1
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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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2
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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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3
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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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4
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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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5
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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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6
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Zhang X. Less is More: Membrane Protein Digestion Beyond Urea-Trypsin Solution for Next-level Proteomics. Mol Cell Proteomics 2015; 14:2441-53. [PMID: 26081834 DOI: 10.1074/mcp.r114.042572] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Indexed: 12/13/2022] Open
Abstract
The goal of next-level bottom-up membrane proteomics is protein function investigation, via high-coverage high-throughput peptide-centric quantitation of expression, modifications and dynamic structures at systems scale. Yet efficient digestion of mammalian membrane proteins presents a daunting barrier, and prevalent day-long urea-trypsin in-solution digestion proved insufficient to reach this goal. Many efforts contributed incremental advances over past years, but involved protein denaturation that disconnected measurement from functional states. Beyond denaturation, the recent discovery of structure/proteomics omni-compatible detergent n-dodecyl-β-d-maltopyranoside, combined with pepsin and PNGase F columns, enabled breakthroughs in membrane protein digestion: a 2010 DDM-low-TCEP (DLT) method for H/D-exchange (HDX) using human G protein-coupled receptor, and a 2015 flow/detergent-facilitated protease and de-PTM digestions (FDD) for integrative deep sequencing and quantitation using full-length human ion channel complex. Distinguishing protein solubilization from denaturation, protease digestion reliability from theoretical specificity, and reduction from alkylation, these methods shifted day(s)-long paradigms into minutes, and afforded fully automatable (HDX)-protein-peptide-(tandem mass tag)-HPLC pipelines to instantly measure functional proteins at deep coverage, high peptide reproducibility, low artifacts and minimal leakage. Promoting-not destroying-structures and activities harnessed membrane proteins for the next-level streamlined functional proteomics. This review analyzes recent advances in membrane protein digestion methods and highlights critical discoveries for future proteomics.
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Affiliation(s)
- Xi Zhang
- From the ‡Department of Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital, Boston, Massachusetts; §Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts
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7
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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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8
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Cheng G, Hao SJ, Yu X, Zheng SY. Nanostructured microfluidic digestion system for rapid high-performance proteolysis. LAB ON A CHIP 2015; 15:650-4. [PMID: 25511010 PMCID: PMC4304898 DOI: 10.1039/c4lc01165a] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
A novel microfluidic protein digestion system with a nanostructured and bioactive inner surface was constructed by an easy biomimetic self-assembly strategy for rapid and effective proteolysis in 2 minutes, which is faster than the conventional overnight digestion methods. It is expected that this work would contribute to rapid online digestion in future high-throughput proteomics.
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Affiliation(s)
- Gong Cheng
- Department of Biomedical Engineering, The Pennsylvania State University, University Park, PA 16802, USA.
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9
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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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10
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Cheng G, Zheng SY. Construction of a high-performance magnetic enzyme nanosystem for rapid tryptic digestion. Sci Rep 2014; 4:6947. [PMID: 25374397 PMCID: PMC4221791 DOI: 10.1038/srep06947] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2014] [Accepted: 10/20/2014] [Indexed: 01/20/2023] Open
Abstract
A magnetic enzyme nanosystem have been designed and constructed by a polydopamine (PDA)-modification strategy. The magnetic enzyme nanosystem has well defined core-shell structure and a relatively high saturation magnetization (Ms) value of 48.3 emu g(-1). The magnetic enzyme system can realize rapid, efficient and reusable tryptic digestion of proteins by taking advantage of its magnetic core and biofunctional shell. Various standard proteins (e.g. cytochrome C (Cyt-C), myoglobin (MYO) and bovine serum albumin (BSA)) have been used to evaluate the effectiveness of the magnetic enzyme nanosystem. The results show that the magnetic enzyme nanosystem can digest the proteins in 30 minutes, and the results are comparable to conventional 12 hours in-solution digestion. Furthermore, the magnetic enzyme nanosystem is also effective in the digestion of low-concentration proteins, even at as low as 5 ng μL(-1) substrate concentration. Importantly, the system can be reused several times, and has excellent stability for storage. Therefore, this work will be highly beneficial for the rapid digestion and identification of proteins in future proteomics.
