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Abstract
Here, we describe a detailed step-by-step protocol for the detection of phosphoproteins in two-dimensional difference gel electrophoresis (2D-DIGE) gels. A standard 2D-DIGE protocol is combined with subsequent post-staining with phosphospecific fluorescent dye. The combination of these two methods complements 2D-DIGE-based proteome profiling by fluorescence detection of phosphoproteins in the same gel providing additional possibility for sensitive and accurate quantification of the differentially regulated phosphoproteins in biological samples.
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Affiliation(s)
- Taras Stasyk
- Institute of Cell Biology, Biocenter, Medical University of Innsbruck, Innsbruck, Austria.
| | - Lukas Alfons Huber
- Institute of Cell Biology, Biocenter, Medical University of Innsbruck, Innsbruck, Austria
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2
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Phosphoproteome Analysis Using Two-Dimensional Electrophoresis Coupled with Chemical Dephosphorylation. Foods 2022; 11:foods11193119. [PMID: 36230195 PMCID: PMC9562008 DOI: 10.3390/foods11193119] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Revised: 09/26/2022] [Accepted: 10/04/2022] [Indexed: 11/22/2022] Open
Abstract
Protein phosphorylation is a reversible post-translational modification (PTM) with major regulatory roles in many cellular processes. However, the analysis of phosphoproteins remains the most challenging barrier in the prevailing proteome research. Recent technological advances in two-dimensional electrophoresis (2-DE) coupled to mass spectrometry (MS) have enabled the identification, characterization, and quantification of protein phosphorylation on a global scale. Most research on phosphoproteins with 2-DE has been conducted using phosphostains. Nevertheless, low-abundant and low-phosphorylated phosphoproteins are not necessarily detected using phosphostains and/or MS. In this study, we report a comparative analysis of 2-DE phosphoproteome profiles using Pro-Q Diamond phosphoprotein stain (Pro-Q DPS) and chemical dephosphorylation of proteins with HF-P from longissimus thoracis (LT) muscle samples of the Rubia Gallega cattle breed. We found statistically significant differences in the number of identified phosphoproteins between methods. More specifically, we found a three-fold increase in phosphoprotein detection with the HF-P method. Unlike Pro-Q DPS, phosphoprotein spots with low volume and phosphorylation rate were identified by HF-P technique. This is the first approach to assess meat phosphoproteome maps using HF-P at a global scale. The results open a new window for 2-DE gel-based phosphoproteome analysis.
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3
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Gao L, Chen L, Peng Y, Zhao Y, Dong J, Mao Z, Jia J, Zhou Y. Iridium tetrazolato complexes as efficient protein staining agents. Dalton Trans 2022; 51:16870-16875. [DOI: 10.1039/d2dt02564g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Iridium tetrazolato complexes have been illustrated as one kind of efficient protein staining agent.
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Affiliation(s)
- Ling Gao
- Department of Immunology, School of Basic Medical Sciences, Nanjing Medical University, Nanjing 211166, Jiangsu, P.R. China
- The Laboratory Center for Basic Medicine Sciences, School of Basic Medical Sciences, Nanjing Medical University, Nanjing 211166, Jiangsu, P.R. China
| | - Luyao Chen
- Department of Immunology, School of Basic Medical Sciences, Nanjing Medical University, Nanjing 211166, Jiangsu, P.R. China
| | - Yu Peng
- Department of Immunology, School of Basic Medical Sciences, Nanjing Medical University, Nanjing 211166, Jiangsu, P.R. China
- The Laboratory Center for Basic Medicine Sciences, School of Basic Medical Sciences, Nanjing Medical University, Nanjing 211166, Jiangsu, P.R. China
| | - Yibo Zhao
- School of Chemistry and Life Sciences, Suzhou University of Science and Technology, Suzhou 215009, Jiangsu, P.R. China
| | - Jianhua Dong
- School of Chemistry and Life Sciences, Suzhou University of Science and Technology, Suzhou 215009, Jiangsu, P.R. China
| | - Ziwang Mao
- School of Chemistry and Life Sciences, Suzhou University of Science and Technology, Suzhou 215009, Jiangsu, P.R. China
| | - Junli Jia
- Department of Immunology, School of Basic Medical Sciences, Nanjing Medical University, Nanjing 211166, Jiangsu, P.R. China
| | - Yuyang Zhou
- School of Chemistry and Life Sciences, Suzhou University of Science and Technology, Suzhou 215009, Jiangsu, P.R. China
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4
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Babak MV, Le Faouder P, Trivelli X, Venkatesan G, Bezzubov SI, Kajjout M, Gushchin AL, Hanif M, Poizat O, Vezin H, Rolando C. Heteroleptic Ruthenium(II) Complexes with Bathophenanthroline and Bathophenanthroline Disulfonate Disodium Salt as Fluorescent Dyes for In-Gel Protein Staining. Inorg Chem 2020; 59:4527-4535. [DOI: 10.1021/acs.inorgchem.9b03679] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Maria V. Babak
- Univ. Lille, CNRS, USR 3290, MSAP, Miniaturisation pour la Synthèse l’Analyse et la Protèomique, F-59 000 Lille, France
| | - Pauline Le Faouder
- Univ. Lille, CNRS, USR 3290, MSAP, Miniaturisation pour la Synthèse l’Analyse et la Protèomique, F-59 000 Lille, France
| | - Xavier Trivelli
- Univ. Lille, CNRS, INRA, Centrale Lille, ENSCL, Univ. Artois, FR 2638 – IMEC - Institut Michel-Eugène Chevreul, F-59000 Lille, France
| | - Gopalakrishnan Venkatesan
- Department of Pharmacy, National University of Singapore, Lower Kent Ridge Road, 18 Science Drive 2, Singapore 119260
| | - Stanislav I. Bezzubov
- Kurnakov Institute of General and Inorganic Chemistry, Russian Academy of Sciences, Leninskii pr. 31, Moscow 119991, Russia
| | - Mohammed Kajjout
- Univ. Lille, CNRS, USR 3290, MSAP, Miniaturisation pour la Synthèse l’Analyse et la Protèomique, F-59 000 Lille, France
| | - Artem L. Gushchin
- Nikolaev Institute of Inorganic Chemistry, Siberian Branch of Russian Academy of Sciences, 3 Acad. Lavrentiev Avenue, Novosibirsk 630090, Russia
- Novosibirsk State University, 2 Pirogov Street, 630090 Novosibirsk, Russia
| | - Muhammad Hanif
- School of Chemical Sciences, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
| | - Olivier Poizat
- Univ. Lille, CNRS, UMR 8516 - LASIRe - Laboratoire Avancé de Spectroscopie pour les Intéractions la Réactivité et l’Environnement, F-59000 Lille, France
| | - Hervé Vezin
- Univ. Lille, CNRS, UMR 8516 - LASIRe - Laboratoire Avancé de Spectroscopie pour les Intéractions la Réactivité et l’Environnement, F-59000 Lille, France
| | - Christian Rolando
- Univ. Lille, CNRS, USR 3290, MSAP, Miniaturisation pour la Synthèse l’Analyse et la Protèomique, F-59 000 Lille, France
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5
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Sarkar A, Kumar R, Das B, Ray PS, Gupta P. A cyclometalated trinuclear Ir(iii)/Pt(ii) complex as a luminescent probe for histidine-rich proteins. Dalton Trans 2020; 49:1864-1872. [DOI: 10.1039/c9dt04720d] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
A trinuclear luminescent organometallic Pt–Ir–Pt complex acts as an efficient protein staining agent due to reversible binding to histidine-rich proteins.
