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Liu Y, Chen X, Zhang Y, Liu J. Advancing single-cell proteomics and metabolomics with microfluidic technologies. Analyst 2019; 144:846-858. [PMID: 30351310 DOI: 10.1039/c8an01503a] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Recent advances in single-cell analysis have unraveled substantial heterogeneity among seemingly identical cells at genomic and transcriptomic levels. These discoveries have urged scientists to develop new tools that are capable of investigating single cells from a broader set of "omics". Proteomics and metabolomics, for instance, are of particular interest as they are closely correlated with a dynamic picture of cellular behaviors and phenotypic identities. The development of such tools requires highly efficient isolation and processing of a large number of individual cells, where techniques such as microfluidics are extremely useful. Here, we review the recent advances in single-cell proteomics and metabolomics, with a focus on microfluidics-based platforms. We highlight a vast array of emerging microfluidic formats for single-cell isolation and manipulation, and how the state-of-the-art analytical tools are coupled with such platforms for proteomic and metabolomic profiling.
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Affiliation(s)
- Yifan Liu
- Jiangsu Key Laboratory for Carbon-based Functional Materials and Devices, Institute of Functional Nano and Soft Materials (FUNSOM), Soochow University, Suzhou, Jiangsu Province 215123, China.
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Hu T, Zhang JL. Mass-spectrometry-based lipidomics. J Sep Sci 2017; 41:351-372. [PMID: 28859259 DOI: 10.1002/jssc.201700709] [Citation(s) in RCA: 94] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Revised: 08/17/2017] [Accepted: 08/18/2017] [Indexed: 01/09/2023]
Abstract
Lipids, which have a core function in energy storage, signalling and biofilm structures, play important roles in a variety of cellular processes because of the great diversity of their structural and physiochemical properties. Lipidomics is the large-scale profiling and quantification of biogenic lipid molecules, the comprehensive study of their pathways and the interpretation of their physiological significance based on analytical chemistry and statistical analysis. Lipidomics will not only provide insight into the physiological functions of lipid molecules but will also provide an approach to discovering important biomarkers for diagnosis or treatment of human diseases. Mass-spectrometry-based analytical techniques are currently the most widely used and most effective tools for lipid profiling and quantification. In this review, the field of mass-spectrometry-based lipidomics was discussed. Recent progress in all essential steps in lipidomics was carefully discussed in this review, including lipid extraction strategies, separation techniques and mass-spectrometry-based analytical and quantitative methods in lipidomics. We also focused on novel resolution strategies for difficult problems in determining C=C bond positions in lipidomics. Finally, new technologies that were developed in recent years including single-cell lipidomics, flux-based lipidomics and multiomics technologies were also reviewed.
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Affiliation(s)
- Ting Hu
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing, PR China
| | - Jin-Lan Zhang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing, PR China
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Amantonico A, Urban PL, Fagerer SR, Balabin RM, Zenobi R. Single-cell MALDI-MS as an analytical tool for studying intrapopulation metabolic heterogeneity of unicellular organisms. Anal Chem 2011; 82:7394-400. [PMID: 20707357 DOI: 10.1021/ac1015326] [Citation(s) in RCA: 108] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Heterogeneity is a characteristic feature of all populations of living organisms. Here we make an attempt to validate a single-cell mass spectrometric method for detection of changes in metabolite levels occurring in populations of unicellular organisms. Selected metabolites involved in central metabolism (ADP, ATP, GTP, and UDP-Glucose) could readily be detected in single cells of Closterium acerosum by means of negative-mode matrix-assisted laser desorption/ionization (MALDI) mass spectrometry (MS). The analytical capabilities of this approach were characterized using standard compounds. The method was then used to study populations of individual cells with different levels of the chosen metabolites. With principal component analysis and support vector machine algorithms, it was possible to achieve a clear separation of individual C. acerosum cells in different metabolic states. This study demonstrates the suitability of mass spectrometric analysis of metabolites in single cells to measure cell-population heterogeneity.
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Affiliation(s)
- Andrea Amantonico
- Department of Chemistry and Applied Biosciences, ETH Zurich, CH-8093 Zurich, Switzerland
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Greving MP, Patti GJ, Siuzdak G. Nanostructure-initiator mass spectrometry metabolite analysis and imaging. Anal Chem 2011; 83:2-7. [PMID: 21049956 PMCID: PMC3012143 DOI: 10.1021/ac101565f] [Citation(s) in RCA: 154] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Nanostructure-Initiator Mass Spectrometry (NIMS) is a matrix-free desorption/ionization approach that is particularly well-suited for unbiased (untargeted) metabolomics. An overview of the NIMS technology and its application in the detection of biofluid and tissue metabolites are presented. (To listen to a podcast about this feature, please go to the Analytical Chemistry multimedia page at pubs.acs.org/page/ancham/audio/index.html .).
