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Xu X, Moreno S, Gentzel M, Zhang K, Wang D, Voit B, Appelhans D. Biomimetic Protocells Featuring Macrophage-Like Capture and Digestion of Protein Pathogens. SMALL METHODS 2023; 7:e2300257. [PMID: 37599260 DOI: 10.1002/smtd.202300257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 06/11/2023] [Indexed: 08/22/2023]
Abstract
Modern medical research develops interest in sophisticated artificial nano- and microdevices for future treatment of human diseases related to biological dysfunctions. This covers the design of protocells capable of mimicking the structure and functionality of eukaryotic cells. The authors use artificial organelles based on trypsin-loaded pH-sensitive polymeric vesicles to provide macrophage-like digestive functions under physiological conditions. Herein, an artificial cell is established where digestive artificial organelles (nanosize) are integrated into a protocell (microsize). With this method, mimicking crossing of different biological barriers, capture of model protein pathogens, and compartmentalized digestive function are possible. This allows the integration of different components (e.g., dextran as stabilizing block) and the diffusion of pathogens in simulated cytosolic environment under physiological conditions. An integrated characterization approach is carried out, with identifying electrospray ionization mass spectrometry as an excellent detection method for the degradation of a small peptide such as β-amyloid. The degradation of model enzymes is measured by enzyme activity assays. This work is an important contribution to effective biomimicry with the design of cell-like functions having potential for therapeutic action.
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Affiliation(s)
- Xiaoying Xu
- Leibniz-Institut für Polymerforschung Dresden e.V., D-01069, Dresden, Germany
- Organic Chemistry of Polymers, Technische Universität Dresden, D-01062, Dresden, Germany
| | - Silvia Moreno
- Leibniz-Institut für Polymerforschung Dresden e.V., D-01069, Dresden, Germany
| | - Marc Gentzel
- Center for Molecular and Cellular Bioengineering (CMCB), Core Facility Mass Spectrometry & Proteomics, Technische Universität Dresden, 01307, Dresden, Germany
| | - Kehu Zhang
- Leibniz-Institut für Polymerforschung Dresden e.V., D-01069, Dresden, Germany
- Organic Chemistry of Polymers, Technische Universität Dresden, D-01062, Dresden, Germany
| | - Dishi Wang
- Leibniz-Institut für Polymerforschung Dresden e.V., D-01069, Dresden, Germany
- Organic Chemistry of Polymers, Technische Universität Dresden, D-01062, Dresden, Germany
| | - Brigitte Voit
- Leibniz-Institut für Polymerforschung Dresden e.V., D-01069, Dresden, Germany
- Organic Chemistry of Polymers, Technische Universität Dresden, D-01062, Dresden, Germany
| | - Dietmar Appelhans
- Leibniz-Institut für Polymerforschung Dresden e.V., D-01069, Dresden, Germany
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2
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Cao W, Bruening ML. Analysis of Protein Glycosylation after Rapid Digestion Using Protease-Containing Membranes in Spin Columns. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023. [PMID: 37127550 DOI: 10.1021/jasms.3c00038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Glycosylation is an important protein post-translational modification that plays a pivotal role in the bioactivity of therapeutic proteins and in the infectivity of viral proteins. Liquid chromatography with tandem mass spectrometry readily identifies protein glycans with site specificity. However, the overnight incubation used in conventional in-solution proteolysis leads to high turnaround times for glycosylation analysis, particularly when sequential in-solution digestions are needed for site-specific glycan identification. Using bovine fetuin as a model glycoprotein, this work first shows that in-membrane digestion in ∼3 min yields similar glycan identification and quantitation when compared to overnight in-solution digestion. Protease-containing membranes in a spin column enable digestion of therapeutic proteins (trastuzumab and erythropoietin) and a viral protein (SARS-CoV-2 receptor binding domain) in ∼30 s. Glycan identification is similar after in-solution and in-membrane digestion, and limited in-membrane digestion enhances the identification of high-mannose glycans in trastuzumab. Finally, stacked membranes containing trypsin and chymotrypsin allow fast sequential proteolytic digestion to site-specifically identify the glycans of SARS-CoV-2 receptor binding domain. One can easily assemble the protease-containing membranes in commercial spin columns, and spinning multiple columns simultaneously will facilitate parallel analyses.
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Affiliation(s)
- Weikai Cao
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Merlin L Bruening
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, Indiana 46556, United States
- Department of Chemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
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3
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Ryan KA, Bruening ML. Online protein digestion in membranes between capillary electrophoresis and mass spectrometry. Analyst 2023; 148:1611-1619. [PMID: 36912593 DOI: 10.1039/d3an00106g] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/10/2023]
Abstract
This research employs pepsin-containing membranes to digest proteins online after a capillary electrophoresis (CE) separation and prior to tandem mass spectrometry. Proteolysis after the separation allows the peptides from a given protein to enter the mass spectrometer in a single plug. Thus, migration time can serve as an additional criterion for confirming the identification of a peptide. The membrane resides in a sheath-flow electrospray ionization (ESI) source to enable digestion immediately before spray into the mass spectrometer, thus limiting separation of the digested peptides. Using the same membrane, digestion occurred reproducibly during 20 consecutive CE analyses performed over a 10 h period. Additionally, after separating a mixture of six unreduced proteins with CE, online digestion facilitated protein identification with at least 2 identifiable peptides for all the proteins. Sequence coverages were >75% for myoglobin and carbonic anhydrase II but much lower for proteins containing disulfide bonds. Development of methods for efficient separation of reduced proteins or identification of cross-linked peptides should enhance sequence coverages for proteins with disulfide bonds. Migration times for the peptides identified from a specific protein differed by <∼30 s, which allows for rejection of some spurious peptide identifications.
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Affiliation(s)
- Kendall A Ryan
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA.
| | - Merlin L Bruening
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA. .,Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, IN 46556, USA
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4
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Lu W, Cao Y, Qing G. Recent advance in solid state nanopores modification and characterization. Chem Asian J 2022; 17:e202200675. [PMID: 35974427 DOI: 10.1002/asia.202200675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 08/16/2022] [Indexed: 11/08/2022]
Abstract
Nanopore, due to its advantages of modifiable, controllability and sensitivity, has made a splash in recent years in the fields of biomolecular sequencing, small molecule detection, salt differential power generation, and biomimetic ion channels, etc. In these applications, the role of chemical or biological modification is indispensable. Compared with small molecules, the modification of polymers is more difficult and the methods are more diverse. Choosing appropriate modification method directly determines the success or not of the research, therefore, it is necessary to summarize the polymer modification methods toward nanopores. In addition, it is also important to provide clear and convincing evidence that the nanopore modification is successful, the corresponding characterization methods are also indispensable. Therefore, this review will summarize the methods of polymer modification of nanopores and efficient characterization methods. And we hope that this review will provide some reference value for like-minded researchers.
