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Lazar IM, Deng J, Smith N. Fast Enzymatic Processing of Proteins for MS Detection with a Flow-through Microreactor. J Vis Exp 2016:e53564. [PMID: 27078683 DOI: 10.3791/53564] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
The vast majority of mass spectrometry (MS)-based protein analysis methods involve an enzymatic digestion step prior to detection, typically with trypsin. This step is necessary for the generation of small molecular weight peptides, generally with MW < 3,000-4,000 Da, that fall within the effective scan range of mass spectrometry instrumentation. Conventional protocols involve O/N enzymatic digestion at 37 ºC. Recent advances have led to the development of a variety of strategies, typically involving the use of a microreactor with immobilized enzymes or of a range of complementary physical processes that reduce the time necessary for proteolytic digestion to a few minutes (e.g., microwave or high-pressure). In this work, we describe a simple and cost-effective approach that can be implemented in any laboratory for achieving fast enzymatic digestion of a protein. The protein (or protein mixture) is adsorbed on C18-bonded reversed-phase high performance liquid chromatography (HPLC) silica particles preloaded in a capillary column, and trypsin in aqueous buffer is infused over the particles for a short period of time. To enable on-line MS detection, the tryptic peptides are eluted with a solvent system with increased organic content directly in the MS ion source. This approach avoids the use of high-priced immobilized enzyme particles and does not necessitate any aid for completing the process. Protein digestion and complete sample analysis can be accomplished in less than ~3 min and ~30 min, respectively.
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Nakagawa K, Tamura A, Chaiya C. Preparation of proteolytic microreactors by freeze-drying immobilization. Chem Eng Sci 2014. [DOI: 10.1016/j.ces.2014.07.054] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Yamaguchi H, Miyazaki M. Enzyme-immobilized reactors for rapid and efficient sample preparation in MS-based proteomic studies. Proteomics 2013; 13:457-66. [DOI: 10.1002/pmic.201200272] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2012] [Revised: 11/03/2012] [Accepted: 11/14/2012] [Indexed: 11/11/2022]
Affiliation(s)
- Hiroshi Yamaguchi
- Liberal Arts Education Center; Tokai University; Minamiaso Kumamoto Japan
| | - Masaya Miyazaki
- Measurement Solution Research Center; National Institute of Advanced Industrial Science and Technology; Tosu Saga Japan
- Interdisciplinary Graduate School of Engineering Science; Kyushu University; Kasuga Fukuoka Japan
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Fiddes LK, Luk VN, Au SH, Ng AHC, Luk V, Kumacheva E, Wheeler AR. Hydrogel discs for digital microfluidics. BIOMICROFLUIDICS 2012; 6:14112-1411211. [PMID: 22662096 PMCID: PMC3365348 DOI: 10.1063/1.3687381] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2011] [Accepted: 01/27/2012] [Indexed: 05/10/2023]
Abstract
Hydrogels are networks of hydrophilic polymer chains that are swollen with water, and they are useful for a wide range of applications because they provide stable niches for immobilizing proteins and cells. We report here the marriage of hydrogels with digital microfluidic devices. Until recently, digital microfluidics, a fluid handling technique in which discrete droplets are manipulated electromechanically on the surface of an array of electrodes, has been used only for homogeneous systems involving liquid reagents. Here, we demonstrate for the first time that the cylindrical hydrogel discs can be incorporated into digital microfluidic systems and that these discs can be systematically addressed by droplets of reagents. Droplet movement is observed to be unimpeded by interaction with the gel discs, and gel discs remain stationary when droplets pass through them. Analyte transport into gel discs is observed to be identical to diffusion in cases in which droplets are incubated with gels passively, but transport is enhanced when droplets are continually actuated through the gels. The system is useful for generating integrated enzymatic microreactors and for three-dimensional cell culture. This paper demonstrates a new combination of techniques for lab-on-a-chip systems which we propose will be useful for a wide range of applications.
