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Jurina T, Sokač Cvetnić T, Šalić A, Benković M, Valinger D, Gajdoš Kljusurić J, Zelić B, Jurinjak Tušek A. Application of Spectroscopy Techniques for Monitoring (Bio)Catalytic Processes in Continuously Operated Microreactor Systems. Catalysts 2023. [DOI: 10.3390/catal13040690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2023] Open
Abstract
In the last twenty years, the application of microreactors in chemical and biochemical industrial processes has increased significantly. The use of microreactor systems ensures efficient process intensification due to the excellent heat and mass transfer within the microchannels. Monitoring the concentrations in the microchannels is critical for a better understanding of the physical and chemical processes occurring in micromixers and microreactors. Therefore, there is a growing interest in performing in-line and on-line analyses of chemical and/or biochemical processes. This creates tremendous opportunities for the incorporation of spectroscopic detection techniques into production and processing lines in various industries. In this work, an overview of current applications of ultraviolet–visible, infrared, Raman spectroscopy, NMR, MALDI-TOF-MS, and ESI-MS for monitoring (bio)catalytic processes in continuously operated microreactor systems is presented. The manuscript includes a description of the advantages and disadvantages of the analytical methods listed, with particular emphasis on the chemometric methods used for spectroscopic data analysis.
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Affiliation(s)
- Tamara Jurina
- Faculty of Food Technology and Biotechnology, University of Zagreb, Pierottijeva ul. 6, 10 000 Zagreb, Croatia
| | - Tea Sokač Cvetnić
- Faculty of Food Technology and Biotechnology, University of Zagreb, Pierottijeva ul. 6, 10 000 Zagreb, Croatia
| | - Anita Šalić
- Faculty of Chemical Engineering and Technology, University of Zagreb, Marulićev trg 19, 10 000 Zagreb, Croatia
| | - Maja Benković
- Faculty of Food Technology and Biotechnology, University of Zagreb, Pierottijeva ul. 6, 10 000 Zagreb, Croatia
| | - Davor Valinger
- Faculty of Food Technology and Biotechnology, University of Zagreb, Pierottijeva ul. 6, 10 000 Zagreb, Croatia
| | - Jasenka Gajdoš Kljusurić
- Faculty of Food Technology and Biotechnology, University of Zagreb, Pierottijeva ul. 6, 10 000 Zagreb, Croatia
| | - Bruno Zelić
- Faculty of Chemical Engineering and Technology, University of Zagreb, Marulićev trg 19, 10 000 Zagreb, Croatia
- Department for Packaging, Recycling and Environmental Protection, University North, Trg dr. Žarka Dolinara 1, 48 000 Koprivnica, Croatia
| | - Ana Jurinjak Tušek
- Faculty of Food Technology and Biotechnology, University of Zagreb, Pierottijeva ul. 6, 10 000 Zagreb, Croatia
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2
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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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3
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Kašička V. Peptide mapping of proteins by capillary electromigration methods. J Sep Sci 2022; 45:4245-4279. [PMID: 36200755 DOI: 10.1002/jssc.202200664] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 09/26/2022] [Accepted: 09/26/2022] [Indexed: 12/13/2022]
Abstract
This review article provides a wide overview of important developments and applications of capillary electromigration methods in the area of peptide mapping of proteins in the period 1997-mid-2022, including review articles on this topic. It deals with all major aspects of peptide mapping by capillary electromigration methods: i) precleavage sample preparation involving purification, preconcentration, denaturation, reduction and alkylation of protein(s) to be analyzed, ii) generation of peptide fragments by off-line or on-line enzymatic and/or chemical cleavage of protein(s), iii) postcleavage preparation of the generated peptide mixture for capillary electromigration separation, iv) separation of the complex peptide mixtures by one-, two- and multidimensional capillary electromigration methods coupled with mass spectrometry detection, and v) a large application of peptide mapping for variable purposes, such as qualitative analysis of monoclonal antibodies and other protein biopharmaceuticals, monitoring of posttranslational modifications, determination of primary structure and investigation of function of proteins in biochemical and clinical research, characterization of proteins of variable origin as well as for protein and peptide identification in proteomic and peptidomic studies.
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Affiliation(s)
- Václav Kašička
- Electromigration Methods, The Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czechia
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4
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Pero-Gascon R, Pont L, Giménez E, Sanz-Nebot V, Benavente F. On-line Immobilized Enzyme Microreactor Capillary Zone Electrophoresis-Mass Spectrometry for Peptide Mapping. Methods Mol Biol 2022; 2531:77-91. [PMID: 35941480 DOI: 10.1007/978-1-0716-2493-7_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Peptide mapping is a routine procedure for protein characterization in proteomics. This bottom-up analysis requires digestion of proteins into peptides before liquid chromatography- or capillary zone electrophoresis-mass spectrometry (LC-MS or CZE-MS, respectively). Proteins are usually digested off-line using proteolytic enzymes, typically trypsin, in solution or immobilized on appropriate supports. As an alternative, here we describe on-line immobilized enzyme microreactor capillary zone electrophoresis-mass spectrometry (IMER-CZE-MS) for a straightforward, rapid, and efficient protein digestion followed by separation, detection, and characterization of the generated peptides.
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Affiliation(s)
- Roger Pero-Gascon
- Department of Chemical Engineering and Analytical Chemistry, Institute for Research on Nutrition and Food Safety (INSA•UB), University of Barcelona, Barcelona, Spain
| | - Laura Pont
- Department of Chemical Engineering and Analytical Chemistry, Institute for Research on Nutrition and Food Safety (INSA•UB), University of Barcelona, Barcelona, Spain
| | - Estela Giménez
- Department of Chemical Engineering and Analytical Chemistry, Institute for Research on Nutrition and Food Safety (INSA•UB), University of Barcelona, Barcelona, Spain
| | - Victoria Sanz-Nebot
- Department of Chemical Engineering and Analytical Chemistry, Institute for Research on Nutrition and Food Safety (INSA•UB), University of Barcelona, Barcelona, Spain
| | - Fernando Benavente
- Department of Chemical Engineering and Analytical Chemistry, Institute for Research on Nutrition and Food Safety (INSA•UB), University of Barcelona, Barcelona, Spain.