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Affiliation(s)
- Ankita Sarkar
- Department of Chemical Sciences
- Indian Institute of Science Education and Research-Kolkata
- Mohanpur
- India
| | - Ravi Kumar
- Department of Biological Sciences
- Indian Institute of Science Education and Research-Kolkata
- Mohanpur
- India
| | - Bishnu Das
- Department of Chemical Sciences
- Indian Institute of Science Education and Research-Kolkata
- Mohanpur
- India
| | - Partho Sarothi Ray
- Department of Biological Sciences
- Indian Institute of Science Education and Research-Kolkata
- Mohanpur
- India
| | - Parna Gupta
- Department of Chemical Sciences
- Indian Institute of Science Education and Research-Kolkata
- Mohanpur
- India
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6
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A Simple, Time-Saving Dye Staining of Proteins in Sodium Dodecyl Sulfate-Polyacrylamide Gel Using Coomassie Blue. Methods Mol Biol 2018. [PMID: 30097927 DOI: 10.1007/978-1-4939-8745-0_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Most traditional post-electrophoretic processes need several hours to several days to finish the whole staining process and traditional staining solutions all contain methanol, acetic acid, or phosphoric acid, which not only produce the unpleasant smell but also cause environmental pollution. Here a fixation-free, fast protein staining method in sodium dodecyl sulfate-polyacrylamide gel electrophoresis using Coomassie blue is described. The protocol includes only staining and quick washing steps, can be completed in 0.5 h. It has a sensitivity of 10 ng. In addition, the dye stain does not contain any acid or methanol.
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7
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Baldelli E, Calvert V, Hodge A, VanMeter A, Petricoin EF, Pierobon M. Reverse Phase Protein Microarrays. Methods Mol Biol 2018; 1606:149-169. [PMID: 28502000 DOI: 10.1007/978-1-4939-6990-6_11] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
While genes and RNA encode information about cellular status, proteins are considered the engine of the cellular machine, as they are the effective elements that drive all cellular functions including proliferation, migration, differentiation, and apoptosis. Consequently, investigations of the cellular protein network are considered a fundamental tool for understanding cellular functions.Alteration of the cellular homeostasis driven by elaborate intra- and extracellular interactions has become one of the most studied fields in the era of personalized medicine and targeted therapy. Increasing interest has been focused on developing and improving proteomic technologies that are suitable for analysis of clinical samples. In this context, reverse-phase protein microarrays (RPPA) is a sensitive, quantitative, high-throughput immunoassay for protein analyses of tissue samples, cells, and body fluids.RPPA is well suited for broad proteomic profiling and is capable of capturing protein activation as well as biochemical reactions such as phosphorylation, glycosylation, ubiquitination, protein cleavage, and conformational alterations across hundreds of samples using a limited amount of biological material. For these reasons, RPPA represents a valid tool for protein analyses and generates data that help elucidate the functional signaling architecture through protein-protein interaction and protein activation mapping for the identification of critical nodes for individualized or combinatorial targeted therapy.
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Affiliation(s)
- Elisa Baldelli
- Center for Applied Proteomics and Molecular Medicine, George Mason University, 10920 George Mason Circle, MS 1A9, Manassas, VA, 20110, USA
| | - Valerie Calvert
- Center for Applied Proteomics and Molecular Medicine, George Mason University, 10920 George Mason Circle, MS 1A9, Manassas, VA, 20110, USA
| | - Alex Hodge
- Center for Applied Proteomics and Molecular Medicine, George Mason University, 10920 George Mason Circle, MS 1A9, Manassas, VA, 20110, USA
| | - Amy VanMeter
- Center for Applied Proteomics and Molecular Medicine, George Mason University, 10920 George Mason Circle, MS 1A9, Manassas, VA, 20110, USA
| | - Emanuel F Petricoin
- Center for Applied Proteomics and Molecular Medicine, George Mason University, 10920 George Mason Circle, MS 1A9, Manassas, VA, 20110, USA
| | - Mariaelena Pierobon
- Center for Applied Proteomics and Molecular Medicine, George Mason University, 10920 George Mason Circle, MS 1A9, Manassas, VA, 20110, USA.
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8
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Abstract
The most commonly used types of gels for separating proteins are SDS gels, either in a 1-D format or as the second dimension of various 2-D separations, and the most common methods of visualizing proteins in these gels use protein binding dyes after fixing the proteins in the gel matrix. In recent years, there has been a continuing trend away from preparing staining solutions in the laboratory to using commercially available kits, which are convenient, save time, have defined shelf lives, and may provide greater reproducibility than stains formulated in research laboratories. In general, when using commercial kits, satisfactory results can be readily obtained by following the manufacturer's protocols. This unit reviews commonly used fixation-based stains and provides a number of manual formulations with staining protocols for those who prefer such staining methods. © 2018 by John Wiley & Sons, Inc.
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Affiliation(s)
- Lynn A Beer
- Molecular and Cellular Oncogenesis Program, The Wistar Institute, Philadelphia, Pennsylvania
| | - David W Speicher
- Molecular and Cellular Oncogenesis Program, The Wistar Institute, Philadelphia, Pennsylvania
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9
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Abstract
Here, we describe the detailed step-by-step protocol for detection of phosphoproteins in two-dimensional difference gel electrophoresis (DIGE) gels. A standard DIGE protocol is combined with subsequent post-staining with phosphospecific fluorescent dye. The combination of these two methods complements DIGE-based proteome profiling by fluorescence detection of phosphoproteins in the same gel providing additional possibility for sensitive and accurate quantification of the differentially regulated phosphoproteins in biological samples.
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Affiliation(s)
- Taras Stasyk
- Division of Cell Biology, Biocenter, Innsbruck Medical University, Innrain 80-82, A-6020, Innsbruck, Austria.
| | - Lukas Alfons Huber
- Division of Cell Biology, Biocenter, Innsbruck Medical University, Innrain 80-82, A-6020, Innsbruck, Austria
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10
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Noaman N, Abbineni PS, Withers M, Coorssen JR. Coomassie staining provides routine (sub)femtomole in-gel detection of intact proteoforms: Expanding opportunities for genuine Top-down Proteomics. Electrophoresis 2017; 38:3086-3099. [PMID: 28872692 DOI: 10.1002/elps.201700190] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Revised: 07/11/2017] [Accepted: 08/25/2017] [Indexed: 01/22/2023]
Abstract
Modified colloidal Coomassie Brilliant Blue (cCBB) staining utilising a novel destain protocol and near-infrared fluorescence detection (nIRFD) rivals the in-gel protein detection sensitivity (DS) of SYPRO Ruby. However, established DS estimates are likely inaccurate in terms of 2DE-resolved proteoform 'spots' since DS is routinely measured from comparatively diffuse protein 'bands' following wide-well 1DE. Here, cCBB DS for 2DE-based proteomics was more accurately determined using narrow-well 1DE. As precise estimates of protein standard monomer concentrations are essential for accurate quantitation, coupling UV absorbance with gel-based purity assessments is described. Further, as cCBB is compatible with both nIRFD and densitometry, the impacts of imaging method (and image resolution) on DS were assessed. Narrow-well 1DE enabled more accurate quantitation of cCBB DS for 2DE, achieving (sub)femtomole DS with either nIRFD or densitometry. While densitometry offers comparative simplicity and affordability, nIRFD has the unique potential for enhanced DS with Deep Imaging. Higher-resolution nIRFD also improved analysis of a 2DE-resolved proteome, surpassing the DS of standard nIRFD and densitometry, with nIRFD Deep Imaging further maximising proteome coverage. cCBB DS for intact proteins rivals that of mass spectrometry (MS) for peptides in complex mixtures, reaffirming that 2DE-MS currently provides the most routine, broadly applicable, robust, and information-rich Top-down approach to Discovery Proteomics.
