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Deracinois B, Flahaut C, Duban-Deweer S, Karamanos Y. Comparative and Quantitative Global Proteomics Approaches: An Overview. Proteomes 2013; 1:180-218. [PMID: 28250403 PMCID: PMC5302699 DOI: 10.3390/proteomes1030180] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2013] [Revised: 10/08/2013] [Accepted: 10/08/2013] [Indexed: 01/14/2023] Open
Abstract
Proteomics became a key tool for the study of biological systems. The comparison between two different physiological states allows unravelling the cellular and molecular mechanisms involved in a biological process. Proteomics can confirm the presence of proteins suggested by their mRNA content and provides a direct measure of the quantity present in a cell. Global and targeted proteomics strategies can be applied. Targeted proteomics strategies limit the number of features that will be monitored and then optimise the methods to obtain the highest sensitivity and throughput for a huge amount of samples. The advantage of global proteomics strategies is that no hypothesis is required, other than a measurable difference in one or more protein species between the samples. Global proteomics methods attempt to separate quantify and identify all the proteins from a given sample. This review highlights only the different techniques of separation and quantification of proteins and peptides, in view of a comparative and quantitative global proteomics analysis. The in-gel and off-gel quantification of proteins will be discussed as well as the corresponding mass spectrometry technology. The overview is focused on the widespread techniques while keeping in mind that each approach is modular and often recovers the other.
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Affiliation(s)
- Barbara Deracinois
- Université Lille Nord de France, Lille F-59000, France.
- Université d'Artois, LBHE, Lens F-62307, France.
- IMPRT-IFR114, Lille F-59000, France.
| | - Christophe Flahaut
- Université Lille Nord de France, Lille F-59000, France.
- Université d'Artois, LBHE, Lens F-62307, France.
- IMPRT-IFR114, Lille F-59000, France.
| | - Sophie Duban-Deweer
- Université Lille Nord de France, Lille F-59000, France.
- Université d'Artois, LBHE, Lens F-62307, France.
- IMPRT-IFR114, Lille F-59000, France.
| | - Yannis Karamanos
- Université Lille Nord de France, Lille F-59000, France.
- Université d'Artois, LBHE, Lens F-62307, France.
- IMPRT-IFR114, Lille F-59000, France.
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Bai HX, Liu XH, Yang F, Yang XR, Wang EK. A Prefractionation Method Can Separate Proteomic Proteins into Multigroups by One-step Extraction. J CHIN CHEM SOC-TAIP 2013. [DOI: 10.1002/jccs.201000140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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3
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Release and antilisterial properties of nisin from zein capsules spray-dried at different temperatures. Lebensm Wiss Technol 2011. [DOI: 10.1016/j.lwt.2011.07.017] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Integration of carboxyl modified magnetic particles and aqueous two-phase extraction for selective separation of proteins. Talanta 2011; 85:304-9. [DOI: 10.1016/j.talanta.2011.03.055] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2010] [Revised: 03/16/2011] [Accepted: 03/24/2011] [Indexed: 11/20/2022]
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Jmeian Y, El Rassi Z. Liquid-phase-based separation systems for depletion, prefractionation and enrichment of proteins in biological fluids for in-depth proteomics analysis. Electrophoresis 2009; 30:249-61. [DOI: 10.1002/elps.200800639] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Zhou J, Lin Y, Deng X, Shen J, He Q, Chen P, Wang X, Liang S. Development and Application of a Two-Phase, On-Membrane Digestion Method in the Analysis of Membrane Proteome. J Proteome Res 2008; 7:1778-83. [DOI: 10.1021/pr070526j] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Jian Zhou
- College of Life Sciences, Hunan Normal University, Changsha 410081, P. R. China
| | - Yong Lin
- College of Life Sciences, Hunan Normal University, Changsha 410081, P. R. China
| | - Xingcan Deng
- College of Life Sciences, Hunan Normal University, Changsha 410081, P. R. China
| | - Jianying Shen
- College of Life Sciences, Hunan Normal University, Changsha 410081, P. R. China
| | - Quanyuan He
