzel K, Mock HP. Recent progress in liquid chromatography-based separation and label-free quantitative plant proteomics. PHYTOCHEMISTRY 2011; 72:963-74. [PMID: 21176926 DOI: 10.1016/j.phytochem.2010.11.009] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2010] [Revised: 11/05/2010] [Accepted: 11/09/2010] [Indexed: 05/26/2023]
Abstract
Recent innovations in liquid chromatography-mass spectrometry (LC-MS)-based methods have facilitated quantitative and functional proteomic analyses of large numbers of proteins derived from complex samples without any need for protein or peptide labelling. Regardless of its great potential, the application of these proteomics techniques to plant science started only recently. Here we present an overview of label-free quantitative proteomics features and their employment for analysing plants. Recent methods used for quantitative protein analyses by MS techniques are summarized and major challenges associated with label-free LC-MS-based approaches, including sample preparation, peptide separation, quantification and kinetic studies, are discussed. Database search algorithms and specific aspects regarding protein identification of non-sequenced organisms are also addressed. So far, label-free LC-MS in plant science has been used to establish cellular or subcellular proteome maps, characterize plant-pathogen interactions or stress defence reactions, and for profiling protein patterns during developmental processes. Improvements in both, analytical platforms (separation technology and bioinformatics/statistical analysis) and high throughput nucleotide sequencing technologies will enhance the power of this method.
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Affiliation(s)
- A Matros
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Department of Physiology and Cell Biology, Corrensstrasse 3, D-06466 Gatersleben, Germany
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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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Li YX, Dan YB, Fang X, Bao JJ. Preliminary studies of a novel multifunctional wide-bore electrophoresis system. Electrophoresis 2010; 31:3247-55. [DOI: 10.1002/elps.201000173] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Affiliation(s)
- Richard N. Zare
- Department of Chemistry, Stanford University, Stanford, California 94305-5080;
| | - Samuel Kim
- Polymer Research Institute and National Core Research Center for Systems Bio-Dynamics, Pohang University of Science and Technology, Pohang, Kyungbuk, Korea;
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Liuni P, Rob T, Wilson DJ. A microfluidic reactor for rapid, low-pressure proteolysis with on-chip electrospray ionization. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2010; 24:315-320. [PMID: 20049884 DOI: 10.1002/rcm.4391] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
A microfluidic reactor that enables rapid digestion of proteins prior to on-line analysis by electrospray ionization mass spectrometry (ESI-MS) is introduced. The device incorporates a wide (1.5 cm), shallow (10 microm) reactor 'well' that is functionalized with pepsin-agarose, a design that facilitates low-pressure operation and high clogging resistance. Electrospray ionization is carried out directly from a short metal capillary integrated into the chip outlet. Fabrication, involving laser ablation of polymethyl methacrylate (PMMA), is exceedingly straightforward and inexpensive. High sequence coverage spectra of myoglobin (Mb), ubiquitin (Ub) and bovine serum albumin (BSA) digests were obtained after <4 s of residence time in the reactor. Stress testing showed little loss of performance over approximately 2 h continuous use at high flow rates (30 microL/min). The device provides a convenient platform for a range of applications in proteomics and structural biology, i.e. to enable high-throughput workflows or to limit back-exchange in spatially resolved hydrogen/deuterium exchange (HDX) experiments.
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Affiliation(s)
- Peter Liuni
- York University Chemistry Department, Toronto, ON, M3J 1P3, Canada
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Abstract
We review microfluidic devices designed for multidimensional sample analysis, with a primer on relevant theory, an emphasis on protein analysis, and an eye towards future improvements and challenges to the field. Image shows results of an on-chip IEF-CE separation of a protein mixture; unpublished surface plot data from A. E. Herr.
