1
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Abstract
Two-dimensional gel electrophoresis has been instrumental in the development of proteomics. Although it is no longer the exclusive scheme used for proteomics, its unique features make it a still highly valuable tool, especially when multiple quantitative comparisons of samples must be made, and even for large samples series. However, quantitative proteomics using two-dimensional gels is critically dependent on the performances of the protein detection methods used after the electrophoretic separations. This chapter therefore examines critically the various detection methods, (radioactivity, dyes, fluorescence, and silver) as well as the data analysis issues that must be taken into account when quantitative comparative analysis of two-dimensional gels is performed.
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2
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Bräunig J, Schiwy S, Broedel O, Müller Y, Frohme M, Hollert H, Keiter SH. Time-dependent expression and activity of cytochrome P450 1s in early life-stages of the zebrafish (Danio rerio). ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2015; 22:16319-16328. [PMID: 25994265 DOI: 10.1007/s11356-015-4673-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Accepted: 05/06/2015] [Indexed: 06/04/2023]
Abstract
Zebrafish embryos are being increasingly used as model organisms for the assessment of single substances and complex environmental samples for regulatory purposes. Thus, it is essential to fully understand the xenobiotic metabolism during the different life-stages of early development. The aim of the present study was to determine arylhydrocarbon receptor (AhR)-mediated activity during selected times of early development using qPCR, enzymatic activity through measurement of 7-ethoxyresorufin-O-deethylase (EROD) activity, and protein expression analysis. In the present study, gene expression of cyp1a, cyp1b1, cyp1c1, cyp1c2, and ahr2 as well as EROD activity were investigated up to 120 h postfertilization (hpf) after exposure to either β-naphthoflavone (BNF) or a polycyclic aromatic hydrocarbons (PAH)-contaminated sediment extract from Vering Kanal in Hamburg (VK). Protein expression was measured at 72 hpf after exposure to 20 μg/L BNF. Altered proteins were identified by matrix assisted laser desorption ionization time-of-flight (MALDI-TOF) peptide mass fingerprinting. Distinct patterns of basal messenger RNA (mRNA) expression were found for each of the cyp1 genes, suggesting specific roles during embryonic development. All transcripts were induced by BNF and VK. ahr2 mRNA expression was significantly upregulated after exposure to VK. All cyp1 genes investigated showed a temporal decline in expression at 72 hpf. The significant decline of Hsp 90β protein at 72 hpf after exposure to BNF may suggest an explanation for the decline of cyp1 genes at this time point as Hsp 90β is of major importance for the functioning of the Ah-receptor. EROD activity measured in embryos was significantly induced after 96 hpf of exposure to BNF or VK. Together, these results demonstrate distinct temporal patterns of cyp1 genes and protein activities in zebrafish embryos as well as show a need to investigate further the xenobiotic biotransformation system during early development of zebrafish.
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Affiliation(s)
- Jennifer Bräunig
- Institute for Environmental Research, RWTH Aachen University, Worringerweg 1, 52074, Aachen, Germany.
- National Research Centre for Environmental Toxicology (Entox), The University of Queensland, 39 Kessels Road, 4108, Brisbane, Queensland, Australia.
| | - Sabrina Schiwy
- Institute for Environmental Research, RWTH Aachen University, Worringerweg 1, 52074, Aachen, Germany
| | - Oliver Broedel
- Molecular Biotechnology and Functional Genomics, Technical University of Applied Sciences Wildau, Hochschulring 1, 15745, Wildau, Germany
| | - Yvonne Müller
- Institute for Environmental Research, RWTH Aachen University, Worringerweg 1, 52074, Aachen, Germany
| | - Marcus Frohme
- Molecular Biotechnology and Functional Genomics, Technical University of Applied Sciences Wildau, Hochschulring 1, 15745, Wildau, Germany
| | - Henner Hollert
- Institute for Environmental Research, RWTH Aachen University, Worringerweg 1, 52074, Aachen, Germany
| | - Steffen H Keiter
- Institute for Environmental Research, RWTH Aachen University, Worringerweg 1, 52074, Aachen, Germany.