- College of Life Sciences, Hunan Normal University, Changsha 410081, P. R. China
| | - Ping Chen
- College of Life Sciences, Hunan Normal University, Changsha 410081, P. R. China
| | - Xianchun Wang
- College of Life Sciences, Hunan Normal University, Changsha 410081, P. R. China
| | - Songping Liang
- College of Life Sciences, Hunan Normal University, Changsha 410081, P. R. China
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Schuchardt S, Borlak J. Quantitative mass spectrometry to investigate epidermal growth factor receptor phosphorylation dynamics. MASS SPECTROMETRY REVIEWS 2008; 27:51-65. [PMID: 18023079 DOI: 10.1002/mas.20155] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Identifying proteins of signaling networks has received much attention, because an array of biological processes are entirely dependent on protein cross-talk and protein-protein interactions. Protein posttranslational modifications (PTM) add an additional layer of complexity, resulting in complex signaling networks. Of particular interest to our working group are the signaling networks of epidermal growth factor (EGF) receptor, a transmembrane receptor tyrosine kinase involved in various cellular processes, including cell proliferation, differentiation, and survival. Ligand binding to the N-terminal residue of the extracellular domain of EGF receptor induces conformational changes, dimerization, and (auto)-phosphorylation of intracellular tyrosine residues. In addition, activated EGF receptor may positively affect survival pathways, and thus determines the pathways for tumor growth and progression. Notably, in many human malignancies exaggerated EGF receptor activities are commonly observed. An understanding of the mechanism that results in aberrant phosphorylation of EGF receptor tyrosine residues and derived signaling cascades is crucial for an understanding of molecular mechanisms in cancer development. Here, we summarize recent labeling methods and discuss the difficulties in quantitative MS-based phosphorylation assays to probe for receptor tyrosine kinase (RTK) activity. We also review recent advances in sample preparation to investigate membrane-bound RTKs, MS-based detection of phosphopeptides, and the diligent use of different quantitative methods for protein labeling.
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Affiliation(s)
- Sven Schuchardt
- Department of Drug Research and Medical Biotechnology, Fraunhofer Institute of Toxicology and Experimental Medicine ITEM, Nikolai-Fuchs-Strasse 1, Hannover, Germany
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Phase equilibrium and protein partitioning in aqueous two-phase systems containing ammonium carbamate and block copolymers PEO–PPO–PEO. Biochem Eng J 2007. [DOI: 10.1016/j.bej.2007.05.010] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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10
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Lopes AS, Garcia JS, Catharino RR, Santos LS, Eberlin MN, Arruda MAZ. Cloud point extraction applied to casein proteins of cow milk and their identification by mass spectrometry. Anal Chim Acta 2007; 590:166-72. [PMID: 17448341 DOI: 10.1016/j.aca.2007.03.043] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2006] [Revised: 03/16/2007] [Accepted: 03/22/2007] [Indexed: 10/23/2022]
Abstract
This work describes the optimization of a cloud point extraction (CPE) method for casein proteins from cow milk samples. To promote phase separation, polyoxyethylene(8) isooctylphenyl ether (Triton X-114) and sodium chloride (NaCl) were used as nonionic surfactant and electrolyte, respectively. Using multivariate studies, four major CPE variables were evaluated: Triton X-114 concentration, sample volume, NaCl concentration, and pH. The results show that surfactant concentration and sample volume were the main variable affecting the CPE process, with the following optimized parameters: 1% (w/v) Triton X-114 concentration, 50 microL of sample volume, 6% (w/v) NaCl concentration and extractions carried out at pH 7.0. At these conditions, 923+/-66 and 67+/-2 microg mL(-1) of total protein were found in the surfactant-rich and surfactant-poor phases, respectively. Finally, matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) was then used to evaluate those target proteins (alpha(s1)-casein, alpha(s2)-casein and beta-casein) separation as well as to check the efficiency of the extraction procedure, making a fingerprint of those target proteins possible.
