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Kohl FJ, Sánchez-Hernández L, Neusüß C. Capillary electrophoresis in two-dimensional separation systems: Techniques and applications. Electrophoresis 2014; 36:144-58. [DOI: 10.1002/elps.201400368] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2014] [Revised: 09/16/2014] [Accepted: 09/17/2014] [Indexed: 12/24/2022]
Affiliation(s)
- Felix J. Kohl
- Department of Chemistry; Aalen University; Aalen Germany
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2
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Grochocki W, Markuszewski MJ, Quirino JP. Multidimensional capillary electrophoresis. Electrophoresis 2014; 36:135-43. [DOI: 10.1002/elps.201400416] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Revised: 09/11/2014] [Accepted: 09/12/2014] [Indexed: 01/26/2023]
Affiliation(s)
- Wojciech Grochocki
- Department of Biopharmaceutics and Pharmacodynamics; Medical University of Gdansk; Gdansk Poland
| | - Michał J. Markuszewski
- Department of Biopharmaceutics and Pharmacodynamics; Medical University of Gdansk; Gdansk Poland
| | - Joselito P. Quirino
- Australian Centre for Research on Separation Science (ACROSS); School of Physical Sciences-Chemistry; University of Tasmania; Hobart Australia
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3
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Wang N, Tang Y, Chen L, Li L. Microbore liquid chromatography ultraviolet detection for quantification of total peptide amount and its application for assessing sample quality in shotgun proteome analysis of hundreds of cells. J Chromatogr A 2014; 1338:51-7. [PMID: 24630977 DOI: 10.1016/j.chroma.2014.02.050] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2013] [Revised: 02/15/2014] [Accepted: 02/17/2014] [Indexed: 11/30/2022]
Abstract
Mass spectrometric profiling of the proteome of a small number of cells requires not only a sensitive instrument for protein/peptide separation and detection, but also a robust sample preparation protocol to process a very small amount of proteins (<1μg) present in few cells. We have developed and evaluated the performance of a microbore liquid chromatography (LC) UV detection system for quantifying the total amount of peptides in a shotgun proteome analysis workflow that is tailored for the analysis of hundreds of cancer cells. Upon the sample injection into a 1-mm-diameter reversed phase column, a step-gradient was used to first remove salts and other impurities and then elute the peptides quickly without much separation. The UV absorbance of eluted peptides at 214nm was used for peptide quantification with the aid of a calibration curve of a tryptic digest of a mixture of four standard proteins. Two linear calibration regions could be obtained in the peptide amount ranging from 0.03μg to 0.3μg and from 0.6μg to 5μg. The limit of quantification (LOQ) was determined to be 30ng (or 39ng in the linear calibration range). However, the presence of background proteins, mainly keratins, introduced during the sample preparation process was found to be the limiting factor in quantifying a lower amount of peptides from a cell lysate digest. With background absorbance from the digest of contaminant proteins in a solution, the LOQ was found to be 200ng. This nondestructive microbore LC-UV method should be useful in assessing sample quality during the development and applications of an efficient sample preparation method for proteome analysis of a small number of cells. As an example, this method was used for quantifying the peptides generated from breast cancer MCF-7 cell extracts with a limited number of cells: 250, 500 and 1000 cells. Using capillary LC quadrupole time-of-flight mass spectrometry, 81-126, 122-154 and 256-282 proteins could be identified from 250, 500, and 1000 cells, respectively, in duplicate experiments. This method was also applied for the analysis of biological triplicate samples of MCF-7 cells. The average numbers of peptides and proteins detected from the experimental triplicate analyses of biological triplicate samples were 400±71 (9 datasets) and 124±14, respectively, from 250 cells, and 531±44 and 162±16, respectively, from 500 cells.
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Affiliation(s)
- Nan Wang
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada
| | - Yanan Tang
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada
| | - Lu Chen
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada
| | - Liang Li
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada.