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Affiliation(s)
- Wenqi Lu
- Chinese Academy of Sciences Dalian Institute of Chemical Physics, CAS Key Laboratory of Separation Science for Analytical Chemistry, 116023, Dalian, CHINA
| | - Yuchen Cao
- Chinese Academy of Sciences Dalian Institute of Chemical Physics, CAS Key Laboratory of Separation Science for Analytical Chemistry, 116023, Dalian, CHINA
| | - Guangyan Qing
- Dalian Institute of Chemical Physics, CAS Key Laboratory of Separation Science for Analytical Chemistry, 457 Zhongshan Road, 116023, Dalian, CHINA
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5
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Schmidt M, Prager A, Schönherr N, Gläser R, Schulze A. Reagent-Free Immobilization of Industrial Lipases to Develop Lipolytic Membranes with Self-Cleaning Surfaces. MEMBRANES 2022; 12:membranes12060599. [PMID: 35736306 PMCID: PMC9229154 DOI: 10.3390/membranes12060599] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 05/30/2022] [Accepted: 06/02/2022] [Indexed: 02/04/2023]
Abstract
Biocatalytic membrane reactors combine the highly efficient biotransformation capability of enzymes with the selective filtration performance of membrane filters. Common strategies to immobilize enzymes on polymeric membranes are based on chemical coupling reactions. Still, they are associated with drawbacks such as long reaction times, high costs, and the use of potentially toxic or hazardous reagents. In this study, a reagent-free immobilization method based on electron beam irradiation was investigated, which allows much faster, cleaner, and cheaper fabrication of enzyme membrane reactors. Two industrial lipase enzymes were coupled onto a polyvinylidene fluoride (PVDF) flat sheet membrane to create self-cleaning surfaces. The response surface methodology (RSM) in the design-of-experiments approach was applied to investigate the effects of three numerical factors on enzyme activity, yielding a maximum activity of 823 ± 118 U m−2 (enzyme concentration: 8.4 g L−1, impregnation time: 5 min, irradiation dose: 80 kGy). The lipolytic membranes were used in fouling tests with olive oil (1 g L−1 in 2 mM sodium dodecyl sulfate), resulting in 100% regeneration of filtration performance after 3 h of self-cleaning in an aqueous buffer (pH 8, 37 °C). Reusability with three consecutive cycles demonstrates regeneration of 95%. Comprehensive membrane characterization was performed by determining enzyme kinetic parameters, permeance monitoring, X-ray photoelectron spectroscopy, FTIR spectroscopy, scanning electron microscopy, and zeta potential, as well as water contact angle measurements.
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Affiliation(s)
- Martin Schmidt
- Leibniz Institute of Surface Engineering (IOM), Permoserstr. 15, 04318 Leipzig, Germany; (M.S.); (A.P.); (N.S.)
| | - Andrea Prager
- Leibniz Institute of Surface Engineering (IOM), Permoserstr. 15, 04318 Leipzig, Germany; (M.S.); (A.P.); (N.S.)
| | - Nadja Schönherr
- Leibniz Institute of Surface Engineering (IOM), Permoserstr. 15, 04318 Leipzig, Germany; (M.S.); (A.P.); (N.S.)
| | - Roger Gläser
- Institute of Chemical Technology, Leipzig University, Linnéstraße 3, 04103 Leipzig, Germany;
| | - Agnes Schulze
- Leibniz Institute of Surface Engineering (IOM), Permoserstr. 15, 04318 Leipzig, Germany; (M.S.); (A.P.); (N.S.)
- Correspondence:
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6
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Microfluidic Immobilized Enzymatic Reactors for Proteomic Analyses—Recent Developments and Trends (2017–2021). MICROMACHINES 2022; 13:mi13020311. [PMID: 35208435 PMCID: PMC8879403 DOI: 10.3390/mi13020311] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 02/13/2022] [Accepted: 02/14/2022] [Indexed: 01/02/2023]
Abstract
Given the strong interdisciplinary nature of microfluidic immobilized enzyme reactor (μ-IMER) technology, several branches of science contribute to its successful implementation. A combination of physical, chemical knowledge and engineering skills is often required. The development and application of μ-IMERs in the proteomic community are experiencing increasing importance due to their attractive features of enzyme reusability, shorter digestion times, the ability to handle minute volumes of sample and the prospect of on-line integration into analytical workflows. The aim of this review is to give an account of the current (2017–2021) trends regarding the preparation of microdevices, immobilization strategies, and IMER configurations. The different aspects of microfabrication (designs, fabrication technologies and detectors) and enzyme immobilization (empty and packed channels, and monolithic supports) are surveyed focusing on μ-IMERs developed for proteomic analysis. Based on the advantages and limitations of the published approaches and the different applications, a probable perspective is given.
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7
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Development of an In-Line Enzyme Reactor Integrated into a Capillary Electrophoresis System. Molecules 2021; 26:molecules26195902. [PMID: 34641446 PMCID: PMC8513095 DOI: 10.3390/molecules26195902] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 09/23/2021] [Accepted: 09/27/2021] [Indexed: 12/03/2022] Open
Abstract
The goal of this paper was to develop an in-line immobilized enzyme reactor (IMER) integrated into a capillary electrophoresis platform. In our research, we created the IMER by adsorbing trypsin onto the inner surface of a capillary in a short section. Enzyme immobilization was possible due to the electrostatic attraction between the oppositely charged fused silica capillary surface and trypsin. The reactor was formed by simply injecting and removing trypsin solution from the capillary inlet (~1–2 cms). We investigated the factors affecting the efficiency of the reactor. The main advantages of the proposed method are the fast, cheap, and easy formation of an IMER with in-line protein digestion capability. Human tear samples were used to test the efficiency of the digestion in the microreactor.
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8
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Nagy C, Huszank R, Gaspar A. Study of the geometry of open channels in a layer-bed-type microfluidic immobilized enzyme reactor. Anal Bioanal Chem 2021; 413:6321-6332. [PMID: 34378068 PMCID: PMC8487885 DOI: 10.1007/s00216-021-03588-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 07/20/2021] [Accepted: 07/28/2021] [Indexed: 01/01/2023]
Abstract
This paper aims at studying open channel geometries in a layer-bed-type immobilized enzyme reactor with computer-aided simulations. The main properties of these reactors are their simple channel pattern, simple immobilization procedure, regenerability, and disposability; all these features make these devices one of the simplest yet efficient enzymatic microreactors. The high surface-to-volume ratio of the reactor was achieved using narrow (25–75 μm wide) channels. The simulation demonstrated that curves support the mixing of solutions in the channel even in strong laminar flow conditions; thus, it is worth including several curves in the channel system. In the three different designs of microreactor proposed, the lengths of the channels were identical, but in two reactors, the liquid flow was split to 8 or 32 parallel streams at the inlet of the reactor. Despite their overall higher volumetric flow rate, the split-flow structures are advantageous due to the increased contact time. Saliva samples were used to test the efficiencies of the digestions in the microreactors.
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Affiliation(s)
- Cynthia Nagy
- Department of Inorganic and Analytical Chemistry, University of Debrecen, Egyetem ter 1, Debrecen, 4032, Hungary
| | - Robert Huszank
- Institute for Nuclear Research (Atomki), P.O. Box 51, Debrecen, 4001, Hungary
| | - Attila Gaspar
- Department of Inorganic and Analytical Chemistry, University of Debrecen, Egyetem ter 1, Debrecen, 4032, Hungary.