- Man-Technology-Environment Research Centre, School of Science and Technology, Örebro University, 70182, Örebro, Sweden.
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3
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Baldassini WA, Braga CP, Chardulo LAL, Silva JAIIV, Malheiros JM, de Albuquerque LG, Fernandes TT, Padilha PDM. Bioanalytical methods for the metalloproteomics study of bovine longissimus thoracis muscle tissue with different grades of meat tenderness in the Nellore breed (Bos indicus). Food Chem 2015; 169:65-72. [DOI: 10.1016/j.foodchem.2014.07.131] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2013] [Revised: 07/07/2014] [Accepted: 07/29/2014] [Indexed: 01/17/2023]
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4
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Abstract
Efficient fractionation of peptides is an essential prerequisite for comprehensive analysis of complex protein mixtures by shotgun mass spectrometry. The separation of peptides by isoelectric focusing is particularly attractive due to its orthogonality to reverse-phase HPLC. Here, we present a protocol for in-gel peptide isoelectric focusing using immobilized pH gradient strips. The method shows high resolving power for up to 1 mg of sample and is highly reproducible.
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5
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Barbosa HS, Arruda SCC, Azevedo RA, Arruda MAZ. New insights on proteomics of transgenic soybean seeds: evaluation of differential expressions of enzymes and proteins. Anal Bioanal Chem 2012; 402:299-314. [PMID: 21947011 DOI: 10.1007/s00216-011-5409-1] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2011] [Revised: 08/25/2011] [Accepted: 09/08/2011] [Indexed: 10/17/2022]
Abstract
This work reports the evaluation of differentially expressed enzymes and proteins from transgenic and nontransgenic soybean seeds. Analysis of malondialdehyde, ascorbate peroxidase (EC 1.11.1.11), glutathione reductase (EC 1.6.4.2), and catalase (EC 1.11.1.6) revealed higher levels (29.8, 30.6, 71.4, and 35.3%, respectively) in transgenic seeds than in nontransgenic seeds. Separation of soybean seed proteins was done by two-dimensional polyacrylamide gel electrophoresis, and 192 proteins were identified by matrix-assisted laser desorption/ionization (MALDI) quadrupole time-of-flight (QTOF) mass spectrometry (MS) and electrospray ionization (ESI) QTOF MS. Additionally, the enzyme CP4 EPSPS, involved in the genetic modification, was identified by enzymatic digestions using either trypsin or chymotrypsin and ESI-QTOF MS/MS for identification. From the proteins identified, actin fragment, cytosolic glutamine synthetase, glycinin subunit G1, and glycine-rich RNA-binding protein were shown to be differentially expressed after analysis using the two-dimensional difference gel electrophoresis technique, and applying a regulator factor of 1.5 or greater.
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Affiliation(s)
- Herbert S Barbosa
- Spectrometry, Sample Preparation and Mechanization Group-GEPAM, Institute of Chemistry, University of Campinas-UNICAMP, Campinas, SP, Brazil
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6
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Abstract
Two-dimensional gel electrophoresis has been instrumental in the development of proteomics. Although it is no longer the exclusive scheme used for proteomics, its unique features make it a still highly valuable tool, especially when multiple quantitative comparisons of samples must be made, and even for large samples series. However, quantitative proteomics using 2D gels is critically dependent on the performances of the protein detection methods used after the electrophoretic separations. This chapter therefore examines critically the various detection methods (radioactivity, dyes, fluorescence, and silver) as well as the data analysis issues that must be taken into account when quantitative comparative analysis of 2D gels is performed.
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Affiliation(s)
- Thierry Rabilloud
- CEA-DSV-iRTSV/CBM and UMR CNRS-UJF 5249, CEA Grenoble, Grenoble, France.