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Affiliation(s)
- Nour Noaman
- Department of Molecular Physiology, and the WSU Molecular Medicine Research Group, School of Medicine, Western Sydney University, Campbelltown, New South Wales, Australia
| | - Prabhodh S Abbineni
- Department of Pharmacology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Michael Withers
- Department of Molecular Physiology, and the WSU Molecular Medicine Research Group, School of Medicine, Western Sydney University, Campbelltown, New South Wales, Australia
| | - Jens R Coorssen
- Departments of Health Sciences and Biological Sciences, Brock University, St Catharines, Ontario, Canada
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11
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Zhang Y, Yu D, Dai J, Wang X, Zhu Z, Huang Y, Sun J, Chen Z, Jin L, Wang Y. A method for rapid and sensitive negative staining of proteins in SDS-PAGE using 2′,7′-dichlorofluorescein. Proteomics 2017; 17. [DOI: 10.1002/pmic.201600346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Revised: 04/24/2017] [Accepted: 04/27/2017] [Indexed: 11/09/2022]
Affiliation(s)
- Yuan Zhang
- School of Pharmaceutical Sciences; Wenzhou Medical University; Wenzhou Zhejiang P. R. China
| | - Dongdong Yu
- School of Pharmaceutical Sciences; Wenzhou Medical University; Wenzhou Zhejiang P. R. China
| | - Jiangbo Dai
- School of Pharmaceutical Sciences; Wenzhou Medical University; Wenzhou Zhejiang P. R. China
| | - Xu Wang
- School of Pharmaceutical Sciences; Wenzhou Medical University; Wenzhou Zhejiang P. R. China
- Wenzhou Undersun Biotechnology Co. Ltd.; Wenzhou Zhejiang P. R. China
| | - Zhongxin Zhu
- School of Pharmaceutical Sciences; Wenzhou Medical University; Wenzhou Zhejiang P. R. China
- Wenzhou Undersun Biotechnology Co. Ltd.; Wenzhou Zhejiang P. R. China
| | - Yewei Huang
- School of Pharmaceutical Sciences; Wenzhou Medical University; Wenzhou Zhejiang P. R. China
| | - Jia Sun
- School of Pharmaceutical Sciences; Wenzhou Medical University; Wenzhou Zhejiang P. R. China
| | - Zhiwei Chen
- School of Pharmaceutical Sciences; Wenzhou Medical University; Wenzhou Zhejiang P. R. China
| | - Litai Jin
- School of Pharmaceutical Sciences; Wenzhou Medical University; Wenzhou Zhejiang P. R. China
- Wenzhou Undersun Biotechnology Co. Ltd.; Wenzhou Zhejiang P. R. China
| | - Yang Wang
- Institute of neuroscience, Department of histology and embryology; Wenzhou Medical University; Wenzhou Zhejiang P. R. China
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12
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Miquel Guennoc C, Rose C, Guinnet F, Miquel I, Labbé J, Deveau A. A New Method for Qualitative Multi-scale Analysis of Bacterial Biofilms on Filamentous Fungal Colonies Using Confocal and Electron Microscopy. J Vis Exp 2017. [PMID: 28190036 PMCID: PMC5352296 DOI: 10.3791/54771] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Bacterial biofilms frequently form on fungal surfaces and can be involved in numerous bacterial-fungal interaction processes, such as metabolic cooperation, competition, or predation. The study of biofilms is important in many biological fields, including environmental science, food production, and medicine. However, few studies have focused on such bacterial biofilms, partially due to the difficulty of investigating them. Most of the methods for qualitative and quantitative biofilm analyses described in the literature are only suitable for biofilms forming on abiotic surfaces or on homogeneous and thin biotic surfaces, such as a monolayer of epithelial cells. While laser scanning confocal microscopy (LSCM) is often used to analyze in situ and in vivo biofilms, this technology becomes very challenging when applied to bacterial biofilms on fungal hyphae, due to the thickness and the three dimensions of the hyphal networks. To overcome this shortcoming, we developed a protocol combining microscopy with a method to limit the accumulation of hyphal layers in fungal colonies. Using this method, we were able to investigate the development of bacterial biofilms on fungal hyphae at multiple scales using both LSCM and scanning electron microscopy (SEM). This report describes the protocol, including microorganism cultures, bacterial biofilm formation conditions, biofilm staining, and LSCM and SEM visualizations.
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Affiliation(s)
| | - Christophe Rose
- Ecologie et Ecophysiologie Forestières - PTEF, UMR 1137, INRA Université de Lorraine
| | - Frédéric Guinnet
- Interactions Arbres - Microorganismes, UMR1136, INRA Université de Lorraine
| | - Igor Miquel
- Interactions Arbres - Microorganismes, UMR1136, INRA Université de Lorraine
| | - Jessy Labbé
- Biosciences Division, Oak Ridge National Laboratory
| | - Aurélie Deveau
- Interactions Arbres - Microorganismes, UMR1136, INRA Université de Lorraine;
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13
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Liu B, Pang Y, Bouhenni R, Duah E, Paruchuri S, McDonald L. A step toward simplified detection of serum albumin on SDS-PAGE using an environment-sensitive flavone sensor. Chem Commun (Camb) 2016; 51:11060-3. [PMID: 26068596 DOI: 10.1039/c5cc03516c] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
In this study, we report a series of novel flavone-based sensors that exhibit a superior fluorescence response when interacting with serum albumin in real serum samples and in acrylamide gels. The detection limit of probe 4 for serum albumin solution is 0.09 μg mL(-1), and the detectable volume for monkey serum reaches as low as 0.03 μL.
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Affiliation(s)
- Bin Liu
- Department of Chemistry, University of Akron, Akron, Ohio 44325, USA.
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14
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LaCava J, Molloy KR, Taylor MS, Domanski M, Chait BT, Rout MP. Affinity proteomics to study endogenous protein complexes: pointers, pitfalls, preferences and perspectives. Biotechniques 2015; 58:103-19. [PMID: 25757543 PMCID: PMC4465938 DOI: 10.2144/000114262] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Accepted: 02/17/2015] [Indexed: 01/13/2023] Open
Abstract
Dissecting and studying cellular systems requires the ability to specifically isolate distinct proteins along with the co-assembled constituents of their associated complexes. Affinity capture techniques leverage high affinity, high specificity reagents to target and capture proteins of interest along with specifically associated proteins from cell extracts. Affinity capture coupled to mass spectrometry (MS)-based proteomic analyses has enabled the isolation and characterization of a wide range of endogenous protein complexes. Here, we outline effective procedures for the affinity capture of protein complexes, highlighting best practices and common pitfalls.
