1
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Han Z, Porter AE. In situ Electron Microscopy of Complex Biological and Nanoscale Systems: Challenges and Opportunities. FRONTIERS IN NANOTECHNOLOGY 2020. [DOI: 10.3389/fnano.2020.606253] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
In situ imaging for direct visualization is important for physical and biological sciences. Research endeavors into elucidating dynamic biological and nanoscale phenomena frequently necessitate in situ and time-resolved imaging. In situ liquid cell electron microscopy (LC-EM) can overcome certain limitations of conventional electron microscopies and offer great promise. This review aims to examine the status-quo and practical challenges of in situ LC-EM and its applications, and to offer insights into a novel correlative technique termed microfluidic liquid cell electron microscopy. We conclude by suggesting a few research ideas adopting microfluidic LC-EM for in situ imaging of biological and nanoscale systems.
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2
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Lu X, Wang Z, Gao Y, Chen W, Wang L, Huang P, Gao W, Ke M, He A, Tian R. AutoProteome Chip System for Fully Automated and Integrated Proteomics Sample Preparation and Peptide Fractionation. Anal Chem 2020; 92:8893-8900. [DOI: 10.1021/acs.analchem.0c00752] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Xue Lu
- Department of Chemistry, Southern University of Science and Technology, Shenzhen 518055, China
| | - Zhikun Wang
- Department of Chemistry, Southern University of Science and Technology, Shenzhen 518055, China
| | - Yan Gao
- Hochuen Medical Technology Co., Ltd., Shenzhen 518109, China
| | - Wendong Chen
- Department of Chemistry, Southern University of Science and Technology, Shenzhen 518055, China
| | - Lingjue Wang
- Department of Chemistry, Southern University of Science and Technology, Shenzhen 518055, China
| | - Peiwu Huang
- Department of Chemistry, Southern University of Science and Technology, Shenzhen 518055, China
| | - Weina Gao
- Department of Chemistry, Southern University of Science and Technology, Shenzhen 518055, China
| | - Mi Ke
- Department of Chemistry, Southern University of Science and Technology, Shenzhen 518055, China
| | - An He
- Department of Chemistry, Southern University of Science and Technology, Shenzhen 518055, China
| | - Ruijun Tian
- Department of Chemistry, Southern University of Science and Technology, Shenzhen 518055, China
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3
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Ke M, Liu J, Chen W, Chen L, Gao W, Qin Y, He A, Chu B, Tang J, Xu R, Deng Y, Tian R. Integrated and Quantitative Proteomic Approach for Charting Temporal and Endogenous Protein Complexes. Anal Chem 2018; 90:12574-12583. [PMID: 30280895 DOI: 10.1021/acs.analchem.8b02667] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
| | | | | | | | | | | | | | | | - Jun Tang
- Shenzhen People’s Hospital, The Second Clinical Medical College of Jinan University, Shenzhen 518020, China
| | - Ruilian Xu
- Shenzhen People’s Hospital, The Second Clinical Medical College of Jinan University, Shenzhen 518020, China
| | - Yi Deng
- Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research, Shenzhen 518055, China
| | - Ruijun Tian
- Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research, Shenzhen 518055, China
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4
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Tan C, Xie D, Liu Y, Peng W, Li X, Ai L, Wu C, Wen C, Huang X, Guo J. Identification of Different Bile Species and Fermentation Times of Bile Arisaema Based on an Intelligent Electronic Nose and Least Squares Support Vector Machine. Anal Chem 2018; 90:3460-3466. [PMID: 29397686 DOI: 10.1021/acs.analchem.7b05189] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Fermentation is one of the most traditionally utilized methods to process the raw materials of traditional Chinese medicine (TCM). Bile Arisaema (BA) is produced by the fermentation of the roots of Arisaema heterophyllum with bile. Fermentation time and bile species are the key factors in producing BA. The study was aimed to develop a new and rapid method for the identification of different fermentation times and bile species of BA. The polysaccharide content (PC), protease activity (PA), and amylase activity (AC) of BA were determined. The changes of PC, PA, and AC were significant indicators for the evaluation of different fermentation times. On the basis of the odor data of BA obtained by electronic nose technology (E-nose), the principal component analysis (PCA) was used to identify bile species. The results were further verified by the least squares support vector machine (LS-SVM). The trained LS-SVM was also used to predict the PC, PA, and AC of the samples to identify fermentation time. The present study indicated that E-nose combined with LS-SVM could effectively predict the PC, PA, and AC of the samples and identify the bile species and fermentation time of BA, and it was proved to be a useful strategy for quality control of fermented products of TCMs.