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Affiliation(s)
- Gong Cheng
- Department of Biomedical engineering, The Pennsylvania State University, University Park, PA 16802, (USA)
| | - Si-Yang Zheng
- Department of Biomedical engineering, The Pennsylvania State University, University Park, PA 16802, (USA)
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11
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Cheng G, Chen P, Wang ZG, Sui XJ, Zhang JL, Ni JZ. Immobilization of trypsin onto multifunctional meso-/macroporous core-shell microspheres: A new platform for rapid enzymatic digestion. Anal Chim Acta 2014; 812:65-73. [DOI: 10.1016/j.aca.2013.12.035] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2013] [Revised: 12/16/2013] [Accepted: 12/24/2013] [Indexed: 10/25/2022]
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12
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Wang C, Gao M, Zhang P, Zhang X. Efficient Proteolysis of Glycoprotein Using a Hydrophilic Immobilized Enzyme Reactor Coupled with MALDI-QIT-TOF-MS Detection and μHPLC Analysis. Chromatographia 2014. [DOI: 10.1007/s10337-013-2622-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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13
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Evaluating the potential nonthermal microwave effects of microwave-assisted proteolytic reactions. J Proteomics 2013; 80:160-70. [DOI: 10.1016/j.jprot.2013.01.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2012] [Revised: 01/09/2013] [Accepted: 01/09/2013] [Indexed: 11/18/2022]
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14
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Switzar L, Giera M, Niessen WMA. Protein Digestion: An Overview of the Available Techniques and Recent Developments. J Proteome Res 2013; 12:1067-77. [DOI: 10.1021/pr301201x] [Citation(s) in RCA: 164] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Linda Switzar
- AIMMS Division of BioMolecular
Analysis, Faculty of Sciences, VU University Amsterdam, De Boelelaan 1083, 1081 HV, Amsterdam, The Netherlands
| | - Martin Giera
- Division of Molecular Cell Physiology,
Faculty of Earth and Life Sciences, VU University Amsterdam, De Boelelaan 1085, 1081 HV, Amsterdam, The Netherlands
- Biomolecular Mass Spectrometry
Unit, Department of Parasitology, Leiden University Medical Center, P.O. Box 9600, 2300 RC Leiden, The Netherlands
| | - Wilfried M. A. Niessen
- AIMMS Division of BioMolecular
Analysis, Faculty of Sciences, VU University Amsterdam, De Boelelaan 1083, 1081 HV, Amsterdam, The Netherlands
- hyphen MassSpec, de Wetstraat 8, 2332 XT Leiden, The Netherlands
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15
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Rey M, Yang M, Burns KM, Yu Y, Lees-Miller SP, Schriemer DC. Nepenthesin from monkey cups for hydrogen/deuterium exchange mass spectrometry. Mol Cell Proteomics 2012. [PMID: 23197791 DOI: 10.1074/mcp.m112.025221] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Studies of protein dynamics, structure and interactions using hydrogen/deuterium exchange mass spectrometry (HDX-MS) have sharply increased over the past 5-10 years. The predominant technology requires fast digestion at pH 2-3 to retain deuterium label. Pepsin is used almost exclusively, but it provides relatively low efficiency under the constraints of the experiment, and a selectivity profile that renders poor coverage of intrinsically disordered regions. In this study we present nepenthesin-containing secretions of the pitcher plant Nepenthes, commonly called monkey cups, for use in HDX-MS. We show that nepenthesin is at least 1400-fold more efficient than pepsin under HDX-competent conditions, with a selectivity profile that mimics pepsin in part, but also includes efficient cleavage C-terminal to "forbidden" residues K, R, H, and P. High efficiency permits a solution-based analysis with no detectable autolysis, avoiding the complication of immobilized enzyme reactors. Relaxed selectivity promotes high coverage of disordered regions and the ability to "tune" the mass map for regions of interest. Nepenthesin-enriched secretions were applied to an analysis of protein complexes in the nonhomologous end-joining DNA repair pathway. The analysis of XRCC4 binding to the BRCT domains of Ligase IV points to secondary interactions between the disordered C-terminal tail of XRCC4 and remote regions of the BRCT domains, which could only be identified with a nepenthesin-based workflow. HDX data suggest that stalk-binding to XRCC4 primes a BRCT conformation in these remote regions to support tail interaction, an event which may be phosphoregulated. We conclude that nepenthesin is an effective alternative to pepsin for all HDX-MS applications, and especially for the analysis of structural transitions among intrinsically disordered proteins and their binding partners.