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Yamaguchi H, Miyazaki M, Maeda H. Limited proteolysis in proteomics using protease-immobilized microreactors. Methods Mol Biol 2012; 815:187-198. [PMID: 22130993 DOI: 10.1007/978-1-61779-424-7_15] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Proteolysis is the key step for proteomic studies integrated with MS analysis. Compared with the conventional method of in-solution digestion, proteolysis by a protease-immobilized microreactor has a number of advantages for proteomic analysis; i.e., rapid and efficient digestion, elimination of a purification step of the digests prior to MS, and high stability against a chemical or thermal denaturant. This chapter describes the preparation of the protease-immobilized microreactors and proteolysis performance of these microreactors. Immobilization of proteases by the formation of a polymeric membrane consisting solely of protease-proteins on the inner wall of the microchannel is performed. This was realized either by a cross-linking reaction in a laminar flow between lysine residues sufficiently present on the protein surfaces themselves or in the case of acidic proteins by mixing them with poly-lysine prior to the crosslink-reaction. The present procedure is simple and widely useful not only for proteases but also for several other enzymes.
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Affiliation(s)
- Hiroshi Yamaguchi
- Measurement Solution Research Center, National Institute of Advanced Industrial Science and Technology, Tosu, Saga, Japan
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Forster S, McArthur SL. Stable low-fouling plasma polymer coatings on polydimethylsiloxane. BIOMICROFLUIDICS 2012; 6:36504. [PMID: 24062864 PMCID: PMC3470602 DOI: 10.1063/1.4754600] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2012] [Accepted: 09/10/2012] [Indexed: 05/15/2023]
Abstract
Polydimethylsiloxane (DMS) is a popular material for microfluidics, but it is hydrophobic and is prone to non-specific protein adsorption. In this study, we explore methods for producing stable, protein resistant, tetraglyme plasma polymer coatings on PDMS by combining extended baking processes with multiple plasma polymer coating steps. We demonstrate that by using this approach, it is possible to produce a plasma polymer coatings that resist protein adsorption (<10 ng/cm(2)) and are stable to storage over at least 100 days. This methodology can translate to any plasma polymer system, enabling the introduction of a wide range of surface functionalities on PDMS surfaces.
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Affiliation(s)
- S Forster
- Department of Engineering Materials, Kroto Research Institute, University of Sheffield, Sheffield Biotactical Engineering Group, IRIS, Faculty of Engineering and Industrial Sciences, Swinburne University of Technology, Hawthorn 3122, Australia
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Pereira-Medrano AG, Forster S, Fowler GJS, McArthur SL, Wright PC. Rapid fabrication of glass/PDMS hybrid µIMER for high throughput membrane proteomics. LAB ON A CHIP 2010; 10:3397-406. [PMID: 20949197 DOI: 10.1039/c0lc00147c] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Mass spectrometry (MS) based proteomics has brought a radical approach to systems biology, offering a platform to study complex biological functions. However, key proteomic technical challenges remain, mainly the inability to characterise the complete proteome of a cell due to the thousands of diverse, complex proteins expressed at an extremely wide concentration range. Currently, high throughput and efficient techniques to unambiguously identify and quantify proteins on a proteome-wide scale are in demand. Miniaturised analytical systems placed upstream of MS help us to attain these goals. One time-consuming step in traditional techniques is the in-solution digestion of proteins (4-20 h). This also has other drawbacks, including enzyme autoproteolysis, low efficiency, and manual operation. Furthermore, the identification of α-helical membrane proteins has remained a challenge due to their high hydrophobicity and lack of trypsin cleavage targets in transmembrane helices. We demonstrate a new rapidly produced glass/PDMS micro Immobilised Enzyme Reactor (µIMER) with enzymes covalently immobilised onto polyacrylic acid plasma-modified surfaces for the purpose of rapidly (as low as 30 s) generating peptides suitable for MS analysis. This µIMER also allows, for the first time, rapid digestion of insoluble proteins. Membrane protein identification through this method was achieved after just 4 min digestion time, up to 9-fold faster than either dual-stage in-solution digestion approaches or other commonly used bacterial membrane proteomic workflows.