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Affiliation(s)
- Chaoqun Tan
- College of Pharmacy , Chengdu University of Traditional Chinese Medicine , Chengdu , Sichuan 611731 , P. R. China.,Institute of Digital Medicine , Chengdu University of Traditional Chinese Medicine , Chengdu , Sichuan 611731 , P. R. China
| | - Dashuai Xie
- College of Pharmacy , Chengdu University of Traditional Chinese Medicine , Chengdu , Sichuan 611731 , P. R. China
| | - Yujie Liu
- College of Pharmacy , Chengdu University of Traditional Chinese Medicine , Chengdu , Sichuan 611731 , P. R. China
| | - Wei Peng
- College of Pharmacy , Chengdu University of Traditional Chinese Medicine , Chengdu , Sichuan 611731 , P. R. China
| | - Xinyi Li
- College of Pharmacy , Chengdu University of Traditional Chinese Medicine , Chengdu , Sichuan 611731 , P. R. China
| | - Li Ai
- College of Pharmacy , Chengdu University of Traditional Chinese Medicine , Chengdu , Sichuan 611731 , P. R. China
| | - Chunjie Wu
- College of Pharmacy , Chengdu University of Traditional Chinese Medicine , Chengdu , Sichuan 611731 , P. R. China
| | - Chuanbiao Wen
- Institute of Digital Medicine , Chengdu University of Traditional Chinese Medicine , Chengdu , Sichuan 611731 , P. R. China
| | - Xiwei Huang
- Ministry of Education Key Lab of RF Circuits and Systems , Hangzhou Dianzi University , Hangzhou , Zhejiang 310018 , China
| | - Jinhong Guo
- Institute of Digital Medicine , Chengdu University of Traditional Chinese Medicine , Chengdu , Sichuan 611731 , P. R. China.,School of Information and Communication Engineering , University of Electronic Science and Technology of China , Chengdu , Sichuan 611731 , P. R. China.,Institute of Medical Equipment , University of Electronic Science and Technology of China , Chengdu , Sichuan 611731 , P. R. China
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5
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ZHANG Q, ZHENG F, QIN WJ, QIAN XH. Preparation and Application of Novel Thermo-sensitive Matrix-based Immobilized Enzyme for Fast and Highly Efficient Proteome Research. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2016. [DOI: 10.1016/s1872-2040(16)60973-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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6
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Chen W, Wang S, Adhikari S, Deng Z, Wang L, Chen L, Ke M, Yang P, Tian R. Simple and Integrated Spintip-Based Technology Applied for Deep Proteome Profiling. Anal Chem 2016; 88:4864-71. [PMID: 27062885 DOI: 10.1021/acs.analchem.6b00631] [Citation(s) in RCA: 91] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Great efforts have been taken for developing high-sensitive mass spectrometry (MS)-based proteomic technologies, among which sample preparation is one of the major focus. Here, a simple and integrated spintip-based proteomics technology (SISPROT) consisting of strong cation exchange beads and C18 disk in one pipet tip was developed. Both proteomics sample preparation steps, including protein preconcentration, reduction, alkylation, and digestion, and reversed phase (RP)-based desalting and high-pH RP-based peptide fractionation can be achieved in a fully integrated manner for the first time. This easy-to-use technology achieved high sensitivity with negligible sample loss. Proteomic analysis of 2000 HEK 293 cells readily identified 1270 proteins within 1.4 h of MS time, while 7826 proteins were identified when 100000 cells were processed and analyzed within only 22 h of MS time. More importantly, the SISPROT can be easily multiplexed on a standard centrifuge with good reproducibility (Pearson correlation coefficient > 0.98) for both single-shot analysis and deep proteome profiling with five-step high-pH RP fractionation. The SISPROT was exemplified by the triplicate analysis of 100000 stem cells from human exfoliated deciduous teeth (SHED). This led to the identification of 9078 proteins containing 3771 annotated membrane proteins, which was the largest proteome data set for dental stem cells reported to date. We expect that the SISPROT will be well suited for deep proteome profiling for fewer than 100000 cells and applied for translational studies where multiplexed technology with good label-free quantification precision is required.