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Affiliation(s)
- Samuel Tia
- Department of Bioengineering, University of California, Berkeley, 308B Stanley Hall, MC # 1762 Berkeley, CA 94720-1762, USA
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Zhou Y, Shen H, Yi T, Wen D, Pang N, Liao J, Liu H. Synergistic design of electric field and membrane in facilitating continuous adsorption for cleanup and enrichment of proteins in direct ESI-MS analysis. Anal Chem 2009; 80:8920-9. [PMID: 18954078 DOI: 10.1021/ac800816k] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We designed and fabricated a novel microdevice to facilitate continuous adsorption phenomena for biological sample preparation. Using the device, we also developed an online, highly integrated, multifunctional strategy, with a promise of accepting a large volume of crude tissue extracts with the end point generation of a reliable MS identification within 20 min. Under an external electric field, charged membranes can adsorb multiple layers of proteins, which exceed the capacity limit of common resins or membranes. It enlarges sample loading and trapping efficiency, thus bypasses the tradeoff between sample capacity and downstream detection sensitivity. This integrated approach, formed by synergistic utilization among electric field, membrane, and fluidic handling at the microscale, reduces the overall complexity of crude samples in one step for direct MS analysis. The sample preparation goals, including enrichment, desalting, removal of noncharged contaminants, and initial fractionation, can be rapidly performed in a single device. The strategy facilitates reproducible MS quantification by circumventing traditional laborious and time-consuming sample preparation steps. In addition, MEPD extended the ion trap linear dynamic range from 2 to at least 4 orders of magnitude by eliminating ion suppression effect, enriching target analyte(s), and decreasing sample loss during integrated sample preparation.
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Affiliation(s)
- Yu Zhou
- Beijing National Laboratory for Molecular Sciences, Key Lab of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Inst. of Analytical Chemistry, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
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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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Guo L, Qiu B, Xue L, Chen G. CE with a new electrochemiluminescent detection system for separation and detection of proteins labeled with tris(1,10-phenanthroline) ruthenium(II). Electrophoresis 2009; 30:2390-6. [DOI: 10.1002/elps.200800715] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Abstract
In the postgenomic era, proteomics has become a dominant field for identifying and quantifying the complex protein machinery of the cell. The expression levels, posttranslational modifications, and specific interactions of proteins control the biology of such processes as development, differentiation, and signal transduction. Studies of the proteins involved in these processes often lead to a better understanding of biology and of human disease. Powerful separation techniques and sensitive detection methods enable researchers to untangle these complicated networks of processes. CE coupled with either MS or LIF are two of the techniques that make this possible. This review will cover proven CE-based methods for proteomics on the cell and tissue level and their application in biological and clinical studies, relevant new developments in enabling technology such as microfluidic CE-MS demonstrated on model systems, and comment on the future of CE in proteomics.
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MESH Headings
- Amino Acid Sequence
- Electrophoresis, Capillary/instrumentation
- Electrophoresis, Capillary/methods
- Humans
- Molecular Sequence Data
- Proteins/analysis
- Proteins/genetics
- Proteome/analysis
- Proteomics/methods
- Sequence Alignment
- Spectrometry, Mass, Electrospray Ionization/instrumentation
- Spectrometry, Mass, Electrospray Ionization/methods
- Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/instrumentation
- Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/methods
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Affiliation(s)
- Bryan R Fonslow
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037, USA
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Wee A, Grayden DB, Zhu Y, Petkovic-Duran K, Smith D. A continuous wavelet transform algorithm for peak detection. Electrophoresis 2008; 29:4215-25. [DOI: 10.1002/elps.200800096] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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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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Levkin PA, Eeltink S, Stratton TR, Brennen R, Robotti K, Yin H, Killeen K, Svec F, Fréchet JMJ. Monolithic porous polymer stationary phases in polyimide chips for the fast high-performance liquid chromatography separation of proteins and peptides. J Chromatogr A 2008; 1200:55-61. [PMID: 18374934 PMCID: PMC2518059 DOI: 10.1016/j.chroma.2008.03.025] [Citation(s) in RCA: 89] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2008] [Revised: 02/25/2008] [Accepted: 03/03/2008] [Indexed: 11/25/2022]
Abstract
Poly(lauryl methacrylate-co-ethylene dimethacrylate) and poly(styrene-co-divinylbenzene) stationary phases in monolithic format have been prepared by thermally initiated free radical polymerization within polyimide chips featuring channels having a cross-section of 200micromx200microm and a length of 6.8cm. These chips were then used for the separation of a mixture of proteins including ribonuclease A, myoglobin, cytochrome c, and ovalbumin, as well as peptides. The separations were monitored by UV adsorption. Both the monolithic phases based on methacrylate and on styrene chemistries enabled the rapid baseline separation of most of the test mixtures. Best performance was achieved with the styrenic monolith leading to fast baseline separation of all four proteins in less than 2.5min. The in situ monolith preparation process affords microfluidic devices exhibiting good batch-to-batch and injection-to-injection repeatability.
