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Hammerling U, Tallsjö A, Grafström R, Ilbäck NG. Comparative Hazard Characterization in Food Toxicology. Crit Rev Food Sci Nutr 2009; 49:626-69. [DOI: 10.1080/10408390802145617] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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102
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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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103
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Malm C, Hadrevi J, Bergström S, Pedrosa‐Domellöf F, Antti H, Svensson M, Frängsmyr L. Evaluation of 2‐D DIGE for skeletal muscle: Protocol and repeatability. Scandinavian Journal of Clinical and Laboratory Investigation 2009; 68:793-800. [DOI: 10.1080/00365510802277464] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Christer Malm
- Umeå University, Department of Integrative Medical Biology, Section for Anatomy, Umeå, Sweden
- Winternet, Boden, Sweden
| | - Jenny Hadrevi
- Umeå University, Department of Integrative Medical Biology, Section for Anatomy, Umeå, Sweden
- Centre for Musculoskeletal Research, University of Gävle, Umeå, Sweden
| | - Sven‐Anders Bergström
- Umeå University, Department of Public Health and Clinical Medicine, Section for Medicine, Umeå, Sweden
| | - Fatima Pedrosa‐Domellöf
- Umeå University, Department of Integrative Medical Biology, Section for Anatomy, Umeå, Sweden
| | - Henrik Antti
- Umeå University, Department of Chemistry, Section for Organic Chemistry, Umeå, Sweden
| | - Michael Svensson
- Umeå University, Department of Surgical and Preoperative Sciences, Section for Sports Medicine, Umeå, Sweden
| | - Lars Frängsmyr
- Umeå University, Department of Integrative Medical Biology, Section for Anatomy, Umeå, Sweden
- Umeå University, Department of Surgical and Preoperative Sciences, Section for Sports Medicine, Umeå, Sweden
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Two-dimensional electrophoresis: an overview. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2009; 519:1-16. [PMID: 19381573 DOI: 10.1007/978-1-59745-281-6_1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Two-dimensional gel electrophoresis (2DE) separates proteins by molecular charge and molecular size. Proteins are first solubilised in a denaturing buffer containing a neutral chaotrope, a zwitterionic or neutral detergent, and a reducing agent. First-dimension isoelectric keywords, focusing, then subjects proteins to a high voltage within a pH gradient. The amphoteric nature of proteins means each migrates to the pH where the net molecular charge is zero. After equilibration, to ensure complete protein unfolding, the second dimension separates by molecular size. Each protein is therefore resolved at a unique isoelectric point/molecular size coordinate. After visualisation by staining proteome changes are revealed by gel image analysis, and protein spots of interest excised and identified by mass spectrometry sequence analysis combined with database comparison. Variations to this procedure include staining or radio-labelling prior to electrophoresis. Although 2DE does have limitations, the most significant being the resolution of membrane and/or hydrophobic proteins, the potential solutions offered by pre-fractionation or adjustments to the electrophoresis regimen mean this technique is likely to remain central to proteomic research.
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105
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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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A comparative study of different dyes for the detection of proteomes derived from Escherichia coli and MDCK cells: Sensitivity and selectivity. J Chromatogr B Analyt Technol Biomed Life Sci 2009; 877:1433-9. [DOI: 10.1016/j.jchromb.2009.03.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2008] [Revised: 02/28/2009] [Accepted: 03/09/2009] [Indexed: 11/22/2022]
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107
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Rapid, antibody-free detection of recombinant proteins on blots using enzyme fragment complementation. Methods Mol Biol 2009. [PMID: 19378077 DOI: 10.1007/978-1-59745-542-8_40] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Alternative, antibody-free techniques to western analysis of protein blots can offer reduced assay times for routine analysis of expression of recombinant proteins. We have adapted the commercially available enzyme fragment complementation technology to provide a rapid protein detection method for protein blots based on significantly reducing the number of incubation and washing steps used in traditional approaches, and eliminating the requirement for antibodies. In this article, we highlight the use of this assay for measuring recombinant protein expressed in mammalian cells for a range of applications, including dot blot screening of large numbers of different cell samples, assessment of protein integrity through detection of degradation bands, and characterization of post-translational protein modifications such as glycosylation.