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Dadouch M, Ladner Y, Bich C, Montels J, Morel J, Perrin C. Fast in-line bottom-up analysis of monoclonal antibodies: Toward an electrophoretic fingerprinting approach. Electrophoresis 2021; 42:1229-1237. [PMID: 33650106 DOI: 10.1002/elps.202000375] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 02/22/2021] [Accepted: 02/24/2021] [Indexed: 01/08/2023]
Abstract
For their characterization and quality control, monoclonal antibodies are frequently analyzed at the bottom-up level to generate specific fingerprints that can be used to tackle post-translational modifications or ensure production consistency between lots. To circumvent time-consuming and labor-intensive off-line sample preparation steps, the implementation of integrated methodologies from sample preparation to separation and detection is highly valuable. In this perspective, capillary zone electrophoresis appears as a choice technique since the capillary can subsequently be used as a vessel for sample preparation and electrophoretic discrimination/detection of the reaction products. Here, a fast in-line methodology for the routine quality control of mAbs at the bottom-up level is reported. Simultaneous denaturation and reduction (pretreatment step) were conducted with RapiGest® surfactant and dithiothreitol before in-line tryptic digestion. Reactant mixing was realized by transverse diffusion of laminar flow profile under controlled temperature. In-line digestion was carried out with a resistant trypsin to autolysis. The main parameters affecting the digestion efficiency (trypsin concentration and incubation conditions) were optimized to generate mAb electrophoretic profiles free from trypsin interferences. An acidic MS-compatible BGE was used to obtain high resolution separation of released peptides and in-line surfactant cleavage. The whole methodology was performed in less than two hours with good repeatability of migration times (RSD = 0.91%, n = 5) and corrected peak areas (RSD = 9.6%, n = 5). CE-fingerprints were successfully established for different mAbs and an antibody-drug conjugate.
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Affiliation(s)
- Meriem Dadouch
- UMR 5247-CNRS-UM-ENSCM, Institut des Biomolécules Max Mousseron (IBMM), Université de Montpellier, Montpellier, France
| | - Yoann Ladner
- UMR 5247-CNRS-UM-ENSCM, Institut des Biomolécules Max Mousseron (IBMM), Université de Montpellier, Montpellier, France
| | - Claudia Bich
- UMR 5247-CNRS-UM-ENSCM, Institut des Biomolécules Max Mousseron (IBMM), Université de Montpellier, Montpellier, France
| | - Jérôme Montels
- UMR 5247-CNRS-UM-ENSCM, Institut des Biomolécules Max Mousseron (IBMM), Université de Montpellier, Montpellier, France
| | - Jacques Morel
- Département de Rhumatologie, Université de Montpellier, Hôpital Lapeyronie, Montpellier Cedex 5, 34295, France
| | - Catherine Perrin
- UMR 5247-CNRS-UM-ENSCM, Institut des Biomolécules Max Mousseron (IBMM), Université de Montpellier, Montpellier, France
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Lu N, Sticker D, Kretschmann A, Petersen NJ, Kutter JP. A thiol-ene microfluidic device enabling continuous enzymatic digestion and electrophoretic separation as front-end to mass spectrometric peptide analysis. Anal Bioanal Chem 2020; 412:3559-3571. [DOI: 10.1007/s00216-020-02609-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 03/13/2020] [Accepted: 03/18/2020] [Indexed: 02/07/2023]
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7
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Practical sample pretreatment techniques coupled with capillary electrophoresis for real samples in complex matrices. Trends Analyt Chem 2020. [DOI: 10.1016/j.trac.2019.115702] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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8
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González-García E, Marina ML, García MC. Nanomaterials in Protein Sample Preparation. SEPARATION & PURIFICATION REVIEWS 2019. [DOI: 10.1080/15422119.2019.1581216] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Estefanía González-García
- Departamento de Química Analítica, Química Física e Ingeniería Química, Instituto de Investigación Química “Andrés M. del Río” (IQAR), Universidad de Alcalá, Alcalá de Henares, Madrid, Spain
| | - María Luisa Marina
- Departamento de Química Analítica, Química Física e Ingeniería Química, Instituto de Investigación Química “Andrés M. del Río” (IQAR), Universidad de Alcalá, Alcalá de Henares, Madrid, Spain
| | - María Concepción García
- Departamento de Química Analítica, Química Física e Ingeniería Química, Instituto de Investigación Química “Andrés M. del Río” (IQAR), Universidad de Alcalá, Alcalá de Henares, Madrid, Spain
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Beutner A, Herl T, Matysik FM. Selectivity enhancement in capillary electrophoresis by means of two-dimensional separation or dual detection concepts. Anal Chim Acta 2018; 1057:18-35. [PMID: 30832915 DOI: 10.1016/j.aca.2018.11.042] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Revised: 11/01/2018] [Accepted: 11/19/2018] [Indexed: 12/18/2022]
Abstract
For the identification and quantification of analytes in complex samples, highly selective analytical strategies are required. The selectivity of single separation techniques such as gas chromatography (GC), liquid chromatography (LC), or capillary electrophoresis (CE) with common detection principles can be enhanced by hyphenating orthogonal separation techniques but also by using complementary detection systems. In this review, two-dimensional systems containing CE in at least one dimension are reviewed, namely LC-CE or 2D CE systems. Particular attention is paid to the aspect of selectivity enhancement due to the orthogonality of the different separation mechanisms. As an alternative concept, dual detection approaches are reviewed using the common detectors of CE such as UV/VIS, laser-induced fluorescence, capacitively coupled contactless conductivity (C4D), electrochemical detection, and mass spectrometry. Special emphasis is given to dual detection systems implementing the highly flexible C4D as one detection component. Selectivity enhancement can be achieved in case of complementarity of the different detection techniques.
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Affiliation(s)
- Andrea Beutner
- Institute of Analytical Chemistry, Chemo- and Biosensors, University of Regensburg, Universitaetsstrasse 31, 93053, Regensburg, Germany
| | - Thomas Herl
- Institute of Analytical Chemistry, Chemo- and Biosensors, University of Regensburg, Universitaetsstrasse 31, 93053, Regensburg, Germany
| | - Frank-Michael Matysik
- Institute of Analytical Chemistry, Chemo- and Biosensors, University of Regensburg, Universitaetsstrasse 31, 93053, Regensburg, Germany.
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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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11
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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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12
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Ramana P, Schejbal J, Houthoofd K, Martens J, Adams E, Augustijns P, Glatz Z, Van Schepdael A. An improved design to capture magnetic microparticles for capillary electrophoresis based immobilized microenzyme reactors. Electrophoresis 2018; 39:981-988. [PMID: 29315710 DOI: 10.1002/elps.201700434] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Revised: 12/22/2017] [Accepted: 12/23/2017] [Indexed: 01/05/2023]
Abstract
In this paper, we demonstrate the effectiveness of a new 3D printed magnet holder that enables capture of magnetic microparticles in commercially available capillary electrophoresis equipment with a liquid or air based coolant system. The design as well as the method to capture magnetic microparticles inside the capillary are discussed. This setup was tested at temperature and pH values suitable for performing enzymatic reactions. To demonstrate its applicability in CE- immobilized microenzyme reactors (IMER) development, human flavin-containing monooxygenase 3 and bovine serum albumin were immobilized on amino functionalized magnetic microparticles using glutaraldehyde. These microparticles were subsequently used to perform in-line capillary electrophoresis with clozapine as a model substrate. This setup could be used further to establish CE-IMERs of other drug metabolic enzymes in a commercially available liquid based capillary coolant system. The CE-IMER setup was successful, although a subsequent decrease in enzyme activity was observed on repeated runs.