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Affiliation(s)
- Pavel A Levkin
- College of Chemistry, University of California, Berkeley, CA 94720-1460, USA
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29
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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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30
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Poitevin M, Peltre G, Descroix S. Use of quasi-isoelectric buffers as anolyte and catholyte to improve capillary isoelectric focusing performances. Electrophoresis 2008; 29:1687-93. [DOI: 10.1002/elps.200700806] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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31
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Balgley BM, Wang W, Fang X, DeVoe DL, Lee CS. Capillary Electrophoretic Separations for Clinical Proteomics. Clin Proteomics 2008. [DOI: 10.1002/9783527622153.ch6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
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32
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Merenbloom SI, Koeniger SL, Bohrer BC, Valentine SJ, Clemmer DE. Improving the efficiency of IMS-IMS by a combing technique. Anal Chem 2008; 80:1918-27. [PMID: 18290667 PMCID: PMC3727147 DOI: 10.1021/ac7018602] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
A simple method for increasing the efficiency of multidimensional ion mobility spectrometry (IMS-IMS) measurements (as defined by the number of two-dimensional data sets necessary to sample all of the ions in a complex mixture) is illustrated. In this approach, components from a packet containing a mixture of ions are introduced into the first IMS drift region where they are separated based on differences in mobility. At the exit of this region, narrow distributions of ions having identical mobilities are selected, subjected to gentle activation conditions that are intended to induce conformational changes, and transmitted into a second IMS drift region where the new conformations are separated. Here, we describe a simple timing sequence associated with selection and activation of multiple distributions at the entrance of the second drift region in a systematic fashion that improves the efficiency of two-dimensional IMS-IMS by a factor of approximately 8. The method is illustrated by examination of a mixture of tryptic peptides from human hemoglobin.
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33
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Yamaguchi S, Yabutsuka T, Hibino M, Yao T. Generation of hydroxyapatite patterns by electrophoretic deposition. JOURNAL OF MATERIALS SCIENCE. MATERIALS IN MEDICINE 2008; 19:1419-24. [PMID: 17914638 DOI: 10.1007/s10856-006-0053-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2006] [Accepted: 11/20/2006] [Indexed: 05/17/2023]
Abstract
Hydroxyapatite (HAp) patterns with distinct boundaries were generated by electrophoretic deposition (EPD) utilizing an insulating mask that partially blocks the electric field. For the EPD process, we selected two types of mask: a polytetrafluoroethylene (PTFE) board with holes and a resist pattern. A porous PTFE film, which differed from the mask PTFE, was employed as a substrate and attached to the mask. EPD was performed with a suspension of wollastonite particles in acetone, which were deposited on the substrate in the form of the patterned mask. The deposited wollastonite particles induced HAp patterns during a soak in simulated body fluid (SBF). As a result, minute HAp patterns, such as dots, lines, and corners were fabricated on the porous PTFE substrate with a minimum line width of about 100 microm.
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Affiliation(s)
- Seiji Yamaguchi
- Graduate School of Energy Science, Kyoto University, Yoshida, Sakyo-ku, Kyoto 606-8501, Japan.