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7
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Two-dimensional gel electrophoresis in proteomics: a tutorial. J Proteomics 2011; 74:1829-41. [PMID: 21669304 DOI: 10.1016/j.jprot.2011.05.040] [Citation(s) in RCA: 169] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2011] [Revised: 05/23/2011] [Accepted: 05/26/2011] [Indexed: 12/12/2022]
Abstract
Two-dimensional electrophoresis of proteins has preceded, and accompanied, the birth of proteomics. Although it is no longer the only experimental scheme used in modern proteomics, it still has distinct features and advantages. The purpose of this tutorial paper is to guide the reader through the history of the field, then through the main steps of the process, from sample preparation to in-gel detection of proteins, commenting the constraints and caveats of the technique. Then the limitations and positive features of two-dimensional electrophoresis are discussed (e.g. its unique ability to separate complete proteins and its easy interfacing with immunoblotting techniques), so that the optimal type of applications of this technique in current and future proteomics can be perceived. This is illustrated by a detailed example taken from the literature and commented in detail. This Tutorial is part of the International Proteomics Tutorial Programme (IPTP 2).
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8
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Deng X, Schröder S, Redweik S, Wätzig H. Quantitative gel electrophoresis: new records in precision by elaborated staining and detection protocols. Electrophoresis 2011; 32:1667-74. [PMID: 21557259 DOI: 10.1002/elps.201000525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2010] [Revised: 10/07/2010] [Accepted: 10/25/2010] [Indexed: 11/08/2022]
Abstract
Gel electrophoresis (GE) is a very common analytical technique for proteome research and protein analysis. Despite being developed decades ago, there is still a considerable need to improve its precision. Using the fluorescence of Colloidal Coomassie Blue -stained proteins in near-infrared (NIR), the major error source caused by the unpredictable background staining is strongly reduced. This result was generalized for various types of detectors. Since GE is a multi-step procedure, standardization of every single step is required. After detailed analysis of all steps, the staining and destaining were identified as the major source of the remaining variation. By employing standardized protocols, pooled percent relative standard deviations of 1.2-3.1% for band intensities were achieved for one-dimensional separations in repetitive experiments. The analysis of variance suggests that the same batch of staining solution should be used for gels of one experimental series to minimize day-to-day variation and to obtain high precision.
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Affiliation(s)
- Xi Deng
- Institute of Pharmaceutical Chemistry, Technical University of Braunschweig, Braunschweig, Germany
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9
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Birdsall RE, Kiley MP, Segu ZM, Palmer CD, Madera M, Gump BB, MacKenzie JA, Parsons PJ, Mechref Y, Novotny MV, Bendinskas KG. Effects of lead and mercury on the blood proteome of children. J Proteome Res 2011; 9:4443-53. [PMID: 20681587 DOI: 10.1021/pr100204g] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Heavy metal exposure in children has been associated with a variety of physiological and neurological problems. The goal of this study was to utilize proteomics to enhance the understanding of biochemical interactions responsible for the health problems related to lead and mercury exposure at concentrations well below CDC guidelines. Blood plasma and serum samples from 34 children were depleted of their most abundant proteins using antibody-based affinity columns and analyzed using two different methods, LC-MS/MS and 2-D electrophoresis coupled with MALDI-TOF/MS and tandem mass spectrometry. Apolipoprotein E demonstrated an inverse significant association with lead concentrations (average being one microgram/deciliter) as deduced from LC-MS/MS and 2-D electrophoresis and confirmed by Western blot analysis. This coincides with prior findings that Apolipoprotein E genotype moderates neurobehavioral effects in individuals exposed to lead. Fifteen other proteins were identified by LC-MS/MS as proteins of interest exhibiting expressional differences in the presence of environmental lead and mercury.
