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Goulden T, Bodachivskyi I, Padula MP, Williams DBG. Concentrated ionic liquids for proteomics: Caveat emptor! Int J Biol Macromol 2023; 253:127438. [PMID: 37839603 DOI: 10.1016/j.ijbiomac.2023.127438] [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: 06/27/2023] [Revised: 10/03/2023] [Accepted: 10/12/2023] [Indexed: 10/17/2023]
Abstract
The use of concentrated ionic liquids (ILs) in the bioanalytical chemistry of proteins is sparse; typically, dilute aqueous IL solutions are used. Concentrated ILs have unique properties that may allow researchers to dissolve previously insoluble protein analytes, to increase the depth and robustness of sample preparation and the analysis of proteins. Previous research using concentrated ILs for this purpose is sparse and there is a need to systematically investigate the structure-activity relationship between the IL structure and its capacity to solubilise proteins. Here, bovine serum albumin was dissolved in various ionic liquids and monitored over time by light microscopy and SDS-PAGE. While qualitative, these measures provide a good estimate of, respectively, the dissolving power of an IL towards the given protein and the retained integrity of the protein. Hydrophilic ILs show the best solubilisation capacity and higher temperatures (in a restricted sense) improve the solubility of the protein. Higher temperatures and longer reaction times reduce the molecular weight of the protein, which could inhibit their applicability in proteomics, unless the conditions are judiciously controlled. Researchers should exercise caution when using concentrated ILs for protein analysis until the full scope and limitations are known, an aspect we are presently investigating.
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Affiliation(s)
- Thomas Goulden
- University of Technology Sydney, School of Mathematical and Physical Sciences, 15 Broadway, Sydney, NSW 2007, Australia
| | - Iurii Bodachivskyi
- University of Technology Sydney, School of Mathematical and Physical Sciences, 15 Broadway, Sydney, NSW 2007, Australia; V.P. Kukhar Institute of Bioorganic Chemistry and Petrochemistry of the National Academy of Sciences of Ukraine, 1 Academician Kukhar St, Kyiv 02094, Ukraine
| | - Matthew P Padula
- University of Technology Sydney, School of Life Sciences, 15 Broadway, Sydney, NSW 2007, Australia
| | - D Bradley G Williams
- University of Technology Sydney, School of Mathematical and Physical Sciences, 15 Broadway, Sydney, NSW 2007, Australia; University of Wollongong, School of Chemistry and Molecular Bioscience, Wollongong, NSW 2522, Australia.
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Vaz BMC, Kholany M, Pinto DCGA, Macário IPE, Veloso T, Caetano T, Pereira JL, Coutinho JAP, Ventura SPM. Recovery of bacterioruberin and proteins using aqueous solutions of surface-active compounds. RSC Adv 2022; 12:30278-30286. [PMID: 36337967 PMCID: PMC9590249 DOI: 10.1039/d2ra02581g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 10/02/2022] [Indexed: 11/30/2022] Open
Abstract
Haloarchaea microorganisms are little explored marine resources that can be a promising source of valuable compounds with unique characteristics, due to their adaptation to extreme environments. In this work, the extraction of bacterioruberin and proteins from Haloferax mediterranei ATCC 33500 was investigated using aqueous solutions of ionic liquids and surfactants, which were further compared with ethanol. Despite the good performance of ethanol in the extraction of bacterioruberin, the use of aqueous solutions of surface-active compounds allowed the simultaneous release of bacterioruberin and proteins in a multi-product process, with the non-ionic surfactants being identified as the most promising. The optimum operational conditions allowed a maximum extraction yield of 0.37 ± 0.01 mgbacterioruberin gwet biomass -1 and 352 ± 9 mgprotein gwet biomass -1 with an aqueous solution of Tween® 20 (at 182.4 mM) as the extraction solvent. In addition, high purities of bacterioruberin were obtained, after performing a simple induced precipitation using ethanol as an antisolvent to recover the proteins present in the initial extract. Finally, a step for polishing the bacterioruberin was performed, to enable solvent recycling, further closing the process to maximize its circularity.