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Nebrich G, Herrmann M, Hartl D, Diedrich M, Kreitler T, Wierling C, Klose J, Giavalisco P, Zabel C, Mao L. PROTEOMER: A workflow-optimized laboratory information management system for 2-D electrophoresis-centered proteomics. Proteomics 2009; 9:1795-808. [DOI: 10.1002/pmic.200800522] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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109
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Wang H, Straubinger RM, Aletta JM, Cao J, Duan X, Yu H, Qu J. Accurate localization and relative quantification of arginine methylation using nanoflow liquid chromatography coupled to electron transfer dissociation and orbitrap mass spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2009; 20:507-19. [PMID: 19110445 PMCID: PMC3351756 DOI: 10.1016/j.jasms.2008.11.008] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2008] [Revised: 11/12/2008] [Accepted: 11/13/2008] [Indexed: 05/21/2023]
Abstract
Protein arginine (Arg) methylation serves an important functional role in eucaryotic cells, and typically occurs in domains consisting of multiple Arg in close proximity. Localization of methylarginine (MA) within Arg-rich domains poses a challenge for mass spectrometry (MS)-based methods; the peptides are highly charged under electrospray ionization (ESI), which limits the number of sequence-informative products produced by collision induced dissociation (CID), and loss of the labile methylation moieties during CID precludes effective fragmentation of the peptide backbone. Here the fragmentation behavior of Arg-rich peptides was investigated comprehensively using electron-transfer dissociation (ETD) and CID for both methylated and unmodified glycine-/Arg-rich peptides (GAR), derived from residues 679-695 of human nucleolin, which contains methylation motifs that are widely-represented in biological systems. ETD produced abundant information for sequencing and MA localization, whereas CID failed to provide credible identification for any available charge state (z = 2-4). Nevertheless, CID produced characteristic neutral losses that can be employed to distinguish among different types of MA, as suggested by previous works and confirmed here with product ion scans of high accuracy/resolution by an LTQ/Orbitrap. To analyze MA-peptides in relatively complex mixtures, a method was developed that employs nano-LC coupled to alternating CID/ETD for peptide sequencing and MA localization/characterization, and an Orbitrap for accurate precursor measurement and relative quantification of MA-peptide stoichiometries. As proof of concept, GAR-peptides methylated in vitro by protein arginine N-methyltransferases PRMT1 and PRMT7 were analyzed. It was observed that PRMT1 generated a number of monomethylated (MMA) and asymmetric-dimethylated peptides, while PRMT7 produced predominantly MMA peptides and some symmetric-dimethylated peptides. This approach and the results may advance understanding of the actions of PRMTs and the functional significance of Arg methylation patterns.
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Affiliation(s)
- Hao Wang
- The Department of Pharmaceutical Sciences, University at Buffalo, State University of New York, Amherst, NY 14260-1200
- New York State Center of Excellence in Bioinformatics and Life Sciences, 701 Ellicott St, Buffalo, NY 14203
| | - Robert M. Straubinger
- The Department of Pharmaceutical Sciences, University at Buffalo, State University of New York, Amherst, NY 14260-1200
- New York State Center of Excellence in Bioinformatics and Life Sciences, 701 Ellicott St, Buffalo, NY 14203
| | - John M. Aletta
- New York State Center of Excellence in Bioinformatics and Life Sciences, 701 Ellicott St, Buffalo, NY 14203
- CH3 BioSystems LLC 1416 Sweet Home Road, Amherst, New York 14228-2784
| | - Jin Cao
- The Department of Pharmaceutical Sciences, University at Buffalo, State University of New York, Amherst, NY 14260-1200
| | - Xiaotao Duan
- The Department of Pharmaceutical Sciences, University at Buffalo, State University of New York, Amherst, NY 14260-1200
- New York State Center of Excellence in Bioinformatics and Life Sciences, 701 Ellicott St, Buffalo, NY 14203
| | - Haoying Yu
- The Department of Pharmaceutical Sciences, University at Buffalo, State University of New York, Amherst, NY 14260-1200
- New York State Center of Excellence in Bioinformatics and Life Sciences, 701 Ellicott St, Buffalo, NY 14203
| | - Jun Qu
- The Department of Pharmaceutical Sciences, University at Buffalo, State University of New York, Amherst, NY 14260-1200
- New York State Center of Excellence in Bioinformatics and Life Sciences, 701 Ellicott St, Buffalo, NY 14203
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Abstract
Posttranslational modifications (PTMs) of proteins perform crucial roles in regulating the biology of the cell. PTMs are enzymatic, covalent chemical modifications of proteins that typically occur after the translation of mRNAs. These modifications are relevant because they can potentially change a protein's physical or chemical properties, activity, localization, or stability. Some PTMs can be added and removed dynamically as a mechanism for reversibly controlling protein function and cell signaling. Extensive investigations have aimed to identify PTMs and characterize their biological functions. This chapter will discuss the existing and emerging techniques in the field of mass spectrometry and proteomics that are available to identify and quantify PTMs. We will focus on the most frequently studied modifications. In addition, we will include an overview of the available tools and technologies in tandem mass spectrometry instrumentation that affect the ability to identify specific PTMs.
