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Thomas SL, Thacker JB, Schug KA, Maráková K. Sample preparation and fractionation techniques for intact proteins for mass spectrometric analysis. J Sep Sci 2020; 44:211-246. [DOI: 10.1002/jssc.202000936] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 10/28/2020] [Accepted: 10/29/2020] [Indexed: 12/17/2022]
Affiliation(s)
- Shannon L. Thomas
- Department of Chemistry & Biochemistry The University of Texas Arlington Arlington Texas USA
| | - Jonathan B. Thacker
- Department of Chemistry & Biochemistry The University of Texas Arlington Arlington Texas USA
| | - Kevin A. Schug
- Department of Chemistry & Biochemistry The University of Texas Arlington Arlington Texas USA
| | - Katarína Maráková
- Department of Pharmaceutical Analysis and Nuclear Pharmacy Faculty of Pharmacy Comenius University in Bratislava Bratislava Slovakia
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2
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Veerapandian R, Paudyal A, Chang A, Vediyappan G. Separation of Bioactive Small Molecules, Peptides from Natural Sources and Proteins from Microbes by Preparative Isoelectric Focusing (IEF) Method. J Vis Exp 2020. [PMID: 32597857 DOI: 10.3791/61101] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Natural products derived from plants and microbes are a rich source of bioactive molecules. Prior to their use, the active molecules from complex extracts must be purified for downstream applications. There are various chromatographic methods available for this purpose yet not all labs can afford high performance methods and isolation from complex biological samples can be difficult. Here we demonstrate that preparative liquid-phase isoelectric focusing (IEF) can separate molecules, including small molecules and peptides from complex plant extracts, based on their isoelectric points (pI). We have used the method for complex biological sample fractionation and characterization. As a proof of concept, we fractionated a Gymnema sylvestre plant extract, isolating a family of terpenoid saponin small molecules and a peptide. We also demonstrated effective microbial protein separation using the Candida albicans fungus as a model system.
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3
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Gel electrophoresis-based plant proteomics: Past, present, and future. Happy 10th anniversary Journal of Proteomics! J Proteomics 2019; 198:1-10. [DOI: 10.1016/j.jprot.2018.08.016] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Revised: 08/21/2018] [Accepted: 08/26/2018] [Indexed: 02/03/2023]
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4
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Grochalová M, Konečná H, Stejskal K, Potěšil D, Fridrichová D, Srbová E, Ornerová K, Zdráhal Z. Deep coverage of the beer proteome. J Proteomics 2017; 162:119-124. [DOI: 10.1016/j.jprot.2017.05.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Revised: 04/12/2017] [Accepted: 05/01/2017] [Indexed: 11/25/2022]
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5
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Pergande MR, Cologna SM. Isoelectric Point Separations of Peptides and Proteins. Proteomes 2017; 5:proteomes5010004. [PMID: 28248255 PMCID: PMC5372225 DOI: 10.3390/proteomes5010004] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2016] [Revised: 01/03/2017] [Accepted: 01/08/2017] [Indexed: 12/20/2022] Open
Abstract
The separation of ampholytic components according to isoelectric point has played an important role in isolating, reducing complexity and improving peptide and protein detection. This brief review outlines the basics of isoelectric focusing, including a summary of the historical achievements and considerations in experimental design. Derivative methodologies of isoelectric focusing are also discussed including common detection methods used. Applications in a variety of fields using isoelectric point based separations are provided as well as an outlook on the field for future studies.
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Affiliation(s)
- Melissa R Pergande
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL 60607, USA.
| | - Stephanie M Cologna
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL 60607, USA.
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6
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Shimura K, Nagai T. Capillary isoelectric focusing after sample enrichment with immunoaffinity chromatography in a single capillary. Sci Rep 2016; 6:39221. [PMID: 27976690 PMCID: PMC5156949 DOI: 10.1038/srep39221] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Accepted: 11/21/2016] [Indexed: 11/12/2022] Open
Abstract
For accurate micro-scale quantification of a specific protein in biological fluids, immunoaffinity chromatography (IAC) and isoelectric focusing (IEF) were combined in a single fused-silica capillary. The inner wall of the capillary was coated with an anti-E-tag antibody at the inlet side to form an IAC column, and polydimethylacrylamide, a neutral polymer, at the outlet side to form the capillary for IEF. After loading a sample, the whole capillary was filled with a carrier ampholyte solution. An anode solution, an acid, was then introduced to fill only the IAC column segment. Focusing was started with a pressure that balances with the electroosmotic flow produced in the acidified IAC column. Fluorescence-labeled recombinant Fab with an E-tag spiked at 16 pM to 10 nM in 50% serum was separated and detected with high precision. The coupling principle allows rapid and high-resolution IEF analysis of a protein in a biological sample without any loss of the immunoaffinity captured protein.