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Affiliation(s)
- Pranov Ramana
- Department of Pharmaceutical and Pharmacological Sciences, Pharmaceutical Analysis, KU Leuven - University of Leuven, Leuven, Belgium
| | - Jan Schejbal
- Department of Biochemistry, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Kristof Houthoofd
- Centre for Surface Chemistry and Catalysis, KU Leuven - University of Leuven, Leuven, Belgium
| | - Johan Martens
- Centre for Surface Chemistry and Catalysis, KU Leuven - University of Leuven, Leuven, Belgium
| | - Erwin Adams
- Department of Pharmaceutical and Pharmacological Sciences, Pharmaceutical Analysis, KU Leuven - University of Leuven, Leuven, Belgium
| | - Patrick Augustijns
- Department of Pharmaceutical and Pharmacological Sciences, Drug Delivery and Disposition, KU Leuven - University of Leuven, Leuven, Belgium
| | - Zdenĕk Glatz
- Department of Biochemistry, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Ann Van Schepdael
- Department of Pharmaceutical and Pharmacological Sciences, Pharmaceutical Analysis, KU Leuven - University of Leuven, Leuven, Belgium
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Huang S, Paul P, Ramana P, Adams E, Augustijns P, Van Schepdael A. Advances in Capillary Electrophoretically Mediated Microanalysis for On-line Enzymatic and Derivatization Reactions. Electrophoresis 2017; 39:97-110. [DOI: 10.1002/elps.201700262] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Revised: 08/10/2017] [Accepted: 08/11/2017] [Indexed: 11/09/2022]
Affiliation(s)
- Shengyun Huang
- KU Leuven - University of Leuven; Department of Pharmaceutical and Pharmacological Sciences, Pharmaceutical Analysis; Leuven Belgium
| | - Prasanta Paul
- KU Leuven - University of Leuven; Department of Pharmaceutical and Pharmacological Sciences, Pharmaceutical Analysis; Leuven Belgium
| | - Pranov Ramana
- KU Leuven - University of Leuven; Department of Pharmaceutical and Pharmacological Sciences, Pharmaceutical Analysis; Leuven Belgium
| | - Erwin Adams
- KU Leuven - University of Leuven; Department of Pharmaceutical and Pharmacological Sciences, Pharmaceutical Analysis; Leuven Belgium
| | - Patrick Augustijns
- KU Leuven - University of Leuven; Department of Pharmaceutical and Pharmacological Sciences, Drug delivery and disposition; Leuven Belgium
| | - Ann Van Schepdael
- KU Leuven - University of Leuven; Department of Pharmaceutical and Pharmacological Sciences, Pharmaceutical Analysis; Leuven Belgium
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Yan X, Sun L, Zhu G, Cox OF, Dovichi NJ. Over 4100 protein identifications from a Xenopus laevis fertilized egg digest using reversed-phase chromatographic prefractionation followed by capillary zone electrophoresis-electrospray ionization-tandem mass spectrometry analysis. Proteomics 2017; 16:2945-2952. [PMID: 27723263 DOI: 10.1002/pmic.201600262] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2016] [Revised: 09/14/2016] [Accepted: 10/07/2016] [Indexed: 12/25/2022]
Abstract
A tryptic digest generated from Xenopus laevis fertilized embryos was fractionated by RPLC. One set of 30 fractions was analyzed by 100-min CZE-ESI-MS/MS separations (50 h total instrument time), and a second set of 15 fractions was analyzed by 3-h UPLC-ESI-MS/MS separations (45 h total instrument time). CZE-MS/MS produced 70% as many protein IDs (4134 versus 5787) and 60% as many peptide IDs (22 535 versus 36 848) as UPLC-MS/MS with similar instrument time (50 h versus 45 h) but with 50 times smaller total consumed sample amount (1.5 μg versus 75 μg). Surprisingly, CZE generated peaks that were 25% more intense than UPLC for peptides that were identified by both techniques, despite the 50-fold lower loading amount; this high sensitivity reflects the efficient ionization produced by the electrokinetically pumped nanospray interface used in CZE. This report is the first comparison of CZE-MS/MS and UPLC-MS/MS for large-scale eukaryotic proteomic analysis. The numbers of protein and peptide identifications produced by CZE-ESI-MS/MS approach those produced by UPLC-MS/MS, but with nearly two orders of magnitude lower sample amounts.