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Affiliation(s)
- Adam R Farley
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
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111
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Abstract
Two-dimensional gel electrophoresis (2-DE) with immobilized pH gradients (IPGs) combined with protein identification by mass spectrometry is currently the workhorse for the majority of ongoing proteome projects. Although alternative/complementary technologies, such as MudPIT, ICAT, or protein arrays, have emerged recently, there is up to now no technology that matches 2-DE in its ability for routine parallel expression profiling of large sets of complex protein mixtures. 2-DE delivers a map of intact proteins, which reflects changes in protein expression level, isoforms, or post-translational modifications. High-resolution 2-DE can resolve up to 5,000 proteins simultaneously ( approximately 2,000 proteins routinely), and detect and quantify <1 ng of protein per spot. Today's 2-DE technology with IPGs has largely overcome the former limitations of carrier ampholyte-based 2-DE with respect to reproducibility, handling, resolution, and separation of very acidic or basic proteins. Current research to further advance 2-DE technology has focused on improved solubilization/separation of hydrophobic proteins, display of low abundance proteins, and reliable protein quantitation by fluorescent dye technologies. Here, we provide a comprehensive protocol of the current high-resolution 2-DE technology with IPGs for proteome analysis and describe in detail the individual steps of this technique, i.e., sample preparation and protein solubilization, isoelectric focusing in IPG strips, IPG strip equilibration, and casting and running of multiple SDS gels. Last but not the least, a section on how to circumvent the major pitfalls is included.
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113
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114
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Penque D. Two-dimensional gel electrophoresis and mass spectrometry for biomarker discovery. Proteomics Clin Appl 2008; 3:155-72. [DOI: 10.1002/prca.200800025] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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115
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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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116
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Hecker M, Antelmann H, Büttner K, Bernhardt J. Gel-based proteomics of Gram-positive bacteria: A powerful tool to address physiological questions. Proteomics 2008; 8:4958-75. [DOI: 10.1002/pmic.200800278] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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117
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Knudsen GM, Davis BM, Deb SK, Loethen Y, Gudihal R, Perera P, Ben-Amotz D, Davisson VJ. Quantification of isotope encoded proteins in 2-D gels using surface enhanced resonance Raman. Bioconjug Chem 2008; 19:2212-20. [PMID: 18925772 PMCID: PMC2654710 DOI: 10.1021/bc800325k] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A strategy for quantification of multiple protein isoforms from a complex sample background is demonstrated, combining isotopomeric rhodamine 6G (R6G) labels and surface-enhanced Raman in polyacrylamide matrix. The procedure involves isotope-encoding by lysine-labeling with (R6G) active ester reagents, isoform separation by 2-DGE, fluorescence quantification using internal standardization to water, and silver nanoparticle deposition followed by surface-enhanced Raman detection. R6G sample encoding and standardization enabled the determination of total protein concentration and the distribution of specific isoforms using the combined detection approach of water-referenced fluorescence spectral imaging and ratiometric quantification. A detection limit of approximately 13.5 picomolar R6G-labeled protein was determined for the surface-enhanced Raman in a gel matrix (15-fold lower than fluorescence). High quantification accuracies for small differences in protein populations at low nanogram abundance were demonstrated for human GMP synthetase (hGMPS) either as purified protein samples in a single-point determination mode (3% relative standard deviation, RSD%) or as HCT116 human cancer cellular lysate in an imaging application (with 16% RSD%). These results represent a prototype for future applications of isotopic surface-enhanced resonance Raman scatter to quantification of protein distributions.