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Affiliation(s)
- Martial Rey
- Department of Biochemistry and Molecular Biology and the Southern Alberta Cancer Research Institute, University of Calgary, Calgary, Alberta T2N 4N1, Canada
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16
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Ji J, Nie L, Qiao L, Li Y, Guo L, Liu B, Yang P, Girault HH. Proteolysis in microfluidic droplets: an approach to interface protein separation and peptide mass spectrometry. LAB ON A CHIP 2012; 12:2625-9. [PMID: 22695710 DOI: 10.1039/c2lc40206h] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
A versatile microreactor protocol based on microfluidic droplets has been developed for on-line protein digestion. Proteins separated by liquid chromatography are fractionated in water-in-oil droplets and digested in sequence. The microfluidic reactor acts also as an electrospray ionization emitter for mass spectrometry analysis of the peptides produced in the individual droplets. Each droplet is an enzymatic micro-reaction unit with efficient proteolysis due to rapid mixing, enhanced mass transfer and automated handling. This droplet approach eliminates sample loss, cross-contamination, non-specific absorption and memory effect. A protein mixture was successfully identified using the droplet-based micro-reactor as interface between reverse phase liquid chromatography and mass spectrometry.
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Affiliation(s)
- Ji Ji
- Department of Chemistry, Institute of Biomedical Sciences and State Key Laboratory of Molecular Engineering of Polymers, Fudan University, Shanghai, China
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17
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Yuan H, Zhou Y, Xia S, Zhang L, Zhang X, Wu Q, Liang Z, Zhang Y. Integrated Platform for Proteome Profiling with Combination of Microreversed Phase Based Protein and Peptide Separation via Online Solvent Exchange and Protein Digestion. Anal Chem 2012; 84:5124-32. [DOI: 10.1021/ac3006796] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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18
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Wu Q, Yuan H, Zhang L, Zhang Y. Recent advances on multidimensional liquid chromatography-mass spectrometry for proteomics: from qualitative to quantitative analysis--a review. Anal Chim Acta 2012; 731:1-10. [PMID: 22652259 DOI: 10.1016/j.aca.2012.04.010] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2012] [Revised: 04/09/2012] [Accepted: 04/09/2012] [Indexed: 02/08/2023]
Abstract
With the acceleration of proteome research, increasing attention has been paid to multidimensional liquid chromatography-mass spectrometry (MDLC-MS) due to its high peak capacity and separation efficiency. Recently, many efforts have been put to improve MDLC-based strategies including "top-down" and "bottom-up" to enable highly sensitive qualitative and quantitative analysis of proteins, as well as accelerate the whole analytical procedure. Integrated platforms with combination of sample pretreatment, multidimensional separations and identification were also developed to achieve high throughput and sensitive detection of proteomes, facilitating highly accurate and reproducible quantification. This review summarized the recent advances of such techniques and their applications in qualitative and quantitative analysis of proteomes.
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Affiliation(s)
- Qi Wu
- Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
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Kim BR, Huyen TT, Han NY, Park JM, Yu US, Lee HK. Acoustic technology-assisted rapid proteolysis for high-throughput proteome analysis. ANALYTICAL SCIENCE AND TECHNOLOGY 2011. [DOI: 10.5806/ast.2011.24.6.510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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20
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Rapid and efficient proteolysis through laser-assisted immobilized enzyme reactors. J Chromatogr A 2011; 1218:8567-71. [DOI: 10.1016/j.chroma.2011.09.084] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2011] [Revised: 09/09/2011] [Accepted: 09/28/2011] [Indexed: 11/20/2022]
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21
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Enzyme digestion of entrapped single-DNA molecules in nanopores. Talanta 2011; 85:2135-41. [PMID: 21872069 DOI: 10.1016/j.talanta.2011.07.058] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2011] [Revised: 07/12/2011] [Accepted: 07/15/2011] [Indexed: 12/21/2022]
Abstract
The real-time digestion of entrapped single-DNA molecules by λ-exonuclease in nanoporous alumina membranes was observed using an epifluorescence microscope. The alumina membrane provides pL (∼ 10(-12)L) containers for confining single-DNA molecules without immobilization. When one end of the DNA molecule was inserted into a nanopore, it was possible to monitor the digestion process outside, near and inside the pore, where the individual DNA molecules exhibited different characteristic digestion modes. The digestion rates calculated from the decrease in fluorescence intensity showed different values according to the location of the individual molecules. Entrapment rather than immobilization allows the DNA strand to be fully exposed to the enzyme and the reaction buffer. These results confirm that the enzymatic digestion of DNA molecules is affected by their three-dimensional (3D) environment.