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Affiliation(s)
- Matthew P Greving
- Center for Metabolomics and Mass Spectrometry, Department of Chemistry, The Scripps Research Institute
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Analytical techniques for single-cell metabolomics: state of the art and trends. Anal Bioanal Chem 2010; 398:2493-504. [DOI: 10.1007/s00216-010-3850-1] [Citation(s) in RCA: 102] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2010] [Revised: 05/09/2010] [Accepted: 05/13/2010] [Indexed: 01/09/2023]
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7
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Petrova YY. A sorption-catalytic procedure for determining histamine. JOURNAL OF ANALYTICAL CHEMISTRY 2010. [DOI: 10.1134/s1061934810050151] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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8
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Chemical and biological single cell analysis. Curr Opin Biotechnol 2010; 21:12-20. [DOI: 10.1016/j.copbio.2010.01.007] [Citation(s) in RCA: 147] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2009] [Accepted: 01/09/2010] [Indexed: 11/20/2022]
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Amantonico A, Oh JY, Sobek J, Heinemann M, Zenobi R. Mass spectrometric method for analyzing metabolites in yeast with single cell sensitivity. Angew Chem Int Ed Engl 2008; 47:5382-5. [PMID: 18543269 DOI: 10.1002/anie.200705923] [Citation(s) in RCA: 110] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Andrea Amantonico
- Department of Chemistry and Applied Biosciences, ETH Zurich, 8093 Zurich, Switzerland
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Amantonico A, Oh J, Sobek J, Heinemann M, Zenobi R. Mass Spectrometric Method for Analyzing Metabolites in Yeast with Single Cell Sensitivity. Angew Chem Int Ed Engl 2008. [DOI: 10.1002/ange.200705923] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Gao N, Li L, Shi Z, Zhang X, Jin W. High-throughput determination of glutathione and reactive oxygen species in single cells based on fluorescence images in a microchannel. Electrophoresis 2007; 28:3966-75. [DOI: 10.1002/elps.200700124] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Rubakhin SS, Churchill JD, Greenough WT, Sweedler JV. Profiling signaling peptides in single mammalian cells using mass spectrometry. Anal Chem 2007; 78:7267-72. [PMID: 17037931 PMCID: PMC2530951 DOI: 10.1021/ac0607010] [Citation(s) in RCA: 77] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The peptide content of individual mammalian cells is profiled using matrix-assisted laser desorption/ionization (MALDI) time-of-flight mass spectrometry. Both enzymatic and nonenzymatic procedures, including a glycerol cell stabilization method, are reported for the isolation of individual mammalian cells in a manner compatible with MALDI MS measurements. Guided microdeposition of MALDI matrix allows samples to be created with suitable analyte-to-matrix ratios. More than 15 peptides are observed in individual rat intermediate pituitary cells. The combination of accurate mass data, expected cleavages by proteolytic enzymes, and postsource decay sequencing allows identification of 14 of these peptides as pro-opiomelanocortin prohormone-derived molecules. These protocols permit the classification of individual mammalian cells by peptide profile, the elucidation of cell-specific prohormone processing, and the discovery of new signaling peptides on a cell-to-cell basis in a wide variety of mammalian cell types.
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Affiliation(s)
| | - James D. Churchill
- Department of Psychology, and the Beckman Institute, University of Illinois, Urbana, IL, 61801
| | - William T. Greenough
- Department of Psychology, and the Beckman Institute, University of Illinois, Urbana, IL, 61801
| | - Jonathan V. Sweedler
- Department of Chemistry, University of Illinois, Urbana, IL, 61801
- CORRESPONDING AUTHOR: Jonathan V. Sweedler, Department of Chemistry, 600 S. Mathews, 64-5, Urbana, IL 61801,
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Foret F, Kusý P. Microdevices in mass spectrometry. EUROPEAN JOURNAL OF MASS SPECTROMETRY (CHICHESTER, ENGLAND) 2007; 13:41-4. [PMID: 17878537 DOI: 10.1255/ejms.834] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Miniaturization of laboratory instrumentation is becoming critical in achieving the speed and throughput required by the current revolutionary progress in biology. This mini review critically summarizes the present status of microfluidic devices designed for use in mass spectrometry.
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Affiliation(s)
- F Foret
- Institute of Analytical Chemistry, Veverí 97, 60200 Brno, Czech Republic
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Abstract
Recent advances of microfluidics systems suitable for multiplexed MS analysis are reviewed with respect to fabrication technologies and applications.