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Affiliation(s)
- Wendong Chen
- Department of Chemistry, Fudan University , Shanghai 200433, China
| | - Shuai Wang
- ENT Institute of Shenzhen University, Shenzhen Longgang ENT Hospital , Shenzhen 518172, China
| | | | - Zuhui Deng
- ENT Institute of Shenzhen University, Shenzhen Longgang ENT Hospital , Shenzhen 518172, China
| | | | | | | | - Pengyuan Yang
- Department of Chemistry, Fudan University , Shanghai 200433, China
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7
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Zhao Q, Fang F, Wu C, Wu Q, Liang Y, Liang Z, Zhang L, Zhang Y. imFASP: An integrated approach combining in-situ filter-aided sample pretreatment with microwave-assisted protein digestion for fast and efficient proteome sample preparation. Anal Chim Acta 2016; 912:58-64. [DOI: 10.1016/j.aca.2016.01.049] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Revised: 01/21/2016] [Accepted: 01/27/2016] [Indexed: 01/02/2023]
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8
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Liu Y, Yan G, Gao M, Deng C, Zhang X. Integrated system for extraction, purification, and digestion of membrane proteins. Anal Bioanal Chem 2016; 408:3495-502. [PMID: 26922343 DOI: 10.1007/s00216-016-9427-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Revised: 01/26/2016] [Accepted: 02/16/2016] [Indexed: 11/29/2022]
Abstract
An integrated system was developed for directly processing living cells into peptides of membrane proteins. Living cells were directly injected into the system and cracked in a capillary column by ultrasonic treatment. Owing to hydrophilicity for broken pieces of the cell membrane, the obtained membranes were retained in a well-designed bi-filter. While cytoplasm proteins were eluted from the bi-filter, the membranes were dissolved and protein released by flushing 4% SDS buffer through the bi-filter. The membrane proteins were subsequently transferred into a micro-reactor and covalently bound in the reactor for purification and digestion. As the system greatly simplified the whole pretreatment processes and minimized both sample loss and contamination, it could be used to analyze the membrane proteome samples of thousand-cell-scales with acceptable reliability and stability. We totally identified 1348 proteins from 5000 HepG2 cells, 615 of which were annotated as membrane proteins. In contrast, with conventional method, only 233 membrane proteins were identified. It is adequately demonstrated that the integrated system shows promising practicability for the membrane proteome analysis of small amount of cells.
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Affiliation(s)
- Yiying Liu
- Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200433, China
| | - Guoquan Yan
- Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200433, China
| | - Mingxia Gao
- Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200433, China
| | - Chunhui Deng
- Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200433, China
| | - Xiangmin Zhang
- Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200433, China.
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9
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Feng X, Liu BF, Li J, Liu X. Advances in coupling microfluidic chips to mass spectrometry. MASS SPECTROMETRY REVIEWS 2015; 34:535-57. [PMID: 24399782 DOI: 10.1002/mas.21417] [Citation(s) in RCA: 87] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2013] [Revised: 11/07/2013] [Accepted: 11/07/2013] [Indexed: 05/26/2023]
Abstract
Microfluidic technology has shown advantages of low sample consumption, reduced analysis time, high throughput, and potential for integration and automation. Coupling microfluidic chips to mass spectrometry (Chip-MS) can greatly improve the overall analytical performance of MS-based approaches and expand their potential applications. In this article, we review the advances of Chip-MS in the past decade, covering innovations in microchip fabrication, microchips coupled to electrospray ionization (ESI)-MS and matrix-assisted laser desorption/ionization (MALDI)-MS. Development of integrated microfluidic systems for automated MS analysis will be further documented, as well as recent applications of Chip-MS in proteomics, metabolomics, cell analysis, and clinical diagnosis.
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MESH Headings
- Animals
- Chromatography, Liquid/instrumentation
- Chromatography, Liquid/methods
- Electrophoresis, Microchip/instrumentation
- Electrophoresis, Microchip/methods
- Equipment Design
- Humans
- Lab-On-A-Chip Devices
- Lipids/analysis
- Metabolomics/instrumentation
- Metabolomics/methods
- Polysaccharides/analysis
- Proteins/analysis
- Proteomics/instrumentation
- Proteomics/methods
- 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)
- Xiaojun Feng
- Britton Chance Center for Biomedical Photonics at Wuhan National Laboratory for Optoelectronics-Hubei Bioinformatics and Molecular Imaging Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Bi-Feng Liu
- Britton Chance Center for Biomedical Photonics at Wuhan National Laboratory for Optoelectronics-Hubei Bioinformatics and Molecular Imaging Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Jianjun Li
- Human Health Therapeutics, National Research Council Canada, Ottawa, Ontario, Canada K1A 0R6
| | - Xin Liu
- Britton Chance Center for Biomedical Photonics at Wuhan National Laboratory for Optoelectronics-Hubei Bioinformatics and Molecular Imaging Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
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10
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Krisp C, Yang H, van Soest R, Molloy MP. Online Peptide fractionation using a multiphasic microfluidic liquid chromatography chip improves reproducibility and detection limits for quantitation in discovery and targeted proteomics. Mol Cell Proteomics 2015; 14:1708-19. [PMID: 25850434 DOI: 10.1074/mcp.m114.046425] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Indexed: 12/19/2022] Open