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4
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El Deeb S, Dawwas HA, Gust R. Recent methodological and instrumental development in MEKC. Electrophoresis 2013; 34:1295-303. [PMID: 23417897 DOI: 10.1002/elps.201200574] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2012] [Revised: 01/04/2013] [Accepted: 01/05/2013] [Indexed: 11/08/2022]
Abstract
The review gives an update about the methodological and instrumental developments in micellar electrokinetic capillary chromatography as a type of CE analytical technique. Here, the last two years development of the technique are particularly presented. Recent approaches to improve sensitivity are discussed. Newly introduced concentration techniques and experimental methods for verification of the different mechanisms and processes of micellar electrokinetic chromatography analysis are highlighted. A theoretical model to explain changes in separation and electrophoretic mobility order of fully charged analytes are demonstrated. Modern approaches for improving compatibility of micellar electrokinetic capillary chromatography to mass spectrometry are also reported.
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Affiliation(s)
- Sami El Deeb
- Department of Pharmaceutical Chemistry, Institute of Pharmacy, Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innsbruck, Austria
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5
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Koshel BM, Wirth MJ. Trajectory of isoelectric focusing from gels to capillaries to immobilized gradients in capillaries. Proteomics 2012; 12:2918-26. [PMID: 22930445 PMCID: PMC3799802 DOI: 10.1002/pmic.201200213] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2012] [Revised: 08/15/2012] [Accepted: 08/20/2012] [Indexed: 12/29/2022]
Abstract
This review presents the need for replacing gels in 2D separations for proteomics, where speed, high-throughput, and the ability to characterize trace level proteins or small samples are the current desires. The theme of the review is isoelectric focusing, which is a valuable tool because it pre-concentrates proteins in addition to separating with high peak capacity. The review traces the technological progress from gel IEF to CIEF to packed capillaries with immobilized gradients for CIEF. Multiple capillary techniques are progressing toward meeting the current desires, providing extremely high sensitivity with regard to concentration and to small samples, integrated automation, and high peak capacity from multiple dimensions of separation. Capillaries with immobilized pH gradients for CIEF are emerging, which will alleviate interference from ampholytes and improve reproducibility in separation times when this valuable technique can be used as one of the dimensions.
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Affiliation(s)
- Brooke M. Koshel
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN 47907
| | - Mary J. Wirth
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN 47907
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6
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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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Chen HC, Chang YS, Chen SJ, Chang PL. Determination of the heterogeneity of DNA methylation by combined bisulfite restriction analysis and capillary electrophoresis with laser-induced fluorescence. J Chromatogr A 2012; 1230:123-9. [DOI: 10.1016/j.chroma.2012.01.049] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2011] [Revised: 01/13/2012] [Accepted: 01/16/2012] [Indexed: 10/14/2022]
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Measurement of ascorbic acid in single rat peritoneal mast cells using capillary electrophoresis with electrochemical detection. J Chromatogr B Analyt Technol Biomed Life Sci 2010; 878:1093-7. [PMID: 20382091 DOI: 10.1016/j.jchromb.2010.03.017] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2009] [Revised: 03/10/2010] [Accepted: 03/11/2010] [Indexed: 11/22/2022]
Abstract
In this paper, the amount of ascorbic acid (AA) in single rat peritoneal mast cell was determined by the method of capillary electrophoresis (CE) with electrochemical detection (ED) at a carbon fiber microdisk bundle electrode. The CE-ED system and the single-cell injection system were rearranged to make the operation more convenient and efficient. In the experiment, a self-made holder made of foam was used to keep the capillary from swing, which kept the stability of the baseline of the electropherogram. The single cell was lysed completely within 5s using the 0.1% sodium dodecylsulfate (SDS) as the cell lysis solution together with the lysis voltage of 2 kV. The quantitation analysis was accomplished by the use of calibration curves, and the amount of AA in single rat peritoneal mast cell was from 2.4 to 7.1 fmol.
