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Hidayah SN, Biabani A, Gaikwad M, Nissen P, Voß H, Riedner M, Schlüter H, Siebels B. Application of sample displacement batch chromatography for fractionation of proteoforms. Proteomics 2024; 24:e2200424. [PMID: 37750450 DOI: 10.1002/pmic.202200424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 09/06/2023] [Accepted: 09/07/2023] [Indexed: 09/27/2023]
Abstract
Fractionation of proteoforms is currently the most challenging topic in the field of proteoform analysis. The need for considering the existence of proteoforms in experimental approaches is not only important in Life Science research in general but especially in the manufacturing of therapeutic proteins (TPs) like recombinant therapeutic antibodies (mAbs). Some of the proteoforms of TPs have significantly decreased actions or even cause side effects. The identification and removal of proteoforms differing from the main species, having the desired action, is challenging because the difference in the composition of atoms is often very small and their concentration in comparison to the main proteoform can be low. In this study, we demonstrate that sample displacement batch chromatography (SDBC) is an easy-to-handle, economical, and efficient method for fractionating proteoforms. As a model sample a commercial ovalbumin fraction was used, containing many ovalbumin proteoforms. The most promising parameters for the SDBC were determined by a screening approach and applied for a 10-segment fractionation of ovalbumin with cation exchange chromatography resins. Mass spectrometry of intact proteoforms was used for characterizing the SDBC fractionation process. By SDBC, a significant separation of different proteoforms was obtained.
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Affiliation(s)
- Siti Nurul Hidayah
- Section Mass Spectrometric Proteomics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Universitas Gadjah Mada, Sleman, Yogyakarta, Indonesia
| | - Ali Biabani
- Section Mass Spectrometric Proteomics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Manasi Gaikwad
- Section Mass Spectrometric Proteomics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Paula Nissen
- Section Mass Spectrometric Proteomics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Hannah Voß
- Section Mass Spectrometric Proteomics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Maria Riedner
- Technology Platform Mass Spectrometry, University of Hamburg, Hamburg, Germany
| | - Hartmut Schlüter
- Section Mass Spectrometric Proteomics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Bente Siebels
- Section Mass Spectrometric Proteomics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
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Begić M, Pečenković S, Gajdošik MŠ, Josić D, Müller E. Salt-tolerant cation exchanger-containing sulfate groups as a viable alternative for mixed-mode type and heparin-based affinity resins. Biotechnol J 2021; 16:e2100100. [PMID: 34347362 DOI: 10.1002/biot.202100100] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 07/02/2021] [Accepted: 07/12/2021] [Indexed: 12/17/2022]
Abstract
Ion-exchange chromatography is still one of the most popular protein separation techniques. Before chromatographic separation, the high salt concentration in various samples necessitates additional steps. Therefore, low salt tolerance of ion-exchange resins is a drawback that needs to be addressed. Herein, the differences in salt tolerance and hydrophobicity of strong cation-exchange TOYOPEARL resins of sulfonium and sulfate-types were investigated. Despite only a minor structural difference, differences in selectivity and salt tolerance between the sulfate and sulfonic groups were detected. In silico calculations were also carried out for model substances representing the sulfonium and sulfate groups, wherein significant differences in hydrophobicity was observed. These experiments confirmed the hypothesis that the salt tolerance, higher affinity, and selectivity for certain vitamin K dependent clotting factors are interrelated and dependent on the presence of the sulfate group. Separation of clotting factor IX from the prothrombin complex concentrate further to confirmed the affinity for these proteins. The results show that the use of only a resin with the sulfate ligand and not with the sulfonic acid ligand allows for a facile and rapid separation of clotting factor IX and other vitamin K dependent clotting factors.
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Affiliation(s)
- Marija Begić
- Faculty of Medicine, University Juraj Dobrila, Pula, Croatia
| | | | | | - Djuro Josić
- Faculty of Medicine, University Juraj Dobrila, Pula, Croatia.,Warren Alpert Medical School, Brown University, Providence, Rhode Island, USA
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Sample Displacement Batch Chromatography of Proteins. Methods Mol Biol 2020. [PMID: 33128756 DOI: 10.1007/978-1-0716-0775-6_19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/27/2023]
Abstract
In downstream processing, large-scale chromatography plays an important role. For its development, screening experiments followed by pilot-plant chromatography are mandatory steps. Here we describe fast, simple, and inexpensive methods for establishing a preparative chromatography for the separation of complex protein mixtures, based on sample displacement batch chromatography. The methods are demonstrated by anion-exchange chromatography of a human plasma protein fraction (Cohn IV-4), including the screening step and upscaling of the chromatography by a factor of one hundred. The results of the screening experiments and the preparative chromatography are monitored by SDS-PAGE electrophoresis. In summary, we provide a protocol, which should be easily adaptable for the chromatographic large-scale purification of other proteins, in the laboratory as well as in the manufacturing of biopharmaceuticals. These protocols cover the initial piloting steps for establishing a large-scale sample batch chromatography. The results from the piloting steps may also be applied for packed columns for performing simulated-moving-bed (SMB) chromatography rather than batch chromatography.