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Affiliation(s)
- John LaCava
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York
- Institute for Systems Genetics, New York University School of Medicine, New York, NY
| | - Kelly R. Molloy
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY
| | - Martin S. Taylor
- High Throughput Biology Center and Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Michal Domanski
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York
- Centre for mRNP Biogenesis and Metabolism, Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Brian T. Chait
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY
| | - Michael P. Rout
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York
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15
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Owen CB, Hughes DJ, Baquero-Perez B, Berndt A, Schumann S, Jackson BR, Whitehouse A. Utilising proteomic approaches to understand oncogenic human herpesviruses (Review). Mol Clin Oncol 2014; 2:891-903. [PMID: 25279171 DOI: 10.3892/mco.2014.341] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2014] [Accepted: 06/10/2014] [Indexed: 12/16/2022] Open
Abstract
The γ-herpesviruses Epstein-Barr virus and Kaposi's sarcoma-associated herpesvirus are successful pathogens, each infecting a large proportion of the human population. These viruses persist for the life of the host and may each contribute to a number of malignancies, for which there are currently no cures. Large-scale proteomic-based approaches provide an excellent means of increasing the collective understanding of the proteomes of these complex viruses and elucidating their numerous interactions within the infected host cell. These large-scale studies are important for the identification of the intricacies of viral infection and the development of novel therapeutics against these two important pathogens.
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Affiliation(s)
- Christopher B Owen
- School of Molecular and Cellular Biology and Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - David J Hughes
- School of Molecular and Cellular Biology and Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Belinda Baquero-Perez
- School of Molecular and Cellular Biology and Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Anja Berndt
- School of Molecular and Cellular Biology and Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Sophie Schumann
- School of Molecular and Cellular Biology and Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Brian R Jackson
- School of Molecular and Cellular Biology and Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Adrian Whitehouse
- School of Molecular and Cellular Biology and Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
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16
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Wright EP, Prasad KAG, Padula MP, Coorssen JR. Deep imaging: how much of the proteome does current top-down technology already resolve? PLoS One 2014; 9:e86058. [PMID: 24489691 PMCID: PMC3904854 DOI: 10.1371/journal.pone.0086058] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2013] [Accepted: 12/10/2013] [Indexed: 11/21/2022] Open
Abstract
Effective proteome analyses are based on interplay between resolution and detection. It had been claimed that resolution was the main factor limiting the use of two-dimensional gel electrophoresis. Improved protein detection now indicates that this is unlikely to be the case. Using a highly refined protocol, the rat brain proteome was extracted, resolved, and detected. In order to overcome the stain saturation threshold, high abundance protein species were excised from the gel following standard imaging. Gels were then imaged again using longer exposure times, enabling detection of lower abundance, less intensely stained protein species. This resulted in a significant enhancement in the detection of resolved proteins, and a slightly modified digestion protocol enabled effective identification by standard mass spectrometric methods. The data indicate that the resolution required for comprehensive proteome analyses is already available, can assess multiple samples in parallel, and preserve critical information concerning post-translational modifications. Further optimization of staining and detection methods promises additional improvements to this economical, widely accessible and effective top-down approach to proteome analysis.
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Affiliation(s)
- Elise P. Wright
- Molecular Physiology, and the UWS Molecular Medicine Research Group, School of Medicine, University of Western Sydney, Campbelltown, NSW, Australia
| | - Kali A. G. Prasad
- Molecular Physiology, and the UWS Molecular Medicine Research Group, School of Medicine, University of Western Sydney, Campbelltown, NSW, Australia
| | - Matthew P. Padula
- Proteomics Core Facility, Faculty of Science, University of Technology, Sydney, NSW, Australia
| | - Jens R. Coorssen
- Molecular Physiology, and the UWS Molecular Medicine Research Group, School of Medicine, University of Western Sydney, Campbelltown, NSW, Australia
- * E-mail:
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17
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Wheelock AM, Goto S. Effects of post-electrophoretic analysis on variance in gel-based proteomics. Expert Rev Proteomics 2014; 3:129-42. [PMID: 16445357 DOI: 10.1586/14789450.3.1.129] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
2D electrophoresis (2DE) is a prominent separation method for complex proteomes. Although recent advances have increased the utility of this method in quantitative proteomics studies, many sources of variance still exist. This review discusses the post-electrophoretic sources of variance in current 2DE analysis. The essential improvements in protein visualization and software algorithms that have made 2DE a leading quantitative proteomics method are briefly reviewed. A number of shortcomings in the post-electrophoretic analysis of 2DE data that require further attention are highlighted. Topics discussed include protein visualization and image acquisition, internal standards and normalization methods, background subtraction algorithms, normality of distribution, and the need for standardized tests for the evaluation of 2DE analysis software packages.
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Affiliation(s)
- Asa M Wheelock
- Kyoto University, Bioinformatics Center, Institute for Chemical Research, Uji, Kyoto, 611-0011, Japan.
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18
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Abstract
During the last decade, a major breakthrough in the field of proteomics has been achieved. This review describes available techniques for proteomic analyses, both gel and non-gel based, particularly concentrating on relative quantification techniques. The principle of the different techniques is discussed, highlighting the advantages and drawbacks of recently available visualization methods in gel-based assays. In addition, recent developments for quantitative analysis in non-gel-based approaches are summarized. This review focuses on applications in Type 1 diabetes. These mainly include proteomic studies on pancreatic islets in animal models and in the human situation. Also discussed are mass spectrometry-based studies on T-cells, and studies on the development of diagnostic markers for diabetic nephropathology by capillary electrophoresis coupled to mass spectrometry.
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Affiliation(s)
- Wannes D'Hertog
- Laboratory for Experimental Medicine & Endocrinology (LEGENDO), University Hospital Gasthuisberg, Herestraat 49, Catholic University of Leuven, Leuven, Belgium.
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Butt RH, Coorssen JR. Coomassie blue as a near-infrared fluorescent stain: a systematic comparison with Sypro Ruby for in-gel protein detection. Mol Cell Proteomics 2013; 12:3834-50. [PMID: 24043422 DOI: 10.1074/mcp.m112.021881] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Quantitative proteome analyses suggest that the well-established stain colloidal Coomassie Blue, when used as an infrared dye, may provide sensitive, post-electrophoretic in-gel protein detection that can rival even Sypro Ruby. Considering the central role of two-dimensional gel electrophoresis in top-down proteomic analyses, a more cost effective alternative such as Coomassie Blue could prove an important tool in ongoing refinements of this important analytical technique. To date, no systematic characterization of Coomassie Blue infrared fluorescence detection relative to detection with SR has been reported. Here, seven commercial Coomassie stain reagents and seven stain formulations described in the literature were systematically compared. The selectivity, threshold sensitivity, inter-protein variability, and linear-dynamic range of Coomassie Blue infrared fluorescence detection were assessed in parallel with Sypro Ruby. Notably, several of the Coomassie stain formulations provided infrared fluorescence detection sensitivity to <1 ng of protein in-gel, slightly exceeding the performance of Sypro Ruby. The linear dynamic range of Coomassie Blue infrared fluorescence detection was found to significantly exceed that of Sypro Ruby. However, in two-dimensional gel analyses, because of a blunted fluorescence response, Sypro Ruby was able to detect a few additional protein spots, amounting to 0.6% of the detected proteome. Thus, although both detection methods have their advantages and disadvantages, differences between the two appear to be small. Coomassie Blue infrared fluorescence detection is thus a viable alternative for gel-based proteomics, offering detection comparable to Sypro Ruby, and more reliable quantitative assessments, but at a fraction of the cost.