Abstract
Comprehensive proteomic profiling of biological specimens usually requires multidimensional chromatographic peptide fractionation prior to mass spectrometry. However, this approach can suffer from poor reproducibility because of the lack of standardization and automation of the entire workflow, thus compromising performance of quantitative proteomic investigations. To address these variables we developed an online peptide fractionation system comprising a multiphasic liquid chromatography (LC) chip that integrates reversed phase and strong cation exchange chromatography upstream of the mass spectrometer (MS). We showed superiority of this system for standardizing discovery and targeted proteomic workflows using cancer cell lysates and nondepleted human plasma. Five-step multiphase chip LC MS/MS acquisition showed clear advantages over analyses of unfractionated samples by identifying more peptides, consuming less sample and often improving the lower limits of quantitation, all in highly reproducible, automated, online configuration. We further showed that multiphase chip LC fractionation provided a facile means to detect many N- and C-terminal peptides (including acetylated N terminus) that are challenging to identify in complex tryptic peptide matrices because of less favorable ionization characteristics. Given as much as 95% of peptides were detected in only a single salt fraction from cell lysates we exploited this high reproducibility and coupled it with multiple reaction monitoring on a high-resolution MS instrument (MRM-HR). This approach increased target analyte peak area and improved lower limits of quantitation without negatively influencing variance or bias. Further, we showed a strategy to use multiphase LC chip fractionation LC-MS/MS for ion library generation to integrate with SWATH(TM) data-independent acquisition quantitative workflows. All MS data are available via ProteomeXchange with identifier PXD001464.
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Affiliation(s)
- Christoph Krisp
- From the ‡Australian Proteome Analysis Facility (APAF), Department of Chemistry and Biomolecular Sciences, Macquarie University, 2109, Sydney, Australia
| | - Hao Yang
- §Eksigent, part of AB SCIEX, 94065, Redwood City, California
| | - Remco van Soest
- §Eksigent, part of AB SCIEX, 94065, Redwood City, California
| | - Mark P Molloy
- From the ‡Australian Proteome Analysis Facility (APAF), Department of Chemistry and Biomolecular Sciences, Macquarie University, 2109, Sydney, Australia;
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11
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Li J, Zhou L, Wang H, Yan H, Li N, Zhai R, Jiao F, Hao F, Jin Z, Tian F, Peng B, Zhang Y, Qian X. A new sample preparation method for the absolute quantitation of a target proteome using 18O labeling combined with multiple reaction monitoring mass spectrometry. Analyst 2015; 140:1281-90. [DOI: 10.1039/c4an02092h] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
A new sample preparation method for target proteome absolute quantitation using 18O labeling-MRM MS.
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12
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Butt A, Farrukh A, Ghaffar A, Duran H, Oluz Z, ur Rehman H, Hussain T, Ahmad R, Tahir A, Yameen B. Design of enzyme-immobilized polymer brush-grafted magnetic nanoparticles for efficient nematicidal activity. RSC Adv 2015. [DOI: 10.1039/c5ra10063a] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Parasitic nematodes adversely affect agricultural industry and global health. An efficient and reusable nematicidal platform is developed by immobilization enzyme on the surface of magnetic NPs.
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Affiliation(s)
- A. Butt
- Department of Chemistry
- SBA School of Science and Engineering
- Lahore University of Management Sciences
- Lahore-54792
- Pakistan
| | - A. Farrukh
- Max-Planck-Institut für Polymerforschung
- 55128 Mainz
- Germany
| | - A. Ghaffar
- Department of Chemistry
- University of Engineering and Technology
- Lahore
- Pakistan
| | - H. Duran
- Department of Materials Science & Nanotechnology Engineering
- TOBB University of Economics and Technology
- 06560 Ankara
- Turkey
| | - Z. Oluz
- Department of Materials Science & Nanotechnology Engineering
- TOBB University of Economics and Technology
- 06560 Ankara
- Turkey
| | - H. ur Rehman
- Department of Chemistry
- SBA School of Science and Engineering
- Lahore University of Management Sciences
- Lahore-54792
- Pakistan
| | - T. Hussain
- The Centre for Advanced Studies in Physics (CASP)
- GC University
- Lahore
- Pakistan
| | - R. Ahmad
- The Centre for Advanced Studies in Physics (CASP)
- GC University
- Lahore
- Pakistan
| | - A. Tahir
- Department of Environmental Sciences
- Lahore College for Women University
- Lahore
- Pakistan
| | - B. Yameen
- Department of Chemistry
- SBA School of Science and Engineering
- Lahore University of Management Sciences
- Lahore-54792
- Pakistan
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13
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Abstract
Sample preparation has lagged far behind the evolution of instrumentation used in mass-linked protein analysis. Trypsin digestion, for example, still takes a day, as it did 50 years ago, while mass spectral analyses are achieved in seconds. Higher order structure of proteins is frequently modified by varying digestion conditions: shifting the initial points of trypsin cleavage, changing digestion pathways, accelerating peptide bond demasking and altering the distribution of miscleaved products at the completion of proteolysis. Reduction and alkylation are even circumvented in many cases. This review focuses on immobilized enzyme reactor technology as a means to achieve accelerated trypsin digestion by exploiting these phenomena.