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Affiliation(s)
- Xiaojing Yan
- Department of Chemistry, University of Notre Dame, Notre Dame, IN, USA
| | - Liangliang Sun
- Department of Chemistry, University of Notre Dame, Notre Dame, IN, USA
| | - Guijie Zhu
- Department of Chemistry, University of Notre Dame, Notre Dame, IN, USA
| | - Olivia F Cox
- Department of Chemistry, University of Notre Dame, Notre Dame, IN, USA
| | - Norman J Dovichi
- Department of Chemistry, University of Notre Dame, Notre Dame, IN, USA
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Opekar F, Tůma P. Coaxial flow-gating interface for capillary electrophoresis. J Sep Sci 2017; 40:3138-3143. [DOI: 10.1002/jssc.201700412] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Revised: 05/22/2017] [Accepted: 05/23/2017] [Indexed: 12/24/2022]
Affiliation(s)
- František Opekar
- Faculty of Science, Department of Analytical Chemistry; Charles University; Prague 2 Czechia
| | - Petr Tůma
- Third Faculty of Medicine, Department of Biochemistry, Cell and Molecular Biology; Charles University; Prague 10 Czechia
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Ramana P, Adams E, Augustijns P, Van Schepdael A. Trapping magnetic nanoparticles for in-line capillary electrophoresis in a liquid based capillary coolant system. Talanta 2017; 164:148-153. [DOI: 10.1016/j.talanta.2016.11.028] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Revised: 11/04/2016] [Accepted: 11/12/2016] [Indexed: 11/28/2022]
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17
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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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Štěpánová S, Kašička V. Recent applications of capillary electromigration methods to separation and analysis of proteins. Anal Chim Acta 2016; 933:23-42. [DOI: 10.1016/j.aca.2016.06.006] [Citation(s) in RCA: 78] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Revised: 05/10/2016] [Accepted: 06/03/2016] [Indexed: 10/21/2022]
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A simple sheathless CE-MS interface with a sub-micrometer electrical contact fracture for sensitive analysis of peptide and protein samples. Anal Chim Acta 2016; 936:157-67. [PMID: 27566351 DOI: 10.1016/j.aca.2016.07.002] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Revised: 06/28/2016] [Accepted: 07/01/2016] [Indexed: 12/11/2022]
Abstract
Online coupling of capillary electrophoresis (CE) to electrospray ionization mass spectrometry (MS) has shown considerable potential, however, technical challenges have limited its use. In this study, we have developed a simple and sensitive sheathless CE-MS interface based on the novel concept of forming a sub-micrometer fracture directly in the capillary. The simple interface design allowed the generation of a stable ESI spray capable of ionization at low nanoliter flow-rates (45-90 nL/min) for high sensitivity MS analysis of challenging samples like those containing proteins and peptides. By analysis of a model peptide (leucine enkephalin), a limit of detection (LOD) of 0.045 pmol/μL (corresponding to 67 attomol in a sample volume of ∼15 nL) was obtained. The merit of the CE-MS approach was demonstrated by analysis of bovine serum albumin (BSA) tryptic peptides. A well-resolved separation profile was achieved and comparable sequence coverage was obtained by the CE-MS method (73%) compared to a representative UPLC-MS method (77%). The CE-MS interface was subsequently used to analyse a more complex sample of pharmaceutically relevant human proteins including insulin, tissue factor and α-synuclein. Efficient separation and protein ESI mass spectra of adequate quality could be achieved using only a small amount of sample (30 fmol). In addition, analysis of ubiquitin samples under both native and denatured conditions, indicate that the CE-MS setup can facilitate native MS applications to probe the conformational properties of proteins. Thus, the described CE-MS setup should be useful for a wide range of high-sensitivity applications in protein research.
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Heemskerk AAM, Deelder AM, Mayboroda OA. CE-ESI-MS for bottom-up proteomics: Advances in separation, interfacing and applications. MASS SPECTROMETRY REVIEWS 2016; 35:259-271. [PMID: 24852088 DOI: 10.1002/mas.21432] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2014] [Accepted: 03/27/2014] [Indexed: 06/03/2023]
Abstract
With the development of more sensitive hyphenation strategies for capillary electrophoresis-electrospray-mass spectrometry the technique has reemerged as technique with high separation power combined with high sensitivity in the analysis of peptides and protein digests. This review will discuss the newly developed hyphenation strategies for CE-ESI-MS and their application in bottom-up proteomics as well as the applications in the same time span, 2009 to present, using co-axial sheathliquid. Subsequently all separate aspects in the development of a CE-ESI-MS method for bottom-up proteomics shall be discussed, highlighting certain applications and discussing pros and cons of the various choices. The separation of peptides in a capillary electrophoresis system is discussed including the great potential for modeling of this migration of peptides due to the simple electrophoretic separation process. Furthermore, the technical aspects of method development are discussed, namely; background electrolyte choice, coating of the separation capillary and chosen loading method. Finally, conclusions and an outlook on future developments in the field of bottom-up proteomics by CE-ESI-MS will be provided.
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Affiliation(s)
- Anthonius A M Heemskerk
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Albinusdreef 2, 2300, RC, Leiden, The Netherlands
| | - André M Deelder
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Albinusdreef 2, 2300, RC, Leiden, The Netherlands
| | - Oleg A Mayboroda
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Albinusdreef 2, 2300, RC, Leiden, The Netherlands
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21
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Kašička V. Recent developments in capillary and microchip electroseparations of peptides (2013-middle 2015). Electrophoresis 2015; 37:162-88. [DOI: 10.1002/elps.201500329] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2015] [Revised: 08/25/2015] [Accepted: 08/25/2015] [Indexed: 12/16/2022]
Affiliation(s)
- Václav Kašička
- Institute of Organic Chemistry and Biochemistry, v.v.i; The Czech Academy of Sciences; Prague Czech Republic
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22
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Štěpánová S, Kašička V. Recent developments and applications of capillary and microchip electrophoresis in proteomic and peptidomic analyses. J Sep Sci 2015; 39:198-211. [DOI: 10.1002/jssc.201500973] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2015] [Revised: 10/06/2015] [Accepted: 10/06/2015] [Indexed: 12/19/2022]
Affiliation(s)
- Sille Štěpánová
- Institute of Organic Chemistry and Biochemistry; The Czech Academy of Sciences; Prague Czech Republic
| | - Václav Kašička
- Institute of Organic Chemistry and Biochemistry; The Czech Academy of Sciences; Prague Czech Republic
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23
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Ghafourifar G, Waldron KC. Fluorescence Microscopy Imaging of an Immobilized Enzyme Microreactor to Investigate Glutaraldehyde-Mediated Crosslinking of Chymotrypsin. ANAL LETT 2015. [DOI: 10.1080/00032719.2015.1075128] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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25
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Verrastro I, Pasha S, Jensen KT, Pitt AR, Spickett CM. Mass spectrometry-based methods for identifying oxidized proteins in disease: advances and challenges. Biomolecules 2015; 5:378-411. [PMID: 25874603 PMCID: PMC4496678 DOI: 10.3390/biom5020378] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Revised: 03/20/2015] [Accepted: 03/23/2015] [Indexed: 01/02/2023] Open
Abstract
Many inflammatory diseases have an oxidative aetiology, which leads to oxidative damage to biomolecules, including proteins. It is now increasingly recognized that oxidative post-translational modifications (oxPTMs) of proteins affect cell signalling and behaviour, and can contribute to pathology. Moreover, oxidized proteins have potential as biomarkers for inflammatory diseases. Although many assays for generic protein oxidation and breakdown products of protein oxidation are available, only advanced tandem mass spectrometry approaches have the power to localize specific oxPTMs in identified proteins. While much work has been carried out using untargeted or discovery mass spectrometry approaches, identification of oxPTMs in disease has benefitted from the development of sophisticated targeted or semi-targeted scanning routines, combined with chemical labeling and enrichment approaches. Nevertheless, many potential pitfalls exist which can result in incorrect identifications. This review explains the limitations, advantages and challenges of all of these approaches to detecting oxidatively modified proteins, and provides an update on recent literature in which they have been used to detect and quantify protein oxidation in disease.