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Affiliation(s)
- Aline Soriano Lopes
- Universidade Estadual de Campinas, Institute of Chemistry, Spectrometry, Sample Preparation and Mechanization Group, P.O. Box 6154, 13084-862 Campinas, São Paulo, Brazil
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Cao Q, Li S, He C, Li K, Liu F. Extraction and determination of papaverin in pericarpium papaveris using aqueous two-phase system of poly(ethylene glycol)–(NH4)2SO4 coupled with high-performance liquid chromatography. Anal Chim Acta 2007; 590:187-94. [PMID: 17448344 DOI: 10.1016/j.aca.2007.03.050] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2006] [Revised: 03/22/2007] [Accepted: 03/23/2007] [Indexed: 11/20/2022]
Abstract
Based on aqueous two-phase system (ATPS) of poly(ethylene glycol) (PEG)-(NH4)2SO4, a simple pretreatment approach was developed for the extraction and determination of papaverin in pericarpium papaveris. The influence factors on phase behavior of the ATPS and partition behavior of papaverin was investigated, and partition mechanism based on the hydrophobic interaction between PEG and analyte molecules was proposed. Under the optimal conditions, the extraction efficiencies for papaverin were 93-96%, and the recoveries of the added standard were 97-106% with relative standard deviations of 1.8-2.5%. Combined with a high-performance liquid chromatography (HPLC) method, this extraction technique has been successfully applied to the determination of papaverin in pericarpium papaveris with the detection limit of 2 ng mL(-1) and the linear range of 0.10-10 microg mL(-1). Compared with the conventional liquid-liquid extraction or solid-phase extraction, this method was more environmentally benign, more cost effective and much simpler due to the direct injection of the upper phase into HPLC system.
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Affiliation(s)
- Qing Cao
- Beijing National Laboratory for Molecular Sciences, The Key Laboratory of Bioorganic Chemistry and Molecular Engineering, Ministry of Education, College of Chemistry, Peking University, Beijing 100871, China
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Dallora NLP, Klemz JGD, Pessôa Filho PDA. Partitioning of model proteins in aqueous two-phase systems containing polyethylene glycol and ammonium carbamate. Biochem Eng J 2007. [DOI: 10.1016/j.bej.2006.12.002] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Roy I, Mondal K, Gupta MN. Leveraging protein purification strategies in proteomics. J Chromatogr B Analyt Technol Biomed Life Sci 2007; 849:32-42. [PMID: 17141589 DOI: 10.1016/j.jchromb.2006.11.016] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2006] [Revised: 11/03/2006] [Accepted: 11/09/2006] [Indexed: 11/25/2022]
Abstract
The proteomic studies, although, tend to be analytical in nature, yet many strategies of preparative protein purification can be usefully employed in such studies. This review points out the importance of purification techniques which are capable of dealing with samples which are suspensions rather than clear solution, e.g. aqueous two phase partitioning, three phase partitioning, expanded bed chromatography, etc. The review also outlines the potential of non-chromatographic techniques in dealing with fractionation of proteomes. Separation protocols which can deal with post-translationally modified (PTM) proteins are also considered.
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Affiliation(s)
- Ipsita Roy
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research (NIPER), Sector 67, SAS Nagar, Punjab 160062, India
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Schindler J, Nothwang HG. Aqueous polymer two-phase systems: effective tools for plasma membrane proteomics. Proteomics 2007; 6:5409-17. [PMID: 16972286 DOI: 10.1002/pmic.200600243] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Plasma membranes (PMs) are of particular importance for all living cells. They form a selectively permeable barrier to the environment. Many essential tasks of PMs are carried out by their proteinaceous components, including molecular transport, cell-cell interactions, and signal transduction. Due to the key role of these proteins for cellular function, they take center-stage in basic and applied research. A major problem towards in-depth identification and characterization of PM proteins by modern proteomic approaches is their low abundance and immense heterogeneity in different cells. Highly selective and efficient purification protocols are hence essential to any PM proteome analysis. An effective tool for preparative isolation of PMs is partitioning in aqueous polymer two-phase systems. In two-phase systems, membranes are separated according to differences in surface properties rather than size and density. Despite their rare application to the fractionation of animal tissues and cells, they represent an attractive alternative to conventional fractionation protocols. Here, we review the principles of partitioning using aqueous polymer two-phase systems and compare aqueous polymer two-phase systems with other methods currently used for the isolation of PMs.
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Affiliation(s)
- Jens Schindler
- Abteilung Tierphysiologie, Fachbereich Biologie, Technische Universität Kaiserslautern, Kaiserslautern, Germany
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