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9
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Andrews WT, Bickner AN, Tobias F, Ryan KA, Bruening ML, Hummon AB. Electroblotting through Enzymatic Membranes to Enhance Molecular Tissue Imaging. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:1689-1699. [PMID: 34110793 PMCID: PMC9241434 DOI: 10.1021/jasms.1c00046] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
MALDI-TOF mass spectrometry imaging (MSI) is a powerful tool for studying biomolecule localization in tissue. Protein distributions in tissue provide important histological information; however, large proteins exhibit a high limit of detection in MALDI-MS when compared to their corresponding smaller proteolytic peptides. As a result, several techniques have emerged to digest proteins into more detectable peptides for imaging. Digestion is typically accomplished through trypsin deposition on the tissue, but this technique increases the complexity of the tissue microenvironment, which can limit the number of detectable species. This proof-of-principle study explores tryptic tissue digestion during electroblotting through a trypsin-containing membrane. This approach actively extracts and enzymatically digests proteins from mouse brain tissue sections while simultaneously reducing the complexity of the tissue microenvironment (compared to trypsin deposition on the surface) to obtain an increased number of detectable peptide fragments. The method does not greatly compromise spatial location or require expensive devices to uniformly deposit trypsin on tissue. Using electrodigestion through membranes, we detected and tentatively identified several tryptic peptides that were not observed after on-tissue digestion. Moreover, the use of pepsin rather than trypsin in digestion membranes allows extraction and digestion at low pH to detect peptides from a complementary subset of tissue proteins. Future studies will aim to further improve the method, including changing the substrate membrane to increase spatial resolution and the number of detected peptides.
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Affiliation(s)
| | | | - Fernando Tobias
- Department of Chemistry and Biochemistry, Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio 43210, United States
| | | | | | - Amanda B Hummon
- Department of Chemistry and Biochemistry, Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio 43210, United States
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10
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Qi L, Qiao J. Design of Switchable Enzyme Carriers Based on Stimuli-Responsive Porous Polymer Membranes for Bioapplications. ACS APPLIED BIO MATERIALS 2021; 4:4706-4719. [PMID: 35007021 DOI: 10.1021/acsabm.1c00338] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Design of efficient enzyme carriers, where enzymes are conjugated to supports, has become an attractive research avenue. Immobilized enzymes are advantageous for practical applications because of their convenience in handling, ease of separation, and good reusability. However, the main challenge is that these traditional enzyme carriers are unable to regulate the enzymolysis efficiency or to protect the enzymes from proteolytic degradation, which restricts their effectiveness of enzymes in bioapplications. Enlightened by the stimuli-responsive channels in the natural cell membranes, conjugation of the enzymes within flat-sheet stimuli-responsive porous polymer membranes (SR-PPMs) as artificial cell membranes is an efficient strategy for circumventing this challenge. Controlled by the external stimuli, the multifunctional polymer chains, which are incorporated within the membranes and attached to the enzyme, change their structures to defend the enzyme from the external environmental disturbances and degradation by proteinases. Specifically, smart SR-PPM enzyme carriers (SR-PPMECs) not only permit convective substrate transfer through the accessible porous network, dramatically improving enzymolysis efficiency due to the adjustable pore sizes and the confinement effect, but they also act as molecular switches for regulating its permeability and selectivity. In this review, the concept of SR-PPMECs is presented. It covers the latest developments in design strategies of flat-sheet SR-PPFMs, fabrication protocols of SR-PPFMECs, strategies for the regulation of enzymolysis efficiency, and their cutting-edge bioapplications.
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Affiliation(s)
- Li Qi
- Beijing National Laboratory of Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China.,School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Juan Qiao
- Beijing National Laboratory of Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China.,School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
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11
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Bickner AN, Champion MM, Hummon AB, Bruening ML. Electroblotting through a tryptic membrane for LC-MS/MS analysis of proteins separated in electrophoretic gels. Analyst 2021; 145:7724-7735. [PMID: 33000802 DOI: 10.1039/d0an01380c] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Digestion of proteins separated via sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) remains a popular method for protein identification using mass-spectrometry based proteomics. Although robust and routine, the in-gel digestion procedure is laborious and time-consuming. Electroblotting to a capture membrane prior to digestion reduces preparation steps but requires on-membrane digestion that yields fewer peptides than in-gel digestion. This paper develops direct electroblotting through a trypsin-containing membrane to a capture membrane to simplify extraction and digestion of proteins separated by SDS-PAGE. Subsequent liquid chromatography-tandem mass spectrometry (LC-MS/MS) identifies the extracted peptides. Analysis of peptides from different capture membrane pieces shows that electrodigestion does not greatly disturb the spatial resolution of a standard protein mixture separated by SDS-PAGE. Electrodigestion of an Escherichia coli (E. coli) cell lysate requires four hours of total sample preparation and results in only 13% fewer protein identifications than in-gel digestion, which can take 24 h. Compared to simple electroblotting and protein digestion on a poly(vinylidene difluoride) (PVDF) capture membrane, adding a trypsin membrane to the electroblot increases the number of protein identifications by 22%. Additionally, electrodigestion experiments using capture membranes coated with polyelectrolyte layers identify a higher fraction of small proteolytic peptides than capture on PVDF or in-gel digestion.
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Affiliation(s)
- A N Bickner
- Department of Chemistry and Biochemistry University of Notre Dame, Notre Dame, Indiana 46556, USA.
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12
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Pankova SM, Sakibaev FA, Holyavka MG, Vyshkvorkina YM, Lukin AN, Artyukhov VG. Studies of the Processes of the Trypsin Interactions with Ion Exchange Fibers and Chitosan. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2021. [DOI: 10.1134/s1068162021030146] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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13
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Zhang S, Peng B, Li M, Diao H, Wang X, Zhao W, Lin W, Sun N, Lin S. Immobilization of Active Substances in Food Using Self‐Organized Patterned Porous Film via Breath Figure Approach. ChemistrySelect 2021. [DOI: 10.1002/slct.202004827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Simin Zhang
- National Engineering Research Center of Seafood School of Food Science and Technology Dalian Polytechnic University Dalian 116034 P. R. China
| | - Bo Peng
- National Engineering Research Center of Seafood School of Food Science and Technology Dalian Polytechnic University Dalian 116034 P. R. China
| | - Meng Li
- National Engineering Research Center of Seafood School of Food Science and Technology Dalian Polytechnic University Dalian 116034 P. R. China
| | - Huayu Diao
- National Engineering Research Center of Seafood School of Food Science and Technology Dalian Polytechnic University Dalian 116034 P. R. China
| | - Xingyu Wang
- National Engineering Research Center of Seafood School of Food Science and Technology Dalian Polytechnic University Dalian 116034 P. R. China
| | - Weiping Zhao
- National Engineering Research Center of Seafood School of Food Science and Technology Dalian Polytechnic University Dalian 116034 P. R. China
| | - Wei Lin
- National Engineering Research Center of Seafood School of Food Science and Technology Dalian Polytechnic University Dalian 116034 P. R. China
| | - Na Sun
- National Engineering Research Center of Seafood School of Food Science and Technology Dalian Polytechnic University Dalian 116034 P. R. China
| | - Songyi Lin
- National Engineering Research Center of Seafood School of Food Science and Technology Dalian Polytechnic University Dalian 116034 P. R. China
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14
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AZHAR I, LIU X, HE HY, QU QS, YANG L. A Syringe-Filter-based Portable Microreactor for Size-selective Proteolysis of Low Molecular-weight Proteins. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2020. [DOI: 10.1016/s1872-2040(20)60061-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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15
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Robinson MR, Vasicek LA, Hoppmann C, Li M, Jokhadze G, Spellman DS. Improving the throughput of immunoaffinity purification and enzymatic digestion of therapeutic proteins using membrane-immobilized reagent technology. Analyst 2020; 145:3148-3156. [PMID: 32191233 DOI: 10.1039/d0an00190b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Continued interest in protein therapeutics has motivated the development of improved bioanalytical tools to support development programs. LC-MS offers specificity, sensitivity, and multiplexing capabilities without the need for target-specific reagents, making it a valuable alternative to ligand binding assays. Immunoaffinity purification (IP) and enzymatic digestion are critical, yet extensive and time-consuming components of the "gold standard" bottom-up approach to LC-MS-based protein quantitation. In the present work, commercially available technology, based on membrane-immobilized reagents in spin column and plate format, is applied to reduce IP and digestion times from hours to minutes. For a standard monoclonal antibody, the lower limit of quantitation was 0.1 ng μL-1 compared to 0.05 ng μL-1 for the standard method. A pharmacokinetics (PK) study dosing Herceptin in rat was analyzed by both the membrane and the standard method with a total sample processing time of 4 h and 20 h, respectively. The calculated concentrations at each time point agreed within 8% between both methods, and PK values including area under the curve (AUC), half-life (T1/2), mean residence time (MRT), clearance (CL), and volume of distribution (Vdss) agreed within 6% underscoring the utility of the membrane methodology for quantitative bioanalysis workflows.