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34
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GUO Y, LIU D, WANG H, YUAN R, BAO JJ. Zone Electrophoresis in an Inner-cooling Wide-bore Electrophoresis System with UV Detection. ANAL SCI 2008; 24:1025-30. [DOI: 10.2116/analsci.24.1025] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Affiliation(s)
- Yugao GUO
- School of Material Science and Chemical Engineering, Tianjin Polytechnic University
- School of Pharmaceutical Science & Technology, Tianjin University
| | - Danning LIU
- School of Pharmaceutical Science & Technology, Tianjin University
| | - Huaifeng WANG
- School of Pharmaceutical Science & Technology, Tianjin University
| | - Ruijuan YUAN
- School of Pharmaceutical Science & Technology, Tianjin University
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35
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Multiplexed high-throughput electrokinetically-controlled immunoassay for the detection of specific bacterial antibodies in human serum. Anal Chim Acta 2008; 606:98-107. [DOI: 10.1016/j.aca.2007.10.052] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2007] [Revised: 10/19/2007] [Accepted: 10/23/2007] [Indexed: 11/19/2022]
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36
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Peng Y, Pallandre A, Tran NT, Taverna M. Recent innovations in protein separation on microchips by electrophoretic methods. Electrophoresis 2008; 29:157-78. [DOI: 10.1002/elps.200700347] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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37
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Phillips TM, Wellner EF. Analysis of inflammatory biomarkers from tissue biopsies by chip-based immunoaffinity CE. Electrophoresis 2007; 28:3041-8. [PMID: 17724696 DOI: 10.1002/elps.200700193] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
To aid in the biochemical analysis of human skin biopsies, a semiautomatic chip-based CE system has been developed for measuring inflammatory biomarkers in microdissected areas of the biopsy. Following solubilization of the dissected tissue, the desired biomarkers were isolated by immunoaffinity capture using a panel of 12 antibodies, immobilized on a disposable glass fiber disk, within the extraction port of the chip. The captured analytes were labeled with a 635 nm light-emitting laser dye and electroeluted into the separation channel. Electrophoretic separation of all of the analytes was achieved in 2.2 min with quantification of each peak being performed by online LIF detection and integration of each peak area. Comparison of the results obtained from the chip-based system to those obtained using commercially available high-sensitivity immunoassays demonstrated that the chip-based assay provides a fast, accurate procedure for studying the concentrations of inflammatory biomarkers in complex biological materials. The degree of accuracy and precision achieved by the chip-based CE is comparable to conventional immunoassays and the system is capable of analyzing circa six samples per hour. With the ever-expanding array of antibodies that are commercially available, this chip-based system can be applied to a wide variety of different biomedical analyses.
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Affiliation(s)
- Terry M Phillips
- Nanoscale Immunodiagnostics, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20892, USA.
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38
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Kang L, Chung BG, Langer R, Khademhosseini A. Microfluidics for drug discovery and development: from target selection to product lifecycle management. Drug Discov Today 2007; 13:1-13. [PMID: 18190858 DOI: 10.1016/j.drudis.2007.10.003] [Citation(s) in RCA: 209] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2007] [Revised: 10/01/2007] [Accepted: 10/05/2007] [Indexed: 01/09/2023]
Abstract
Microfluidic technologies' ability to miniaturize assays and increase experimental throughput have generated significant interest in the drug discovery and development domain. These characteristics make microfluidic systems a potentially valuable tool for many drug discovery and development applications. Here, we review the recent advances of microfluidic devices for drug discovery and development and highlight their applications in different stages of the process, including target selection, lead identification, preclinical tests, clinical trials, chemical synthesis, formulations studies and product management.