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22
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23
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A novel organic-inorganic hybrid monolith for trypsin immobilization. SCIENCE CHINA-LIFE SCIENCES 2011; 54:54-9. [DOI: 10.1007/s11427-010-4108-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2010] [Accepted: 08/17/2010] [Indexed: 10/18/2022]
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24
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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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25
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Hou C, Yuan H, Qiao X, Liu J, Shan Y, Zhang L, Liang Z, Zhang Y. Weak anion and cation exchange mixed-bed microcolumn for protein separation. J Sep Sci 2010; 33:3299-303. [DOI: 10.1002/jssc.201000440] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Yao G, Deng C, Zhang X, Yang P. Efficient Tryptic Proteolysis Accelerated by Laser Radiation for Peptide Mapping in Proteome Analysis. Angew Chem Int Ed Engl 2010; 49:8185-9. [DOI: 10.1002/anie.201004152] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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27
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Efficient Tryptic Proteolysis Accelerated by Laser Radiation for Peptide Mapping in Proteome Analysis. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.201004152] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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28
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Krenkova J, Lacher NA, Svec F. Highly efficient enzyme reactors containing trypsin and endoproteinase LysC immobilized on porous polymer monolith coupled to MS suitable for analysis of antibodies. Anal Chem 2010; 81:2004-12. [PMID: 19186936 DOI: 10.1021/ac8026564] [Citation(s) in RCA: 151] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Capillary enzymatic microreactors containing trypsin and endoproteinase LysC immobilized on a porous polymer monolith have been prepared and used for the characterization and identification of proteins such as cytochrome c, bovine serum albumin, and high-molecular weight human immunoglobulin G. The hydrophilicity of diol functionalities originating from the hydrolyzed poly(glycidyl methacrylate-co-ethylene dimethacrylate) monolith was not sufficient to avoid adsorption of hydrophobic albumin in a highly aqueous mobile phase. Therefore, this monolith was first hydrophilized via photografting of poly(ethylene glycol) methacrylate followed by photografting of a 4-vinyl-2,2-dimethylazlactone to provide the pore surface with reactive functionalities required for immobilization. This new approach reduced the undesired nonspecific adsorption of proteins and peptides and facilitated control of both the enzyme immobilization and protein digestion processes. The enzymatic reactors were coupled off-line with MALDI/TOF MS and/or on-line with ESI/TOF MS. Experimental conditions for digestion were optimized using cytochrome c and bovine serum albumin as model proteins. The optimized reactors were then integrated into a multidimensional system comprised of a monolithic capillary enzyme reactor, an in-line nanoLC separation of peptides using a poly(lauryl methacrylate-co-ethylene dimethacrylate) monolithic column, and ESI/TOF MS. With the use of this system, immunoglobulin G was digested at room temperature in 6 min to an extent similar to that achieved with soluble enzyme at 37 degrees C after 24 h.
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Affiliation(s)
- Jana Krenkova
- The Molecular Foundry, E. O. Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
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29
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López-Ferrer D, Petritis K, Robinson EW, Hixson KK, Tian Z, Lee JH, Lee SW, Tolić N, Weitz KK, Belov ME, Smith RD, Pasa-Tolić L. Pressurized pepsin digestion in proteomics: an automatable alternative to trypsin for integrated top-down bottom-up proteomics. Mol Cell Proteomics 2010; 10:M110.001479. [PMID: 20627868 PMCID: PMC3033671 DOI: 10.1074/mcp.m110.001479] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Integrated top-down bottom-up proteomics combined with on-line digestion has great potential to improve the characterization of protein isoforms in biological systems and is amendable to high throughput proteomics experiments. Bottom-up proteomics ultimately provides the peptide sequences derived from the tandem MS analyses of peptides after the proteome has been digested. Top-down proteomics conversely entails the MS analyses of intact proteins for more effective characterization of genetic variations and/or post-translational modifications. Herein, we describe recent efforts toward efficient integration of bottom-up and top-down LC-MS-based proteomics strategies. Since most proteomics separations utilize acidic conditions, we exploited the compatibility of pepsin (where the optimal digestion conditions are at low pH) for integration into bottom-up and top-down proteomics work flows. Pressure-enhanced pepsin digestions were successfully performed and characterized with several standard proteins in either an off-line mode using a Barocycler or an on-line mode using a modified high pressure LC system referred to as a fast on-line digestion system (FOLDS). FOLDS was tested using pepsin and a whole microbial proteome, and the results were compared against traditional trypsin digestions on the same platform. Additionally, FOLDS was integrated with a RePlay configuration to demonstrate an ultrarapid integrated bottom-up top-down proteomics strategy using a standard mixture of proteins and a monkey pox virus proteome.