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Affiliation(s)
- Michelle R Robinson
- Department of Pharmacokinetics Pharmacodynamics and Drug Metabolism, Merck & Co., Inc., West Point, PA, USA.
| | - Lisa A Vasicek
- Department of Pharmacokinetics Pharmacodynamics and Drug Metabolism, Merck & Co., Inc., West Point, PA, USA.
| | | | - Mandy Li
- Takara Bio USA, Inc., Mountain View, CA, USA
| | | | - Daniel S Spellman
- Department of Pharmacokinetics Pharmacodynamics and Drug Metabolism, Merck & Co., Inc., West Point, PA, USA.
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16
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Nagy C, Kecskemeti A, Gaspar A. Fabrication of immobilized enzyme reactors with pillar arrays into polydimethylsiloxane microchip. Anal Chim Acta 2020; 1108:70-78. [PMID: 32222246 DOI: 10.1016/j.aca.2020.02.048] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 02/23/2020] [Accepted: 02/24/2020] [Indexed: 11/19/2022]
Abstract
This paper demonstrates the design, efficiency and applicability of a simple and inexpensive microfluidic immobilized enzymatic reactor (IMER) for rapid protein digestion. The high surface-to-volume ratio (S/V) of the reactor was achieved by forming pillars in the channel. It was found that pillar arrays including dimensions of 40 μm × 40 μm as pillar diameter and interpillar distance can provide both relatively high S/V and flow rate in the PDMS chip, the fabrication of which was performed by means of soft lithography using average research laboratory infrastructure. CZE peptide maps of IMER-based digestions were compared to peptide maps obtained from standard in-solution digestion of proteins. The peak patterns of the electropherograms and the identified proteins were similar, however, digestion with the IMER requires less than 10 min, while in-solution digestion takes 16 h.
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Affiliation(s)
- Cynthia Nagy
- Department of Inorganic and Analytical Chemistry, University of Debrecen, Egyetem ter 1., Debrecen, 4032, Hungary
| | - Adam Kecskemeti
- Department of Inorganic and Analytical Chemistry, University of Debrecen, Egyetem ter 1., Debrecen, 4032, Hungary
| | - Attila Gaspar
- Department of Inorganic and Analytical Chemistry, University of Debrecen, Egyetem ter 1., Debrecen, 4032, Hungary.
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17
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Burdette MK, Jenkins R, Bandera YP, Jones H, Foulger IK, Dickey A, Nieminen AL, Foulger SH. Click-Engineered, Bioresponsive, and Versatile Particle-Protein-Dye System. ACS APPLIED BIO MATERIALS 2019; 2:3183-3193. [PMID: 31844845 PMCID: PMC6913539 DOI: 10.1021/acsabm.9b00025] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
We present a multifunctional polymer based nanoparticle platform for personalized nanotheranostic applications, which include photodynamic therapy and active targeting. In this system, poly(propargyl acrylate) (PA) particles were surface-modified with organic ligands and fluorophores (the payload) through an environmentally-sensitive linker. An azide modified bovine serum albumin (azBSA) was employed as the linker. This system prevents opsonization and, upon digestion, releases the payload. Attachment of the emitting payload to the particle through azide-modified bovine serum albumin (BSA) quenches emission, which can be again activated with digestion of the azBSA. The emission "turn-on" at a specific location will increase the signal-to-noise ratio. By utilizing human head and neck squamous carcinoma cells (UMSCC22A), photodynamic therapy studies with these particles gave promising reductions in cell growth. Additionally, the particle-protein-dye system is versatile as different fluorophores (such as silicon phthalocyanine or cyanine 3) can be attached to the protein and the same activation/deactivation behavior is observed. Active targeting can be employed to enhance the concentration of the payload in the designated tumor. Human lung carcinoma cells (A549) were utilized in toxicity studies where PA-azBSA particles were modified with a Survivin targeting ligand and indicated an enhanced cell death with the modified particles relative to the "free" Survivin targeting ligand.
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Affiliation(s)
- Mary K. Burdette
- Department of Materials Science and Engineering, Advanced Materials Research Laboratories, Clemson University, Anderson, South Carolina 29625, United States
- Center for Optical Materials Science and Engineering Technologies, Advanced Materials Research Laboratories, Clemson University, Anderson, South Carolina 29625, United States
| | - Ragini Jenkins
- Department of Materials Science and Engineering, Advanced Materials Research Laboratories, Clemson University, Anderson, South Carolina 29625, United States
- Center for Optical Materials Science and Engineering Technologies, Advanced Materials Research Laboratories, Clemson University, Anderson, South Carolina 29625, United States
| | - Yuriy P. Bandera
- Department of Materials Science and Engineering, Advanced Materials Research Laboratories, Clemson University, Anderson, South Carolina 29625, United States
- Center for Optical Materials Science and Engineering Technologies, Advanced Materials Research Laboratories, Clemson University, Anderson, South Carolina 29625, United States
| | - Haley Jones
- Department of Materials Science and Engineering, Advanced Materials Research Laboratories, Clemson University, Anderson, South Carolina 29625, United States
- Center for Optical Materials Science and Engineering Technologies, Advanced Materials Research Laboratories, Clemson University, Anderson, South Carolina 29625, United States
| | - Isabell K. Foulger
- Center for Optical Materials Science and Engineering Technologies, Advanced Materials Research Laboratories, Clemson University, Anderson, South Carolina 29625, United States
- Department of Bioengineering, Clemson University, Clemson, South Carolina 29634, United States
| | - Ashley Dickey
- Center for Optical Materials Science and Engineering Technologies, Advanced Materials Research Laboratories, Clemson University, Anderson, South Carolina 29625, United States
- Department of Chemistry, Advanced Materials Research Laboratories, Clemson University, Anderson, South Carolina 29625, United States
| | - Anna-Liisa Nieminen
- Drug Discovery & Biomedical Sciences, Medical University of South Carolina, Charleston, South Carolina 29425, United States
| | - Stephen H. Foulger
- Department of Materials Science and Engineering, Advanced Materials Research Laboratories, Clemson University, Anderson, South Carolina 29625, United States
- Center for Optical Materials Science and Engineering Technologies, Advanced Materials Research Laboratories, Clemson University, Anderson, South Carolina 29625, United States
- Department of Bioengineering, Clemson University, Clemson, South Carolina 29634, United States
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18
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Label-free protein quantification after ultrafast digestion of complex proteomes using ultrasonic energy and immobilized-trypsin magnetic nanoparticles. Talanta 2019; 196:262-270. [DOI: 10.1016/j.talanta.2018.12.066] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2018] [Revised: 12/20/2018] [Accepted: 12/21/2018] [Indexed: 12/27/2022]
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19
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Enzymes and nanoparticles: Modulation of enzymatic activity via nanoparticles. Int J Biol Macromol 2018; 118:1833-1847. [DOI: 10.1016/j.ijbiomac.2018.07.030] [Citation(s) in RCA: 92] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Revised: 07/09/2018] [Accepted: 07/09/2018] [Indexed: 12/30/2022]
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20