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Affiliation(s)
- Lifeng Kang
- Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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39
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Tran B, Pepaj M, Lundanes E, Greibrokk T. The Behaviour of Reduced, Alkylated and Native Proteins in a pH-Gradient LC System. Chromatographia 2007. [DOI: 10.1365/s10337-007-0390-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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40
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Roman GT, Kennedy RT. Fully integrated microfluidic separations systems for biochemical analysis. J Chromatogr A 2007; 1168:170-88; discussion 169. [PMID: 17659293 DOI: 10.1016/j.chroma.2007.06.010] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2007] [Accepted: 06/05/2007] [Indexed: 10/23/2022]
Abstract
Over the past decade a tremendous amount of research has been performed using microfluidic analytical devices to detect over 200 different chemical species. Most of this work has involved substantial integration of fluid manipulation components such as separation channels, valves, and filters. This level of integration has enabled complex sample processing on miniscule sample volumes. Such devices have also demonstrated high throughput, sensitivity, and separation performance. Although the miniaturization of fluidics has been highly valuable, these devices typically rely on conventional ancillary equipment such as power supplies, detection systems, and pumps for operation. This auxiliary equipment prevents the full realization of a "lab-on-a-chip" device with complete portability, autonomous operation, and low cost. Integration and/or miniaturization of ancillary components would dramatically increase the capability and impact of microfluidic separations systems. This review describes recent efforts to incorporate auxiliary equipment either as miniaturized plug-in modules or directly fabricated into the microfluidic device.
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Affiliation(s)
- Gregory T Roman
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA
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41
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Larson RL, Hill AL, Nuñez A. Characterization of protein changes associated with sugar beet (Beta vulgaris) resistance and susceptibility to Fusarium oxysporum. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2007; 55:7905-15. [PMID: 17715886 DOI: 10.1021/jf070876q] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Fusarium oxysporum (F-19) is a serious threat to sugar beet. Resistance exists, but the basis for resistance and disease is unknown. Protein extracts from sugar beet genotypes C1200.XH024 (resistant, R) and Fus7 (susceptible, S) were analyzed by multidimensional liquid chromatography at 2 and 5 days postinoculation (dpi) and compared to mock-inoculated controls. One hundred twenty-one (R) and 73 (S) protein peaks were induced/repressed by F-19, approximately 12 (R) and 8% (S) of the total proteome detected. Temporal protein regulation occurred within and between each genotype, indicating that the timing of expression may be important for resistance. Thirty-one (R) and 48 (S) of the differentially expressed peaks were identified using matrix-assisted laser desorption-ionization with tandem time-of-flight mass spectrometry; others were below detection level. Comparison between the two genotypes uncovered R- and S-specific proteins with potential roles in resistance and disease development, respectively. Use of these proteins to select for new sources of resistance and to develop novel disease control strategies is discussed.
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Affiliation(s)
- Rebecca L Larson
- Sugarbeet Research Unit, Agricultural Research Service, US Department of Agriculture, 1701 Centre Avenue, Fort Collins, Colorado 80526, USA.
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42
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Jacksén J, Redeby T, Emmer A. Capillary electrophoretic separation and fractionation of hydrophobic peptides onto a pre-structured matrix assisted laser desorption/ ionization target for mass spectrometric analysis. J Sep Sci 2007; 29:288-95. [PMID: 16524105 DOI: 10.1002/jssc.200500338] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
A CE separation of hydrophobic peptides followed by fractionation onto a prestructured MALDI target and off-line MS analysis was performed. An improved and partially automated manufacturing procedure of the previously described MALDI target is presented. This target is structurally coated with silicone and especially developed for hydrophobic peptides and proteins. Here, the target plate was designed specifically for the CE fraction collection. Different solvents were evaluated to meet the requirements of peptide solubility and compatibility to both the CE and MALDI methods and to the fractionation procedure. CE-MALDI-MS analysis of nine highly hydrophobic peptides from cyanogen bromide-digested bacteriorhodopsin is demonstrated.