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14
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Jarvas G, Grym J, Foret F, Guttman A. Simulation-based design of a microfabricated pneumatic electrospray nebulizer. Electrophoresis 2014; 36:386-92. [PMID: 25257095 DOI: 10.1002/elps.201400387] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2014] [Revised: 09/11/2014] [Accepted: 09/11/2014] [Indexed: 11/08/2022]
Abstract
A microfabricated pneumatic electrospray nebulizer has been developed and evaluated using computer simulations and experimental measurements of the MS signals. The microdevice under development is designed for electrospray MS interfacing without the need to fabricate an electrospray needle and can be used as a disposable or an integral part of a reusable system. The design of the chip layout was supported by computational fluid dynamics simulations. The tested microdevices were fabricated in glass using conventional photolithography, followed by wet chemical etching and thermal bonding. The performance of the microfabricated nebulizer was evaluated by means of TOF-MS with a peptide mixture. It was demonstrated that the nebulizer, operating at supersonic speed of the nebulizing gas, produced very stable nanospray (900 nL/min) as documented by less than 0.1% (SE) fluctuation in total mass spectrometric signal intensity.
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Affiliation(s)
- Gabor Jarvas
- CEITEC - Central European Institute of Technology, Brno, Czech Republic; MTA-PE Translational Glycomics Research Group, MUKKI, University of Pannonia, Veszprem, Hungary
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15
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Fan C, Shi Z, Pan Y, Song Z, Zhang W, Zhao X, Tian F, Peng B, Qin W, Cai Y, Qian X. Dual Matrix-Based Immobilized Trypsin for Complementary Proteolytic Digestion and Fast Proteomics Analysis with Higher Protein Sequence Coverage. Anal Chem 2014; 86:1452-8. [DOI: 10.1021/ac402696b] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Chao Fan
- National
Center for Protein Sciences Beijing, State Key Laboratory of Proteomics,
Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 102206, China
- Graduate School of Anhui Medical University, Hefei, Chian
| | - Zhaomei Shi
- National
Center for Protein Sciences Beijing, State Key Laboratory of Proteomics,
Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 102206, China
- Graduate School of Anhui Medical University, Hefei, Chian
| | - Yiting Pan
- National
Center for Protein Sciences Beijing, State Key Laboratory of Proteomics,
Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 102206, China
| | - Zifeng Song
- National
Center for Protein Sciences Beijing, State Key Laboratory of Proteomics,
Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 102206, China
| | - Wanjun Zhang
- National
Center for Protein Sciences Beijing, State Key Laboratory of Proteomics,
Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 102206, China
| | - Xinyuan Zhao
- National
Center for Protein Sciences Beijing, State Key Laboratory of Proteomics,
Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 102206, China
| | - Fang Tian
- National
Center for Protein Sciences Beijing, State Key Laboratory of Proteomics,
Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 102206, China
| | - Bo Peng
- National
Center for Protein Sciences Beijing, State Key Laboratory of Proteomics,
Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 102206, China
| | - Weijie Qin
- National
Center for Protein Sciences Beijing, State Key Laboratory of Proteomics,
Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 102206, China
| | - Yun Cai
- National
Center for Protein Sciences Beijing, State Key Laboratory of Proteomics,
Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 102206, China
| | - Xiaohong Qian
- National
Center for Protein Sciences Beijing, State Key Laboratory of Proteomics,
Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 102206, China
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16
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Choi JW, Lee S, Lee DH, Kim J, deMello AJ, Chang SI. Integrated pneumatic micro-pumps for high-throughput droplet-based microfluidics. RSC Adv 2014. [DOI: 10.1039/c4ra02033b] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Droplet-based microfluidic systems have recently emerged as powerful experimental tools in the chemical and biological sciences.