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Affiliation(s)
- Kiyohito Shimura
- Division of Advanced Chemistry, Fukushima Medical University, 1 Hikarigaoka, Fukushima, 960-1295, Japan
| | - Toshihiko Nagai
- Division of Advanced Chemistry, Fukushima Medical University, 1 Hikarigaoka, Fukushima, 960-1295, Japan
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Nanopore Event-Transduction Signal Stabilization for Wide pH Range under Extreme Chaotrope Conditions. Molecules 2016; 21:346. [PMID: 26985886 PMCID: PMC6272909 DOI: 10.3390/molecules21030346] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Revised: 03/02/2016] [Accepted: 03/02/2016] [Indexed: 11/17/2022] Open
Abstract
Operation of an α-hemolysin nanopore transduction detector is found to be surprisingly robust over a critical range of pH (6-9), including physiological pH = 7.4 and polymerase chain reaction (PCR) pH = 8.4, and extreme chaotrope concentration, including 5 M urea. The engineered transducer molecule that is captured in the standard α-hemolysin nanopore detector, to transform it into a transduction detector, appears to play a central role in this stabilization process by stabilizing the channel against gating during its capture. This enables the nanopore transduction detector to operate as a single molecule "nanoscope" in a wide range of conditions, where tracking on molecular state is possible in a variety of different environmental conditions. In the case of streptavidin biosensing, results are shown for detector operation when in the presence of extreme (5 M) urea concentration. Complications involving degenerate states are encountered at higher chaotrope concentrations, but since the degeneracy is only of order two, this is easily absorbed into the classification task as in prior work. This allows useful detector operation over a wide range of conditions relevant to biochemistry, biomedical engineering, and biotechnology.
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Kabytaev K, Durairaj A, Shin D, Rohlfing CL, Connolly S, Little RR, Stoyanov AV. Two-step ion-exchange chromatographic purification combined with reversed-phase chromatography to isolate C-peptide for mass spectrometric analysis. J Sep Sci 2016; 39:676-81. [PMID: 26717885 PMCID: PMC6053671 DOI: 10.1002/jssc.201500989] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Revised: 12/04/2015] [Accepted: 12/15/2015] [Indexed: 11/10/2022]
Abstract
A liquid chromatography with mass spectrometry on-line platform that includes the orthogonal techniques of ion exchange and reversed phase chromatography is applied for C-peptide analysis. Additional improvement is achieved by the subsequent application of cation- and anion-exchange purification steps that allow for isolating components that have their isoelectric points in a narrow pH range before final reversed-phase mass spectrometry analysis. The utility of this approach for isolating fractions in the desired "pI window" for profiling complex mixtures is discussed.
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Affiliation(s)
| | | | - Dmitriy Shin
- University of Missouri, School of Medicine, One Hospital Drive, Columbia, MO 65212, USA
| | - Curt L. Rohlfing
- University of Missouri, School of Medicine, One Hospital Drive, Columbia, MO 65212, USA
| | - Shawn Connolly
- University of Missouri, School of Medicine, One Hospital Drive, Columbia, MO 65212, USA
| | - Randie R. Little
- University of Missouri, School of Medicine, One Hospital Drive, Columbia, MO 65212, USA
| | - Alexander V. Stoyanov
- University of Missouri, School of Medicine, One Hospital Drive, Columbia, MO 65212, USA
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Patrie SM. Top-Down Mass Spectrometry: Proteomics to Proteoforms. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 919:171-200. [PMID: 27975217 DOI: 10.1007/978-3-319-41448-5_8] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
This chapter highlights many of the fundamental concepts and technologies in the field of top-down mass spectrometry (TDMS), and provides numerous examples of contributions that TD is making in biology, biophysics, and clinical investigations. TD workflows include variegated steps that may include non-specific or targeted preparative strategies, orthogonal liquid chromatography techniques, analyte ionization, mass analysis, tandem mass spectrometry (MS/MS) and informatics procedures. This diversity of experimental designs has evolved to manage the large dynamic range of protein expression and diverse physiochemical properties of proteins in proteome investigations, tackle proteoform microheterogeneity, as well as determine structure and composition of gas-phase proteins and protein assemblies.
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Affiliation(s)
- Steven M Patrie
- Computational and Systems Biology & Biomedical Engineering Graduate Programs, University of Texas Southwestern Medical Center, Dallas, TX, USA. .,Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, USA. .,Department of Bioengineering, University of Texas at Dallas, Richardson, TX, USA.