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Affiliation(s)
- Johan Jacksén
- Department of Chemistry, Division of Analytical Chemistry, Royal Institute of Technology, Stockholm, Sweden
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43
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Braun RJ, Kinkl N, Beer M, Ueffing M. Two-dimensional electrophoresis of membrane proteins. Anal Bioanal Chem 2007; 389:1033-45. [PMID: 17680235 DOI: 10.1007/s00216-007-1514-6] [Citation(s) in RCA: 91] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2007] [Revised: 07/10/2007] [Accepted: 07/13/2007] [Indexed: 01/26/2023]
Abstract
One third of all genes of various organisms encode membrane proteins, emphasizing their crucial cellular role. However, due to their high hydrophobicity, membrane proteins demonstrate low solubility and a high tendency for aggregation. Indeed, conventional two-dimensional gel electrophoresis (2-DE), a powerful electrophoretic method for the separation of complex protein samples that applies isoelectric focusing (IEF) in the first dimension and sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) in the second dimension, has a strong bias against membrane proteins. This review describes two-dimensional electrophoretic techniques that can be used to separate membrane proteins. Alternative methods for performing conventional 2-DE are highlighted; these involve replacing the IEF with electrophoresis using cationic detergents, namely 16-benzyldimethyl-n-hexadecylammonium chloride (16-BAC) and cetyl trimethyl ammonium bromide (CTAB), or the anionic detergent SDS. Finally, the separation of native membrane protein complexes through the application of blue and clear native gel electrophoresis (BN/CN-PAGE) is reviewed, as well as the free-flow electrophoresis (FFE) of membranes.
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Affiliation(s)
- Ralf J Braun
- GSF-National Research Center for Environment and Health, Institute of Human Genetics, Ingolstaedter Landstrasse 1, 85764, Munich-Neuherberg, Germany
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44
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Manicone AM, McGuire JK. Matrix metalloproteinases as modulators of inflammation. Semin Cell Dev Biol 2007; 19:34-41. [PMID: 17707664 PMCID: PMC2235912 DOI: 10.1016/j.semcdb.2007.07.003] [Citation(s) in RCA: 394] [Impact Index Per Article: 23.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2007] [Revised: 07/02/2007] [Accepted: 07/03/2007] [Indexed: 12/21/2022]
Abstract
An increased expression of members of the matrix metalloproteinase (MMP) family of enzymes is seen in almost every human tissue in which inflammation is present. Through the use of models of human disease in mice with targeted deletions of individual MMPs, it has become clear that MMPs act broadly in inflammation to regulate barrier function, inflammatory cytokine and chemokine activity, and the generation of chemokine gradients. Individual MMPs regulate both normal and pathological inflammatory processes, and therefore, developing rational therapies requires further identification of specific MMP substrates and characterization of the downstream consequences of MMP proteolytic activity.
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Affiliation(s)
- Anne M. Manicone
- Center for Lung Biology, University of Washington, Seattle, WA
- Pulmonary and Critical Care Medicine, University of Washington, Seattle, WA
| | - John K. McGuire
- Center for Lung Biology, University of Washington, Seattle, WA
- Department of Pediatrics, University of Washington, Seattle, WA
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45
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Abstract
This review summarizes applications of CEC for the analysis of proteins and peptides. This "hybrid" technique is useful for the analysis of a broad spectrum of proteins and peptides and is a complementary approach to liquid chromatographic and capillary electrophoretic analysis. All modes of CEC are described--granular packed columns, monolithic stationary phases as well as open-tubular CEC. Attention is also paid to pressurized CEC and the chip-based platform.
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Affiliation(s)
- Ivan Miksík
- Institute of Physiology, Academy of Sciences of the Czech Republic, Prague, Czech Republic.
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46
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Jacksén J, Frisk T, Redeby T, Parmar V, van der Wijngaart W, Stemme G, Emmer A. Off-line integration of CE and MALDI-MS using a closed–open–closed microchannel system. Electrophoresis 2007; 28:2458-65. [PMID: 17577881 DOI: 10.1002/elps.200600735] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
In this work, a new technique for off-line hyphenation between CE and MALDI-MS is presented. Two closed fused-silica capillaries were connected via a silicon chip comprising an open microcanal. The EOF in the system was evaluated using mesityloxide or leucine-enkephalin as a sample and with a running buffer that rendered the analyte neutrally charged. Comparison was made between the EOF in a closed system (first capillary solely included in the electrical circuit) and in a closed-open system (first capillary and microcanal included in the electrical circuit). It was concluded that the experimental values of the EOF agreed with the theory. The influence of the capillary outer diameter on the peak dispersion was investigated using a closed-open-closed system (first capillary, microcanal and second capillary included in the electrical circuit). It was clearly seen that a capillary with 375 microm od induced considerably higher peak dispersion than a 150 microm od capillary, due to a larger liquid dead volume in the connection between the first capillary outlet and the microcanal. Mass spectrometric analysis has also been performed following CE separation runs in a closed-open-closed system with cytochrome c and lysozyme as model proteins. It was demonstrated that a signal distribution profile of the separated analytes could be recorded over a 30 mm long microcanal.