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Affiliation(s)
- Daniel López-Ferrer
- Biological Science Division, Pacific Northwest National Laboratory, Richland, Washington 99354, USA.
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30
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Sun L, Ma J, Qiao X, Liang Y, Zhu G, Shan Y, Liang Z, Zhang L, Zhang Y. Integrated Device for Online Sample Buffer Exchange, Protein Enrichment, and Digestion. Anal Chem 2010; 82:2574-9. [DOI: 10.1021/ac902835p] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Liangliang Sun
- National Chromatographic R. & A. Center, Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian 116023, China, and Graduate School of Chinese Academy of Sciences, Beijing 100039, China
| | - Junfeng Ma
- National Chromatographic R. & A. Center, Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian 116023, China, and Graduate School of Chinese Academy of Sciences, Beijing 100039, China
| | - Xiaoqiang Qiao
- National Chromatographic R. & A. Center, Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian 116023, China, and Graduate School of Chinese Academy of Sciences, Beijing 100039, China
| | - Yu Liang
- National Chromatographic R. & A. Center, Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian 116023, China, and Graduate School of Chinese Academy of Sciences, Beijing 100039, China
| | - Guijie Zhu
- National Chromatographic R. & A. Center, Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian 116023, China, and Graduate School of Chinese Academy of Sciences, Beijing 100039, China
| | - Yichu Shan
- National Chromatographic R. & A. Center, Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian 116023, China, and Graduate School of Chinese Academy of Sciences, Beijing 100039, China
| | - Zhen Liang
- National Chromatographic R. & A. Center, Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian 116023, China, and Graduate School of Chinese Academy of Sciences, Beijing 100039, China
| | - Lihua Zhang
- National Chromatographic R. & A. Center, Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian 116023, China, and Graduate School of Chinese Academy of Sciences, Beijing 100039, China
| | - Yukui Zhang
- National Chromatographic R. & A. Center, Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian 116023, China, and Graduate School of Chinese Academy of Sciences, Beijing 100039, China
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31
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Yuan H, Zhang L, Hou C, Zhu G, Tao D, Liang Z, Zhang Y. Integrated platform for proteome analysis with combination of protein and peptide separation via online digestion. Anal Chem 2010; 81:8708-14. [PMID: 19788244 DOI: 10.1021/ac900310y] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
An integrated platform with the combination of protein and peptide separation was established via online protein digestion, by which proteins were first separated by a microcolumn packed with mixed weak anion and weak cation exchange (WAX/WCX) particles under a series of salt steps, online digested by a trypsin immobilized microenzymatic reactor (IMER), trapped and desalted by two parallel C8 precolumns, separated by microreversed-phase liquid chromatography (muRPLC) under a linear gradient of organic modifier concentration, and finally identified by electrospray ionization-MS/MS (ESI-MS/MS). To evaluate the performance of such a platform, a mixture of myoglobin, cytochrome c, bovine serum albumin (BSA), and alpha-casein, with mass ranging from 25 ng to 2 microg, was analyzed. Compared to the methods by off-line protein fractionation and shotgun based strategy, the analysis time, including sample preparation, digestion, desalting, separation, and detection, was shortened from ca. 30 to 5 h, and cytochrome c with abundance of 25 ng could be identified with improved sequence coverage. Furthermore, such an integrated platform was successfully applied into the analysis of proteins extracted from human lung cancer cells. Compared with the results obtained by the shotgun approach, the identified protein number was increased by 30%. All these results demonstrated that such an integrated approach would be an attractive alternative to commonly applied approaches for proteome research.