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Affiliation(s)
- Ivan Verrastro
- School of Life and Health Sciences, Aston University, Aston Triangle, Birmingham, B4 7ET, UK.
| | - Sabah Pasha
- School of Life and Health Sciences, Aston University, Aston Triangle, Birmingham, B4 7ET, UK.
| | - Karina Tveen Jensen
- School of Life and Health Sciences, Aston University, Aston Triangle, Birmingham, B4 7ET, UK.
| | - Andrew R Pitt
- School of Life and Health Sciences, Aston University, Aston Triangle, Birmingham, B4 7ET, UK.
| | - Corinne M Spickett
- School of Life and Health Sciences, Aston University, Aston Triangle, Birmingham, B4 7ET, UK.
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26
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Moritz B, Schnaible V, Kiessig S, Heyne A, Wild M, Finkler C, Christians S, Mueller K, Zhang L, Furuya K, Hassel M, Hamm M, Rustandi R, He Y, Solano OS, Whitmore C, Park SA, Hansen D, Santos M, Lies M. Evaluation of capillary zone electrophoresis for charge heterogeneity testing of monoclonal antibodies. J Chromatogr B Analyt Technol Biomed Life Sci 2015; 983-984:101-10. [DOI: 10.1016/j.jchromb.2014.12.024] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2014] [Revised: 12/19/2014] [Accepted: 12/22/2014] [Indexed: 01/30/2023]
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27
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Coussot G, Ladner Y, Bayart C, Faye C, Vigier V, Perrin C. On-line capillary electrophoresis-based enzymatic methodology for the study of polymer-drug conjugates. J Chromatogr A 2015; 1376:159-66. [DOI: 10.1016/j.chroma.2014.12.029] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2014] [Revised: 11/17/2014] [Accepted: 12/08/2014] [Indexed: 01/08/2023]
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28
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Kohl FJ, Sánchez-Hernández L, Neusüß C. Capillary electrophoresis in two-dimensional separation systems: Techniques and applications. Electrophoresis 2014; 36:144-58. [DOI: 10.1002/elps.201400368] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2014] [Revised: 09/16/2014] [Accepted: 09/17/2014] [Indexed: 12/24/2022]
Affiliation(s)
- Felix J. Kohl
- Department of Chemistry; Aalen University; Aalen Germany
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29
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Grochocki W, Markuszewski MJ, Quirino JP. Multidimensional capillary electrophoresis. Electrophoresis 2014; 36:135-43. [DOI: 10.1002/elps.201400416] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Revised: 09/11/2014] [Accepted: 09/12/2014] [Indexed: 01/26/2023]
Affiliation(s)
- Wojciech Grochocki
- Department of Biopharmaceutics and Pharmacodynamics; Medical University of Gdansk; Gdansk Poland
| | - Michał J. Markuszewski
- Department of Biopharmaceutics and Pharmacodynamics; Medical University of Gdansk; Gdansk Poland
| | - Joselito P. Quirino
- Australian Centre for Research on Separation Science (ACROSS); School of Physical Sciences-Chemistry; University of Tasmania; Hobart Australia
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Yuan H, Zhang L, Zhang Y. Preparation of high efficiency and low carry-over immobilized enzymatic reactor with methacrylic acid-silica hybrid monolith as matrix for on-line protein digestion. J Chromatogr A 2014; 1371:48-57. [PMID: 25456586 DOI: 10.1016/j.chroma.2014.10.067] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2014] [Revised: 09/05/2014] [Accepted: 10/20/2014] [Indexed: 11/28/2022]
Abstract
In this work, a novel kind of organic-silica hybrid monolith based immobilized enzymatic reactor (IMER) was developed. The monolithic support was prepared by a single step "one-pot" strategy via the polycondensation of tetramethoxysilane and vinyltrimethoxysilane and in situ copolymerization of methacrylic acid and vinyl group on the precondensed siloxanes with ammonium persulfate as the thermal initiator. Subsequently, the monolith was activated by N-(3-dimethylaminopropyl) - N'-ethylcarbodiimide (EDC) and N-hydroxysuccinimide (NHS), followed by the modification of branched polyethylenimine (PEI) to improve the hydrophilicity. Finally, after activated by EDC and NHS, trypsin was covalently immobilized onto the monolithic support. The performance of such a microreactor was evaluated by the in sequence digestion of bovine serum albumin (BSA) and myoglobin, followed by MALDI-TOF-MS analysis. Compared to those obtained by traditional in-solution digestion, not only higher sequence coverages for BSA (74±1.4% vs. 59.5±2.7%, n=6) and myoglobin (93±3% vs. 81±4.5%, n=6) were obtained, but also the digestion time was shortened from 24h to 2.5 min, demonstrating the high digestion efficiency of such an IMER. The carry-over of these two proteins on the IMER was investigated, and peptides from BSA could not be found in mass spectrum of myoglobin digests, attributed to the good hydrophilicity of our developed monolithic support. Moreover, the dynamic concentration range for protein digestion was proved to be four orders of magnitude, and the IMER could endure at least 7-day consecutive usage. Furthermore, such an IMER was coupled with nano-RPLC-ESI/MS/MS for the analysis of extracted proteins from Escherichia coli. Compared to formerly reported silica hybrid monolith based IMER and the traditional in-solution counterpart, by our developed IMER, although the identified protein number was similar, the identified distinct peptide number was improved by 7% and 25% respectively, beneficial to improve the reliability of protein identification. The IMER was further online integrated with two-dimensional nano-HPLC-MS/MS system for the analysis of protein extracts from hepatocellular carcinoma (HCC) cells with low metastasis rate, and more than 3000 protein groups were identified, with only 46 proteins identified from the residues of the IMER. All these results demonstrated that such a hybrid monolith based IMER would be of great promise in the high throughput and high confidence proteome analysis.
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Affiliation(s)
- Huiming Yuan
- 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
| | - 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.