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Affiliation(s)
- Johan Jacksén
- Department of Chemistry, Division of Analytical Chemistry, School of Chemical Science and Engineering, Royal Institute of Technology, Stockholm, Sweden
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47
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Sahlin E. Two-dimensional capillary electrophoresis using tangentially connected capillaries. J Chromatogr A 2007; 1154:454-9. [PMID: 17459399 DOI: 10.1016/j.chroma.2007.04.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2007] [Revised: 03/29/2007] [Accepted: 04/02/2007] [Indexed: 11/24/2022]
Abstract
A novel type of fused silica capillary system is described where channels with circular cross-sections are tangentially in contact with each other and connected through a small opening at the contact area. Since the channels are not crossing each other in the same plane, the capillaries can easily be filled with different solutions, i.e. different solutions will be in contact with each other at the contact point. The system has been used to perform different types of two-dimensional separations and the complete system is fully automated where a high voltage switch is used to control the location of the high voltage in the system. Using two model compounds it is demonstrated that a type of two-dimensional separation can be performed using capillary zone electrophoresis at two different pH values. It is also shown that a compound with acid/base properties can be concentrated using a dynamic pH junction mechanism when transferred from the first separation to the second separation. In addition, the system has been used to perform a comprehensive two-dimensional capillary electrophoresis separation of tryptic digest of bovine serum albumin using capillary zone electrophoresis followed by micellar electrokinetic chromatography.
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Affiliation(s)
- Eskil Sahlin
- Department of Chemistry, Göteborg University, 412 96 Göteborg, Sweden.
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48
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Cañas B, Piñeiro C, Calvo E, López-Ferrer D, Gallardo JM. Trends in sample preparation for classical and second generation proteomics. J Chromatogr A 2007; 1153:235-58. [PMID: 17276441 DOI: 10.1016/j.chroma.2007.01.045] [Citation(s) in RCA: 122] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2006] [Revised: 12/18/2006] [Accepted: 01/12/2007] [Indexed: 11/16/2022]
Abstract
Sample preparation is a fundamental step in the proteomics workflow. However, it is not easy to find compiled information updating this subject. In this paper, the strategies and protocols for protein extraction and identification, following either classical or second generation proteomics methodologies, are reviewed. Procedures for: tissue disruption, cell lysis, sample pre-fractionation, protein separation by 2-DE, protein digestion, mass spectrometry analysis, multidimensional peptide separations and quantification of protein expression level are described.
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Affiliation(s)
- Benito Cañas
- Dept. Química Analítica, Facultad de CC, Químicas, UCM, Av.Complutense s/n, Madrid 28040, Spain.
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49
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Chang PL, Lee KH, Hu CC, Chang HT. CE with sequential light-emitting diode-induced fluorescence and electro-chemiluminescence detections for the determination of amino acids and alkaloids. Electrophoresis 2007; 28:1092-9. [PMID: 17330227 DOI: 10.1002/elps.200600546] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
This paper describes the determination of alkaloids and amino acids (AAs) using CE in conjunction with sequential light-emitting diode-induced fluorescence (LEDIF) and electrochemiluminescence (ECL) detections. In the CE-LEDIF-ECL system, the ECL detector was located in the outlet of the capillary, while the LEDIF detector was positioned 12 cm from the outlet. Naphthalene-2,3-dicarboxaldehyde (NDA) was used to form fluorescent AA-NDA derivatives from AAs possessing primary amino groups, while Ru(bpy)(3) (2+) was used to obtain ECL signals for analytes having secondary and tertiary amino groups. In the presence of poly(ethylene oxide), we accomplished the CE-LEDIF-ECL separation of a mixture of 12 AA-NDA derivatives, anabasine, nicotine, and proline within 11 min. This low-cost CE-LEDIF-ECL system allows the analysis of these AA-NDA derivatives and alkaloids at concentrations in the ranges of 49 nM-0.2 microM and 0.66-4.7 microM, respectively. We applied our CE-LEDIF-ECL system to the analysis of a urine sample and also to tobacco extracts. We obtained good qualitative and quantitative results when using this method with these analytes: the RSDs were below 3.0 and 2.8%, respectively. This CE-LEDIF-ECL system provides the advantages of high efficiency, speed, and sensitivity for the analysis of analytes possessing amino groups.