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Immobilization of trypsin onto Fe3O4@SiO2 –NH2 and study of its activity and stability. Colloids Surf B Biointerfaces 2018; 170:553-562. [DOI: 10.1016/j.colsurfb.2018.06.022] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Revised: 06/12/2018] [Accepted: 06/14/2018] [Indexed: 11/30/2022]
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21
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Vanangamudi A, Saeki D, Dumée LF, Duke M, Vasiljevic T, Matsuyama H, Yang X. Surface-Engineered Biocatalytic Composite Membranes for Reduced Protein Fouling and Self-Cleaning. ACS APPLIED MATERIALS & INTERFACES 2018; 10:27477-27487. [PMID: 30048587 DOI: 10.1021/acsami.8b07945] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
A new biocatalytic nanofibrous composite ultrafiltration membrane was developed to reduce protein fouling interactions and self-clean the membrane surface. The dual-layer poly(vinylidenefluoride)/nylon-6,6/chitosan composite membrane contains a hydrophobic poly(vinylidenefluoride) cast support layer and a hydrophilic functional nylon-6,6/chitosan nanofibrous surface layer where enzymes were chemically attached. The intrinsic surface chemistry and high surface area of the nanofibers allowed optimal and stable immobilization of trypsin (TR) and α-chymotrypsin enzymes via direct covalent binding. The enzyme immobilization was confirmed by X-ray photoelectron spectroscopy and visualized by confocal microscopy analysis. The prepared biocatalytic composite membranes were nanoporous with superior permeability offering stable protein antiadhesion and self-cleaning properties owing to the repulsive mechanism and digestion of proteins into peptides and amino acids, which was quantified by the gel electrophoresis technique. The TR-immobilized composite membranes exhibited 2.7-fold higher permeance and lower surface protein contamination with 3-fold greater permeance recovery, when compared to the pristine membrane after two ultrafiltration cycles with the model feed solution containing bovine serum albumin/NaCl/CaCl2. The biocatalytic membranes retained about 50% of the enzyme activity after six reuse cycles but were regenerated to 100% activity after enzyme reloading, leading to a simple and cost-effective water remediation operation. Such surface- and pore-engineered membranes with self-cleaning properties offer a viable solution for severe surface protein contamination in food and water applications.
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Affiliation(s)
- Anbharasi Vanangamudi
- Institute for Frontier Materials , Deakin University , Waurn Ponds , Victoria 3216 , Australia
| | - Daisuke Saeki
- Department of Chemical Science and Engineering , Kobe University , 1-1 Rokkodai-cho , Nada, Kobe , Hyogo 657-8501 , Japan
| | - Ludovic F Dumée
- Institute for Frontier Materials , Deakin University , Waurn Ponds , Victoria 3216 , Australia
| | | | | | - Hideto Matsuyama
- Department of Chemical Science and Engineering , Kobe University , 1-1 Rokkodai-cho , Nada, Kobe , Hyogo 657-8501 , Japan
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22
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Liu W, Pang Y, Tan HY, Patel N, Jokhadze G, Guthals A, Bruening ML. Enzyme-containing spin membranes for rapid digestion and characterization of single proteins. Analyst 2018; 143:3907-3917. [PMID: 30039812 DOI: 10.1039/c8an00969d] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Proteolytic digestion is an important step in characterizing protein sequences and post-translational modifications (PTMs) using mass spectrometry (MS). This study uses pepsin- or trypsin-containing spin membranes for rapid digestion of single proteins or simple protein mixtures prior to ultrahigh-resolution Orbitrap MS analysis. Centrifugation of 100 μL of pretreated protein solutions through the functionalized membranes requires less than 1 min and conveniently digests proteins into large peptides that aid in confirming specific protein sequence variations and PTMs. Peptic and tryptic peptides from spin digestion of apomyoglobin and four commercial monoclonal antibodies (mAbs) typically cover 100% of the protein sequences in direct infusion MS analysis. Increasing the spin rate leads to a higher fraction of large peptic peptides for apomyoglobin, and MS analysis of peptic and tryptic peptides reveals mAb PTMs such as N-terminal pyroglutamate formation, C-terminal lysine clipping and glycosylation. Relative to overnight in-solution digestion of mAbs, spin digestion yields higher sequence coverages. Spin-membrane digestion followed by infusion MS readily differentiates a mAb to the Ebola virus from a related antibody that differs by addition of a single amino acid.
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Affiliation(s)
- Weijing Liu
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, USA
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23
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Shen X, Sun L. Systematic Evaluation of Immobilized Trypsin-Based Fast Protein Digestion for Deep and High-Throughput Bottom-Up Proteomics. Proteomics 2018; 18:e1700432. [PMID: 29577644 DOI: 10.1002/pmic.201700432] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Revised: 03/02/2018] [Indexed: 11/08/2022]
Abstract
Immobilized trypsin (IM) has been recognized as an alternative to free trypsin (FT) for accelerating protein digestion 30 years ago. However, some questions of IM still need to be answered. How does the solid matrix of IM influence its preference for protein cleavage and how well can IM perform for deep bottom-up proteomics compared to FT? By analyzing Escherichia coli proteome samples digested with amine or carboxyl functionalized magnetic bead-based IM (IM-N or IM-C) or FT, it is observed that IM-N with the nearly neutral solid matrix, IM-C with the negatively charged solid matrix, and FT have similar cleavage preference considering the microenvironment surrounding the cleavage sites. IM-N (15 min) and FT (12 h) both approach 9000 protein identifications (IDs) from a mouse brain proteome. Compared to FT, IM-N has no bias in the digestion of proteins that are involved in various biological processes, are located in different components of cells, have diverse functions, and are expressed in varying abundance. A high-throughput bottom-up proteomics workflow comprising IM-N-based rapid protein cleavage and fast CZE-MS/MS enables the completion of protein sample preparation, CZE-MS/MS analysis, and data analysis in only 3 h, resulting in 1000 protein IDs from the mouse brain proteome.
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Affiliation(s)
- Xiaojing Shen
- Department of Chemistry, Michigan State University, East Lansing, MI, USA
| | - Liangliang Sun
- Department of Chemistry, Michigan State University, East Lansing, MI, USA
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24
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Kecskemeti A, Gaspar A. Particle-based immobilized enzymatic reactors in microfluidic chips. Talanta 2018; 180:211-228. [DOI: 10.1016/j.talanta.2017.12.043] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 12/13/2017] [Indexed: 10/18/2022]
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25
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Dizge N, Epsztein R, Cheng W, Porter CJ, Elimelech M. Biocatalytic and salt selective multilayer polyelectrolyte nanofiltration membrane. J Memb Sci 2018. [DOI: 10.1016/j.memsci.2017.12.026] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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26
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Liu B, Wu L, Zhou X, Wu H, Zheng B. Porous polydimethylsiloxane monolith for protein digestion. J Mater Chem B 2018; 6:824-829. [DOI: 10.1039/c7tb02738a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
We developed a simple method to prepare interconnected porous PDMS monolith using glass microbubbles as the template.