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10
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Arruda SCC, Barbosa HDS, Azevedo RA, Arruda MAZ. Two-dimensional difference gel electrophoresis applied for analytical proteomics: fundamentals and applications to the study of plant proteomics. Analyst 2011; 136:4119-26. [DOI: 10.1039/c1an15513j] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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11
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Valledor L, Jorrín J. Back to the basics: Maximizing the information obtained by quantitative two dimensional gel electrophoresis analyses by an appropriate experimental design and statistical analyses. J Proteomics 2011; 74:1-18. [PMID: 20656082 DOI: 10.1016/j.jprot.2010.07.007] [Citation(s) in RCA: 124] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2010] [Revised: 07/13/2010] [Accepted: 07/15/2010] [Indexed: 10/19/2022]
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12
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Weist S, Brunkau C, Wittke J, Eravci M, Broedel O, Krause E, Stephanowitz H, Eravci S, Baumgartner A. Effects of thawing, refreezing and storage conditions of tissue samples and protein extracts on 2-DE spot intensity. Proteomics 2010; 10:1515-21. [PMID: 20127687 DOI: 10.1002/pmic.200900471] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
We report that reliable quantitative proteome analyses can be performed with tissue samples stored at -80 degrees C for up to 10 years. However, storing protein extracts at 4 degrees C for 24 h and freezing protein extracts at -80 degrees C and thawing them significantly altered 41.6 and 17.5% of all spot intensities on 2-DE gels, respectively. Fortunately, these storing effects did not impair the reliability of quantifying 2-DE experiments. Nonetheless, the results show that freezing and storage conditions should be carefully controlled in proteomic experiments.
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Affiliation(s)
- Stephanie Weist
- Department of Radiology and Nuclear Medicine (Radiochemistry), Charité Universitätsmedizin, Campus Benjamin Franklin, Berlin, Germany
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13
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Brandão AR, Barbosa HS, Arruda MAZ. Image analysis of two-dimensional gel electrophoresis for comparative proteomics of transgenic and non-transgenic soybean seeds. J Proteomics 2010; 73:1433-40. [PMID: 20123049 DOI: 10.1016/j.jprot.2010.01.009] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2009] [Revised: 01/08/2010] [Accepted: 01/16/2010] [Indexed: 11/28/2022]
Abstract
Considering the importance of bidimensional electrophoresis and image analysis in comparative proteomics, the parameters that influence the analysis of protein expression of transgenic and non-transgenic soybean seeds were evaluated. The loaded mass of the proteins (150-500 microg), the pH separation range (3-10 or 4-7), and manual/automatic image editing were evaluated. Additionally, after optimizing the conditions, histograms and matchings were obtained in order to accurately analyze the variations (90%) in protein expression. From this, 10 proteins displayed significant differences in expression, and eight of them were characterized and identified by mass spectrometry.
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Affiliation(s)
- A R Brandão
- Spectrometry, Sample Preparation and Mechanization Group-GEPAM, Institute of Chemistry, University of Campinas-UNICAMP, Campinas, SP, Brazil
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14
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Westermeier R, Schickle H. The current state of the art in high-resolution two-dimensional electrophoresis. Arch Physiol Biochem 2009; 115:279-85. [PMID: 19874117 DOI: 10.3109/13813450903338090] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The study of the "proteomes" of human cells, tissues, and body fluids is a big challenge, and several highly sophisticated workflow approaches are pursued to achieve as comprehensive information as possible. Initially proteome analysis was exclusively based on the gel-based workflow, employing two-dimensional electrophoresis of protein extracts followed by mass spectrometry of the tryptic peptide digests of protein spots. Meanwhile several additional proteomics workflows are applied, which are mostly based on separation and analysis of tryptic peptides without separating the protein mixture. However, direct information on quantitative and qualitative changes of protein expressions can only be obtained by methods operating on the protein level, no other method can replace two-dimensional electrophoresis. In this review we compile the different techniques of high-resolution two-dimensional electrophoresis and their further developments to increase the degree of reliance of the method.