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Papasotiriou DG, Markoutsa S, Gorka J, Schleiff E, Karas M, Meyer B. MALDI analysis of proteins after extraction from dissolvable ethylene glycol diacrylate cross-linked polyacrylamide gels. Electrophoresis 2013; 34:2484-94. [DOI: 10.1002/elps.201300132] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2013] [Revised: 04/20/2013] [Accepted: 05/12/2013] [Indexed: 12/23/2022]
Affiliation(s)
- Dimitrios G. Papasotiriou
- Institute of Pharmaceutical Chemistry; Cluster of Excellence “Macromolecular Complexes”, Goethe University; Frankfurt am Main Germany
| | - Stavroula Markoutsa
- Institute of Pharmaceutical Chemistry; Cluster of Excellence “Macromolecular Complexes”, Goethe University; Frankfurt am Main Germany
| | - Jan Gorka
- Institute of Pharmaceutical Chemistry; Cluster of Excellence “Macromolecular Complexes”, Goethe University; Frankfurt am Main Germany
| | - Enrico Schleiff
- Molecular Cell Biology of Plants; Cluster of Excellence “Macromolecular Complexes”, Goethe University; Frankfurt am Main Germany
| | - Michael Karas
- Institute of Pharmaceutical Chemistry; Cluster of Excellence “Macromolecular Complexes”, Goethe University; Frankfurt am Main Germany
| | - Bjoern Meyer
- Institute for Instrumental Analysis and Bioanalysis; Mannheim University of Applied Sciences; Mannheim Germany
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Okumura N, Tsujihata M, Momohara C, Yoshioka I, Suto K, Nonomura N, Okuyama A, Takao T. Diversity in protein profiles of individual calcium oxalate kidney stones. PLoS One 2013; 8:e68624. [PMID: 23874695 PMCID: PMC3706363 DOI: 10.1371/journal.pone.0068624] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2013] [Accepted: 05/30/2013] [Indexed: 02/03/2023] Open
Abstract
Calcium oxalate kidney stones contain low amounts of proteins, some of which have been implicated in progression or prevention of kidney stone formation. To gain insights into the pathophysiology of urolithiasis, we have characterized protein components of calcium oxalate kidney stones by proteomic approaches. Proteins extracted from kidney stones showed highly heterogeneous migration patterns in gel electrophoresis as reported. This was likely to be mainly due to proteolytic degradation and protein-protein crosslinking of Tamm-Horsfall protein and prothrombin. Protein profiles of calcium oxalate kidney stones were obtained by in-solution protease digestion followed by nanoLC-MALDI-tandem mass spectrometry, which resulted in identification of a total of 92 proteins in stones from 9 urolithiasis patients. Further analysis showed that protein species and their relative amounts were highly variable among individual stones. Although proteins such as prothrombin, osteopontin, calgranulin A and calgranulin B were found in most stones tested, some samples had high contents of prothrombin and osteopontin, while others had high contents of calgranulins. In addition, calgranulin-rich stones had various neutrophil-enriched proteins such as myeloperoxidase and lactotransferrin. These proteomic profiles of individual kidney stones suggest that multiple systems composed of different groups of proteins including leucocyte-derived ones are differently involved in pathogenesis of individual kidney stones depending on situations.
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Affiliation(s)
- Nobuaki Okumura
- Laboratory of Homeostatic Integration, Division of Integrated Protein Functions, Institute for Protein Research, Osaka University, Suita, Osaka, Japan.
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Drews O. High-resolution separation of cardiovascular proteomes: two-dimensional electrophoresis and liquid chromatography. ACTA ACUST UNITED AC 2013; 5:592. [PMID: 23074339 DOI: 10.1161/circgenetics.110.958637] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Oliver Drews
- Institute of Physiology and Pathophysiology, Division of Cardiovascular Physiology, University of Heidelberg, Heidelberg, Germany.
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Gauci VJ, Padula MP, Coorssen JR. Coomassie blue staining for high sensitivity gel-based proteomics. J Proteomics 2013; 90:96-106. [PMID: 23428344 DOI: 10.1016/j.jprot.2013.01.027] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2012] [Accepted: 01/27/2013] [Indexed: 11/26/2022]
Abstract
Gel electrophoresis, particularly one- (1DE) and two-dimensional electrophoresis (2DE), remain among the most widely used top-down methods for resolving and analysing proteomes. Detection of the resulting protein maps relies on staining (i.e. colloidal coomassie blue (CCB) or SYPRO Ruby (SR), in addition to many others). Fluorescent in-gel protein stains are generally preferred for higher sensitivity, reduced background, and wider dynamic range. Although traditionally used for densitometry, CBB has fluorescent properties. Indeed, infrared detection of CCB stained protein was comparable to SR, with BioSafe (Bio-Rad) and the Neuhoff formulation (NCCB) identified as potentially superior to SR; a minor sensitivity issue encountered in gel-resolved proteomes; might have been due to the unified staining protocol used. Here the staining protocol for both CCB formulations was optimised, yielding improved selectivity without affecting sensitivity; the resulting linear dynamic range was similar for BioSafe and NCCB and somewhat better than SR. 2D gel-based analyses of mouse brain and Arabidopsis thaliana (leaf) proteomes indicated markedly superior spot detection using the NCCB formulation. Thus more sensitive, quantitative in-gel protein analyses can be achieved using NCCB, at a fraction of the cost.
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Affiliation(s)
- Victoria J Gauci
- Molecular Physiology, and the Molecular Medicine Research Group, School of Medicine, University of Western Sydney, Sydney, Australia
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Jung YH, Jeong SH, Kim SH, Singh R, Lee JE, Cho YS, Agrawal GK, Rakwal R, Jwa NS. Secretome analysis of Magnaporthe oryzae using in vitro systems. Proteomics 2012; 12:878-900. [PMID: 22539438 DOI: 10.1002/pmic.201100142] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Magnaporthe oryzae is a devastating blast fungal pathogen of rice (Oryza sativa L.) that causes dramatic decreases in seed yield and quality. During the early stages of infection by this pathogen, the fungal spore senses the rice leaf surface, germinates, and penetrates the cell via an infectious structure known as an appressorium. During this process, M. oryzae secretes several proteins; however, these proteins are largely unknown mainly due to the lack of a suitable method for isolating secreted proteins during germination and appressoria formation. We examined the secretome of M. oryzae by mimicking the early stages of infection in vitro using a glass plate (GP), PVDF membrane, and liquid culture medium (LCM). Microscopic observation of M. oryzae growth revealed appressorium formation on the GP and PVDF membrane resembling natural M. oryzae-rice interactions; however, appresorium formation was not observed in the LCM. Secreted proteins were collected from the GP (3, 8, and 24 h), PVDF membrane (24 h), and LCM (48 h) and identified by two-dimensional gel electrophoresis (2DE) followed by tandem mass spectrometry. The GP, PVDF membrane, and LCM-derived 2D gels showed distinct protein patterns, indicating that they are complementary approaches. Collectively, 53 nonredundant proteins including previously known and novel secreted proteins were identified. Six biological functions were assigned to the proteins, with the predominant functional classes being cell wall modification, reactive oxygen species detoxification, lipid modification, metabolism, and protein modification. The in vitro system using GPs and PVDF membranes applied in this study to survey the M. oryzae secretome, can be used to further our understanding of the early interactions between M. oryzae and rice leaves.