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Affiliation(s)
- Baishu Liu
- Department of Chemistry
- The Chinese University of Hong Kong
- China
| | - Liang Wu
- Department of Chemistry
- The Chinese University of Hong Kong
- China
| | - Xiaohu Zhou
- Department of Chemistry
- The Chinese University of Hong Kong
- China
| | - Han Wu
- Department of Chemistry
- The Chinese University of Hong Kong
- China
| | - Bo Zheng
- Department of Chemistry
- The Chinese University of Hong Kong
- China
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27
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Kim H, Kim HS, Lee D, Shin D, Shin D, Kim J, Kim J. Microwave-Assisted Protein Digestion in a Plate Well for Facile Sampling and Rapid Digestion. Anal Chem 2017; 89:10655-10660. [PMID: 28945068 DOI: 10.1021/acs.analchem.7b02169] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Protein digestion is one of the most important processes in proteomic analysis. Here, we report microwave-assisted protein digestion in a plate well, which allows for facile sampling as well as rapid protein digestion based on the combination of highly stable enzyme immobilization and 3D printing technologies. Trypsin (TR) was immobilized on polystyrene-based nanofibers via an enzyme coating (EC) approach. The EC with stabilized TR activity was assembled with the 3D-printed structure in the plate well (EC/3D), which provides two separated compartments for the solution sampling and the TR-catalyzed protein digestion, respectively. EC/3D can effectively prevent the interference of sampling by accommodating EC in the separated compartment from the sampling hole in the middle. EC/3D in the plate well maintained its protein digestion performance under shaking over 160 days. Microwave irradiation enabled the digestion of bovine serum albumin within 10 min, generating the MALDI-TOF MS results of 75.0% sequence coverage and 61 identified peptides. EC/3D maintained its protein digestion performance under microwave irradiation after 30 times of recycled uses. EC/3D in the plate well has demonstrated its potential as a robust and facile tool for the development of an automated protein digestion platform. The combination of stable immobilized enzymes and 3D-printed structures can be potentially utilized not only for the protein digestion, but also for many other enzyme applications, including bioconversion and biosensors.
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Affiliation(s)
- Hyeonil Kim
- Department of Chemical and Biological Engineering, Korea University , Seoul 02841, Republic of Korea
| | - Han Sol Kim
- Department of Chemical and Biological Engineering, Korea University , Seoul 02841, Republic of Korea
| | - Dabin Lee
- Department of Chemistry, Chungnam National University , Daejeon 34134, Republic of Korea
| | - Dongwon Shin
- Department of Chemistry, Chungnam National University , Daejeon 34134, Republic of Korea
| | - Daeho Shin
- Bio Medical Technologies Co., Ltd., Seoul 04598, Republic of Korea
| | - Jeongkwon Kim
- Department of Chemistry, Chungnam National University , Daejeon 34134, Republic of Korea
| | - Jungbae Kim
- Department of Chemical and Biological Engineering, Korea University , Seoul 02841, Republic of Korea
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28
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Paper and Fiber-Based Bio-Diagnostic Platforms: Current Challenges and Future Needs. APPLIED SCIENCES-BASEL 2017. [DOI: 10.3390/app7080863] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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29
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Atacan K, Çakıroğlu B, Özacar M. Efficient protein digestion using immobilized trypsin onto tannin modified Fe 3 O 4 magnetic nanoparticles. Colloids Surf B Biointerfaces 2017; 156:9-18. [DOI: 10.1016/j.colsurfb.2017.04.055] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Revised: 03/24/2017] [Accepted: 04/27/2017] [Indexed: 12/11/2022]
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30
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Stability and activity of immobilized trypsin on carboxymethyl chitosan-functionalized magnetic nanoparticles cross-linked with carbodiimide and glutaraldehyde. J Chromatogr B Analyt Technol Biomed Life Sci 2017; 1054:57-63. [DOI: 10.1016/j.jchromb.2017.04.016] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2016] [Revised: 03/06/2017] [Accepted: 04/07/2017] [Indexed: 11/19/2022]
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31
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Development of an enzymatic reactor applying spontaneously adsorbed trypsin on the surface of a PDMS microfluidic device. Anal Bioanal Chem 2017; 409:3573-3585. [DOI: 10.1007/s00216-017-0295-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Revised: 02/23/2017] [Accepted: 03/02/2017] [Indexed: 10/20/2022]
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32
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Wouters B, Dapic I, Valkenburg TS, Wouters S, Niezen L, Eeltink S, Corthals GL, Schoenmakers PJ. A cyclic-olefin-copolymer microfluidic immobilized-enzyme reactor for rapid digestion of proteins from dried blood spots. J Chromatogr A 2017; 1491:36-42. [DOI: 10.1016/j.chroma.2017.01.078] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Revised: 01/19/2017] [Accepted: 01/27/2017] [Indexed: 11/27/2022]
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33
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Kecskemeti A, Gaspar A. Preparation and characterization of a packed bead immobilized trypsin reactor integrated into a PDMS microfluidic chip for rapid protein digestion. Talanta 2017; 166:275-283. [PMID: 28213235 DOI: 10.1016/j.talanta.2017.01.060] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Revised: 01/20/2017] [Accepted: 01/24/2017] [Indexed: 01/20/2023]
Abstract
This paper demonstrates the design, efficiency and applicability of a simple, inexpensive and high sample throughput microchip immobilized enzymatic reactor (IMER) for rapid protein digestion. The IMER contains conventional silica particles with covalently immobilized trypsin packed inside of a poly(dimethylsiloxane) (PDMS) microchip channel (10mm×1mm×35µm). The microchip consists of 9 different channels, enabling 9 simultaneous protein digestions. Trypsin was covalently immobilized using carbodiimide activation, the ideal trypsin/silica particle ratio (i.e. measured mass ratio before the immobilization reaction) was determined. The amount of immobilized trypsin was 10-15μg trypsin for 1mg silica particle. Migration times of CZE peptide maps showed good repeatability and reproducibility (RSD%=0.02-0.31%). The IMER maintained its activity for 2 months, in this period it was used effectively for rapid proteolysis. Four proteins (myoglobin, lysozyme, hemoglobin and albumin) in a wide size range (15-70kDa) were digested to demonstrate the applicability of the reactor. Their CZE peptide maps were compared to peptide maps obtained from standard in-solution digestion of the four proteins. The number of peptide peaks correlated well with the theoretically expected peptide number in both cases, the peak patterns of the electropherograms were similar, however, digestion with the microchip IMER requires only <10s, while in-solution digestion takes 16h. LC-MS/MS peptide mapping was also carried out, the four proteins were identified with satisfying sequence coverages (29-50%), trypsin autolysis peptides were not detected. The protein content of human serum was digested with the IMER and with in-solution digestion.
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Affiliation(s)
- Adam Kecskemeti
- Department of Inorganic and Analytical Chemistry, University of Debrecen, Egyetem ter 1, Debrecen 4032, Hungary
| | - Attila Gaspar
- Department of Inorganic and Analytical Chemistry, University of Debrecen, Egyetem ter 1, Debrecen 4032, Hungary.