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15
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Schröder S, Brandmüller A, Deng X, Ahmed A, Wätzig H. Improving precision in gel electrophoresis by stepwisely decreasing variance components. J Pharm Biomed Anal 2009; 50:320-7. [DOI: 10.1016/j.jpba.2009.04.034] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2009] [Revised: 04/27/2009] [Accepted: 04/29/2009] [Indexed: 11/30/2022]
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16
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Broedel O, Krause E, Stephanowitz H, Schuemann M, Eravci M, Weist S, Brunkau C, Wittke J, Eravci S, Baumgartner A. In-Gel 18O Labeling for Improved Identification of Proteins from 2-DE Gel Spots in Comparative Proteomic Experiments. J Proteome Res 2009; 8:3771-7. [DOI: 10.1021/pr8010765] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Oliver Broedel
- Department of Radiology and Nuclear Medicine (Radiochemistry), Charité Universitätsmedizin, Campus Benjamin Franklin, Berlin, Germany, A+M Proteome Science, Berlin, Germany, and Leibniz Institute for Molecular Pharmacology (FMP), Berlin, Germany
| | - Eberhard Krause
- Department of Radiology and Nuclear Medicine (Radiochemistry), Charité Universitätsmedizin, Campus Benjamin Franklin, Berlin, Germany, A+M Proteome Science, Berlin, Germany, and Leibniz Institute for Molecular Pharmacology (FMP), Berlin, Germany
| | - Heike Stephanowitz
- Department of Radiology and Nuclear Medicine (Radiochemistry), Charité Universitätsmedizin, Campus Benjamin Franklin, Berlin, Germany, A+M Proteome Science, Berlin, Germany, and Leibniz Institute for Molecular Pharmacology (FMP), Berlin, Germany
| | - Michael Schuemann
- Department of Radiology and Nuclear Medicine (Radiochemistry), Charité Universitätsmedizin, Campus Benjamin Franklin, Berlin, Germany, A+M Proteome Science, Berlin, Germany, and Leibniz Institute for Molecular Pharmacology (FMP), Berlin, Germany
| | - Murat Eravci
- Department of Radiology and Nuclear Medicine (Radiochemistry), Charité Universitätsmedizin, Campus Benjamin Franklin, Berlin, Germany, A+M Proteome Science, Berlin, Germany, and Leibniz Institute for Molecular Pharmacology (FMP), Berlin, Germany
| | - Stephanie Weist
- Department of Radiology and Nuclear Medicine (Radiochemistry), Charité Universitätsmedizin, Campus Benjamin Franklin, Berlin, Germany, A+M Proteome Science, Berlin, Germany, and Leibniz Institute for Molecular Pharmacology (FMP), Berlin, Germany
| | - Cindy Brunkau
- Department of Radiology and Nuclear Medicine (Radiochemistry), Charité Universitätsmedizin, Campus Benjamin Franklin, Berlin, Germany, A+M Proteome Science, Berlin, Germany, and Leibniz Institute for Molecular Pharmacology (FMP), Berlin, Germany
| | - Janosch Wittke
- Department of Radiology and Nuclear Medicine (Radiochemistry), Charité Universitätsmedizin, Campus Benjamin Franklin, Berlin, Germany, A+M Proteome Science, Berlin, Germany, and Leibniz Institute for Molecular Pharmacology (FMP), Berlin, Germany
| | - Selda Eravci
- Department of Radiology and Nuclear Medicine (Radiochemistry), Charité Universitätsmedizin, Campus Benjamin Franklin, Berlin, Germany, A+M Proteome Science, Berlin, Germany, and Leibniz Institute for Molecular Pharmacology (FMP), Berlin, Germany
| | - Andreas Baumgartner
- Department of Radiology and Nuclear Medicine (Radiochemistry), Charité Universitätsmedizin, Campus Benjamin Franklin, Berlin, Germany, A+M Proteome Science, Berlin, Germany, and Leibniz Institute for Molecular Pharmacology (FMP), Berlin, Germany
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17
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Eravci M, Mansmann U, Broedel O, Weist S, Buetow S, Wittke J, Brunkau C, Hummel M, Eravci S, Baumgartner A. Strategies for a Reliable Biostatistical Analysis of Differentially Expressed Spots from Two-Dimensional Electrophoresis Gels. J Proteome Res 2009; 8:2601-7. [DOI: 10.1021/pr800532f] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Murat Eravci
- Department of Radiology and Nuclear Medicine (Radiochemistry), Charité Universitätsmedizin, Campus Benjamin Franklin, Berlin, Germany, A+M Proteome Science, Berlin, Germany, and Department of Medical Informatics, Biometry and Epidemiology, University of Munich, Munich, Germany
| | - Ulrich Mansmann
- Department of Radiology and Nuclear Medicine (Radiochemistry), Charité Universitätsmedizin, Campus Benjamin Franklin, Berlin, Germany, A+M Proteome Science, Berlin, Germany, and Department of Medical Informatics, Biometry and Epidemiology, University of Munich, Munich, Germany
| | - Oliver Broedel