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Affiliation(s)
- Bárbara M. C. Vaz
- CICECO – Aveiro Institute of Materials, Department of Chemistry, University of Aveiro, Campus Universitário de Santiago3810-193 AveiroPortugal
| | - Mariam Kholany
- CICECO – Aveiro Institute of Materials, Department of Chemistry, University of Aveiro, Campus Universitário de Santiago3810-193 AveiroPortugal
| | - Diana C. G. A. Pinto
- LAQV – REQUIMTE, Department of Chemistry, University of Aveiro3810-193 AveiroPortugal
| | - Inês P. E. Macário
- CICECO – Aveiro Institute of Materials, Department of Chemistry, University of Aveiro, Campus Universitário de Santiago3810-193 AveiroPortugal,CESAM – Centre for Environmental and Marine Studies, Department of Biology, University of Aveiro Campus Universitário de Santiago3810-193 AveiroPortugal
| | - Telma Veloso
- CICECO – Aveiro Institute of Materials, Department of Chemistry, University of Aveiro, Campus Universitário de Santiago3810-193 AveiroPortugal,CESAM – Centre for Environmental and Marine Studies, Department of Biology, University of Aveiro Campus Universitário de Santiago3810-193 AveiroPortugal
| | - Tânia Caetano
- CESAM – Centre for Environmental and Marine Studies, Department of Biology, University of Aveiro Campus Universitário de Santiago3810-193 AveiroPortugal
| | - Joana L. Pereira
- CESAM – Centre for Environmental and Marine Studies, Department of Biology, University of Aveiro Campus Universitário de Santiago3810-193 AveiroPortugal
| | - João A. P. Coutinho
- CICECO – Aveiro Institute of Materials, Department of Chemistry, University of Aveiro, Campus Universitário de Santiago3810-193 AveiroPortugal
| | - Sónia P. M. Ventura
- CICECO – Aveiro Institute of Materials, Department of Chemistry, University of Aveiro, Campus Universitário de Santiago3810-193 AveiroPortugal
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Blaga AC, Tucaliuc A, Kloetzer L. Applications of Ionic Liquids in Carboxylic Acids Separation. MEMBRANES 2022; 12:membranes12080771. [PMID: 36005686 PMCID: PMC9414664 DOI: 10.3390/membranes12080771] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 07/31/2022] [Accepted: 08/04/2022] [Indexed: 05/26/2023]
Abstract
Ionic liquids (ILs) are considered a green viable organic solvent substitute for use in the extraction and purification of biosynthetic products (derived from biomass-solid/liquid extraction, or obtained through fermentation-liquid/liquid extraction). In this review, we analyzed the ionic liquids (greener alternative for volatile organic media in chemical separation processes) as solvents for extraction (physical and reactive) and pertraction (extraction and transport through liquid membranes) in the downstream part of organic acids production, focusing on current advances and future trends of ILs in the fields of promoting environmentally friendly products separation.
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Ionic liquid modification of metal-organic framework endows high selectivity for phosphoproteins adsorption. Anal Chim Acta 2021; 1147:144-154. [PMID: 33485572 DOI: 10.1016/j.aca.2020.12.046] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 12/18/2020] [Accepted: 12/22/2020] [Indexed: 02/02/2023]
Abstract
Zr-based metal-organic framework, UiO-66-NH2, provides favorable adsorption capacity to phosphoproteins, however, it exhibits obvious nonspecific adsorption to other proteins. In the present work, we report a facile strategy to reduce the nonspecific adsorption of nonphosphoproteins by modifying UiO-66-NH2 with imidazolium ionic liquids (ILs). With respect to bare UiO-66-NH2, the modified counterpart, UiO@IL, exhibits much improved selectivity to phosphoproteins while maintains comparable adsorption performance. The surface of UiO@IL presents a strong hydrophilicity due to the modification of ILs. Hydrophobic and electrostatic interaction between the absorbent and nonphosphoprotein is significantly reduced. In addition, the interaction between imidazole group of ILs moiety and phosphate group in phosphoprotein ensures the favorable adsorption capacity of UiO@IL for phosphoproteins. Anionic moieties of ILs, i.e., Cl-, Br-, BF4-, CF3SO3-, play negligible effect in the adsorption process. As a representative, phosphoprotein β-casein (β-ca) is selectively enriched at a mass ratio of BSA:β-ca = 100:1. UiO@IL was further applied for the selective enrichment of phosphoprotein in milk.