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34
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Dong J, Ning W, Liu W, Bruening ML. Limited proteolysis in porous membrane reactors containing immobilized trypsin. Analyst 2017; 142:2578-2586. [DOI: 10.1039/c7an00778g] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Trypsin-containing membranes effect limited digestion to identify facile digestion sites in protein structures.
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Affiliation(s)
- Jinlan Dong
- Department of Chemistry
- Michigan State University
- East Lansing
- USA
| | - Wenjing Ning
- Department of Chemistry
- Michigan State University
- East Lansing
- USA
| | - Weijing Liu
- Department of Chemistry
- University of Notre Dame
- Notre Dame
- USA
| | - Merlin L. Bruening
- Department of Chemistry
- University of Notre Dame
- Notre Dame
- USA
- Department of Chemical & Biomolecular Engineering
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35
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Kayili HM, Salih B. Fast and efficient proteolysis by reusable pepsin-encapsulated magnetic sol-gel material for mass spectrometry-based proteomics applications. Talanta 2016; 155:78-86. [DOI: 10.1016/j.talanta.2016.04.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2015] [Revised: 03/30/2016] [Accepted: 04/05/2016] [Indexed: 01/11/2023]
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36
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Development of immobilized-pepsin microreactors coupled to nano liquid chromatography and tandem mass spectrometry for the quantitative analysis of human butyrylcholinesterase. J Chromatogr A 2016; 1461:84-91. [DOI: 10.1016/j.chroma.2016.07.058] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Revised: 07/21/2016] [Accepted: 07/22/2016] [Indexed: 01/25/2023]
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37
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Ruan G, Wu Z, Huang Y, Wei M, Su R, Du F. An easily regenerable enzyme reactor prepared from polymerized high internal phase emulsions. Biochem Biophys Res Commun 2016; 473:54-60. [DOI: 10.1016/j.bbrc.2016.03.049] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Accepted: 03/11/2016] [Indexed: 12/15/2022]
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38
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Wichert WRA, Han D, Bohn PW. Effects of molecular confinement and crowding on horseradish peroxidase kinetics using a nanofluidic gradient mixer. LAB ON A CHIP 2016; 16:877-883. [PMID: 26792298 DOI: 10.1039/c5lc01413a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The effects of molecular confinement and crowding on enzyme kinetics were studied at length scales and under conditions similar to those found in biological cells. These experiments were carried out using a nanofluidic network of channels constituting a nanofluidic gradient mixer, providing the basis for measuring multiple experimental conditions simultaneously. The 100 nm × 40 μm nanochannels were wet etched directly into borosilicate glass, then annealed and characterized with fluorescein emission prior to kinetic measurements. The nanofluidic gradient mixer was then used to measure the kinetics of the conversion of the horseradish peroxidase (HRP)-catalyzed conversion of non-fluorescent Amplex Red (AR) to the fluorescent product resorufin in the presence of hydrogen peroxide (H2O2). The design of the gradient mixer allows reaction kinetics to be studied under multiple (five) unique solution compositions in a single experiment. To characterize the efficiency of the device the effects of confinement on HRP-catalyzed AR conversion kinetics were studied by varying the starting ratio of AR : H2O2. Equimolar concentrations of Amplex Red and H2O2 yielded the highest reaction rates followed by 2 : 1, 1 : 2, 5 : 1, and finally 1 : 5 [AR] : [H2O2]. Under all conditions, initial reaction velocities were decreased by excess H2O2. Crowding effects on kinetics were studied by increasing solution viscosity in the nanochannels in the range 1.0-1.6 cP with sucrose. Increasing the solution viscosities in these confined geometries decreases the initial reaction velocity at the highest concentration from 3.79 μM min(-1) at 1.00 cP to 0.192 μM min(-1) at 1.59 cP. Variations in reaction velocity are interpreted in the context of models for HRP catalysis and for molecular crowding.
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Affiliation(s)
- William R A Wichert
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA.
| | - Donghoon Han
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Paul W Bohn
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA. and Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, IN 46556, USA
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39
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Qiao J, Kim JY, Wang YY, Qi L, Wang FY, Moon MH. Trypsin immobilization in ordered porous polymer membranes for effective protein digestion. Anal Chim Acta 2015; 906:156-164. [PMID: 26772135 DOI: 10.1016/j.aca.2015.11.042] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Revised: 11/26/2015] [Accepted: 11/28/2015] [Indexed: 02/01/2023]
Abstract
Fast and effective protein digestion is a vital process for mass spectrometry (MS) based protein analysis. This study introduces a porous polymer membrane enzyme reactor (PPMER) coupled to nanoflow liquid chromatography-tandem MS (nLC-ESI-MS/MS) for on-line digestion and analysis of proteins. Poly (styrene-co-maleic anhydride) (PS-co-MAn) was fabricated by the breath figure method to make a porous polymer membrane in which the MAn group was covalently bound to enzyme. Based on this strategy, microscale PPMER (μPPMER) was constructed for on-line connection with the nLC-ESI-MS/MS system. Its capability for enzymatic digestion with bovine serum albumin (BSA) was evaluated with varied digestion periods. The on-line proteolysis of BSA and subsequent analysis with μPPMER-nLC-ESI-MS/MS revealed that peptide sequence coverage increased from 10.3% (digestion time 10 min) to 89.1% (digestion time 30 min). μPPMER can efficiently digest proteins due to the microscopic confinement effect, showing its potential application in fast protein identification and protease immobilization. Applications of on-line digestion using μPPMER with human plasma and urinary proteome samples showed that the developed on-line method yielded equivalent or better performance in protein coverage and identified more membrane proteins than the in-solution method. This may be due to easy accommodation of hydrophobic membrane proteins within membrane pores.
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Affiliation(s)
- Juan Qiao
- Beijing National Laboratory for Molecular Sciences; Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, No. 2 Zhongguancun Beiyijie, Beijing 100190, PR China
| | - Jin Yong Kim
- Department of Chemistry, Yonsei University, 50 Yonsei-ro, Seoul 120-749, South Korea
| | - Yuan Yuan Wang
- Beijing National Laboratory for Molecular Sciences; Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, No. 2 Zhongguancun Beiyijie, Beijing 100190, PR China
| | - Li Qi
- Beijing National Laboratory for Molecular Sciences; Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, No. 2 Zhongguancun Beiyijie, Beijing 100190, PR China.
| | - Fu Yi Wang
- Beijing National Laboratory for Molecular Sciences; Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, No. 2 Zhongguancun Beiyijie, Beijing 100190, PR China
| | - Myeong Hee Moon
- Department of Chemistry, Yonsei University, 50 Yonsei-ro, Seoul 120-749, South Korea.