- Department of Radiology and Nuclear Medicine (Radiochemistry), Charité Universitätsmedizin, Campus Benjamin Franklin, Berlin, Germany, A+M Proteome Science, Berlin, Germany, and Department of Medical Informatics, Biometry and Epidemiology, University of Munich, Munich, Germany
| | - Stephanie Weist
- Department of Radiology and Nuclear Medicine (Radiochemistry), Charité Universitätsmedizin, Campus Benjamin Franklin, Berlin, Germany, A+M Proteome Science, Berlin, Germany, and Department of Medical Informatics, Biometry and Epidemiology, University of Munich, Munich, Germany
| | - Sandra Buetow
- Department of Radiology and Nuclear Medicine (Radiochemistry), Charité Universitätsmedizin, Campus Benjamin Franklin, Berlin, Germany, A+M Proteome Science, Berlin, Germany, and Department of Medical Informatics, Biometry and Epidemiology, University of Munich, Munich, Germany
| | - Janosch Wittke
- Department of Radiology and Nuclear Medicine (Radiochemistry), Charité Universitätsmedizin, Campus Benjamin Franklin, Berlin, Germany, A+M Proteome Science, Berlin, Germany, and Department of Medical Informatics, Biometry and Epidemiology, University of Munich, Munich, Germany
| | - Cindy Brunkau
- Department of Radiology and Nuclear Medicine (Radiochemistry), Charité Universitätsmedizin, Campus Benjamin Franklin, Berlin, Germany, A+M Proteome Science, Berlin, Germany, and Department of Medical Informatics, Biometry and Epidemiology, University of Munich, Munich, Germany
| | - Manuela Hummel
- Department of Radiology and Nuclear Medicine (Radiochemistry), Charité Universitätsmedizin, Campus Benjamin Franklin, Berlin, Germany, A+M Proteome Science, Berlin, Germany, and Department of Medical Informatics, Biometry and Epidemiology, University of Munich, Munich, Germany
| | - Selda Eravci
- Department of Radiology and Nuclear Medicine (Radiochemistry), Charité Universitätsmedizin, Campus Benjamin Franklin, Berlin, Germany, A+M Proteome Science, Berlin, Germany, and Department of Medical Informatics, Biometry and Epidemiology, University of Munich, Munich, Germany
| | - Andreas Baumgartner
- Department of Radiology and Nuclear Medicine (Radiochemistry), Charité Universitätsmedizin, Campus Benjamin Franklin, Berlin, Germany, A+M Proteome Science, Berlin, Germany, and Department of Medical Informatics, Biometry and Epidemiology, University of Munich, Munich, Germany
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18
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Garcia JS, Souza GHMF, Eberlin MN, Arruda MAZ. Evaluation of metal-ion stress in sunflower (Helianthus annuus L.) leaves through proteomic changes. Metallomics 2009. [DOI: 10.1039/b816146a] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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19
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Grussenmeyer T, Meili-Butz S, Dieterle T, Traunecker E, Carrel TP, Lefkovits I. Quantitative proteome analysis in cardiovascular physiology and pathology. I. Data processing. J Proteome Res 2008; 7:5211-20. [PMID: 19367704 DOI: 10.1021/pr8005292] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Methodological evaluation of the proteomic analysis of cardiovascular-tissue material has been performed with a special emphasis on establishing examinations that allow reliable quantitative analysis of silver-stained readouts. Reliability, reproducibility, robustness and linearity were addressed and clarified. In addition, several types of normalization procedures were evaluated and new approaches are proposed. It has been found that the silver-stained readout offers a convenient approach for quantitation if a linear range for gel loading is defined. In addition, a broad range of a 10-fold input (loading 20-200 microg per gel) fulfills the linearity criteria, although at the lowest input (20 microg) a portion of protein species will remain undetected. The method is reliable and reproducible within a range of 65-200 microg input. The normalization procedure using the sum of all spot intensities from a silver-stained 2D pattern has been shown to be less reliable than other approaches, namely, normalization through median or through involvement of interquartile range. A special refinement of the normalization through virtual segmentation of pattern, and calculation of normalization factor for each stratum provides highly satisfactory results. The presented results not only provide evidence for the usefulness of silver-stained gels for quantitative evaluation, but they are directly applicable to the research endeavor of monitoring alterations in cardiovascular pathophysiology.