| | - 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
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31
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Kler PA, Sydes D, Huhn C. Column–coupling strategies for multidimensional electrophoretic separation techniques. Anal Bioanal Chem 2014; 407:119-38. [DOI: 10.1007/s00216-014-8099-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Revised: 08/06/2014] [Accepted: 08/08/2014] [Indexed: 10/24/2022]
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32
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Sun L, Zhu G, Yan X, Mou S, Dovichi NJ. Uncovering immobilized trypsin digestion features from large-scale proteome data generated by high-resolution mass spectrometry. J Chromatogr A 2014; 1337:40-7. [PMID: 24636566 PMCID: PMC4000775 DOI: 10.1016/j.chroma.2014.02.014] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2013] [Revised: 02/01/2014] [Accepted: 02/03/2014] [Indexed: 12/21/2022]
Abstract
Immobilized trypsin produces very fast protein digestion, which is attractive for application to high throughput bottom-up proteomics. While there is a rich literature on the preparation of immobilized trypsin, there are very few studies that investigate its application to complex proteomic samples. In this work, we compared solution-phase trypsin with trypsin immobilized on magnetic microspheres for digestion of two complex proteomes, Escherichia coli and the MCF7 cell line. The digests were separated by HPLC, and detected with a Q-Exactive mass spectrometer, which generated high resolution and high quality parent- and fragment-ion mass spectra. The data were analyzed using MaxQuant. We make several conclusions about the features of immobilized trypsin digestion of complex proteomes. First, both immobilized and solution-phase trypsin generate peptides that sample the same protein pool. Second, immobilized trypsin can digest complex proteomes two orders of magnitude faster than solution-phase trypsin while retaining similar numbers of protein identifications and proteome depth. Digestion using immobilized trypsin for 5-min produces a similar number of missed cleavages as solution-based trypsin digestion for 4-h; digestion using immobilized trypsin for 20-min produces a similar number of missed cleavages as solution-based trypsin digestion for 12-h. Third, immobilized trypsin produces quantitatively reproducible digestion of complex proteomes. Finally, there is small but measurable loss of peptide due to non-specific adsorption to the immobilization matrix. This adsorption generates a bias against detection of basic peptides.
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Affiliation(s)
- Liangliang Sun
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Guijie Zhu
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Xiaojing Yan
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Si Mou
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Norman J Dovichi
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA.
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33
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Yin Z, Zhao W, Tian M, Zhang Q, Guo L, Yang L. A capillary electrophoresis-based immobilized enzyme reactor using graphene oxide as a support via layer by layer electrostatic assembly. Analyst 2014; 139:1973-9. [DOI: 10.1039/c3an02241b] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Using graphene oxide as an enzyme support, we developed a novel CE-based microreactor via layer-by-layer electrostatic assembly, which can be used for accurate on-line analysis and characterization of peptides and proteins.
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Affiliation(s)
- Zhengri Yin
- Faculty of Chemistry
- Northeast Normal University
- Changchun, P. R. China
| | - Wenwen Zhao
- Faculty of Chemistry
- Northeast Normal University
- Changchun, P. R. China
| | - Miaomiao Tian
- Faculty of Chemistry
- Northeast Normal University
- Changchun, P. R. China
| | - Qian Zhang
- Faculty of Chemistry
- Northeast Normal University
- Changchun, P. R. China
| | - Liping Guo
- Faculty of Chemistry
- Northeast Normal University
- Changchun, P. R. China
| | - Li Yang
- Faculty of Chemistry
- Northeast Normal University
- Changchun, P. R. China
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34
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Sun L, Li Y, Champion MM, Zhu G, Wojcik R, Dovichi NJ. Capillary zone electrophoresis-multiple reaction monitoring from 100 pg of RAW 264.7 cell lysate digest. Analyst 2013; 138:3181-8. [PMID: 23591184 DOI: 10.1039/c3an00287j] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Capillary zone electrophoresis-multiple/single reaction monitoring (CZE-MRM/SRM), which employed an electrokinetically driven sheath-flow electrospray interface, was used for the rapid and highly sensitive detection of protein analytes in complex tryptic digests. MRM channels were developed against a commercial exponential mixture of bovine proteins. Five proteins spanning four orders of magnitude concentration range were confidently detected from only 2.5 ng of the digest mixture; the mass detection limits (S/N = 3) of two detected proteins, alpha-casein and glutamate dehydrogenase were about 600 zmol and 30 amol, respectively. This technique was then applied to a RAW 264.7 cell lysate digest. Three proteins were confidently and reproducibly detected from 100 pg of this digest. The sample amount corresponds to the approximate protein content from a single cell, which suggests that CZE-MRM may be a useful analytical tool in chemical cytometry. In addition to providing highly sensitive detection of proteins in complex mixtures, this system is highly rapid; migration time of the protein digests was less than 10 min.
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Affiliation(s)
- Liangliang Sun
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
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35
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Flaherty RJ, Huge BJ, Bruce SM, Dada OO, Dovichi NJ. Nicked-sleeve interface for two-dimensional capillary electrophoresis. Analyst 2013; 138:3621-5. [PMID: 23702824 DOI: 10.1039/c3an00284e] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report an improved interface for two-dimensional capillary electrophoresis. This interface is based on capillary tubing and a Plexiglas chip, both of which were milled using a micro-dicing saw. The interface was evaluated and compared to a traditional interface design for both pseudo one-dimensional and two-dimensional capillary electrophoresis. We observe less than 70% transfer efficiency for the traditional design and greater than 90% transfer efficiency with this new interface.
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Affiliation(s)
- Ryan J Flaherty
- Department of Chemistry, University of Notre Dame, Notre Dame, IN 46556, USA
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36
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Kašička V. Recent developments in capillary and microchip electroseparations of peptides (2011-2013). Electrophoresis 2013; 35:69-95. [PMID: 24255019 DOI: 10.1002/elps.201300331] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2013] [Revised: 09/10/2013] [Accepted: 09/10/2013] [Indexed: 01/15/2023]
Abstract
The review presents a comprehensive survey of recent developments and applications of capillary and microchip electroseparation methods (zone electrophoresis, ITP, IEF, affinity electrophoresis, EKC, and electrochromatography) for analysis, isolation, purification, and physicochemical and biochemical characterization of peptides. Advances in the investigation of electromigration properties of peptides, in the methodology of their analysis, including sample preseparation, preconcentration and derivatization, adsorption suppression and EOF control, as well as in detection of peptides, are presented. New developments in particular CE and CEC modes are reported and several types of their applications to peptide analysis are described: conventional qualitative and quantitative analysis, determination in complex (bio)matrices, monitoring of chemical and enzymatical reactions and physical changes, amino acid, sequence and chiral analysis, and peptide mapping of proteins. Some micropreparative peptide separations are shown and capabilities of CE and CEC techniques to provide relevant physicochemical characteristics of peptides are demonstrated.
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Affiliation(s)
- Václav Kašička
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Prague, Czech Republic
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37
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Bao H, Zhang L, Chen G. Immobilization of trypsin via graphene oxide-silica composite for efficient microchip proteolysis. J Chromatogr A 2013; 1310:74-81. [PMID: 23998335 DOI: 10.1016/j.chroma.2013.08.040] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2013] [Revised: 08/01/2013] [Accepted: 08/12/2013] [Indexed: 11/15/2022]
Abstract
In this report, trypsin was covalently immobilized in the graphene oxide (GO)-silica composite coating on the channel wall of poly(methyl methacrylate) (PMMA) microchips to fabricate microfluidic bioreactors for highly efficient proteolysis. A mixture solution containing GO nanosheets and silica gel was injected into the channels to form coating. 1-Ethyl-3-(3-dimethylaminopropyl)carbodiimide and N-hydroxysuccinimide were used as carboxyl activating agents to crosslink the primary amino groups of trypsin to the carboxyl groups of the entrapped GO sheets in the composite to realize covalent immobilization. The feasibility and performance of the novel GO-based microfluidic bioreactors were demonstrated by the digestion of hemoglobin (HEM), cytochrome c (Cyt-c), myoglobin (MYO), and ovalbumin (OVA) and the digestion time was significantly reduced to 5s. The obtained digests were identified by MALDI-TOF MS with the sequence coverages of 95%, 76%, 69%, and 55% for HEM, Cyt-c, MYO, and OVA, respectively. The suitability of the prepared bioreactors to complex proteins was demonstrated by digesting human serum.