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Affiliation(s)
- Huiming Yuan
- Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
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32
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Accelerated digestion for high-throughput proteomics analysis of whole bacterial proteomes. J Microbiol Methods 2010; 80:56-62. [DOI: 10.1016/j.mimet.2009.10.019] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2009] [Revised: 10/27/2009] [Accepted: 10/29/2009] [Indexed: 11/21/2022]
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33
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Percy AJ, Schriemer DC. Rheostatic control of tryptic digestion in a microscale fluidic system. Anal Chim Acta 2010; 657:53-9. [DOI: 10.1016/j.aca.2009.10.019] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2009] [Revised: 09/17/2009] [Accepted: 10/09/2009] [Indexed: 11/25/2022]
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34
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Chen SP, Yu XD, Xu JJ, Chen HY. Lab-on-a-chip for analysis of triglycerides based on a replaceable enzyme carrier using magnetic beads. Analyst 2010; 135:2979-86. [DOI: 10.1039/c0an00231c] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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35
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Whiteaker JR, Zhao L, Anderson L, Paulovich AG. An automated and multiplexed method for high throughput peptide immunoaffinity enrichment and multiple reaction monitoring mass spectrometry-based quantification of protein biomarkers. Mol Cell Proteomics 2009; 9:184-96. [PMID: 19843560 DOI: 10.1074/mcp.m900254-mcp200] [Citation(s) in RCA: 286] [Impact Index Per Article: 19.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
There is an urgent need for quantitative assays in verifying and validating the large numbers of protein biomarker candidates produced in modern "-omics" experiments. Stable isotope standards with capture by anti-peptide antibodies (SISCAPA) has shown tremendous potential to meet this need by combining peptide immunoaffinity enrichment with quantitative mass spectrometry. In this study, we describe three significant advances to the SISCAPA technique. First, we develop a method for an automated magnetic bead-based platform capable of high throughput processing. Second, we implement the automated method in a multiplexed SISCAPA assay (nine targets in one assay) and assess the performance characteristics of the multiplexed assay. Using the automated, multiplexed platform, we demonstrate detection limits in the physiologically relevant ng/ml range (from 10 microl of plasma) with sufficient precision (median coefficient of variation, 12.6%) for quantifying biomarkers. Third, we demonstrate that enrichment of peptides from larger volumes of plasma (1 ml) can extend the limits of detection to the low pg/ml range of protein concentration. The method is generally applicable to any protein or biological specimen of interest and holds great promise for analyzing large numbers of biomarker candidates.
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36
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Gao M, Zhang P, Hong G, Guan X, Yan G, Deng C, Zhang X. Novel monolithic enzymatic microreactor based on single-enzyme nanoparticles for highly efficient proteolysis and its application in multidimensional liquid chromatography. J Chromatogr A 2009; 1216:7472-7. [DOI: 10.1016/j.chroma.2009.05.003] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2009] [Revised: 04/25/2009] [Accepted: 05/04/2009] [Indexed: 10/20/2022]
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37
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Yuan H, Zhou Y, Zhang L, Liang Z, Zhang Y. Integrated protein analysis platform based on column switch recycling size exclusion chromatography, microenzymatic reactor and μRPLC–ESI-MS/MS. J Chromatogr A 2009; 1216:7478-82. [DOI: 10.1016/j.chroma.2009.06.019] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2009] [Revised: 05/31/2009] [Accepted: 06/03/2009] [Indexed: 11/25/2022]
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38
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Overview on modern approaches to speed up protein identification workflows relying on enzymatic cleavage and mass spectrometry-based techniques. Anal Chim Acta 2009; 650:151-9. [DOI: 10.1016/j.aca.2009.07.034] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2009] [Revised: 07/14/2009] [Accepted: 07/15/2009] [Indexed: 11/19/2022]
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39
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López-Ferrer D, Petritis K, Lourette NM, Clowers B, Hixson KK, Heibeck T, Prior DC, Pasa-Tolić L, Camp DG, Belov ME, Smith RD. On-line digestion system for protein characterization and proteome analysis. Anal Chem 2009; 80:8930-6. [PMID: 19551971 DOI: 10.1021/ac800927v] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
An efficient on-line digestion system that reduces the number of sample manipulation steps has been demonstrated for high-throughput proteomics. By incorporating a pressurized sample loop into a liquid chromatography-based separation system, both sample and enzyme (e.g., trypsin) can be simultaneously introduced to produce a complete, yet rapid digestion. Both standard proteins and a complex Shewanella oneidensis global protein extract were digested and analyzed using the automated online pressurized digestion system coupled to an ion mobility time-of-flight mass spectrometer, an ion trap mass spectrometer, or both. The system denatured, digested, and separated product peptides in a manner of minutes, making it amenable to on-line high-throughput applications. In addition to simplifying and expediting sample processing, the system was easy to implement and no cross-contamination was observed among samples. As a result, the online digestion system offers a powerful approach for high-throughput screening of proteins that could prove valuable in biochemical research (rapid screening of protein-based drugs).