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Affiliation(s)
- Po-Ling Chang
- Department of Chemistry, National Taiwan University, Taipei, Taiwan
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50
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Yoo C, Patwa TH, Kreunin P, Miller FR, Huber CG, Nesvizhskii AI, Lubman DM. Comprehensive analysis of proteins of pH fractionated samples using monolithic LC/MS/MS, intact MW measurement and MALDI-QIT-TOF MS. JOURNAL OF MASS SPECTROMETRY : JMS 2007; 42:312-34. [PMID: 17206599 PMCID: PMC3426914 DOI: 10.1002/jms.1163] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
A comprehensive platform that integrates information from the protein and peptide levels by combining various MS techniques has been employed for the analysis of proteins in fully malignant human breast cancer cells. The cell lysates were subjected to chromatofocusing fractionation, followed by tryptic digestion of pH fractions for on-line monolithic RP-HPLC interfaced with linear ion trap MS analysis for rapid protein identification. This unique approach of direct analysis of pH fractions resulted in the identification of large numbers of proteins from several selected pH fractions, in which approximately 1.5 microg of each of the pH fraction digests was consumed for an analysis time of ca 50 min. In order to combine valuable information retained at the protein level with the protein identifications obtained from the peptide level information, the same pH fraction was analyzed using nonporous (NPS)-RP-HPLC/ESI-TOF MS to obtain intact protein MW measurements. In order to further validate the protein identification procedures from the fraction digest analysis, NPS-RP-HPLC separation was performed for off-line protein collection to closely examine each protein using MALDI-TOF MS and MALDI-quadrupole ion trap (QIT)-TOF MS, and excellent agreement of protein identifications was consistently observed. It was also observed that the comparison to intact MW and other MS information was particularly useful for analyzing proteins whose identifications were suggested by one sequenced peptide from fraction digest analysis.
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Affiliation(s)
- Chul Yoo
- Department of Chemistry, The University of Michigan, Ann Arbor, MI 48109, USA
| | - Tasneem H. Patwa
- Department of Chemistry, The University of Michigan, Ann Arbor, MI 48109, USA
| | - Paweena Kreunin
- Department of Chemistry, The University of Michigan, Ann Arbor, MI 48109, USA
| | - Fred R. Miller
- Barbara Ann Karmanos Cancer Institute, Wayne State University, Detroit, MI 48201, USA
| | - Christian G. Huber
- Department of Chemistry, Instrumental Analysis and Bioanalysis, Saarland University, 66123 Saarbrucken, Germany
| | - Alexey I. Nesvizhskii
- Department of Pathology, The University of Michigan Medical Center, Ann Arbor, MI 48109, USA
| | - David M. Lubman
- Department of Surgery, The University of Michigan Medical Center, Ann Arbor, MI 48109, USA
- Department of Chemistry, The University of Michigan, Ann Arbor, MI 48109, USA
- Department of Pathology, The University of Michigan Medical Center, Ann Arbor, MI 48109, USA
- Comprehensive Cancer Center, The University of Michigan Medical Center, Ann Arbor, MI 48109, USA
- Correspondence to: David M. Lubman, University of Michigan Medical Center, Department of Surgery, MSRBI, A510B, Box 0658, Ann Arbor, MI 48109, USA.
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