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Affiliation(s)
- Jae-Won Choi
- Department of Biochemistry
- Chungbuk National University
- Cheongju 361-763, Republic of Korea
| | - Sangmin Lee
- Department of Mechanical Engineering
- Pohang University of Science and Technology
- Pohang 790-784, Republic of Korea
| | - Dong-Hun Lee
- Department of Microbiology
- Chungbuk National University
- Cheongju 361-763, Republic of Korea
| | - Joonwon Kim
- Department of Mechanical Engineering
- Pohang University of Science and Technology
- Pohang 790-784, Republic of Korea
| | - Andrew J. deMello
- Department of Chemistry and Applied Biosciences
- ETH Zürich
- Zürich CH-8093, Switzerland
| | - Soo-Ik Chang
- Department of Biochemistry
- Chungbuk National University
- Cheongju 361-763, Republic of Korea
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17
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He X, Chen Q, Zhang Y, Lin JM. Recent advances in microchip-mass spectrometry for biological analysis. Trends Analyt Chem 2014. [DOI: 10.1016/j.trac.2013.09.013] [Citation(s) in RCA: 76] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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18
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Mayne J, Starr AE, Ning Z, Chen R, Chiang CK, Figeys D. Fine Tuning of Proteomic Technologies to Improve Biological Findings: Advancements in 2011–2013. Anal Chem 2013; 86:176-95. [DOI: 10.1021/ac403551f] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Janice Mayne
- Ottawa Institute of
Systems Biology, Department of Biochemistry, Microbiology
and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, ON, Canada K1H8M5
| | - Amanda E. Starr
- Ottawa Institute of
Systems Biology, Department of Biochemistry, Microbiology
and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, ON, Canada K1H8M5
| | - Zhibin Ning
- Ottawa Institute of
Systems Biology, Department of Biochemistry, Microbiology
and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, ON, Canada K1H8M5
| | - Rui Chen
- Ottawa Institute of
Systems Biology, Department of Biochemistry, Microbiology
and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, ON, Canada K1H8M5
| | - Cheng-Kang Chiang
- Ottawa Institute of
Systems Biology, Department of Biochemistry, Microbiology
and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, ON, Canada K1H8M5
| | - Daniel Figeys
- Ottawa Institute of
Systems Biology, Department of Biochemistry, Microbiology
and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, ON, Canada K1H8M5
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19
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Reverse PCA, a systematic approach for identifying genes important for the physical interaction between protein pairs. PLoS Genet 2013; 9:e1003838. [PMID: 24130505 PMCID: PMC3794912 DOI: 10.1371/journal.pgen.1003838] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2013] [Accepted: 08/13/2013] [Indexed: 12/26/2022] Open
Abstract
Protein-protein interactions (PPIs) are of central importance for many areas of biological research. Several complementary high-throughput technologies have been developed to study PPIs. The wealth of information that emerged from these technologies led to the first maps of the protein interactomes of several model organisms. Many changes can occur in protein complexes as a result of genetic and biochemical perturbations. In the absence of a suitable assay, such changes are difficult to identify, and thus have been poorly characterized. In this study, we present a novel genetic approach (termed “reverse PCA”) that allows the identification of genes whose products are required for the physical interaction between two given proteins. Our assay starts with a yeast strain in which the interaction between two proteins of interest can be detected by resistance to the drug, methotrexate, in the context of the protein-fragment complementation assay (PCA). Using synthetic genetic array (SGA) technology, we can systematically screen mutant libraries of the yeast Saccharomyces cerevisiae to identify those mutations that disrupt the physical interaction of interest. We were able to successfully validate this novel approach by identifying mutants that dissociate the conserved interaction between Cia2 and Mms19, two proteins involved in Iron-Sulfur protein biogenesis and genome stability. This method will facilitate the study of protein structure-function relationships, and may help in elucidating the mechanisms that regulate PPIs. Protein–protein interactions (PPI) occur when two or more proteins bind together to form large molecular machines. The importance of PPIs led to the development of multitude technologies to detect them, and to the first maps of the protein interactomes. One important challenge in biology is to understand how protein complexes respond to genetic perturbations; however, in the absence of a suitable assay, such changes have been poorly characterized. Here, we present a novel systematic genetic approach (termed “reverse PCA”), that demonstrates how the yeast protein complementation assay (PCA), coupled with the synthetic genetic array (SGA) technology may be used to study the modulation of protein–protein interactions in-vivo in response to genetic perturbations. Our assay starts with a yeast strain in which the interaction between given proteins can be detected by resistance to the drug, methotrexate. Using the SGA technology, we can systematically identify yeast mutants that reverse this interaction. We were able to successfully validate this approach by identifying mutants that dissociate the conserved interaction between Cia2 and Mms19, two proteins involved in Iron-Sulfur protein biogenesis and genome stability. This method will facilitate the study of protein structure-function relationships, and elucidate the mechanisms that regulate PPIs.