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Affiliation(s)
- Young-Ho Jung
- Department of Molecular Biology, Sejong University, Gunja-dong, Seoul, South Korea
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25
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Jia J, Fei H, Zhou M. Luminescent iridium(III) complexes as novel protein staining agents. Electrophoresis 2012; 33:1397-401. [DOI: 10.1002/elps.201100693] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- Junli Jia
- Division of Nanobiomedicine,; Suzhou Institute of Nano-Tech and Nano-Bionics; Chinese Academy of Sciences; Suzhou; Jiangsu; P. R. China
| | - Hao Fei
- Division of Nanobiomedicine,; Suzhou Institute of Nano-Tech and Nano-Bionics; Chinese Academy of Sciences; Suzhou; Jiangsu; P. R. China
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26
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Proteomics: Bases for protein complexity understanding. Thromb Res 2012; 129:257-62. [DOI: 10.1016/j.thromres.2011.12.035] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2011] [Revised: 12/19/2011] [Accepted: 12/22/2011] [Indexed: 01/10/2023]
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Pierobon M, Vanmeter AJ, Moroni N, Galdi F, Petricoin EF. Reverse-phase protein microarrays. Methods Mol Biol 2012; 823:215-35. [PMID: 22081348 DOI: 10.1007/978-1-60327-216-2_14] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Cancer is the consequence of intra- and extracellular signaling network deregulation that derives from alteration of genetic and proteomic cellular homeostasis. Mapping the individual molecular circuitry of a patient's tumor cells is the starting point for rational personalized therapy.While genes and RNA encode information about cellular status, proteins are considered the engine of the cellular machine, as they are the effective elements that drive cellular functions, such as proliferation, migration, differentiation, and apoptosis. Consequently, investigations of the cellular protein network are considered a fundamental tool to understand cellular functions. In the last decades, increasing interest has been focused on the improvement of new technologies for proteomic analysis. In this context, reverse-phase protein microarrays (RPMAs) have been developed to study and analyze posttranslational modifications that are responsible for principal cell functions and activities. This innovative technology allows the investigation of protein activation as a consequence of protein-protein interaction or biochemical reactions, such as phosphorylation, glycosylation, ubiquitination, protein cleavage, and conformational alterations.Intracellular balance is carefully conserved by constant rearrangements of proteins through the activity of a series of kinases and phosphatases. Therefore, knowledge of the key cellular signaling cascades reveal information regarding the cellular processes driving a tumor's growth (such as cellular survival, proliferation, invasion, and cell death) and response to treatment.Alteration to cellular homeostasis, driven by elaborate intra- and extracellular interactions, has become one of the most studied fields in the era of personalized medicine and targeted therapy. RPMA technology is a valid tool that can be applied to protein analysis of several diseases for the potential to generate protein interaction and activation maps that lead to the identification of critical nodes for individualized or combinatorial target therapy.
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Affiliation(s)
- Mariaelena Pierobon
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA, USA.
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28
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Simple, time-saving dye staining of proteins for sodium dodecyl sulfate-polyacrylamide gel electrophoresis using Coomassie blue. PLoS One 2011; 6:e22394. [PMID: 21850222 PMCID: PMC3151240 DOI: 10.1371/journal.pone.0022394] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2011] [Accepted: 06/20/2011] [Indexed: 11/25/2022] Open
Abstract
A fixation-free and fast protein-staining method for sodium dodecyl sulfate–polyacrylamide gel electrophoresis using Coomassie blue is described. The protocol comprises staining and quick washing steps, which can be completed in 0.5 h. It has a sensitivity of 10 ng, comparable with that of conventional Coomassie Brilliant Blue G staining with phosphoric acid in the staining solution. In addition, the dye stain does not contain any amount of acid and methanol, such as phosphoric acid. Considering the speed, simplicity, and low cost, the dye stain may be of more practical value than other dye-based protein stains in routine proteomic research.
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Gallagher RI, Silvestri A, Petricoin EF, Liotta LA, Espina V. Reverse phase protein microarrays: fluorometric and colorimetric detection. Methods Mol Biol 2011; 723:275-301. [PMID: 21370072 DOI: 10.1007/978-1-61779-043-0_18] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
The Reverse Phase Protein Microarray (RPMA) is an array platform used to quantitate proteins and their posttranslationally modified forms. RPMAs are applicable for profiling key cellular signaling pathways and protein networks, allowing direct comparison of the activation state of proteins from multiple samples within the same array. The RPMA format consists of proteins immobilized directly on a nitrocellulose substratum. The analyte is subsequently probed with a primary antibody and a series of reagents for signal amplification and detection. Due to the diversity, low concentration, and large dynamic range of protein analytes, RPMAs require stringent signal amplification methods, high quality image acquisition, and software capable of precisely analyzing spot intensities on an array. Microarray detection strategies can be either fluorescent or colorimetric. The choice of a detection system depends on (a) the expected analyte concentration, (b) type of microarray imaging system, and (c) type of sample. The focus of this chapter is to describe RPMA detection and imaging using fluorescent and colorimetric (diaminobenzidine (DAB)) methods.
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Affiliation(s)
- Rosa I Gallagher
- George Mason University, Center for Applied Proteomics and Molecular Medicine, Manassas, VA, USA
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31
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Yarmoluk SM, Kovalska VB, Volkova KD. Optimized Dyes for Protein and Nucleic Acid Detection. ADVANCED FLUORESCENCE REPORTERS IN CHEMISTRY AND BIOLOGY III 2011. [DOI: 10.1007/978-3-642-18035-4_5] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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32
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Espina V, Mueller C, Liotta LA. Phosphoprotein stability in clinical tissue and its relevance for reverse phase protein microarray technology. Methods Mol Biol 2011; 785:23-43. [PMID: 21901591 DOI: 10.1007/978-1-61779-286-1_3] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Phosphorylated proteins reflect the activity of specific cell signaling nodes in biological kinase protein networks. Cell signaling pathways can be either activated or deactivated depending on the phosphorylation state of the constituent proteins. The state of these kinase pathways reflects the in vivo activity of the cells and tissue at any given point in time. As such, cell signaling pathway information can be extrapolated to infer which phosphorylated proteins/pathways are driving an individual tumor's growth. Reverse phase protein microarrays (RPMAs) are a sensitive and precise platform that can be applied to the quantitative measurement of hundreds of phosphorylated signal proteins from a small sample of tissue. Pre-analytical variability originating from tissue procurement and preservation may cause significant variability and bias in downstream molecular analysis. Depending on the ex vivo delay time in tissue processing, and the manner of tissue handling, protein biomarkers such as signal pathway phosphoproteins will be elevated or suppressed in a manner that does not represent the biomarker levels at the time of excision. Consequently, assessment of the state of these kinase networks requires stabilization, or preservation, of the phosphoproteins immediately post-tissue procurement. We have employed RPMA analysis of phosphoproteins to study the factors influencing stability of phosphoproteins in tissue following procurement. Based on this analysis we have established tissue procurement guidelines for clinical research with an emphasis on quantifying phosphoproteins by RPMA.