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Abstract
The urinary proteome is the focus of many studies due to the ease of urine collection and the relative proteome stability. Systems biology allows the combination of multiple omics studies, forming a link between proteomics, metabolomics, genomics and transcriptomics. In-depth data interpretation is achieved by bioinformatics analysis of -omics data sets. It is expected that the contribution of systems biology to the study of the urinary proteome will offer novel insights. The main focus of this review is on technical aspects of proteomics studies, available tools for systems biology analysis and the application of urinary proteomics in clinical studies and systems biology.
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11
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Xia L, Lin F, Wu X, Liu C, Wang J, Tang Q, Yu S, Huang K, Deng Y, Geng L. On-chip protein isoelectric focusing using a photoimmobilized pH gradient†. J Sep Sci 2014; 37:3174-80. [DOI: 10.1002/jssc.201400795] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2014] [Revised: 07/23/2014] [Accepted: 08/02/2014] [Indexed: 02/01/2023]
Affiliation(s)
- Lin Xia
- School of Life Science; Beijing Institute of Technology; Beijing P. R. China
| | - FengMing Lin
- School of Life Science; Beijing Institute of Technology; Beijing P. R. China
| | - Xin Wu
- School of Life Science; Beijing Institute of Technology; Beijing P. R. China
| | - Chuanli Liu
- School of Life Science; Beijing Institute of Technology; Beijing P. R. China
| | - Jianshe Wang
- School of Life Science; Beijing Institute of Technology; Beijing P. R. China
| | - Qi Tang
- School of Life Science; Beijing Institute of Technology; Beijing P. R. China
| | - Shiyong Yu
- School of Life Science; Beijing Institute of Technology; Beijing P. R. China
| | - Kunjie Huang
- School of Life Science; Beijing Institute of Technology; Beijing P. R. China
| | - Yulin Deng
- School of Life Science; Beijing Institute of Technology; Beijing P. R. China
| | - Lina Geng
- School of Life Science; Beijing Institute of Technology; Beijing P. R. China
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Chaijaroenkul W, Thiengsusuk A, Rungsihirunrat K, Ward SA, Na-Bangchang K. Proteomics analysis of antimalarial targets of Garcinia mangostana Linn. Asian Pac J Trop Biomed 2014; 4:515-9. [PMID: 25183269 DOI: 10.12980/apjtb.4.2014apjtb-2014-0043] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Accepted: 06/15/2014] [Indexed: 10/25/2022] Open
Abstract
OBJECTIVE To investigate possible protein targets for antimalarial activity of Garcinia mangostana Linn. (G. mangostana) (pericarp) in 3D7 Plasmodium falciparum clone using 2-dimensional electrophoresis and liquid chromatography mass-spectrometry (LC/MS/MS). METHODS 3D7 Plasmodium falciparum was exposed to the crude ethanolic extract of G. mangostana Linn. (pericarp) at the concentrations of 12µg/mL (IC50 level: concentration that inhibits parasite growth by 50%) and 30 µg/mL (IC90 level: concentration that inhibits parasite growth by 90%) for 12 h. Parasite proteins were separated by 2-dimensional electrophoresis and identified by LC/MS/MS. RESULTS At the IC50 concentration, about 82% of the expressed parasite proteins were matched with the control (non-exposed), while at the IC90 concentration, only 15% matched proteins were found. The selected protein spots from parasite exposed to the plant extract at the concentration of 12 µg/mL were identified as enzymes that play role in glycolysis pathway, i.e., phosphoglycerate mutase putative, L-lactate dehydrogenase/glyceraldehyde-3-phosphate dehydrogenase, and fructose-bisphosphate aldolase/phosphoglycerate kinase. The proteosome was found in parasite exposed to 30 µg/mL of the extract. CONCLUSIONS Results suggest that proteins involved in the glycolysis pathway may be the targets for antimalarial activity of G. mangostana Linn. (pericarp).