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20
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Bandow JE, Baker JD, Berth M, Painter C, Sepulveda OJ, Clark KA, Kilty I, VanBogelen RA. Improved image analysis workflow for 2-D gels enables large-scale 2-D gel-based proteomics studies - COPD biomarker discovery study. Proteomics 2008; 8:3030-41. [DOI: 10.1002/pmic.200701184] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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21
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Weist S, Eravci M, Broedel O, Fuxius S, Eravci S, Baumgartner A. Results and reliability of protein quantification for two-dimensional gel electrophoresis strongly depend on the type of protein sample and the method employed. Proteomics 2008; 8:3389-96. [DOI: 10.1002/pmic.200800236] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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22
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Fuxius S, Eravci M, Broedel O, Weist S, Mansmann U, Eravci S, Baumgartner A. Technical strategies to reduce the amount of “false significant” results in quantitative proteomics. Proteomics 2008; 8:1780-4. [DOI: 10.1002/pmic.200701074] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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23
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Ge Y, Preston RJ, Owen RD. Toxicoproteomics and its application to human health risk assessment. Proteomics Clin Appl 2007; 1:1613-24. [DOI: 10.1002/prca.200700490] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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24
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Berth M, Moser FM, Kolbe M, Bernhardt J. The state of the art in the analysis of two-dimensional gel electrophoresis images. Appl Microbiol Biotechnol 2007; 76:1223-43. [PMID: 17713763 PMCID: PMC2279157 DOI: 10.1007/s00253-007-1128-0] [Citation(s) in RCA: 140] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2007] [Revised: 07/13/2007] [Accepted: 07/14/2007] [Indexed: 11/21/2022]
Abstract
Software-based image analysis is a crucial step in the biological interpretation of two-dimensional gel electrophoresis experiments. Recent significant advances in image processing methods combined with powerful computing hardware have enabled the routine analysis of large experiments. We cover the process starting with the imaging of 2-D gels, quantitation of spots, creation of expression profiles to statistical expression analysis followed by the presentation of results. Challenges for analysis software as well as good practices are highlighted. We emphasize image warping and related methods that are able to overcome the difficulties that are due to varying migration positions of spots between gels. Spot detection, quantitation, normalization, and the creation of expression profiles are described in detail. The recent development of consensus spot patterns and complete expression profiles enables one to take full advantage of statistical methods for expression analysis that are well established for the analysis of DNA microarray experiments. We close with an overview of visualization and presentation methods (proteome maps) and current challenges in the field.
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Affiliation(s)
- Matthias Berth
- DECODON GmbH, Rathenau-Strasse 49a, 17489 Greifswald, Germany
| | | | - Markus Kolbe
- DECODON GmbH, Rathenau-Strasse 49a, 17489 Greifswald, Germany
| | - Jörg Bernhardt
- DECODON GmbH, Rathenau-Strasse 49a, 17489 Greifswald, Germany
- Institute of Microbiology, Greifswald University, Jahnstrasse 15, 17487 Greifswald, Germany
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