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Frey C, Arad M, Ku K, Hare R, Balagtas R, Shi Y, Moon KM, Foster LJ, Ghafourifar G. Development of automated proteomic workflows utilizing silicon-based coupling agents. J Proteomics 2024; 303:105215. [PMID: 38843981 DOI: 10.1016/j.jprot.2024.105215] [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] [Received: 05/10/2024] [Revised: 05/28/2024] [Accepted: 06/03/2024] [Indexed: 06/16/2024]
Abstract
Automated methods for enzyme immobilization via 4-triethoxysilylbutyraldehyde (TESB) derived silicone-based coupling agents were developed. TESB and its oxidized derivative, 4-triethoxysilylbutanoic acid (TESBA), were determined to be the most effective. The resulting immobilized enzyme particles (IEPs) displayed robustness, rapid digestion, and immobilization efficiency of 51 ± 8%. Furthermore, we automated the IEP procedure, allowing for multiple enzymes, and/or coupling agents to be fabricated at once, in a fraction of the time via an Agilent Bravo. The automated trypsin TESB and TESBA IEPs were shown to rival a classical in-gel digestion method. Moreover, pepsin IEPs favored cleavage at leucine (>50%) over aromatic and methionine residues. The IEP method was then adapted for an in-situ immobilized enzyme microreactor (IMER) fabrication. We determined that TESBA could functionalize the silica capillary's inner wall while simultaneously acting as an enzyme coupler. The IMER digestion of bovine serum albumin (BSA), mirroring IEP digestion conditions, yielded a 33-40% primary sequence coverage per LC-MS/MS analysis in as little as 15 min. Overall, our findings underscore the potential of both IEP and IMER methods, paving the way for automated analysis and a reduction in enzyme waste through reuse, thereby contributing to a more cost-effective and timely study of the proteome. SIGNIFICANCE: This research introduces 4-triethoxysilylbutyraldehyde (TESB) and its derivatives as silicon-based enzyme coupling agents and an automated liquid handling method for bottom-up proteomics (BUP) while streamlining sample preparation for high-throughput processing. Additionally, immobilized enzyme particle (IEP) fabrication and digestion within the 96-well plate allows for flexibility in protocol where different enzyme-coupler combinations can be employed simultaneously. By enabling the digestion of entire microplates and reducing manual labor, the proposed method enhances reproducibility and offers a more efficient alternative to classical in-gel techniques. Furthermore, pepsin IEPs were noted to favor cleavage at leucine residues which represents an interesting finding when compared to the literature that warrants further study. The capability of immobilized enzyme microreactors (IMER) for rapid digestion (in as little as 15 min) demonstrated the system's efficiency and potential for rapid proteomic analysis. This advancement in BUP not only improves efficiency, but also opens avenues for a fully automated, mass spectrometry-integrated proteomics workflow, promising to expedite research and discoveries in complex biological studies.
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Affiliation(s)
- Connor Frey
- Department of Chemistry, University of the Fraser Valley, 33844 King Road, Abbotsford, BC V2S 7M8, Canada; Faculty of Medicine, University of British Columbia, 2194 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada.
| | - Maor Arad
- Department of Chemistry, University of the Fraser Valley, 33844 King Road, Abbotsford, BC V2S 7M8, Canada; Department of Biochemistry and Molecular Biology, Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T1Z4, Canada.
| | - Kenneth Ku
- Department of Chemistry, University of the Fraser Valley, 33844 King Road, Abbotsford, BC V2S 7M8, Canada
| | - Rhien Hare
- Department of Chemistry, University of the Fraser Valley, 33844 King Road, Abbotsford, BC V2S 7M8, Canada; Faculty of Health Sciences, Simon Fraser University, 8888 University Drive, Burnaby, BC V5A 1S6, Canada.
| | - Ronald Balagtas
- Department of Chemistry, University of the Fraser Valley, 33844 King Road, Abbotsford, BC V2S 7M8, Canada.
| | - Yuming Shi
- Department of Biochemistry and Molecular Biology, Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T1Z4, Canada.
| | - Kyung-Mee Moon
- Department of Biochemistry and Molecular Biology, Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T1Z4, Canada.
| | - Leonard J Foster
- Department of Biochemistry and Molecular Biology, Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T1Z4, Canada.
| | - Golfam Ghafourifar
- Department of Chemistry, University of the Fraser Valley, 33844 King Road, Abbotsford, BC V2S 7M8, Canada.