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Affiliation(s)
- Virginia Espina
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA, USA.
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33
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Gauci VJ, Wright EP, Coorssen JR. Quantitative proteomics: assessing the spectrum of in-gel protein detection methods. J Chem Biol 2011; 4:3-29. [PMID: 21686332 PMCID: PMC3022124 DOI: 10.1007/s12154-010-0043-5] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2010] [Accepted: 06/02/2010] [Indexed: 11/28/2022] Open
Abstract
Proteomics research relies heavily on visualization methods for detection of proteins separated by polyacrylamide gel electrophoresis. Commonly used staining approaches involve colorimetric dyes such as Coomassie Brilliant Blue, fluorescent dyes including Sypro Ruby, newly developed reactive fluorophores, as well as a plethora of others. The most desired characteristic in selecting one stain over another is sensitivity, but this is far from the only important parameter. This review evaluates protein detection methods in terms of their quantitative attributes, including limit of detection (i.e., sensitivity), linear dynamic range, inter-protein variability, capacity for spot detection after 2D gel electrophoresis, and compatibility with subsequent mass spectrometric analyses. Unfortunately, many of these quantitative criteria are not routinely or consistently addressed by most of the studies published to date. We would urge more rigorous routine characterization of stains and detection methodologies as a critical approach to systematically improving these critically important tools for quantitative proteomics. In addition, substantial improvements in detection technology, particularly over the last decade or so, emphasize the need to consider renewed characterization of existing stains; the quantitative stains we need, or at least the chemistries required for their future development, may well already exist.
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Affiliation(s)
- Victoria J. Gauci
- Molecular Physiology, School of Medicine, and Molecular Medicine Research Group, University of Western Sydney, Campbelltown, NSW 1797 Australia
| | - Elise P. Wright
- Molecular Physiology, School of Medicine, and Molecular Medicine Research Group, University of Western Sydney, Campbelltown, NSW 1797 Australia
| | - Jens R. Coorssen
- Molecular Physiology, School of Medicine, and Molecular Medicine Research Group, University of Western Sydney, Campbelltown, NSW 1797 Australia
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Mueller C, Liotta LA, Espina V. Reverse phase protein microarrays advance to use in clinical trials. Mol Oncol 2010; 4:461-81. [PMID: 20974554 PMCID: PMC2981612 DOI: 10.1016/j.molonc.2010.09.003] [Citation(s) in RCA: 102] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2010] [Revised: 09/15/2010] [Accepted: 09/16/2010] [Indexed: 12/18/2022] Open
Abstract
Individualizing cancer therapy for molecular targeted inhibitors requires a new class of molecular profiling technology that can map the functional state of the cancer cell signal pathways containing the drug targets. Reverse phase protein microarrays (RPMA) are a technology platform designed for quantitative, multiplexed analysis of specific phosphorylated, cleaved, or total (phosphorylated and non-phosphorylated) forms of cellular proteins from a limited amount of sample. This class of microarray can be used to interrogate tissue samples, cells, serum, or body fluids. RPMA were previously a research tool; now this technology has graduated to use in research clinical trials with clinical grade sensitivity and precision. In this review we describe the application of RPMA for multiplexed signal pathway analysis in therapeutic monitoring, biomarker discovery, and evaluation of pharmaceutical targets, and conclude with a summary of the technical aspects of RPMA construction and analysis.
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Affiliation(s)
- Claudius Mueller
- George Mason University, Center for Applied Proteomics and Molecular Medicine, Manassas, VA 20110, USA
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35
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Chevalier F. Standard Dyes for Total Protein Staining in Gel-Based Proteomic Analysis. MATERIALS 2010; 3:4784-4792. [PMID: 28883353 PMCID: PMC5445784 DOI: 10.3390/ma3104784] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/08/2010] [Revised: 10/13/2010] [Accepted: 10/15/2010] [Indexed: 12/02/2022]
Abstract
Staining of two-dimensional gels is a primary concern in proteomic studies using two-dimensional gel electrophoresis with respect to the number of proteins analyzed, the accuracy of spot quantification and reproducibility. In this review article, the efficiency of the most widely used dyes was investigated. Visible dyes (Coomassie blue and silver nitrate), fluorescent dyes (Sypro Ruby, Deep Purple) and cyanine labeled methods were compared.
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36
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Chevalier F. Highlights on the capacities of "Gel-based" proteomics. Proteome Sci 2010; 8:23. [PMID: 20426826 PMCID: PMC2873371 DOI: 10.1186/1477-5956-8-23] [Citation(s) in RCA: 128] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2010] [Accepted: 04/28/2010] [Indexed: 11/18/2022] Open
Abstract
Gel-based proteomic is the most popular and versatile method of global protein separation and quantification. This is a mature approach to screen the protein expression at the large scale, and a cheaper approach as compared with gel-free proteomics. Based on two independent biochemical characteristics of proteins, two-dimensional electrophoresis combines isoelectric focusing, which separates proteins according to their isoelectric point, and SDS-PAGE, which separates them further according to their molecular mass. The next typical steps of the flow of gel-based proteomics are spots visualization and evaluation, expression analysis and finally protein identification by mass spectrometry. For the study of differentially expressed proteins, two-dimensional electrophoresis allows simultaneously to detect, quantify and compare up to thousand protein spots isoforms, including post-translational modifications, in the same gel and in a wide range of biological systems. In this review article, the limits, benefits, and perspectives of gel-based proteomic approaches are discussed using concrete examples.
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37
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Volkova K, Kovalska V, Yarmoluk S. Modern techniques for protein detection on polyacrylamide gels: problems arising from the use of dyes of undisclosed structures for scientific purposes. Biotech Histochem 2009; 82:201-8. [DOI: 10.1080/10520290701707660] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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38
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Lin CY, Wang V, Shui HA, Juang RH, Hour AL, Chen PS, Huang HM, Wu SY, Lee JC, Tsai TL, Chen HM. A comprehensive evaluation of imidazole-zinc reverse stain for current proteomic researches. Proteomics 2009; 9:696-709. [PMID: 19137546 DOI: 10.1002/pmic.200700470] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
In this paper, we comprehensively evaluated the capability of imidazole-zinc reverse stain (ZN) in comparative proteomics. Three commonly used protein gel staining methods, including silver (SN), SYPRO Ruby (SR), and CB stain were investigated alongside for comparison purpose. A transparency scanning procedure, which may deliver more even and contrasting gel images, was found best for documenting ZN stained gels. Our results showed that ZN was more sensitive than SN, SR, and CB. It may reveal as few as 1.8 ng of proteins in a gel. Moreover, ZN was found to provide a linear dynamic range of staining for revealing proteins up to 140 ng, and show an insignificant staining preference. To analyze a ZN stained 2-D gel image that generally comprises an apparent but even background, the Melanie 4 software was found more suitable than others. Furthermore, ZN demonstrated an equivalent or better MS compatibility than the other three staining methods. Intense and comprehensive MS profiles were frequently observed for ZN stained gel spots. Approximate two-third of ZN stained gel spots were successfully identified for protein identities. Taken together, our results suggest that the prompt, cost effective and versatile ZN is well suited for current proteomic researches.