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Nice EC. The separation sciences, the front end to proteomics: An historical perspective. Biomed Chromatogr 2020; 35:e4995. [DOI: 10.1002/bmc.4995] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 09/18/2020] [Accepted: 09/23/2020] [Indexed: 02/06/2023]
Affiliation(s)
- Edouard C. Nice
- Department of Biochemistry and Molecular Biology Monash University Clayton Victoria Australia
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Prediction of the elution profiles of proteins in mixed salt systems in hydrophobic interaction chromatography. Sep Purif Technol 2020. [DOI: 10.1016/j.seppur.2019.116006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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Andjelković U, Tufegdžić S, Popović M. Use of monolithic supports for high-throughput protein and peptide separation in proteomics. Electrophoresis 2017; 38:2851-2869. [DOI: 10.1002/elps.201700260] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Revised: 09/02/2017] [Accepted: 09/03/2017] [Indexed: 01/08/2023]
Affiliation(s)
- Uroš Andjelković
- Department of Chemistry-Institute of Chemistry; Technology and Metallurgy; University of Belgrade; Belgrade Serbia
- Department of Biotechnology; University of Rijeka; Rijeka Croatia
| | - Srdjan Tufegdžić
- Department of Chemistry-Institute of Chemistry; Technology and Metallurgy; University of Belgrade; Belgrade Serbia
| | - Milica Popović
- Faculty of Chemistry; University of Belgrade; Belgrade Serbia
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Martinović T, Josić D. Polymethacrylate-based monoliths as stationary phases for separation of biopolymers and immobilization of enzymes. Electrophoresis 2017; 38:2821-2826. [DOI: 10.1002/elps.201700255] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Revised: 07/20/2017] [Accepted: 07/14/2017] [Indexed: 12/17/2022]
Affiliation(s)
| | - Djuro Josić
- Department of Biotechnology; University of Rijeka; Rijeka Croatia
- Warren Alpert Medical School; Brown University; Providence RI USA
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Influence of mixed electrolytes on the adsorption of lysozyme, PEG, and PEGylated lysozyme on a hydrophobic interaction chromatography resin. Biotechnol Prog 2017; 33:1104-1115. [DOI: 10.1002/btpr.2474] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Revised: 03/23/2017] [Indexed: 11/07/2022]
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Černigoj U, Martinuč U, Cardoso S, Sekirnik R, Krajnc NL, Štrancar A. Sample displacement chromatography of plasmid DNA isoforms. J Chromatogr A 2015; 1414:103-9. [DOI: 10.1016/j.chroma.2015.08.035] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2015] [Revised: 08/13/2015] [Accepted: 08/14/2015] [Indexed: 10/23/2022]
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Henning AK, Albrecht D, Riedel K, Mettenleiter TC, Karger A. An alternative method for serum protein depletion/enrichment by precipitation at mildly acidic pH values and low ionic strength. Proteomics 2015; 15:1935-40. [PMID: 25644273 DOI: 10.1002/pmic.201400257] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2014] [Revised: 12/15/2014] [Accepted: 01/28/2015] [Indexed: 01/05/2023]
Abstract
Serum proteome analysis is severely hampered by the extreme dynamic range of protein concentrations, but tools for the specific depletion of highly abundant serum proteins lack for most farm and companion animals. A well-established alternative strategy to reduce the dynamic range of plasma protein concentrations, treatment with combinatorial peptide ligand libraries (CPLL), is generally applicable but requires large amounts of sample. Therefore, additional depletion/enrichment protocols for plasma and serum samples from animals are desirable. In this respect, we have tested a protein precipitate that formed after withdrawal of salt from human, bovine, or porcine serum at pH 4.2. The bovine sample was composed of over 300 proteins making it a potential source for biomarker discovery. Precipitation was highly reproducible and the concentrations of albumin and other highly abundant serum proteins were strongly reduced. In comparison to the CPLL treatment, precipitation did not introduce any selection bias based on hydrophathy or pI. However, the composition of both preparations was partially complementary. Salt withdrawal at pH 4.2 is suggested as additional depletion/enrichment strategy for serum samples. Also, we point out that the removal of precipitates from serum samples under the described conditions bears the risk of losing a valuable protein fraction.
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Affiliation(s)
- Ann-Kristin Henning
- Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Dirk Albrecht
- Institute for Microbiology, Ernst-Moritz-Arndt-University Greifswald, Greifswald, Germany
| | - Katharina Riedel
- Institute for Microbiology, Ernst-Moritz-Arndt-University Greifswald, Greifswald, Germany
| | - Thomas C Mettenleiter
- Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Axel Karger
- Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
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Jozala AF, de Lencastre Novaes LC, Mazzola PG, Oliveira-Nascimento L, Vessoni Penna TC, Teixeira JA, Passarinha LA, Queiroz JA, Pessoa A. Low-cost purification of nisin from milk whey to a highly active product. FOOD AND BIOPRODUCTS PROCESSING 2015. [DOI: 10.1016/j.fbp.2013.12.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Werner A, Hackemann E, Hasse H. Temperature dependence of adsorption of PEGylated lysozyme and pure polyethylene glycol on a hydrophobic resin: Comparison of isothermal titration calorimetry and van’t Hoff data. J Chromatogr A 2014; 1356:188-96. [DOI: 10.1016/j.chroma.2014.06.056] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2014] [Revised: 06/17/2014] [Accepted: 06/17/2014] [Indexed: 10/25/2022]
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Werner A, Hasse H. Experimental study and modeling of the influence of mixed electrolytes on adsorption of macromolecules on a hydrophobic resin. J Chromatogr A 2013; 1315:135-44. [DOI: 10.1016/j.chroma.2013.09.071] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2013] [Revised: 09/19/2013] [Accepted: 09/23/2013] [Indexed: 11/28/2022]
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