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Morellon-Sterling R, Tavano O, Bolivar JM, Berenguer-Murcia Á, Vela-Gutiérrez G, Sabir JSM, Tacias-Pascacio VG, Fernandez-Lafuente R. A review on the immobilization of pepsin: A Lys-poor enzyme that is unstable at alkaline pH values. Int J Biol Macromol 2022; 210:682-702. [PMID: 35508226 DOI: 10.1016/j.ijbiomac.2022.04.224] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 04/28/2022] [Accepted: 04/29/2022] [Indexed: 11/05/2022]
Abstract
Pepsin is a protease used in many different applications, and in many instances, it is utilized in an immobilized form to prevent contamination of the reaction product. This enzyme has two peculiarities that make its immobilization complex. The first one is related to the poor presence of primary amino groups on its surface (just one Lys and the terminal amino group). The second one is its poor stability at alkaline pH values. Both features make the immobilization of this enzyme to be considered a complicated goal, as most of the immobilization protocols utilize primary amino groups for immobilization. This review presents some of the attempts to get immobilized pepsin biocatalyst and their applications. The high density of anionic groups (Asp and Glu) make the anion exchange of the enzyme simpler, but this makes many of the strategies utilized to immobilize the enzyme (e.g., amino-glutaraldehyde supports) more related to a mixed ion exchange/hydrophobic adsorption than to real covalent immobilization. Finally, we propose some possibilities that can permit not only the covalent immobilization of this enzyme, but also their stabilization via multipoint covalent attachment.
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Affiliation(s)
- Roberto Morellon-Sterling
- Departamento de Biocatálisis, ICP-CSIC, Marie Curie 2, Campus UAM-CSIC Cantoblanco, 28049 Madrid, Spain; Student of Departamento de Biología Molecular, Universidad Autónoma de Madrid, Darwin 2, Campus UAM-CSIC, Cantoblanco, 28049 Madrid, Spain
| | - Olga Tavano
- Faculty of Nutrition, Alfenas Federal Univ., 700 Gabriel Monteiro da Silva St, Alfenas, MG 37130-000, Brazil
| | - Juan M Bolivar
- Chemical and Materials Engineering Department, Faculty of Chemical Sciences, Complutense University of Madrid, Complutense Ave., Madrid 28040, Spain
| | - Ángel Berenguer-Murcia
- Departamento de Química Inorgánica e Instituto Universitario de Materiales, Universidad de Alicante, Alicante, Spain
| | - Gilber Vela-Gutiérrez
- Facultad de Ciencias de la Nutrición y Alimentos, Universidad de Ciencias y Artes de Chiapas, Lib. Norte Pte. 1150, 29039 Tuxtla Gutiérrez, Chiapas, Mexico
| | - Jamal S M Sabir
- Centre of Excellence in Bionanoscience Research, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Veymar G Tacias-Pascacio
- Facultad de Ciencias de la Nutrición y Alimentos, Universidad de Ciencias y Artes de Chiapas, Lib. Norte Pte. 1150, 29039 Tuxtla Gutiérrez, Chiapas, Mexico; Tecnológico Nacional de México, Instituto Tecnológico de Tuxtla Gutiérrez, Carretera Panamericana Km. 1080, 29050 Tuxtla Gutiérrez, Chiapas, Mexico.
| | - Roberto Fernandez-Lafuente
- Departamento de Biocatálisis, ICP-CSIC, Marie Curie 2, Campus UAM-CSIC Cantoblanco, 28049 Madrid, Spain; Center of Excellence in Bionanoscience Research, External Scientific Advisory Academics, King Abdulaziz University, Jeddah 21589, Saudi Arabia.