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20
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SONG Z, ZHANG Q, ZHANG Y, QIN W, QIAN X. Trypsin immobilization on silica beads modified by squamous polymer for ultra fast and highly efficient proteome digestion. Se Pu 2013; 30:549-54. [DOI: 10.3724/sp.j.1123.2012.02006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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21
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Zhao Q, Liang Y, Yuan H, Sui Z, Wu Q, Liang Z, Zhang L, Zhang Y. Biphasic Microreactor for Efficient Membrane Protein Pretreatment with a Combination of Formic Acid Assisted Solubilization, On-Column pH Adjustment, Reduction, Alkylation, and Tryptic Digestion. Anal Chem 2013; 85:8507-12. [DOI: 10.1021/ac402076u] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Qun Zhao
- National Chromatographic R. & A. Center, Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian 116023, China
- University of Chinese Academy of Sciences, Beijing 100039, China
| | - Yu Liang
- National Chromatographic R. & A. Center, Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian 116023, China
| | - Huiming Yuan
- National Chromatographic R. & A. Center, Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian 116023, China
| | - Zhigang Sui
- National Chromatographic R. & A. Center, Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian 116023, China
| | - Qi Wu
- National Chromatographic R. & A. Center, Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian 116023, China
- University of Chinese Academy of Sciences, Beijing 100039, China
| | - Zhen Liang
- National Chromatographic R. & A. Center, Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian 116023, China
| | - Lihua Zhang
- National Chromatographic R. & A. Center, Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian 116023, China
| | - Yukui Zhang
- National Chromatographic R. & A. Center, Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian 116023, China
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22
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Kim JY, Lee SY, Kim SK, Park SR, Kang D, Moon MH. Development of an Online Microbore Hollow Fiber Enzyme Reactor Coupled with Nanoflow Liquid Chromatography-Tandem Mass Spectrometry for Global Proteomics. Anal Chem 2013; 85:5506-13. [DOI: 10.1021/ac400625k] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Jin Yong Kim
- Department of Chemistry, Yonsei University, Seoul, 120-749, Korea
| | - Sun Young Lee
- Center for Bioanalysis, Division
of Metrology for Quality of Life, Korea Research Institute of Standards and Science, Daejeon, 305-340, Korea
| | - Sook-Kyung Kim
- Center for Bioanalysis, Division
of Metrology for Quality of Life, Korea Research Institute of Standards and Science, Daejeon, 305-340, Korea
| | - Sang Ryoul Park
- Center for Bioanalysis, Division
of Metrology for Quality of Life, Korea Research Institute of Standards and Science, Daejeon, 305-340, Korea
| | - Dukjin Kang
- Center for Bioanalysis, Division
of Metrology for Quality of Life, Korea Research Institute of Standards and Science, Daejeon, 305-340, Korea
| | - Myeong Hee Moon
- Department of Chemistry, Yonsei University, Seoul, 120-749, Korea
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23
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Recent Progresses in Optical Colorimetric/Fluorometric Sensor Array. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2013. [DOI: 10.1016/s1872-2040(13)60658-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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24
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Nge PN, Rogers CI, Woolley AT. Advances in microfluidic materials, functions, integration, and applications. Chem Rev 2013; 113:2550-83. [PMID: 23410114 PMCID: PMC3624029 DOI: 10.1021/cr300337x] [Citation(s) in RCA: 519] [Impact Index Per Article: 47.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Pamela N. Nge
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT 84602
| | - Chad I. Rogers
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT 84602
| | - Adam T. Woolley
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT 84602
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25
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Quantitative microfluidic biomolecular analysis for systems biology and medicine. Anal Bioanal Chem 2013; 405:5743-58. [PMID: 23568613 DOI: 10.1007/s00216-013-6930-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2013] [Revised: 03/10/2013] [Accepted: 03/19/2013] [Indexed: 12/12/2022]
Abstract
In the postgenome era, biology and medicine are rapidly evolving towards quantitative and systems studies of complex biological systems. Emerging breakthroughs in microfluidic technologies and innovative applications are transforming systems biology by offering new capabilities to address the challenges in many areas, such as single-cell genomics, gene regulation networks, and pathology. In this review, we focus on recent progress in microfluidic technology from the perspective of its applications to promoting quantitative and systems biomolecular analysis in biology and medicine.