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Affiliation(s)
- Ana G Pereira-Medrano
- Biological and Environmental Systems Group, ChELSI Institute, Chemical and Biological Engineering, The University of Sheffield, Mappin Street, Sheffield, S1 3JD, UK
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Yamaguchi H, Miyazaki M, Honda T, Briones-Nagata MP, Arima K, Maeda H. Rapid and efficient proteolysis for proteomic analysis by protease-immobilized microreactor. Electrophoresis 2009; 30:3257-64. [PMID: 19722210 DOI: 10.1002/elps.200900134] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Proteolysis is an important part of protein identification in proteomics analysis. The conventional method of in-solution digestion of proteins is time-consuming and has limited sensitivity. In this study, trypsin- or alpha-chymotrypsin-immobilized microreactors prepared by a microfluidics-based enzyme-immobilization technique were studied for rapid sample preparation in proteomic analysis. The kinetic studies for hydrolysis of substrate by microreactors revealed that immobilized proteases had higher hydrolytic efficiency than those performed by in-solution digestion. The performance of the microreactors was evaluated by digesting cytochrome c and BSA. Protein digestion was achieved within a short period of time (approximately 5 min) at 30 degrees C without any complicated reduction and alkylation procedures. The efficiency of digestion by trypsin-immobilized reactor was evaluated by analyzing the sequence coverage, which was 47 and 12% for cytochrome c and BSA, respectively. These values were higher than those performed by in-solution digestion. Besides, because of higher stability against high concentration of denaturant, the microreactors can be useful for immediate digestion of the denaturated protein. In the present study, we propose a protease-immobilized microreactor digestion method, which can utilize as a proteome technique for biological and clinical research.
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Affiliation(s)
- Hiroshi Yamaguchi
- Nanotechnology Research Institute, National Institute of Advanced Industrial Science and Technology, Tosu, Saga, Japan
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Qian K, Wan J, Qiao L, Huang X, Tang J, Wang Y, Kong J, Yang P, Yu C, Liu B. Macroporous Materials as Novel Catalysts for Efficient and Controllable Proteolysis. Anal Chem 2009; 81:5749-56. [DOI: 10.1021/ac900550q] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Kun Qian
- Department of Chemistry and Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Institute of Biomedical Sciences, Fudan University, Shanghai 200433, P. R. China
| | - Jingjing Wan
- Department of Chemistry and Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Institute of Biomedical Sciences, Fudan University, Shanghai 200433, P. R. China
| | - Liang Qiao
- Department of Chemistry and Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Institute of Biomedical Sciences, Fudan University, Shanghai 200433, P. R. China
| | - Xiaodan Huang
- Department of Chemistry and Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Institute of Biomedical Sciences, Fudan University, Shanghai 200433, P. R. China
| | - Jiawei Tang
- Department of Chemistry and Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Institute of Biomedical Sciences, Fudan University, Shanghai 200433, P. R. China
| | - Yunhua Wang
- Department of Chemistry and Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Institute of Biomedical Sciences, Fudan University, Shanghai 200433, P. R. China
| | - Jilie Kong
- Department of Chemistry and Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Institute of Biomedical Sciences, Fudan University, Shanghai 200433, P. R. China
| | - Pengyuan Yang
- Department of Chemistry and Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Institute of Biomedical Sciences, Fudan University, Shanghai 200433, P. R. China
| | - Chengzhong Yu
- Department of Chemistry and Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Institute of Biomedical Sciences, Fudan University, Shanghai 200433, P. R. China
| | - Baohong Liu
- Department of Chemistry and Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Institute of Biomedical Sciences, Fudan University, Shanghai 200433, P. R. China
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Xu X, Wang X, Liu Y, Liu B, Wu H, Yang P. Trypsin entrapped in poly(diallyldimethylammonium chloride) silica sol-gel microreactor coupled to matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2008; 22:1257-1264. [PMID: 18383213 DOI: 10.1002/rcm.3478] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
An enzyme-immobilized capillary microreactor for rapid protein digestion and proteomics analysis is reported. The inner surface of the fused-silica capillary was coated with poly(diallyldimethylammonium chloride) (PDDA)-entrapped silica sol-gel matrix, followed by assembly of trypsin onto the PDDA-modified surface via electrostatic adsorption. The immobilization parameters such as PDDA content in the sol-gel matrix, trypsin concentration and pH were investigated in detail. Protein samples including beta-casein, myoglobin and cytochrome c could be effectively digested and electrophoretically separated simultaneously in such a modified capillary. Just 2.26 ng (corresponding to 0.10-0.14 picomole) of sample was sufficient for on-line capillary electrophoresis peptide mapping. The efficiency of the digestion was further demonstrated by digestion of a human liver cytoplasm sample and 253 proteins were identified in one unique run.
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Affiliation(s)
- Xuejiao Xu
- Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
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