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Zhang H, Bai Y, Zhu N, Xu J. Microfluidic reactor with immobilized enzyme-from construction to applications: A review. Chin J Chem Eng 2021. [DOI: 10.1016/j.cjche.2020.12.011] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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4
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Currivan SA, Chen WQ, Wilson R, Sanz Rodriguez E, Upadhyay N, Connolly D, Nesterenko PN, Paull B. Multi-lumen capillary based trypsin micro-reactor for the rapid digestion of proteins. Analyst 2018; 143:4944-4953. [PMID: 30221288 DOI: 10.1039/c8an01330f] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
In this work we evaluated a novel microreactor prepared using a surface modified, high surface-to-volume ratio multi-lumen fused silica capillary (MLC). The MLC investigated contained 126 parallel channels, each of 4 μm internal diameter. The MLC, along with conventional fused silica capillaries of 25 μm and 50 μm internal diameter, were treated by (3-aminopropyl)triethoxysilane (APTES) and then modified with gold nanoparticles, of ∼20 nm in diameter, to ultimately provide immobilisation sites for the proteolytic enzyme, trypsin. The modified capillaries and MLCs were characterised and profiled using non-invasive scanning capacitively coupled contactless conductivity detection (sC4D). The sC4D profiles confirmed a significantly higher amount of enzyme was immobilised to the MLC when compared to the fused silica capillaries, attributable to the increased surface to volume ratio. The MLC was used for dynamic protein digestion, where peptide fragments were collected and subjected to off-line chromatographic evaluation. The digestion was achieved with the MLC reactor, using a residence time of just 1.26 min, following which the HPLC peak associated with the intact protein decreased by >70%. The MLC reactors behaved similarly to the classical in vitro or in-solution approach, but provided a reduction in digestion time, and fewer peaks associated with trypsin auto-digestion, which is common using in-solution digestion. The digestion of cytochrome C using both the MLC-IMER and the in-solution approach, resulted in a sequence coverage of ∼80%. The preparation of the MLC microreactor was reproducible with <2.5% RSD between reactors (n = 3) as determined by sC4D.
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Affiliation(s)
- S A Currivan
- Australian Centre for Research on Separation Science, School of Natural Sciences, University of Tasmania, Tasmania, Australia.
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Höldrich M, Sievers-Engler A, Lämmerhofer M. Gold nanoparticle-conjugated pepsin for efficient solution-like heterogeneous biocatalysis in analytical sample preparation protocols. Anal Bioanal Chem 2016; 408:5415-27. [DOI: 10.1007/s00216-016-9657-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Revised: 04/28/2016] [Accepted: 05/19/2016] [Indexed: 11/30/2022]
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6
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Szałapata K, Osińska-Jaroszuk M, Bryjak J, Jaszek M, Jarosz-Wilkołazka A. NOVEL APPLICATION OF POROUS AND CELLULAR MATERIALS FOR COVALENT IMMOBILIZATION OF PEPSIN. BRAZILIAN JOURNAL OF CHEMICAL ENGINEERING 2016. [DOI: 10.1590/0104-6632.20160332s20140111] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
| | | | - J. Bryjak
- Wroclaw University of Technology, Poland
| | - M. Jaszek
- Maria Curie-Sklodowska University, Poland
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7
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Álvarez Porebski PW, Lynen F. Offline comprehensive liquid chromatography in combination with a Deoxyribonuclease I immobilized enzymatic reactor for selective screening of oligonucleotide mixtures. J Chromatogr A 2016; 1451:164-168. [PMID: 27208984 DOI: 10.1016/j.chroma.2016.05.021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Revised: 05/01/2016] [Accepted: 05/04/2016] [Indexed: 10/21/2022]
Abstract
The development of a comprehensive ion-pair chromatography-immobilized enzyme reactor×ion-pair chromatography (IPC-IMER×IPC) methodology for the advanced characterization of DNA/RNA oligonucleotides (ONs) mixtures has been carried out. More in detail, a DNase I IMER has been coupled to IPC in the post column configuration, followed by the collection of the eluting fractions and reanalysis by IPC. The effect of the mobile phase over the IMER activity was qualitatively evaluated. The methodology proved to generate relevant ON degradation profiles that might be correlated with the ON stability towards nucleases. Moreover, this platform shows potential for its further implementation in selective analysis of ON mixtures and in mapping studies.