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Affiliation(s)
- Giselle M. Knudsen
- Department of Medicinal Chemistry & Molecular Pharmacology and the Bindley Bioscience Center at Discovery Park, Purdue University, West Lafayette, IN 47907
| | - Brandon M. Davis
- Department of Chemistry, Purdue University, West Lafayette, IN 47907
| | - Shirshendu K. Deb
- Department of Medicinal Chemistry & Molecular Pharmacology and the Bindley Bioscience Center at Discovery Park, Purdue University, West Lafayette, IN 47907
| | - Yvette Loethen
- Department of Chemistry, Purdue University, West Lafayette, IN 47907
| | - Ravindra Gudihal
- Department of Medicinal Chemistry & Molecular Pharmacology and the Bindley Bioscience Center at Discovery Park, Purdue University, West Lafayette, IN 47907
| | - Pradeep Perera
- Department of Chemistry, Purdue University, West Lafayette, IN 47907
| | - Dor Ben-Amotz
- Department of Chemistry, Purdue University, West Lafayette, IN 47907
| | - V. Jo Davisson
- Department of Medicinal Chemistry & Molecular Pharmacology and the Bindley Bioscience Center at Discovery Park, Purdue University, West Lafayette, IN 47907
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Roger E, Grunau C, Pierce RJ, Hirai H, Gourbal B, Galinier R, Emans R, Cesari IM, Cosseau C, Mitta G. Controlled chaos of polymorphic mucins in a metazoan parasite (Schistosoma mansoni) interacting with its invertebrate host (Biomphalaria glabrata). PLoS Negl Trop Dis 2008; 2:e330. [PMID: 19002242 PMCID: PMC2576457 DOI: 10.1371/journal.pntd.0000330] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2008] [Accepted: 10/10/2008] [Indexed: 01/21/2023] Open
Abstract
Invertebrates were long thought to possess only a simple, effective and hence non-adaptive defence system against microbial and parasitic attacks. However, recent studies have shown that invertebrate immunity also relies on immune receptors that diversify (e.g. in echinoderms, insects and mollusks (Biomphalaria glabrata)). Apparently, individual or population-based polymorphism-generating mechanisms exists that permit the survival of invertebrate species exposed to parasites. Consequently, the generally accepted arms race hypothesis predicts that molecular diversity and polymorphism also exist in parasites of invertebrates. We investigated the diversity and polymorphism of parasite molecules (Schistosoma mansoni Polymorphic Mucins, SmPoMucs) that are key factors for the compatibility of schistosomes interacting with their host, the mollusc Biomphalaria glabrata. We have elucidated the complex cascade of mechanisms acting both at the genomic level and during expression that confer polymorphism to SmPoMuc. We show that SmPoMuc is coded by a multi-gene family whose members frequently recombine. We show that these genes are transcribed in an individual-specific manner, and that for each gene, multiple splice variants exist. Finally, we reveal the impact of this polymorphism on the SmPoMuc glycosylation status. Our data support the view that S. mansoni has evolved a complex hierarchical system that efficiently generates a high degree of polymorphism—a “controlled chaos”—based on a relatively low number of genes. This contrasts with protozoan parasites that generate antigenic variation from large sets of genes such as Trypanosoma cruzi, Trypanosoma brucei and Plasmodium falciparum. Our data support the view that the interaction between parasites and their invertebrate hosts are far more complex than previously thought. While most studies in this matter have focused on invertebrate host diversification, we clearly show that diversifying mechanisms also exist on the parasite side of the interaction. Our findings shed new light on how and why invertebrate immunity develops. Contrary to the traditional view that immunity in invertebrates is limited to non-specific mechanisms, recent studies have shown that they have diverse, specific immune receptors. An example is provided by the FREPs of the mollusk Biomphalaria glabrata, polymorphic members of the immunoglobulin superfamily. This capacity for an individual or population-based polymorphic immune response raises the question of whether a corresponding polymorphism exists in parasites of invertebrates, as would be expected in an “arms race” between host and parasite. We have indeed identified such polymorphic molecules in Schistosoma mansoni, a flatworm parasite of B. glabrata, by comparing two strains of schistosome that are respectively compatible and incompatible with the same mollusk host strain. However, in contrast to antigenic variation in protozoan parasites that is based on an extensive gene repertoire, we show here that a high level of polymorphism in these S. mansoni polymorphic mucins (SmPoMucs) is generated from a low number of genes by a complex cascade of mechanisms, a “controlled chaos”.