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Affiliation(s)
- Wanna Chaijaroenkul
- Chulabhorn International College of Medicine, Thammasat University (Rangsit Campus), Pathumtani 12121, Thailand
| | - Artitiya Thiengsusuk
- Chulabhorn International College of Medicine, Thammasat University (Rangsit Campus), Pathumtani 12121, Thailand
| | | | - Stephen Andrew Ward
- Molecular and Biochemical Parasitology, Liverpool School of Tropical Medicine, University of Liverpool, Liverpool L3 5QA, United Kingdom
| | - Kesara Na-Bangchang
- Chulabhorn International College of Medicine, Thammasat University (Rangsit Campus), Pathumtani 12121, Thailand
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13
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Moreda-Piñeiro A, García-Otero N, Bermejo-Barrera P. A review on preparative and semi-preparative offgel electrophoresis for multidimensional protein/peptide assessment. Anal Chim Acta 2014; 836:1-17. [PMID: 24974865 DOI: 10.1016/j.aca.2014.04.053] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2013] [Revised: 04/23/2014] [Accepted: 04/27/2014] [Indexed: 11/29/2022]
Abstract
Mass spectrometry (MS) techniques are commonly used for protein identification and further analysis of selected protein spots after high resolution 2-D electrophoresis. Complementary gel-free approaches have been developed during the last few years and have shown to be useful tools in modern proteomics. The development and application of various gel-free electrophoresis devices for performing protein fractionation according to the pI differences is therefore a topic of interest. This review describes the current state of isoelectric focusing (IEF) gel-free electrophoresis based on the Agilent offgel 3100 fractionator. The review includes, therefore, (i) an overview on IEF as well as other previous IEF gel-free electrophoresis developments; (ii) offgel fundamentals and future trends; (iii) advantages and disadvantages of current offgel procedures; (iv) requirements of isolated protein pellets for further offgel fractionation; (v) offgel fraction requirements to perform the second dimensional analysis by advance electrophoresis and chromatographic techniques; and (vi) effect of the offgel operating conditions on the stability of metal-protein complexes.
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Affiliation(s)
- Antonio Moreda-Piñeiro
- Department of Analytical Chemistry, Nutrition and Bromatology, Faculty of Chemistry, University of Santiago de Compostela, Avenida das Ciencias, s/n. 15782 Santiago de Compostela, Spain.
| | - Natalia García-Otero
- Department of Analytical Chemistry, Nutrition and Bromatology, Faculty of Chemistry, University of Santiago de Compostela, Avenida das Ciencias, s/n. 15782 Santiago de Compostela, Spain
| | - Pilar Bermejo-Barrera
- Department of Analytical Chemistry, Nutrition and Bromatology, Faculty of Chemistry, University of Santiago de Compostela, Avenida das Ciencias, s/n. 15782 Santiago de Compostela, Spain
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Smejkal P, Bottenus D, Breadmore MC, Guijt RM, Ivory CF, Foret F, Macka M. Microfluidic isotachophoresis: A review. Electrophoresis 2013; 34:1493-509. [DOI: 10.1002/elps.201300021] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2013] [Revised: 03/06/2013] [Accepted: 03/07/2013] [Indexed: 12/22/2022]
Affiliation(s)
- Petr Smejkal
- ACROSS and School of Chemistry; University of Tasmania; Hobart; Australia
| | - Danny Bottenus
- Voiland School of Chemical Engineering and Bioengineering; Washington State University; Pullman; WA; USA
| | | | - Rosanne M. Guijt
- ACROSS and School of Pharmacy; University of Tasmania; Hobart; Australia
| | - Cornelius F. Ivory
- Voiland School of Chemical Engineering and Bioengineering; Washington State University; Pullman; WA; USA
| | - František Foret
- Institute of Analytical Chemistry of the Academy of Sciences of the Czech Republic; v.v.i., Brno; Czech Republic
| | - Mirek Macka
- ACROSS and School of Chemistry; University of Tasmania; Hobart; Australia
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Stoyanov AV, Connolly S, Rohlfing CL, Rogatsky E, Stein D, Little RR. Human C-peptide Quantitation by LC-MS Isotope-Dilution Assay in Serum or Urine Samples. ACTA ACUST UNITED AC 2013; 4. [PMID: 31942247 PMCID: PMC6961834 DOI: 10.4172/2157-7064.1000172] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
In this communication we report a simple and efficient approach to C-peptide quantitation using isotope dilution mass-spectrometry analysis. The method facilitates quantitation of C-peptide levels at least one order of magnitude lower compared to concentration levels achieved with an IDA method reported previously. The improvement was due to more intensive sample preparation procedure that, in turn, makes it possible to increase the sample load without a corresponding increase in matrix effects. We also show the results of a comparison study with a second laboratory using a similar previously reported method for C-peptide quantitation.
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Affiliation(s)
| | - Shawn Connolly
- University of Missouri, School of Medicine, Columbia MO, USA
| | - Curt L Rohlfing
- University of Missouri, School of Medicine, Columbia MO, USA
| | - Eduard Rogatsky
- Albert Einstein College of Medicine, Yeshiva University, Bronx NY, USA
| | - Daniel Stein
- Albert Einstein College of Medicine, Yeshiva University, Bronx NY, USA
| | - Randie R Little
- University of Missouri, School of Medicine, Columbia MO, USA
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