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Affiliation(s)
- Piotr Wiktor Álvarez Porebski
- Separation Science Group, Department of Organic and Macromolecular Chemistry, Universiteit Gent, Krijgslaan 281 S4-bis, 9000 Gent, Belgium.
| | - Frederic Lynen
- Separation Science Group, Department of Organic and Macromolecular Chemistry, Universiteit Gent, Krijgslaan 281 S4-bis, 9000 Gent, Belgium.
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Foo HC, Smith NW, Stanley SM. Fabrication of an on-line enzyme micro-reactor coupled to liquid chromatography–tandem mass spectrometry for the digestion of recombinant human erythropoietin. Talanta 2015; 135:18-22. [DOI: 10.1016/j.talanta.2014.12.033] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Revised: 12/19/2014] [Accepted: 12/20/2014] [Indexed: 11/30/2022]
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9
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Lakouraj MM, Maashsani A, Norouzian RS, Mohadjerani M. Immobilization of Pepsin on Chitosan Magnetic Nanoparticles and Its Application in Deacetylation of Amides. J Carbohydr Chem 2015. [DOI: 10.1080/07328303.2015.1009534] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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10
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Hong T, Chi C, Ji Y. Pepsin-modified chiral monolithic column for affinity capillary electrochromatography. J Sep Sci 2014; 37:3377-83. [DOI: 10.1002/jssc.201400424] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2014] [Revised: 08/10/2014] [Accepted: 08/10/2014] [Indexed: 01/31/2023]
Affiliation(s)
- Tingting Hong
- Department of Analytical Chemistry; China Pharmaceutical University; Nanjing China
- Key Laboratory of Drug Quality Control and Pharmacovigilance; Ministry of Education; Nanjing China
| | - Cuijie Chi
- Department of Analytical Chemistry; China Pharmaceutical University; Nanjing China
- Key Laboratory of Drug Quality Control and Pharmacovigilance; Ministry of Education; Nanjing China
| | - Yibing Ji
- Department of Analytical Chemistry; China Pharmaceutical University; Nanjing China
- Key Laboratory of Drug Quality Control and Pharmacovigilance; Ministry of Education; Nanjing China
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12
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Zhang Z, Zhang L, Zhang C, Zhang W. Hybrid organic–inorganic monolithic enzymatic reactor with SBA-15 nanoparticles incorporated. Talanta 2014; 119:485-91. [DOI: 10.1016/j.talanta.2013.11.037] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2013] [Revised: 11/11/2013] [Accepted: 11/13/2013] [Indexed: 10/26/2022]
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13
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Safdar M, Sproß J, Jänis J. Microscale immobilized enzyme reactors in proteomics: Latest developments. J Chromatogr A 2014; 1324:1-10. [DOI: 10.1016/j.chroma.2013.11.045] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2013] [Revised: 11/18/2013] [Accepted: 11/24/2013] [Indexed: 01/10/2023]
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14
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Elagli A, Laurette S, Treizebre A, Bocquet B, Froidevaux R. Diffusion based kinetic selectivity modulation of enzymatic proteolysis in a microfluidic reactor: experimental analysis and stochastic modeling. RSC Adv 2014. [DOI: 10.1039/c3ra46005c] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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15
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Safdar M, Spross J, Jänis J. Microscale enzyme reactors comprising gold nanoparticles with immobilized trypsin for efficient protein digestion. JOURNAL OF MASS SPECTROMETRY : JMS 2013; 48:1281-1284. [PMID: 24338882 DOI: 10.1002/jms.3297] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2013] [Revised: 10/11/2013] [Accepted: 10/15/2013] [Indexed: 06/03/2023]
Affiliation(s)
- Muhammad Safdar
- Department of Chemistry, University of Eastern Finland, Yliopistokatu 7, FI-80101, Joensuu, Finland
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16
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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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17