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Kim BY, Yang J, Gong M, Flachsbart BR, Shannon MA, Bohn PW, Sweedler JV. Multidimensional separation of chiral amino acid mixtures in a multilayered three-dimensional hybrid microfluidic/nanofluidic device. Anal Chem 2009; 81:2715-22. [PMID: 19271741 DOI: 10.1021/ac802630p] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Microscale total analysis systems (microTAS) allow high-throughput analyses by integrating multiple processes, parallelization, and automation. Here we combine unit operations of microTAS to create a device that can perform multidimensional separations using a three-dimensional hybrid microfluidic/nanofluidic device composed of alternating layers of patterned poly(methyl methacrylate) and nanocapillary array membranes constructed from nuclear track-etched polycarbonate. Two consecutive electrophoretic separations are performed, the first being an achiral separation followed by a chiral separation of a selected analyte band. Separation conditions are optimized for a racemic mixture of fluorescein-isothiocyanate-labeled amino acids, serine and aspartic acid, chosen because there are endogenous D-forms of these amino acids in animals. The chiral separation is implemented using micellar electrokinetic chromatography using beta-cyclodextrin as the chiral selector and sodium taurocholate as the micelle-forming agent. Analyte separation is monitored by dual-beam laser-induced fluorescence detection. After separation in the first electrophoretic channel, the preselected analyte is sampled by the second-stage separation using an automated collection sequence with a zero-crossing algorithm. The controlled fluidic environment inherent to the three-dimensional architecture enables a series of separations in varying fluidic environments and allows sample stacking via different background electrolyte pH conditions. The ability to interface sequential separations, selected analyte capture, and other fluidic manipulations in the third dimension significantly improves the functionality of multilayer microfluidic devices.
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Affiliation(s)
- Bo Young Kim
- Department of Chemistry and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
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10
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Qiao X, Wang L, Ma J, Deng Q, Liang Z, Zhang L, Peng X, Zhang Y. High sensitivity analysis of water-soluble, cyanine dye labeled proteins by high-performance liquid chromatography with fluorescence detection. Anal Chim Acta 2009; 640:114-20. [DOI: 10.1016/j.aca.2009.03.021] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2008] [Revised: 02/14/2009] [Accepted: 03/09/2009] [Indexed: 10/21/2022]
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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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12
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Silva M. Micellar electrokinetic chromatography: Methodological and instrumental advances focused on practical aspects. Electrophoresis 2009; 30:50-64. [DOI: 10.1002/elps.200800414] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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13
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Sun X, Niu Y, Bi S, Zhang S. Determination of ascorbic acid in individual rat hepatocyte cells based on capillary electrophoresis with electrochemiluminescence detection. Electrophoresis 2008; 29:2918-24. [PMID: 18546168 DOI: 10.1002/elps.200700792] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
A novel method to detect ascorbic acid (AA) in individual rat hepatocyte cells was developed by combining CE with electrochemiluminescence (ECL) based on tris(2,2'-bipyridine) ruthenium(II) (Ru(bpy)(3)2+). A single cell, followed by 0.1% SDS as cell lysis solution, was injected into the inlet of the separation capillary by electromigration. After optimizing the analytical conditions, the RSDs of migration time and peak height were 0.38% and 2.6% for 1.0x10(-5) M AA (n=10), respectively. The linear range of AA was from 1.0x10(-8) to 5.0x10(-5) M with a correlation coefficient of 0.9979 and the LOD (S/N=3) was estimated to be 1.0x10(-8) M. This method has been successfully applied to determine AA in single rat hepatocytes and the amount of AA in seven rat hepatocytes ranged from 16 to 62 fmol. The above results demonstrated that CE coupled with ECL is convenient, sensitive, and will become an attractive alternative method for single-cell analysis.
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Affiliation(s)
- Xuemei Sun
- Key Laboratory of Eco-chemical Engineering, Ministry of Education, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao, China
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14
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Lowry M, Fakayode SO, Geng ML, Baker GA, Wang L, McCarroll ME, Patonay G, Warner IM. Molecular Fluorescence, Phosphorescence, and Chemiluminescence Spectrometry. Anal Chem 2008; 80:4551-74. [DOI: 10.1021/ac800749v] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Mark Lowry
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, Department of Chemistry, Winston-Salem State University, Winston-Salem, North Carolina 27110, Department of Chemistry, Nanoscience and Nanotechnology Institute and the Optical Science and Technology Center, University of Iowa, Iowa City, Iowa 52242, Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, Department of Chemistry and Biochemistry, Southern Illinois University, Carbondale,
| | - Sayo O. Fakayode