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26
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LIU J, WANG FJ, ZHANG ZB, ZOU HF. Reversed Phase Monolithic Column Based Enzyme Reactor for Protein Analysis. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2013. [DOI: 10.1016/s1872-2040(13)60619-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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27
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Choi JW, Kang DK, Park H, deMello AJ, Chang SI. High-Throughput Analysis of Protein–Protein Interactions in Picoliter-Volume Droplets Using Fluorescence Polarization. Anal Chem 2012; 84:3849-54. [DOI: 10.1021/ac300414g] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Jae-Won Choi
- Department of Biochemistry, Chungbuk National University, Cheongju 361-763, Republic
of Korea,
| | - Dong-Ku Kang
- Department of Biochemistry, Chungbuk National University, Cheongju 361-763, Republic
of Korea,
- Department of
Chemistry, Imperial College London, London
SW7 2AZ, United Kingdom,
| | - Hyun Park
- Department of Biochemistry, Chungbuk National University, Cheongju 361-763, Republic
of Korea,
| | - Andrew J. deMello
- Department of Chemistry and Applied Biosciences, ETH Zürich, Zürich CH-8093, Switzerland
| | - Soo-Ik Chang
- Department of Biochemistry, Chungbuk National University, Cheongju 361-763, Republic
of Korea,
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28
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Gorbatsova J, Borissova M, Kaljurand M. Electrowetting-on-dielectric actuation of droplets with capillary electrophoretic zones for off-line mass spectrometric analysis. J Chromatogr A 2012; 1234:9-15. [DOI: 10.1016/j.chroma.2011.12.052] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2011] [Revised: 11/21/2011] [Accepted: 12/16/2011] [Indexed: 01/03/2023]
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29
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Qin W, Song Z, Fan C, Zhang W, Cai Y, Zhang Y, Qian X. Trypsin Immobilization on Hairy Polymer Chains Hybrid Magnetic Nanoparticles for Ultra Fast, Highly Efficient Proteome Digestion, Facile 18O Labeling and Absolute Protein Quantification. Anal Chem 2012; 84:3138-44. [DOI: 10.1021/ac2029216] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Weijie Qin
- State Key Laboratory of Proteomics, Beijing Proteome
Research Center, Beijing Institute of Radiation Medicine, No. 33 Life Science Park Road, Changping District, Beijing 102206,
P. R. China
| | - Zifeng Song
- State Key Laboratory of Proteomics, Beijing Proteome
Research Center, Beijing Institute of Radiation Medicine, No. 33 Life Science Park Road, Changping District, Beijing 102206,
P. R. China
| | - Chao Fan
- State Key Laboratory of Proteomics, Beijing Proteome
Research Center, Beijing Institute of Radiation Medicine, No. 33 Life Science Park Road, Changping District, Beijing 102206,
P. R. China
| | - Wanjun Zhang
- State Key Laboratory of Proteomics, Beijing Proteome
Research Center, Beijing Institute of Radiation Medicine, No. 33 Life Science Park Road, Changping District, Beijing 102206,
P. R. China
| | - Yun Cai
- State Key Laboratory of Proteomics, Beijing Proteome
Research Center, Beijing Institute of Radiation Medicine, No. 33 Life Science Park Road, Changping District, Beijing 102206,
P. R. China
| | - Yangjun Zhang
- State Key Laboratory of Proteomics, Beijing Proteome
Research Center, Beijing Institute of Radiation Medicine, No. 33 Life Science Park Road, Changping District, Beijing 102206,
P. R. China
| | - Xiaohong Qian
- State Key Laboratory of Proteomics, Beijing Proteome
Research Center, Beijing Institute of Radiation Medicine, No. 33 Life Science Park Road, Changping District, Beijing 102206,
P. R. China
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30
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Kovarik ML, Gach PC, Ornoff DM, Wang Y, Balowski J, Farrag L, Allbritton NL. Micro total analysis systems for cell biology and biochemical assays. Anal Chem 2012; 84:516-40. [PMID: 21967743 PMCID: PMC3264799 DOI: 10.1021/ac202611x] [Citation(s) in RCA: 180] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Michelle L. Kovarik
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Phillip C. Gach
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Douglas M. Ornoff
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599
- Department of Pharmacology, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Yuli Wang
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Joseph Balowski
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Lila Farrag
- School of Medicine, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Nancy L. Allbritton
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599
- Department of Biomedical Engineering, University of North Carolina, Chapel Hill, NC 27599 and North Carolina State University, Raleigh, NC 27695
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31
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Abstract
Proteomic analysis requires the combination of an extensive suite of technologies including protein processing and separation, micro-flow HPLC, MS and bioinformatics. Although proteomic technologies are still in flux, approaches that bypass gel electrophoresis (gel-free approaches) are dominating the field of proteomics. Along with the development of gel-free proteomics, came the development of devices for the processing of proteomic samples termed proteomic reactors. These microfluidic devices provide rapid, robust and efficient pre-MS sample procession by performing protein sample preparation/concentration, digestion and peptide fractionation. The proteomic reactor has advanced in two major directions: immobilized enzyme reactor and ion exchange-based proteomic reactor. This review summarizes the technical developments and biological applications of the proteomic reactor over the last decade.
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Affiliation(s)
- Hu Zhou
- Ottawa Institute of Systems Biology (OISB), University of Ottawa, Ottawa, ON, Canada
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