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Affiliation(s)
- Huimin Bao
- School of Pharmacy, Department of Chemistry, Fudan University, 220 Handan Road, Shanghai 200433, China
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38
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Sun L, Zhu G, Yan X, Dovichi NJ. High sensitivity capillary zone electrophoresis-electrospray ionization-tandem mass spectrometry for the rapid analysis of complex proteomes. Curr Opin Chem Biol 2013; 17:795-800. [PMID: 23911612 DOI: 10.1016/j.cbpa.2013.07.018] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2013] [Revised: 07/02/2013] [Accepted: 07/03/2013] [Indexed: 12/15/2022]
Abstract
The vast majority of bottom-up proteomic studies employ reversed-phase separation of tryptic digests coupled with electrospray ionization tandem mass spectrometry. These studies are remarkably successful for the analysis of samples containing micrograms of protein. However, liquid chromatography tends to perform poorly for samples containing nanogram amounts of protein, presumably due to loss of trace-level peptides within the chromatographic system. Capillary zone electrophoresis provides a much simpler flow system and would appear to be an attractive alternative to liquid chromatography for separation of small peptide samples before electrospray ionization and mass spectrometry detection. However, capillary zone electrophoresis has received very little attention as a tool for analysis of complex proteomes. In 2012, we reported the use of capillary zone electrophoresis for the analysis of the secretome of Mycobacterium marinum, a model system for tuberculosis. Roughly 400 peptides and over 100 proteins were identified from this medium-complexity proteome; this identification required analysis of a set of 11 fractions and occupied three hours of mass spectrometer time. We have recently employed an improved capillary zone electrophoresis system for the analysis of 100 ng of the Escherichia coli proteome and observed over 1300 peptides and nearly 350 proteins in a single separation. More interestingly, analysis of 1 ng of the E. coli proteome yielded over 600 peptide and 140 protein groups. This sample size approaches that of a large eukaryotic cell, suggesting that capillary zone electrophoresis may ultimately be a useful tool for chemical cytometry.
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Affiliation(s)
- Liangliang Sun
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Guijie Zhu
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Xiaojing Yan
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Norman J Dovichi
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
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Yan X, Essaka DC, Sun L, Zhu G, Dovichi NJ. Bottom-up proteome analysis of E. coli using capillary zone electrophoresis-tandem mass spectrometry with an electrokinetic sheath-flow electrospray interface. Proteomics 2013; 13:2546-51. [PMID: 23798545 DOI: 10.1002/pmic.201300062] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2013] [Revised: 04/10/2013] [Accepted: 05/27/2013] [Indexed: 01/15/2023]
Abstract
The Escherichia coli proteome was digested with trypsin and fractionated using SPE on a C18 SPE column. Seven fractions were collected and analyzed by CZE-ESI-MS/MS. The separation was performed in a 60-cm-long linear polyacrylamide-coated capillary with a 0.1% v/v formic acid separation buffer. An electrokinetic sheath-flow electrospray interface was used to couple the separation capillary with an Orbitrap-Velos operating in higher-energy collisional dissociation mode. Each CZE-ESI-MS/MS run lasted 50 min and total MS time was 350 min. A total of 23 706 peptide spectra matches, 4902 peptide IDs, and 871 protein group IDs were generated using MASCOT with false discovery rate less than 1% on the peptide level. The total mass spectrometer analysis time was less than 6 h, the sample identification rate (145 proteins/h) was more than two times higher than previous studies of the E. coli proteome, and the amount of sample consumed (<1 μg) was roughly fourfold less than previous studies. These results demonstrate that CZE is a useful tool for the bottom-up analysis of prokaryote proteomes.
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Affiliation(s)
- Xiaojing Yan
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, USA
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40
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Capillary electrophoresis applied to screening of trypsin inhibitors using microreactor with trypsin immobilized by glutaraldehyde. Anal Biochem 2013; 438:32-8. [DOI: 10.1016/j.ab.2013.03.010] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2012] [Revised: 03/09/2013] [Accepted: 03/11/2013] [Indexed: 11/19/2022]
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41
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Ghafourifar G, Fleitz A, Waldron KC. Development of glutaraldehyde-crosslinked chymotrypsin and an in situ immobilized enzyme microreactor with peptide mapping by capillary electrophoresis. Electrophoresis 2013; 34:1804-11. [PMID: 23686566 DOI: 10.1002/elps.201200663] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2012] [Revised: 02/10/2013] [Accepted: 02/19/2013] [Indexed: 11/06/2022]
Abstract
Immobilized proteolytic enzymes present several advantages over their soluble form, not the least of which is suppression of autoproteolysis peaks even at high enzyme-to-substrate ratios. We have made immobilized chymotrypsin by directly crosslinking it with glutaraldehyde to produce polymeric particles. Digestion of two model substrates using the particles was followed by CE peptide mapping with detection by UV absorbance or LIF. Results showed that autoproteolysis was highly suppressed and that different storage conditions of the particles in the short term (24 h) did not affect digestion of denatured BSA. As well, the chymotrypsin particles were indifferent to the presence of fluorescein groups on a casein substrate. Glutaraldehyde crosslinking of chymotrypsin inside a fused silica capillary column to make an immobilized enzyme reactor (IMER) was achieved in a series of reagent addition and washing steps, entirely automated using a commercial CE instrument. Digestion of myoglobin in the IMER for 30 min at 37°C followed by peptide mapping by CE-MS of the collected digest allowed identification of 17 chymotryptic peptides of myoglobin, or 83% primary sequence coverage.