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, Department of Chemistry, Winston-Salem State University, Winston-Salem, North Carolina 27110, Department of Chemistry, Nanoscience and Nanotechnology Institute and the Optical Science and Technology Center, University of Iowa, Iowa City, Iowa 52242, Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, Department of Chemistry and Biochemistry, Southern Illinois University, Carbondale,
| | - Maxwell L. Geng
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, Department of Chemistry, Winston-Salem State University, Winston-Salem, North Carolina 27110, Department of Chemistry, Nanoscience and Nanotechnology Institute and the Optical Science and Technology Center, University of Iowa, Iowa City, Iowa 52242, Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, Department of Chemistry and Biochemistry, Southern Illinois University, Carbondale,
| | - Gary A. Baker
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, Department of Chemistry, Winston-Salem State University, Winston-Salem, North Carolina 27110, Department of Chemistry, Nanoscience and Nanotechnology Institute and the Optical Science and Technology Center, University of Iowa, Iowa City, Iowa 52242, Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, Department of Chemistry and Biochemistry, Southern Illinois University, Carbondale,
| | - Lin Wang
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, Department of Chemistry, Winston-Salem State University, Winston-Salem, North Carolina 27110, Department of Chemistry, Nanoscience and Nanotechnology Institute and the Optical Science and Technology Center, University of Iowa, Iowa City, Iowa 52242, Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, Department of Chemistry and Biochemistry, Southern Illinois University, Carbondale,
| | - Matthew E. McCarroll
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, Department of Chemistry, Winston-Salem State University, Winston-Salem, North Carolina 27110, Department of Chemistry, Nanoscience and Nanotechnology Institute and the Optical Science and Technology Center, University of Iowa, Iowa City, Iowa 52242, Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, Department of Chemistry and Biochemistry, Southern Illinois University, Carbondale,
| | - Gabor Patonay
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, Department of Chemistry, Winston-Salem State University, Winston-Salem, North Carolina 27110, Department of Chemistry, Nanoscience and Nanotechnology Institute and the Optical Science and Technology Center, University of Iowa, Iowa City, Iowa 52242, Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, Department of Chemistry and Biochemistry, Southern Illinois University, Carbondale,
| | - Isiah M. Warner
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, Department of Chemistry, Winston-Salem State University, Winston-Salem, North Carolina 27110, Department of Chemistry, Nanoscience and Nanotechnology Institute and the Optical Science and Technology Center, University of Iowa, Iowa City, Iowa 52242, Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, Department of Chemistry and Biochemistry, Southern Illinois University, Carbondale,
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Kostal V, Katzenmeyer J, Arriaga EA. Capillary electrophoresis in bioanalysis. Anal Chem 2008; 80:4533-50. [PMID: 18484738 DOI: 10.1021/ac8007384] [Citation(s) in RCA: 108] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Vratislav Kostal
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, USA
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16
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Huang WH, Ai F, Wang ZL, Cheng JK. Recent advances in single-cell analysis using capillary electrophoresis and microfluidic devices. J Chromatogr B Analyt Technol Biomed Life Sci 2008; 866:104-22. [DOI: 10.1016/j.jchromb.2008.01.030] [Citation(s) in RCA: 86] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2007] [Revised: 01/10/2008] [Accepted: 01/18/2008] [Indexed: 01/09/2023]
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Frumkin D, Wasserstrom A, Itzkovitz S, Harmelin A, Rechavi G, Shapiro E. Amplification of multiple genomic loci from single cells isolated by laser micro-dissection of tissues. BMC Biotechnol 2008; 8:17. [PMID: 18284708 PMCID: PMC2266725 DOI: 10.1186/1472-6750-8-17] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2007] [Accepted: 02/20/2008] [Indexed: 01/30/2023] Open
Abstract
BACKGROUND Whole genome amplification (WGA) and laser assisted micro-dissection represent two recently developed technologies that can greatly advance biological and medical research. WGA allows the analysis of multiple genomic loci from a single genome and has been performed on single cells from cell suspensions and from enzymatically-digested tissues. Laser micro-dissection makes it possible to isolate specific single cells from heterogeneous tissues. RESULTS Here we applied for the first time WGA on laser micro-dissected single cells from stained tissue sections, and developed a protocol for sequentially performing the two procedures. The combined procedure allows correlating the cell's genome with its natural morphology and precise anatomical position. From each cell we amplified 122 genomic and mitochondrial loci. In cells obtained from fresh tissue sections, 64.5% of alleles successfully amplified to approximately 700000 copies each, and mitochondrial DNA was amplified successfully in all cells. Multiplex PCR amplification and analysis of cells from pre-stored sections yielded significantly poorer results. Sequencing and capillary electrophoresis of WGA products allowed detection of slippage mutations in microsatellites (MS), and point mutations in P53. CONCLUSION Comprehensive genomic analysis of single cells from stained tissue sections opens new research opportunities for cell lineage and depth analyses, genome-wide mutation surveys, and other single cell assays.