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Kang SH, Lee S, Yeung ES. Atypical mobilities of single native DNA molecules in microchip electrophoresis revealed by differential interference contrast microscopy. Electrophoresis 2006; 27:4149-57. [PMID: 17001741 DOI: 10.1002/elps.200600154] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
A transmitted-light optical microscope using differential interference contrast (DIC) was employed to follow the real-time dynamics of different kb-sized single native dsDNA molecules without fluorescent-dye labeling. In a PDMS/glass microchip, the electrophoretic migration velocities of large dsDNA molecules are lower than small dsDNA molecules in a running buffer of 0.25% v/v nonionic polymeric surfactant C16E6 (n-alkyl polyoxyethylene ether) in 100 mM N-tris(hydroxymethyl)methyl-2-aminoethanesulfonic acid (TES) buffer because the C16E6 behaved as a dynamic polymer. However, the order of migration reversed in 50 mM Gly-Gly buffer. The radial positions of individual DNA molecules (i.e., center or walls of the microchip) did not change the migration order. The atypical migration order correlated well with the results in CE. The alignment of the deformable molecules due to viscous drag is likely responsible for these observations.
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Affiliation(s)
- Seong Ho Kang
- Department of Chemistry, Chonbuk National University, Jeonju, South Korea.
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McClain MA, Culbertson CT, Jacobson SC, Allbritton NL, Sims CE, Ramsey JM. Microfluidic devices for the high-throughput chemical analysis of cells. Anal Chem 2004; 75:5646-55. [PMID: 14588001 DOI: 10.1021/ac0346510] [Citation(s) in RCA: 287] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A microfluidic device is reported that integrated cell handling, rapid cell lysis, and electrophoretic separation and detection of fluorescent cytosolic dyes. The device function was demonstrated using Jurkat cells that were loaded with the fluorogenic dyes - carboxyfluorescein diacetate, Oregon green carboxylic acid diacetate, or Calcein AM. The loaded cells were hydrodynamically transported from the cell-containing reservoir to a region on the microfluidic device where they were focused and then rapidly lysed using an electric field. Complete lysis was accomplished in <33 ms. The hydrolyzed, fluorescent dyes in the cell lysate were automatically injected into a separation channel on the device and detected 3 mm downstream of the injection point. The total separation time was approximately 2.2 s with absolute migration time reproducibilities of <1% and efficiencies ranging from 2300 to 4000 theoretical plates. Results from 139 cells are reported. A small fraction of these cells, approximately 9%, were found to enzymatically hydrolyze the loaded dyes in a manner significantly different from the majority of the cells. Cell analysis rates of 7-12 cells/min were demonstrated and are >100 times faster than those reported using standard bench-scale capillary electrophoresis.
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Affiliation(s)
- Maxine A McClain
- Oak Ridge National Laboratory, P.O. Box 2008, Oak Ridge, Tennessee 37831-6142, USA
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Oguri S, Yoneya Y. Assay and biological relevance of endogenous histamine and its metabolites: application of microseparation techniques. J Chromatogr B Analyt Technol Biomed Life Sci 2002; 781:165-79. [PMID: 12450658 DOI: 10.1016/s1570-0232(02)00534-2] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
This review provides an overview of the assay methods used to determine the presence of endogenous histamine (HA) including its metabolites, and also discusses their biological significance. Firstly, this review briefly summarizes the biological significance of HA and its biological pathways. Next, the assay methods with microseparation techniques, such as gas-chromatography (GC), liquid-chromatography (LC), capillary electrophoresis (CE) and capillary electrochromatography (CEC) are looked at from a developmental viewpoint. Finally, the use of these methods, including flow cytometry techniques, for the determination of HA and its metabolites in biological samples, such as blood, urine, brain and cells, is described. The merits and demerits associated with each of these various methods are also discussed, along with their applications.
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Affiliation(s)
- Shigeyuki Oguri
- Laboratory of Food Science, Department of Home Economics, Aichi-Gakusen University, 28 Kamikawanari, Hegoshi-Cho, Okazaki City, 444-8520, Japan.
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Cannon DM, Winograd N, Ewing AG. Quantitative chemical analysis of single cells. ANNUAL REVIEW OF BIOPHYSICS AND BIOMOLECULAR STRUCTURE 2001; 29:239-63. [PMID: 10940249 DOI: 10.1146/annurev.biophys.29.1.239] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
A fundamental perspective can be achieved by targeting single cells for analysis with the goal of deconvoluting complex biological functions. However, single-cell studies have their own difficulties, such as minute volumes and sample amounts. Quantitative chemical analysis of single cells has emerged as a powerful new area in recent years due to several technological advancements. The development of microelectrodes has allowed the measurement of redox-active species as a function of cellular dynamics. This miniaturization trend is also evident in the separation sciences with the application of small column separations to single cells. Desorption ionization methods with mass spectrometric detection have shown single-cell capability owing to numerous technological developments. Finally, fluorescence imaging has also progressed to the point where single-cell dynamics can be probed by native fluorescence utilizing either single or multiple photon excitation. The results of these studies are reviewed with an emphasis on the quantitation of single-cell dynamics.
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Affiliation(s)
- D M Cannon
- Department of Chemistry, Pennsylvania State University, University Park 16802, USA.
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Cells on the target matrix-assisted laser-desorption/ionization time-of-flight mass-spectrometric analysis of mammalian cells grown on the target. Chromatographia 1999. [DOI: 10.1007/bf02468975] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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