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Çelebi B, Bayraktar A, Tuncel A. Synthesis of a monolithic, micro-immobilised enzyme reactor via click-chemistry. Anal Bioanal Chem 2012; 403:2655-63. [DOI: 10.1007/s00216-012-6075-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2011] [Revised: 04/19/2012] [Accepted: 04/21/2012] [Indexed: 10/28/2022]
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Bachmann S, Bakry R, Huck CW, Polato F, Corradini D, Bonn GK. Peptide mapping using capillary electrophoresis offline coupled to matrix-assisted laser desorption ionization time of flight mass spectrometry. Electrophoresis 2011; 32:2830-9. [PMID: 21953317 DOI: 10.1002/elps.201000653] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2010] [Revised: 03/14/2011] [Accepted: 03/14/2011] [Indexed: 01/20/2023]
Abstract
This article reports the results of a study carried out to evaluate the offline hyphenation of capillary zone electrophoresis with matrix-assisted lased desorption ionization time of flight mass spectrometry (MALDI-TOF-MS) for the analysis of low-abundant complex samples, represented by the tryptic phosphorylated peptides of phosphoproteins, such as α-casein, β-casein, and fetuin. The proposed method employs a latex-coated capillary and consists in the online preconcentration of the tryptic peptides by a pH-mediated stacking method, their separation by capillary zone electrophoresis, and subsequent deposition of the separated analytes onto a MALDI target for their MS analysis. The online preconcentration method allows loading a large sample volume (∼150 nL), which is introduced into the capillary after the hydrodynamic injection of a short plug of 1.0 M ammonium hydroxide solution and is sandwiched between two plugs of the acidic background electrolyte solution (BGE) filling the capillary. The sample spotting of the separated analytes onto the MALDI target is performed either during or postseparation using an automatic spotting device connected to the exit of the separation capillary. The proposed method allows the separation and identification of multiphosphorylated peptides from other peptides and enables their identification at femtomole level with improved efficiency compared with LC approaches hyphenated to MS.
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Affiliation(s)
- Stefan Bachmann
- Institute of Analytical Chemistry and Radiochemistry, Leopold-Franzens University, Innsbruck, Austria
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Liang Y, Tao D, Ma J, Sun L, Liang Z, Zhang L, Zhang Y. Hydrophilic monolith based immobilized enzyme reactors in capillary and on microchip for high-throughput proteomic analysis. J Chromatogr A 2011; 1218:2898-905. [DOI: 10.1016/j.chroma.2011.02.073] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2010] [Revised: 02/25/2011] [Accepted: 02/28/2011] [Indexed: 12/29/2022]
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Vitorino R, Krenkova J, Foret F, Domingues P, Amado F. Protein identification using nano-HPLC-MS: ESI-MS and MALDI-MS interfaces. Methods Mol Biol 2011; 790:31-46. [PMID: 21948404 DOI: 10.1007/978-1-61779-319-6_3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Body fluids and body tissues have a myriad of peptides and proteins that, very often, the traditional methodologies of proteomics, such as conventional gel electrophoresis or mass spectrometry, are unable to characterize. We describe two protocols to characterize high molecular weight peptides (>3 kDa) and intact proteins involving on-line trypsin digestion, separation of the digests by nano-HPLC, and analysis by mass spectrometry using two different ionization sources (matrix-assisted laser desorption and electrospray ionization). These protocols have the advantage of promoting protein denaturation in an aqueous-organic solvent, which reduces the derivatization of the sample and facilitates an in-depth analysis for detection and identification of proteins. Additional advantages include the following: (1) integration of these protocols into standard proteomic workflows after the preprocessing of samples and separation; (2) use of high-resolution monolithic columns; and (3) the ability to acquire information from minimal amounts of sample.