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Affiliation(s)
- Dan Frumkin
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot, Israel.
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19
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Cohen D, Dickerson JA, Whitmore CD, Turner EH, Palcic MM, Hindsgaul O, Dovichi NJ. Chemical cytometry: fluorescence-based single-cell analysis. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2008; 1:165-190. [PMID: 20636078 DOI: 10.1146/annurev.anchem.1.031207.113104] [Citation(s) in RCA: 90] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Cytometry deals with the analysis of the composition of single cells. Flow and image cytometry employ antibody-based stains to characterize a handful of components in single cells. Chemical cytometry, in contrast, employs a suite of powerful analytical tools to characterize a large number of components. Tools have been developed to characterize nucleic acids, proteins, and metabolites in single cells. Whereas nucleic acid analysis employs powerful polymerase chain reaction-based amplification techniques, protein and metabolite analysis tends to employ capillary electrophoresis separation and ultrasensitive laser-induced fluorescence detection. It is now possible to detect yoctomole amounts of many analytes in single cells.
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Affiliation(s)
- Daniella Cohen
- Department of Chemistry, University of Washington, Seattle, 98195, USA
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20
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Edwards JL, Edwards RL, Reid KR, Kennedy RT. Effect of decreasing column inner diameter and use of off-line two-dimensional chromatography on metabolite detection in complex mixtures. J Chromatogr A 2007; 1172:127-34. [PMID: 17961581 PMCID: PMC2710303 DOI: 10.1016/j.chroma.2007.09.075] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2007] [Revised: 08/30/2007] [Accepted: 09/24/2007] [Indexed: 11/29/2022]
Abstract
Capillary liquid chromatography coupled with electrospray ionization to a quadrupole ion trap mass spectrometer was explored as a method for the analysis of polar anionic compounds in complex metabolome mixtures. A ternary mobile phase gradient, consisting of aqueous acidic, aqueous neutral and organic phases in combination with an aqueous compatible reversed-phase stationary phase allowed metabolites with a wide range of polarities to be resolved and detected. Detection limits in the full scan mode for glycolysis and tricarboxylic acid cycle intermediates were from 0.9 to 36fmol. Using this system, 111+/-9 (n=3) metabolites were detected in Escherichia coli lysate samples. Reducing column I.D. from 50 to 25microm increased the number of metabolites detected to 156+/-17 (n=3). The improvement in number of metabolites detected was attributed to an increase in separation efficiency, an increase in sensitivity, and a decrease in adduct formation. Implementation of a second separation mode, strong anion exchange, to fractionate the sample prior to capillary RPLC increased the number of metabolites detected to 244+/-21 (n=3). This improvement was attributed to the increased peak capacity which decreased co-elution of molecules enabling more sensitive detection by mass spectrometry. This system was also applied to islets of Langerhans where more significant improvements in metabolite detection were observed. In islets, 391+/-33 small molecules were detected using the two-dimensional separation. The results demonstrate that column miniaturization and use of two-dimensional separations can yield a significant improvement in the coverage of the metabolome.
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Affiliation(s)
- James L. Edwards
- Department of Chemistry University of Michigan Ann Arbor, MI USA
| | - Rachel L. Edwards
- Department of Microbiology and Immunology University of Michigan Ann Arbor, MI USA
| | - Kendra R. Reid
- Department of Chemistry University of Michigan Ann Arbor, MI USA
| | - Robert T. Kennedy
- Department of Chemistry University of Michigan Ann Arbor, MI USA
- Department of Pharmacology University of Michigan Ann Arbor, MI USA
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21
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Emrich CA, Medintz IL, Chu WK, Mathies RA. Microfabricated Two-Dimensional Electrophoresis Device for Differential Protein Expression Profiling. Anal Chem 2007; 79:7360-6. [PMID: 17822308 DOI: 10.1021/ac0711485] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A microfluidic separation system is developed to perform two-dimensional differential gel electrophoretic (DIGE) separations of complex, cellular protein mixtures produced by induced protein expression in E. coli. The micro-DIGE analyzer is a two-layer borosilicate glass microdevice consisting of a single 3.75 cm long channel for isoelectric focusing, which is sampled in parallel by 20 channels effecting a second-dimension separation by native electrophoresis. The connection between the orthogonal separation systems is accomplished by smaller channels comprising a microfluidic interface (MFI) that prevents media leakage between the two dimensions and enables facile loading of discontinuous gel systems in each dimension. Proteins are covalently labeled with Cy2 and Cy3 DIGE and detected simultaneously with a rotary confocal fluorescence scanner. Reproducible two-dimensional separations of both purified proteins and complex protein mixtures are performed with minimal run-to-run variation by including 7 M urea in the second-dimension separation matrix. The capabilities of the micro-DIGE analyzer are demonstrated by following the induced expression of maltose binding protein in E. coli. Although the absence of sodium dodecyl sulfate (SDS) in the second-dimension sizing separation limits the orthogonality and peak capacity of the separation, this analyzer is a significant first step toward the reproducible two-dimensional analysis of complex protein samples in microfabricated devices. Furthermore, the microchannel interface structures developed here will facilitate other multidimensional separations in microdevices.