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Liu C, Si X, Yan S, Zhao X, Qian X, Ying W, Zhao L. Development of the C12Im-Cl-assisted method for rapid sample preparation in proteomic application. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2021; 13:776-781. [PMID: 33492312 DOI: 10.1039/d0ay02079f] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Chromatography and mass spectrometry (MS) techniques have greatly improved the power of proteomic analyses. However, sample processing methods used prior to MS, including protein extraction and digestion, remain bottlenecks in the large-scale clinical application of proteomics. Ionic liquids, composed entirely of ions, have high solubility in various solvents. In this study, the effects of the cationic surfactant 1-dodecyl-3-methylimidazolium chloride (C12Im-Cl) on protein digestion were evaluated for clinical proteomic applications. C12Im-Cl was compatible with trypsin and reduced the protein digestion time from 16 h to 1 h. Residual C12Im-Cl was easily removed with a strong anion exchange membrane before MS. We evaluated the performance of C12Im-Cl extraction and rapid protein digestion using formalin-fixed paraffin-embedded liver cancer tissues. The number of proteins and peptides identified was nearly equal to that identified by the traditional filter-aided sample preparation method (2705 vs. 2739 and 16 682 vs. 17 214). In general, the C12Im-Cl-aided rapid sample preparation method is promising for proteomic applications.
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Affiliation(s)
- Chang Liu
- Beijing Key Laboratory of Environmental and Viral Oncology, Faculty of Environment and Life, Beijing University of Technology, Beijing 100124, China.
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Chen Y, Jiang B, Yuan H, Zhu X, Liu J, Zhang X, Liang Z, Wang L, Zhang L, Zhang Y. Fully integrated protein absolute quantification platform for analysis of multiple tumor markers in human plasma. Talanta 2021; 226:122102. [PMID: 33676658 DOI: 10.1016/j.talanta.2021.122102] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 01/04/2021] [Accepted: 01/09/2021] [Indexed: 11/18/2022]
Abstract
In this study, we developed a fully integrated protein absolute quantification platform for simultaneous analysis of multiple tumor markers in human plasma, by which multiple target proteins (alpha-fetoprotein, prostate-specific antigen, carcino-embryonic antigen and mucin-1) were firstly enriched by aptamers immobilized capillary column using graphene oxide modified polymer microsphere as the separation matrix, and then the eluted target proteins were online denatured, reduced, desalted and digested by our developed fully automated sample treatment device (FAST), finally the resulting peptides were analyzed by parallel reaction monitoring (PRM) on LTQ-orbitrap velos mass spectrometry. Compared to traditional ELISA assay, the platform exhibited significant advantages such as short analysis time, low limit of detection, and ease of automation. Furthermore, our developed platform was also applied in the absolute quantification of tumor markers from clinical human plasma samples, and the results were comparable to those obtained by clinical immunoassay. All the results demonstrated that such a platform could provide a promising tool for achieving high sensitivity, high accuracy, and high throughput detection of disease related protein markers in the routine physical examination and clinical disease diagnosis.