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Affiliation(s)
- Daniel López-Ferrer
- Biological Sciences Division, Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99352, USA
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40
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Ma J, Liu J, Sun L, Gao L, Liang Z, Zhang L, Zhang Y. Online Integration of Multiple Sample Pretreatment Steps Involving Denaturation, Reduction, and Digestion with Microflow Reversed-Phase Liquid Chromatography−Electrospray Ionization Tandem Mass Spectrometry for High-Throughput Proteome Profiling. Anal Chem 2009; 81:6534-40. [DOI: 10.1021/ac900971w] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Junfeng Ma
- Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China and Graduate School of Chinese Academy of Sciences, Beijing 100039, China
| | - Jinxiang Liu
- Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China and Graduate School of Chinese Academy of Sciences, Beijing 100039, China
| | - Liangliang Sun
- Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China and Graduate School of Chinese Academy of Sciences, Beijing 100039, China
| | - Liang Gao
- Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China and Graduate School of Chinese Academy of Sciences, Beijing 100039, China
| | - Zhen Liang
- Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China and Graduate School of Chinese Academy of Sciences, Beijing 100039, China
| | - Lihua Zhang
- Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China and Graduate School of Chinese Academy of Sciences, Beijing 100039, China
| | - Yukui Zhang
- Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China and Graduate School of Chinese Academy of Sciences, Beijing 100039, China
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41
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Abstract
An accelerated protein digestion procedure is described that features a microscale trypsin cartridge operated under aqueous-organic conditions. High sequence coverage digestions obtained in seconds with small amounts of enzyme are possible with the approach, which also supports online integration of digestion with reversed-phase protein separation. The construction and operation of effective digestor cartridges for rapid sample processing are described. For workflows involving chromatographic protein separation an easily assembled fluidic system is presented, which inserts the digestion step after column-based separation. Successful integration requires dynamic effluent titration immediately prior to transmission through the digestor. This is achieved through the co-ordination of the column gradient system with an inverse gradient system to produce steady pH and organic solvent levels. System assembly and operation sufficient for achieving digestion and identification of subnanogram levels of protein are described.
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42
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Ma J, Zhang L, Liang Z, Zhang W, Zhang Y. Recent advances in immobilized enzymatic reactors and their applications in proteome analysis. Anal Chim Acta 2009; 632:1-8. [DOI: 10.1016/j.aca.2007.08.045] [Citation(s) in RCA: 100] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2007] [Revised: 08/26/2007] [Accepted: 08/28/2007] [Indexed: 11/26/2022]
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43
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Functionalized magnetic carbonaceous microspheres for trypsin immobilization and the application to fast proteolysis. J Chromatogr A 2008; 1215:82-91. [DOI: 10.1016/j.chroma.2008.10.114] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2008] [Revised: 10/24/2008] [Accepted: 10/29/2008] [Indexed: 11/18/2022]
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44
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Tran BQ, Loftheim H, Reubsaet L, Lundanes E, Greibrokk T. On-Line multitasking analytical proteomics: How to separate, reduce, alkylate and digest whole proteins in an on-Line multidimensional chromatography system coupled to MS. J Sep Sci 2008; 31:2913-23. [DOI: 10.1002/jssc.200800275] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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45
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Pesek JJ, Matyska MT, Venkat JP. Evaluation of protein, peptide, and amino acid retention on C5 hydride-based stationary phases. J Sep Sci 2008; 31:2560-6. [DOI: 10.1002/jssc.200800169] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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46
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Pepsin immobilized in dextran-modified fused-silica capillaries for on-line protein digestion and peptide mapping. Anal Chim Acta 2008; 619:231-8. [DOI: 10.1016/j.aca.2008.04.060] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2008] [Revised: 04/27/2008] [Accepted: 04/28/2008] [Indexed: 11/21/2022]
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47