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Affiliation(s)
- Rui Vitorino
- Department of Chemistry, Mass Spectrometry Center, QOPNA, University of Aveiro, Campus Universitário de Santiago, Aveiro, Portugal.
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Tao D, Zhang L, Shan Y, Liang Z, Zhang Y. Recent advances in micro-scale and nano-scale high-performance liquid-phase chromatography for proteome research. Anal Bioanal Chem 2010; 399:229-41. [PMID: 20683586 DOI: 10.1007/s00216-010-3946-7] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2010] [Revised: 06/18/2010] [Accepted: 06/20/2010] [Indexed: 10/25/2022]
Abstract
High-performance liquid chromatography-electrospray ionization tandem mass spectrometry (HPLC-ESI-MS-MS) is regarded as one of the most powerful techniques for separation and identification of proteins. Recently, much effort has been made to improve the separation capacity, detection sensitivity, and analysis throughput of micro- and nano-HPLC, by increasing column length, reducing column internal diameter, and using integrated techniques. Development of HPLC columns has also been rapid, as a result of the use of submicrometer packing materials and monolithic columns. All these innovations result in clearly improved performance of micro- and nano-HPLC for proteome research.
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Affiliation(s)
- Dingyin Tao
- 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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Ma X, Chan ECY. On-line chromatographic screening of matrix metalloproteinase inhibitors using immobilized MMP-9 enzyme reactor. J Chromatogr B Analyt Technol Biomed Life Sci 2010; 878:1777-83. [DOI: 10.1016/j.jchromb.2010.04.040] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2010] [Revised: 04/22/2010] [Accepted: 04/28/2010] [Indexed: 10/19/2022]
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23
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Yah WO, Yamamoto K, Jiravanichanun N, Otsuka H, Takahara A. Imogolite Reinforced Nanocomposites: Multifaceted Green Materials. MATERIALS 2010. [PMCID: PMC5445889 DOI: 10.3390/ma3031709] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
This paper presents an overview on recent developments of imogolite reinforced nanocomposites, including fundamental structure, synthesis/purification of imogolite, physicochemical properties of nanocomposites and potential applications in industry. The naturally derived nanotubular material of imogolite represents a distinctive class of nanofiller for industrially significant polymer. The incompatibility between the surface properties of inorganic nanofiller and organic matrix has prompted the need to surface modify the imogolite. Early problems in increasing the binding properties of surface modifier to imogolite have been overcome by using a phosphonic acid group. Different approaches have been used to gain better control over the dispersal of nanofiller and to further improve the physicochemical properties of nanocomposites. Among these, polymer grafting, in situ synthesis of imogolite in polymer matrix, and spin-assembly are some of the promising methods that will be described herein. This imogolite reinforced nanocomposite of enhanced optical and mechanical properties, and with unique biological and electronic properties, is expected to become an important category of hybrid material that shows potential for industrial applications.