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Ning W, Bruening ML. Rapid Protein Digestion and Purification with Membranes Attached to Pipet Tips. Anal Chem 2015; 87:11984-9. [DOI: 10.1021/acs.analchem.5b03679] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Wenjing Ning
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, United States
| | - Merlin L. Bruening
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, United States
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Dulay MT, Eberlin LS, Zare RN. Protein Analysis by Ambient Ionization Mass Spectrometry Using Trypsin-Immobilized Organosiloxane Polymer Surfaces. Anal Chem 2015; 87:12324-30. [PMID: 26567450 DOI: 10.1021/acs.analchem.5b03669] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
In the growing field of proteomic research, rapid and simple protein analysis is a crucial component of protein identification. We report the use of immobilized trypsin on hybrid organic-inorganic organosiloxane (T-OSX) polymers for the on-surface, in situ digestion of four model proteins: melittin, cytochrome c, myoglobin, and bovine serum albumin. Tryptic digestion products were sampled, detected, and identified using desorption electrospray ionization mass spectrometry (DESI-MS) and nanoDESI-MS. These novel, reusable T-OSX arrays on glass slides allow for protein digestion in methanol:water solvents (1:1, v/v) and analysis directly from the same polymer surface without the need for sample preparation, high temperature, and pH conditions typically required for in-solution trypsin digestions. Digestion reactions were conducted with 2 μL protein sample droplets (0.35 mM) at incubation temperatures of 4, 25, 37, and 65 °C and digestion reaction times between 2 and 24 h. Sequence coverages were dependent on the hydrophobicity of the OSX polymer support and varied by temperature and digestion time. Under the best conditions, the sequence coverages, determined by DESI-MS, were 100% for melittin, 100% for cytochrome c, 90% for myoglobin, and 65% for bovine serum albumin.
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Affiliation(s)
- Maria T Dulay
- Department of Chemistry, Stanford University , Stanford, California 94305, United States
| | - Livia S Eberlin
- Department of Chemistry, Stanford University , Stanford, California 94305, United States
| | - Richard N Zare
- Department of Chemistry, Stanford University , Stanford, California 94305, United States
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Dong J, Bruening ML. Functionalizing Microporous Membranes for Protein Purification and Protein Digestion. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2015; 8:81-100. [PMID: 26001953 DOI: 10.1146/annurev-anchem-071114-040255] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
This review examines advances in the functionalization of microporous membranes for protein purification and the development of protease-containing membranes for controlled protein digestion prior to mass spectrometry analysis. Recent studies confirm that membranes are superior to bead-based columns for rapid protein capture, presumably because convective mass transport in membrane pores rapidly brings proteins to binding sites. Modification of porous membranes with functional polymeric films or TiO₂ nanoparticles yields materials that selectively capture species ranging from phosphopeptides to His-tagged proteins, and protein-binding capacities often exceed those of commercial beads. Thin membranes also provide a convenient framework for creating enzyme-containing reactors that afford control over residence times. With millisecond residence times, reactors with immobilized proteases limit protein digestion to increase sequence coverage in mass spectrometry analysis and facilitate elucidation of protein structures. This review emphasizes the advantages of membrane-based techniques and concludes with some challenges for their practical application.
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Affiliation(s)
- Jinlan Dong
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824;
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Li Y, Yan L, Liu Y, Qian K, Liu B, Yang P, Liu B. High-efficiency nano/micro-reactors for protein analysis. RSC Adv 2015. [DOI: 10.1039/c4ra12333f] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
This article reviews the recent advances regarding the development of nanomaterial-based nanoreactors and microfluidic droplet reactors and their applications in protein analysis.
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Affiliation(s)
- Yixin Li
- Department of Chemistry and Institutes of Biomedical Sciences
- Fudan University
- Shanghai 200433
- China
| | - Ling Yan
- Department of Chemistry and Institutes of Biomedical Sciences
- Fudan University
- Shanghai 200433
- China
| | - Yun Liu
- Department of Chemistry and Institutes of Biomedical Sciences
- Fudan University
- Shanghai 200433
- China
| | - Kun Qian
- Center for Bio-Nano-Chips and Diagnostics in Translational Medicine
- School of Biomedical Engineering and Med-X Research Institute
- Shanghai Jiao Tong University
- Shanghai
- China
| | - Bin Liu
- Center for Bio-Nano-Chips and Diagnostics in Translational Medicine
- School of Biomedical Engineering and Med-X Research Institute
- Shanghai Jiao Tong University
- Shanghai
- China
| | - Pengyuan Yang
- Department of Chemistry and Institutes of Biomedical Sciences
- Fudan University
- Shanghai 200433
- China
| | - Baohong Liu
- Department of Chemistry and Institutes of Biomedical Sciences
- Fudan University
- Shanghai 200433
- China
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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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Zhang Y, Sargent JL, Boudouris BW, Phillip WA. Nanoporous membranes generated from self-assembled block polymer precursors:Quo Vadis? J Appl Polym Sci 2014. [DOI: 10.1002/app.41683] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Yizhou Zhang
- Department of Chemical and Biomolecular Engineering; University of Notre Dame; Notre Dame Indiana 46556
| | - Jessica L. Sargent
- School of Chemical Engineering, Purdue University; West Lafayette Indiana 47907
| | - Bryan W. Boudouris
- School of Chemical Engineering, Purdue University; West Lafayette Indiana 47907
| | - William A. Phillip
- Department of Chemical and Biomolecular Engineering; University of Notre Dame; Notre Dame Indiana 46556
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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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Shi C, Deng C, Li Y, Zhang X, Yang P. Hydrophilic polydopamine-coated magnetic graphene nanocomposites for highly efficient tryptic immobilization. Proteomics 2014; 14:1457-63. [DOI: 10.1002/pmic.201300487] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2013] [Revised: 01/10/2014] [Accepted: 04/01/2014] [Indexed: 11/10/2022]
Affiliation(s)
- Chenyi Shi
- Department of Chemistry and Institutes of Biomedical Sciences; Fudan University; Shanghai P. R. China
| | - Chunhui Deng
- Department of Chemistry and Institutes of Biomedical Sciences; Fudan University; Shanghai P. R. China
| | - Yan Li
- Pharmaceutical Analysis Department; School of Pharmacy, Fudan University; Shanghai P. R. China
| | - Xiangmin Zhang
- Department of Chemistry and Institutes of Biomedical Sciences; Fudan University; Shanghai P. R. China
| | - Pengyuan Yang
- Department of Chemistry and Institutes of Biomedical Sciences; Fudan University; Shanghai P. R. China
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Çelikbıçak Ö, Atakay M, Güler Ü, Salih B. A Trypsin Immobilized Sol-Gel for Protein Indentification in MALDI-MS Applications. ANAL LETT 2014. [DOI: 10.1080/00032719.2013.831423] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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A colorimetric method for monitoring tryptic digestion prior to shotgun proteomics. INTERNATIONAL JOURNAL OF PROTEOMICS 2014; 2014:125482. [PMID: 24678421 PMCID: PMC3941143 DOI: 10.1155/2014/125482] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/22/2013] [Accepted: 12/23/2013] [Indexed: 11/17/2022]
Abstract
Tryptic digestion is an important preanalytical step in shotgun proteomics because inadequate or excessive digestion can result in a failed or incomplete experiment. Unfortunately, this step is not routinely monitored before mass spectrometry because methods available for protein digestion monitoring either are time/sample consuming or require expensive equipment. To determine if a colorimetric method (ProDM Kit) can be used to identify the extent of tryptic digestion that yields the best proteomics outcome, plasma and serum digested for 8 h and 24 h were screened with ProDM, Bioanalyzer, and LC/MS/MS, and the effect of digestion on the number of proteins identified and sequence coverage was compared. About 6% and 16% less proteins were identified when >50% of proteins were digested in plasma and serum, respectively, compared to when ~46% of proteins were digested. Average sequence coverage for albumin, haptoglobin, and serotransferrin after 2 h, 8 h, and 24 h digestion was 52%, 45%, and 45% for serum and 54%, 47%, and 42% for plasma, respectively. This paper reiterates the importance of optimizing the tryptic digestion step and demonstrates the extent to which ProDM can be used to monitor and standardize protein digestion to achieve better proteomics outcomes.
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