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Affiliation(s)
- Ching-Yu Lin
- Graduate Institute of Applied Science and Engineering, Catholic Fu-Jen University, Taipei, Taiwan, Republic of China
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Cong WT, Hwang SY, Jin LT, Choi JK. Improved conditions for fluorescent staining of proteins with 4,4'-dianilino-1,1'-binaphthyl-5,5'-disulfonic acid in SDS-PAGE. Electrophoresis 2009; 29:4487-94. [PMID: 19035403 DOI: 10.1002/elps.200800124] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
A simple and sensitive fluorescent staining method for the detection of proteins in SDS-PAGE, namely IB (improved 4,4'-dianilino-1,1'-binaphthyl-5,5'-disulfonic acid) stain, is described. Non-covalent hydrophobic probe 4,4'-dianilino-1,1'-binaphthyl-5,5'-disulfonic acid was applied as a fluorescent dye, which can bind to hydrophobic sites in proteins non-specifically. As low as 1 ng of protein band can be detected briefly by 30 min washing followed by 15 min staining without the aiding of stop or destaining step. The sensitivity of the new presented protocol is similar to that of SYPRO Ruby, which has been widely accepted in proteomic research. Comparative analysis of the MS compatibility of IB stain and SYPRO Ruby stain allowed us to address that IB stain is compatible with the downstream of protein identification by PMF.
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Affiliation(s)
- Wei-Tao Cong
- College of Pharmacy & Research Institute of Drug Development, Chonnam National University, Gwangju, South Korea
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Apweiler R, Aslanidis C, Deufel T, Gerstner A, Hansen J, Hochstrasser D, Kellner R, Kubicek M, Lottspeich F, Maser E, Mewes HW, Meyer HE, Müllner S, Mutter W, Neumaier M, Nollau P, Nothwang HG, Ponten F, Radbruch A, Reinert K, Rothe G, Stockinger H, Tarnok A, Taussig MJ, Thiel A, Thiery J, Ueffing M, Valet G, Vandekerckhove J, Verhuven W, Wagener C, Wagner O, Schmitz G. Approaching clinical proteomics: current state and future fields of application in fluid proteomics. Clin Chem Lab Med 2009; 47:724-44. [DOI: 10.1515/cclm.2009.167] [Citation(s) in RCA: 98] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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43
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Jin LT, Li XK, Cong WT, Hwang SY, Choi JK. Previsible silver staining of protein in electrophoresis gels with mass spectrometry compatibility. Anal Biochem 2008; 383:137-43. [DOI: 10.1016/j.ab.2008.04.048] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2008] [Revised: 04/08/2008] [Accepted: 04/10/2008] [Indexed: 11/25/2022]
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Cong WT, Hwang SY, Jin LT, Choi JK. Sensitive fluorescent staining for proteomic analysis of proteins in 1-D and 2-D SDS-PAGE and its comparison with SYPRO Ruby by PMF. Electrophoresis 2008; 29:4304-15. [DOI: 10.1002/elps.200800150] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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45
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Filtration-based staining of proteins on membranes. Anal Biochem 2008; 379:121-3. [DOI: 10.1016/j.ab.2008.04.030] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2008] [Revised: 03/29/2008] [Accepted: 04/20/2008] [Indexed: 11/23/2022]
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46
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Riederer BM. Non-covalent and covalent protein labeling in two-dimensional gel electrophoresis. J Proteomics 2008; 71:231-44. [DOI: 10.1016/j.jprot.2008.05.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2008] [Revised: 05/03/2008] [Accepted: 05/06/2008] [Indexed: 12/16/2022]
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47
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Abstract
This unit has been recently updated to include information on preformulated gel stains as well as new protocols for Sypro Ruby and silver staining, and gel imaging methodology. Other previously published protocols are also provided for both rapid and acid-based Coomassie blue staining, and alternate methods for silver staining (i.e., nonammoniacal silver staining, rapid silver staining, and an enhanced-background, two-stage method).
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Affiliation(s)
- Lynn A Echan
- The Wistar Institute, Philadelphia, Pennsylvania, USA
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Liumbruno GM. Proteomics: applications in transfusion medicine. BLOOD TRANSFUSION = TRASFUSIONE DEL SANGUE 2008; 6:70-85. [PMID: 18946951 PMCID: PMC2626841 DOI: 10.2450/2008.0038-07] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Subscribe] [Scholar Register] [Received: 08/02/2007] [Accepted: 12/20/2007] [Indexed: 12/30/2022]
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49
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Harvey DJ. Analysis of carbohydrates and glycoconjugates by matrix-assisted laser desorption/ionization mass spectrometry: an update covering the period 2001-2002. MASS SPECTROMETRY REVIEWS 2008; 27:125-201. [PMID: 18247413 DOI: 10.1002/mas.20157] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
This review is the second update of the original review on the application of MALDI mass spectrometry to the analysis of carbohydrates and glycoconjugates that was published in 1999. It covers fundamental aspects of the technique as applied to carbohydrates, fragmentation of carbohydrates, studies of specific carbohydrate types such as those from plant cell walls and those attached to proteins and lipids, studies of glycosyl-transferases and glycosidases, and studies where MALDI has been used to monitor products of chemical synthesis. Use of the technique shows a steady annual increase at the expense of older techniques such as FAB. There is an increasing emphasis on its use for examination of biological systems rather than on studies of fundamental aspects and method development and this is reflected by much of the work on applications appearing in tabular form.
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Affiliation(s)
- David J Harvey
- Department of Biochemistry, Oxford Glycobiology Institute, South Parks Road, Oxford OX1 3QU, UK.
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Nock CM, Ball MS, White IR, Skehel JM, Bill L, Karuso P. Mass spectrometric compatibility of Deep Purple and SYPRO Ruby total protein stains for high-throughput proteomics using large-format two-dimensional gel electrophoresis. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2008; 22:881-886. [PMID: 18293286 DOI: 10.1002/rcm.3483] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
In order to identify putative biomarkers from two-dimensional (2D) gel electrophoresis it is necessary to use a visualization technique that is sensitive, has a large dynamic range and does not interfere with the identification of the protein. As mass spectrometry increases in sensitivity more pressure is placed on visualization techniques that facilitate proteomic workflows but do not interfere with downstream processing. Two stains reported to meet these requirements are SYPRO Ruby (Invitrogen) and Deep Purple (GE Healthcare). This study examined the compatibility of these stains with protein identification by selecting spots from replicate 2D gels of human plasma and subjecting these to protein identification using liquid chromatography/tandem mass spectrometry (LC/MS/MS). Using a test of two populations of proportions it was found that proteins were statistically more likely to be identified from gels stained with Deep Purple. Additionally, the identifications from Deep Purple stained gels are of higher quality because they are based on multiple peptides.
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Affiliation(s)
- Christina M Nock
- GlaxoSmithKline Pharmaceuticals, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, UK
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