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Affiliation(s)
- Weng On Yah
- Graduate School of Engineering, Kyushu University, 744 Mootoka, Nishi-ku, Fukuoka 819-0395, Japan; E-Mail: (W.O.Y)
| | - Kazuya Yamamoto
- Kitakyushu College of Technology, 5-20-1 Shii, Kokuraminami, Kitakyusyu, Fukuoka 802-0985, Japan; E-Mail: (K.Y)
| | - Nattha Jiravanichanun
- Institute for Materials Chemistry and Engineering, Kyushu University, 744 Mootoka, Nishi-ku, Fukuoka 819-0395, Japan; E-Mails: (N.J); (H.O)
| | - Hideyuki Otsuka
- Graduate School of Engineering, Kyushu University, 744 Mootoka, Nishi-ku, Fukuoka 819-0395, Japan; E-Mail: (W.O.Y)
- Institute for Materials Chemistry and Engineering, Kyushu University, 744 Mootoka, Nishi-ku, Fukuoka 819-0395, Japan; E-Mails: (N.J); (H.O)
| | - Atsushi Takahara
- Graduate School of Engineering, Kyushu University, 744 Mootoka, Nishi-ku, Fukuoka 819-0395, Japan; E-Mail: (W.O.Y)
- Institute for Materials Chemistry and Engineering, Kyushu University, 744 Mootoka, Nishi-ku, Fukuoka 819-0395, Japan; E-Mails: (N.J); (H.O)
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +81-92-802-2517; Fax: +81-92-802-2518
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Rietschel B, Bornemann S, Arrey TN, Baeumlisberger D, Karas M, Meyer B. Membrane protein analysis using an improved peptic in-solution digestion protocol. Proteomics 2010; 9:5553-7. [PMID: 20017156 DOI: 10.1002/pmic.200900532] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
In the proteomic analysis of membrane proteins, less-specific proteases have become a promising tool to overcome fundamental limitations of trypsin with its unique specificity for basic residues. Pepsin is well-known to be utilized for specific applications that require acidic conditions, but in terms of membrane protein identification and characterization, it has been disregarded for the most part. This work presents an optimization of an existing peptic digest protocol for the analysis of membrane proteins using bacteriorhodopsin from purple membranes as reference.
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Affiliation(s)
- Benjamin Rietschel
- Cluster of Excellence Macromolecular Complexes, Institute for Pharmaceutical Chemistry, Goethe-University, Frankfurt am Main, Germany
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25
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Cingöz A, Hugon-Chapuis F, Pichon V. Total on-line analysis of a target protein from plasma by immunoextraction, digestion and liquid chromatography–mass spectrometry. J Chromatogr B Analyt Technol Biomed Life Sci 2010; 878:213-21. [DOI: 10.1016/j.jchromb.2009.07.032] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2009] [Revised: 07/17/2009] [Accepted: 07/27/2009] [Indexed: 10/20/2022]
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26
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Hahn HW, Rainer M, Ringer T, Huck CW, Bonn GK. Ultrafast Microwave-Assisted In-Tip Digestion of Proteins. J Proteome Res 2009; 8:4225-30. [DOI: 10.1021/pr900188x] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Hans W. Hahn
- Institute of Analytical Chemistry and Radiochemistry, Leopold-Franzens University, Innrain 52a, 6020 Innsbruck, Austria
| | - Matthias Rainer
- Institute of Analytical Chemistry and Radiochemistry, Leopold-Franzens University, Innrain 52a, 6020 Innsbruck, Austria
| | - Thomas Ringer
- Institute of Analytical Chemistry and Radiochemistry, Leopold-Franzens University, Innrain 52a, 6020 Innsbruck, Austria
| | - Christian W. Huck
- Institute of Analytical Chemistry and Radiochemistry, Leopold-Franzens University, Innrain 52a, 6020 Innsbruck, Austria
| | - Günther K. Bonn
- Institute of Analytical Chemistry and Radiochemistry, Leopold-Franzens University, Innrain 52a, 6020 Innsbruck, Austria
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27
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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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28
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Lin W, Skinner CD. Design and optimization of porous polymer enzymatic digestors for proteomics. J Sep Sci 2009; 32:2642-52. [DOI: 10.1002/jssc.200900221] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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29
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Stigter E, de Jong G, van Bennekom W. Development of an on-line SPR-digestion-nanoLC-MS/MS system for the quantification and identification of interferon-γ in plasma. Biosens Bioelectron 2009; 24:2184-90. [DOI: 10.1016/j.bios.2008.11.020] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2008] [Revised: 10/29/2008] [Accepted: 11/20/2008] [Indexed: 01/01/2023]
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30
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