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Affiliation(s)
- Charles A Emrich
- Biophysics Graduate Group, University of California, Berkeley, California 94720, USA
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Pierce KM, Hoggard JC, Mohler RE, Synovec RE. Recent advancements in comprehensive two-dimensional separations with chemometrics. J Chromatogr A 2007; 1184:341-52. [PMID: 17697686 DOI: 10.1016/j.chroma.2007.07.059] [Citation(s) in RCA: 134] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2007] [Revised: 07/17/2007] [Accepted: 07/18/2007] [Indexed: 11/30/2022]
Abstract
Comprehensive two-dimensional (2D) separations provide the analyst with a tremendous amount of complex data. In order to glean useful information from this complex data, advancements in commercially available software that implement chemometrics are currently available and continue to evolve. Future advancements will no doubt involve commercializing (or adapting) specialized, in-house chemometric techniques that are currently found only in the hands of technical experts and researchers in industry, government, and academia. In order to make timely advancements, future commercialization of novel chemometric techniques should involve collaborations among instrument software manufacturers, professional programmers, technical experts, and researchers. During the last decade, this field has seen a steady advancement from single analyte target analysis to comprehensive non-target analysis of entire multidimensional sample profiles (involving sample classification and/or data mining for discovery-based sample comparisons). The advancements in instrumentation and chemometric software tools have a tremendous impact in various applications: fuels, food, environmental, pharmaceuticals, metabolomics, etc. Most of the development has been for software to apply with gas chromatography-based instrumentation, such as comprehensive two-dimensional gas chromatography (GC x GC) and comprehensive two-dimensional gas chromatography with time-of-flight mass spectrometry (GC x GC-TOF-MS). More recently there have been notable advancements in liquid-phase instrumentation as well.
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Affiliation(s)
- Karisa M Pierce
- Department of Chemistry, Box 351700, University of Washington, Seattle, WA 98195-1700 USA
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Sobhani K, Fink SL, Cookson BT, Dovichi NJ. Repeatability of chemical cytometry: 2-DE analysis of single RAW 264.7 macrophage cells. Electrophoresis 2007; 28:2308-13. [PMID: 17557367 DOI: 10.1002/elps.200700017] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
This report presents the use of 2-DE with ultrasensitive fluorescence detection as a chemical cytometry tool to characterize the protein and biogenic amine content of single cells from the RAW 264.7 murine macrophage cell line. Cells were sorted by cell cycle prior to 2-DE analysis. Cells in the G2/M phase of the cell cycle were aspirated into the first-dimensional capillary and lysed. The cellular contents were fluorescently labeled and first separated by capillary sieving electrophoresis (CSE). Over 380 fractions were transferred from the first-dimensional capillary to the second-dimensional capillary, where components were further separated by MEKC and detected by laser-induced fluorescence. Twenty-five spots common to the four electropherograms were fit with a 2-D Gaussian surface to determine spot position, width, and amplitude. The RSD in CSE mobility was 1.0 +/- 0.6%. The mean uncertainty in spot position was 1.3 times larger than the mean spot width in the CSE dimension. The average SD in MEKC migration time was 0.37 +/- 0.13 s, which is smaller than the average spot size in this dimension. Spot capacity was 200. The RSD in spot amplitude was 50%, reflecting a large cell-to-cell variation in component expression.
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Affiliation(s)
- Kimia Sobhani
- Department of Chemistry, University of Washington, Seattle, WA 98195-1700, USA
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