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Hu F, Deng C, Zhang X. Development of high performance liquid chromatography with immobilized enzyme onto magnetic nanospheres for screening enzyme inhibitor. J Chromatogr B Analyt Technol Biomed Life Sci 2008; 871:67-71. [PMID: 18606577 DOI: 10.1016/j.jchromb.2008.06.036] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2008] [Revised: 06/12/2008] [Accepted: 06/23/2008] [Indexed: 11/30/2022]
Abstract
A novel-immobilized enzyme strategy created by magnetic nanospheres for monitoring enzyme activity and screening inhibitors followed by high performance liquid chromatography (HPLC) has been demonstrated. Through the reaction of the aldehyde groups with amine groups, alpha-glycosidase was simply and stably immobilized onto magnetic nanospheres by the cross-linking agent glutaraldehyde. In order to profiling the activity of the immobilized alpha-glucosidase, the natural substrate was hydrolyzed by it and the yield of product was determined by HPLC. Compared with traditional bioassay approach, the prepared immobilized alpha-glucosidase displays a high activity and stability which allows it to be easily reused for 10 times. Enzyme inhibition assays by known inhibitor glucobay and three candidate traditional Chinese medicines (TCMs) were then investigated using a similar methodology. This assay was able to readily detect the change of the immobilized enzyme activity based on measuring a decrease of product formation using HPLC. The approach is general and offers many attractive advantages including easy product isolation, inexpensive cost, and high efficiency in terms of reagent consumption.
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Affiliation(s)
- Fengli Hu
- Department of Chemistry, Fudan University, Shanghai, China
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48
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Lin S, Yao G, Qi D, Li Y, Deng C, Yang P, Zhang X. Fast and Efficient Proteolysis by Microwave-Assisted Protein Digestion Using Trypsin-Immobilized Magnetic Silica Microspheres. Anal Chem 2008; 80:3655-65. [DOI: 10.1021/ac800023r] [Citation(s) in RCA: 103] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Shuang Lin
- Department of Chemistry & Institute of Biomedical Sciences, Fudan University, Shanghai 200433, China
| | - Guoping Yao
- Department of Chemistry & Institute of Biomedical Sciences, Fudan University, Shanghai 200433, China
| | - Dawei Qi
- Department of Chemistry & Institute of Biomedical Sciences, Fudan University, Shanghai 200433, China
| | - Yan Li
- Department of Chemistry & Institute of Biomedical Sciences, Fudan University, Shanghai 200433, China
| | - Chunhui Deng
- Department of Chemistry & Institute of Biomedical Sciences, Fudan University, Shanghai 200433, China
| | - Pengyuan Yang
- Department of Chemistry & Institute of Biomedical Sciences, Fudan University, Shanghai 200433, China
| | - Xiangmin Zhang
- Department of Chemistry & Institute of Biomedical Sciences, Fudan University, Shanghai 200433, China
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49
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Wang S, Bao H, Yang P, Chen G. Immobilization of trypsin in polyaniline-coated nano-Fe3O4/carbon nanotube composite for protein digestion. Anal Chim Acta 2008; 612:182-9. [DOI: 10.1016/j.aca.2008.02.035] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2007] [Revised: 02/15/2008] [Accepted: 02/19/2008] [Indexed: 10/22/2022]
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50
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Ma J, Liang Z, Qiao X, Deng Q, Tao D, Zhang L, Zhang Y. Organic−Inorganic Hybrid Silica Monolith Based Immobilized Trypsin Reactor with High Enzymatic Activity. Anal Chem 2008; 80:2949-56. [DOI: 10.1021/ac702343a] [Citation(s) in RCA: 180] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Junfeng Ma
- National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China, and Graduate School of the Chinese Academy of Sciences, Beijing 100039, China
| | - Zhen Liang
- National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China, and Graduate School of the Chinese Academy of Sciences, Beijing 100039, China
| | - Xiaoqiang Qiao
- National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China, and Graduate School of the Chinese Academy of Sciences, Beijing 100039, China
| | - Qiliang Deng
- National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China, and Graduate School of the Chinese Academy of Sciences, Beijing 100039, China
| | - Dingyin Tao
- National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China, and Graduate School of the Chinese Academy of Sciences, Beijing 100039, China
| | - Lihua Zhang
- National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China, and Graduate School of the Chinese Academy of Sciences, Beijing 100039, China
| | - Yukui Zhang
- National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China, and Graduate School of the Chinese Academy of Sciences, Beijing 100039, China
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