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Affiliation(s)
- Yuanbo Chen
- National Chromatographic Research and Analysis Center, Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian, 116023, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Bo Jiang
- National Chromatographic Research and Analysis Center, Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian, 116023, China
| | - Huiming Yuan
- National Chromatographic Research and Analysis Center, Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian, 116023, China.
| | - Xudong Zhu
- National Chromatographic Research and Analysis Center, Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian, 116023, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jianhui Liu
- National Chromatographic Research and Analysis Center, Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian, 116023, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiaodan Zhang
- National Chromatographic Research and Analysis Center, Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian, 116023, China
| | - Zhen Liang
- National Chromatographic Research and Analysis Center, Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian, 116023, China
| | - Liming Wang
- The Second Affiliated Hospital of Dalian Medical University, Dalian, 116027, China
| | - Lihua Zhang
- National Chromatographic Research and Analysis Center, Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian, 116023, China.
| | - Yukui Zhang
- National Chromatographic Research and Analysis Center, Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian, 116023, China
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Fang F, Zhao Q, Chu H, Liu M, Zhao B, Liang Z, Zhang L, Li G, Wang L, Qin J, Zhang Y. Molecular Dynamics Simulation-assisted Ionic Liquid Screening for Deep Coverage Proteome Analysis. Mol Cell Proteomics 2020; 19:1724-1737. [PMID: 32675193 PMCID: PMC8015004 DOI: 10.1074/mcp.tir119.001827] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 07/08/2020] [Indexed: 11/06/2022] Open
Abstract
In-depth coverage of proteomic analysis could enhance our understanding to the mechanism of the protein functions. Unfortunately, many highly hydrophobic proteins and low-abundance proteins, which play critical roles in signaling networks, are easily lost during sample preparation, mainly attributed to the fact that very few extractants can simultaneously satisfy the requirements on strong solubilizing ability to membrane proteins and good enzyme compatibility. Thus, it is urgent to screen out ideal extractant from the huge compound libraries in a fast and effective way. Herein, by investigating the interior mechanism of extractants on the membrane proteins solubilization and trypsin compatibility, a molecular dynamics simulation system was established as complement to the experimental procedure to narrow down the scope of candidates for proteomics analysis. The simulation data shows that the van der Waals interaction between cation group of ionic liquid and membrane protein is the dominant factor in determining protein solubilization. In combination with the experimental data, 1-dodecyl-3-methylimidazolium chloride (C12Im-Cl) is on the shortlist for the suitable candidates from comprehensive aspects. Inspired by the advantages of C12Im-Cl, an ionic liquid-based filter-aided sample preparation (i-FASP) method was developed. Using this strategy, over 3,300 proteins were confidently identified from 103 HeLa cells (∼100 ng proteins) in a single run, an improvement of 53% over the conventional FASP method. Then the i-FASP method was further successfully applied to the label-free relative quantitation of human liver cancer and para-carcinoma tissues with obviously improved accuracy, reproducibility and coverage than the commonly used urea-based FASP method. The above results demonstrated that the i-FASP method could be performed as a versatile tool for the in-depth coverage proteomic analysis of biological samples.
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Affiliation(s)
- Fei Fang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Science, National Chromatographic Research and Analysis Center, Dalian, China
| | - Qun Zhao
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Science, National Chromatographic Research and Analysis Center, Dalian, China
| | - Huiying Chu
- Laboratory of Molecular Modeling and Design, State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian, China
| | - Mingwei Liu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine; National Center for Protein Sciences, Beijing, China
| | - Baofeng Zhao
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Science, National Chromatographic Research and Analysis Center, Dalian, China
| | - Zhen Liang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Science, National Chromatographic Research and Analysis Center, Dalian, China
| | - Lihua Zhang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Science, National Chromatographic Research and Analysis Center, Dalian, China.
| | - Guohui Li
- Laboratory of Molecular Modeling and Design, State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian, China.
| | - Liming Wang
- Division of Hepatobiliary and Pancreatic Surgery, Department of General Surgery, The Second Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Jun Qin
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine; National Center for Protein Sciences, Beijing, China; Alkek Center for Molecular Discovery, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas, USA
| | - Yukui Zhang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Science, National Chromatographic Research and Analysis Center, Dalian, China
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