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42
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Sun L, Zhu G, Dovichi NJ. Integrated capillary zone electrophoresis-electrospray ionization tandem mass spectrometry system with an immobilized trypsin microreactor for online digestion and analysis of picogram amounts of RAW 264.7 cell lysate. Anal Chem 2013; 85:4187-94. [PMID: 23510126 DOI: 10.1021/ac400523x] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
A capillary zone electrophoresis (CZE) electrospray ionization (ESI) tandem mass spectrometry (MS/MS) system was integrated with an immobilized trypsin microreactor. The system was evaluated and then applied for online digestion and analysis of picogram loadings of RAW 264.7 cell lysate. Protein samples were dissolved in a buffer containing 50% (v/v) acetonitrile (ACN), and then directly loaded into the capillary for digestion, followed by CZE separation and MS/MS identification. The organic solvent (50% (v/v) ACN) assisted the immobilized trypsin digestion and simplified the protein sample preparation protocol. Neither protein reduction nor alkylation steps were employed, which minimized sample loss and contamination. The integrated CZE-ESI-MS/MS system generated confident identification of bovine serum albumin (BSA) with 19% sequence coverage and 14 peptide identifications (IDs) when 20 fmol was loaded. When only 1 fmol of BSA was injected, one BSA peptide was consistently detected. For the analysis of a standard protein mixture, the integrated system produced efficient protein digestion and confident identification for proteins with different molecular weights and isoelectric points when a low-femtomole amount was loaded for each protein. We further applied the system for triplicate analysis of a RAW 264.7 cell lysate; 2 ± 1 and 7 ± 2 protein groups were confidently identified from only 300 pg and 3 ng loadings, respectively. The 300 pg sample loading corresponds to the protein content of three RAW 264.7 cells. In addition to high-sensitivity analysis, the integrated CZE-ESI-MS/MS system produces good reproducibility in terms of peptide and protein IDs, peptide migration time, and peptide intensity.
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Affiliation(s)
- Liangliang Sun
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
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43
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Zhang Z, Zhang F, Liu Y. Recent Advances in Enhancing the Sensitivity and Resolution of Capillary Electrophoresis. J Chromatogr Sci 2013; 51:666-83. [DOI: 10.1093/chromsci/bmt012] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
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44
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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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45
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Iqbal J, Iqbal S, Müller CE. Advances in immobilized enzyme microbioreactors in capillary electrophoresis. Analyst 2013; 138:3104-16. [DOI: 10.1039/c3an00031a] [Citation(s) in RCA: 71] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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46
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Li Y, Zhang X, Deng C. Functionalized magnetic nanoparticles for sample preparation in proteomics and peptidomics analysis. Chem Soc Rev 2013; 42:8517-39. [DOI: 10.1039/c3cs60156k] [Citation(s) in RCA: 139] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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47
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Klepárník K. Recent advances in the combination of capillary electrophoresis with mass spectrometry: From element to single-cell analysis. Electrophoresis 2012; 34:70-85. [DOI: 10.1002/elps.201200488] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2012] [Revised: 10/08/2012] [Accepted: 10/08/2012] [Indexed: 11/11/2022]
Affiliation(s)
- Karel Klepárník
- Institute of Analytical Chemistry; Academy of Sciences of the Czech Republic; Brno; Czech Republic
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48
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Haselberg R, de Jong GJ, Somsen GW. CE-MS for the analysis of intact proteins 2010-2012. Electrophoresis 2012; 34:99-112. [DOI: 10.1002/elps.201200439] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2012] [Revised: 10/08/2012] [Accepted: 10/09/2012] [Indexed: 12/18/2022]
Affiliation(s)
- Rob Haselberg
- Biomolecular Analysis; Utrecht University; CG Utrecht; The Netherlands
| | | | - Govert W. Somsen
- Biomolecular Analysis; Utrecht University; CG Utrecht; The Netherlands
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49
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Sun L, Zhu G, Li Y, Yang P, Dovichi NJ. Coupling methanol denaturation, immobilized trypsin digestion, and accurate mass and time tagging for liquid-chromatography-based shotgun proteomics of low nanogram amounts of RAW 264.7 cell lysate. Anal Chem 2012; 84:8715-21. [PMID: 22971241 PMCID: PMC3477608 DOI: 10.1021/ac3019608] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We report the shotgun proteomic analysis of mammalian cell lysates that contain low nanogram amounts of protein. Proteins were denatured using methanol, digested using immobilized trypsin, and analyzed by UPLC-ESI-MS/MS. The approach generated more peptides and higher sequence coverage for a mixture of three standard proteins than the use of free trypsin solution digestion of heat- or urea-denatured proteins. We prepared triplicate RAW 264.7 cell lysates that contained 6, 30, 120, and 300 ng of protein. An average of 2 ± 1, 23 ± 2, 134 ± 11, and 218 ± 26 proteins were detected for each sample size, respectively. The numbers of both protein and peptide IDs scaled linearly with the amount of sample taken for analysis. Our approach also outperformed traditional methods (free trypsin digestion of heat- or urea-denatured proteins) for 6-300 ng RAW 264.7 cell protein analysis in terms of number of peptides and proteins identified. The use of accurate mass and time (AMT) tags resulted in the identification of an additional 16 proteins based on 20 peptides from the 6 ng cell lysate prepared with our approach. When AMT analysis was performed for the 6 ng cell lysate prepared with traditional methods, no reasonable peptide signal could be obtained. In all cases, roughly ∼30% of the digested sample was taken for analysis, corresponding to the analysis of a 2 ng aliquot of homogenate from the 6 ng cell lysate.
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Affiliation(s)
- Liangliang Sun
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Guijie Zhu
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Yihan Li
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Ping Yang
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Norman J. Dovichi
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
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50
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Krenkova J, Foret F. On-line CE/ESI/MS interfacing: recent developments and applications in proteomics. Proteomics 2012; 12:2978-90. [PMID: 22888067 DOI: 10.1002/pmic.201200140] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2012] [Revised: 05/17/2012] [Accepted: 06/12/2012] [Indexed: 12/13/2022]
Abstract
After shining as the ultimate separation - sequencing technique used for the successful completion of the Human Genome Project, in the early 2000s CE experienced lowered popularity among separation scientists. The renewed interest in recent years relates to the separation needs, especially in proteomics, metabolomics, and glycomics, where CE complements liquid chromatography techniques. This interest is further boosted by the regulators requiring additional separation techniques for characterization of newly developed pharmaceuticals. This paper gives a short overview of recent developments in the on-line interfacing of CE separation techniques with electrospray ionization/mass spectrometric analysis. Both the instrumentation and selected CE/ESI/MS applications including analyses of peptides, proteins, and glycans are discussed with the stress on research published in the past 3 years. Techniques related to the proteomic and glycomic analyses such as sample preconcentration, on-line protein digestion, and analyte derivatization prior CE/ESI/MS analysis are also included.
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Affiliation(s)
- Jana Krenkova
- Institute of Analytical Chemistry of the ASCR, Brno, Czech Republic.
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