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Affiliation(s)
- Emmanuel Roger
- Parasitologie Fonctionnelle et Evolutive, UMR 5244, CNRS Université de Perpignan, Perpignan, France
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119
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Nesatyy VJ, Suter MJF. Analysis of environmental stress response on the proteome level. MASS SPECTROMETRY REVIEWS 2008; 27:556-574. [PMID: 18553564 DOI: 10.1002/mas.20177] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Thousands of man-made chemicals are annually released into the environment by agriculture, transport, industries, and other human activities. In general, chemical analysis of environmental samples used to assess the pollution status of a specific ecosystem is complicated by the complexity of the mixture, and in some cases by the very low toxicity thresholds of chemicals present. In that sense, a proteomics approach, capable of detecting subtle changes in the level and structure of individual proteins within the whole proteome in response to the altered surroundings, has obvious applications in the field of ecotoxicology. In addition to identifying new protein biomarkers, it can also help to provide an insight into underlying mechanisms of toxicity. Despite being a comparatively new field with a number of caveats, proteomics applications have spread from microorganisms and plants to invertebrates and vertebrates, gradually becoming an established technology used in environmental research. This review article highlights recent advances in the field of environmental proteomics, mainly focusing on experimental approaches with a potential to understand toxic modes of action and to identify novel ecotoxicological biomarkers.
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Affiliation(s)
- Victor J Nesatyy
- Eawag-Swiss Federal Institute of Aquatic Science and Technology, Ueberlandstrasse 133, PO Box 611, 8600 Duebendorf, Switzerland
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120
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Lee CJ, Ariztia EV, Fishman DA. Conventional and Proteomic Technologies for the Detection of Early Stage Malignancies: Markers for Ovarian Cancer. Crit Rev Clin Lab Sci 2008; 44:87-114. [PMID: 17175521 DOI: 10.1080/10408360600778885] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Our understanding of the tumor microenvironment continues to evolve and allows for the identification of biomarkers that should detect the presence of early stage malignancies. Recent advances in computational analysis and biomedical technologies have come together to elucidate signatures associated with cancer and that are capable of identifying unique tumor-specific proteins. Within the tumor microenvironment, we continue to characterize the proteophysiology of the different steps associated with tumor progression. The urgent need for biomarkers accurately detecting early-stage epithelial ovarian cancer has prompted us, and others, to engage in a search for specific peptide signatures that may discriminate transformed cells from those of the normal ovarian microenvironment. This endeavor also provides new insights into the biology of the disease, which may not only be applicable to detection but may also help to initiate new therapies and optimize patient care.
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Affiliation(s)
- Catherine J Lee
- Department of Obstetrics and Gynecology, New York University School of Medicine, New York, New York 10016, USA
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121
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Manuel González-Buitrago J, Ferreira L, Del Carmen Muñiz M. Proteómica clínica y nuevos biomarcadores en los líquidos biológicos. Med Clin (Barc) 2008; 131:426-34. [DOI: 10.1157/13126219] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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122
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Filanoski B, Rastogi SK, Cameron A, Cameron E, Mishra NN, Maki W, Maki G. Non-enzymatic aqueous peroxyoxalate chemiluminescence immune detection using a CCD camera and a CMOS device. LUMINESCENCE 2008; 23:296-302. [DOI: 10.1002/bio.1033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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123
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Chakravarti B, Louie M, Ratanaprayul W, Raval A, Gallagher S, Chakravarti DN. A highly uniform UV transillumination imaging system for quantitative analysis of nucleic acids and proteins. Proteomics 2008; 8:1789-97. [PMID: 18398876 DOI: 10.1002/pmic.200700891] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The digital fluorescent imaging for documentation and analysis of gel electrophoretic separations of nucleic acids and proteins is widely used in quantitative biology. Most fluorescent stains used in postelectrophoretic analysis of proteins and nucleic acids have significant excitation peaks with UV light (300-365 nm), making midrange UV (UV-B) as the excitation source of choice. However, coupling quantitative CCD imaging with UV is difficult due to lack of uniformity found in typical UV transilluminators. The apparent amount of those macromolecules depends on the position of the gel band on the imaging surface of the transilluminator. Here, we report the development and validation of a highly uniform UV transillumination system. Using a novel high density lighting system containing a single lamp formed into a high density grid, an electronic ballast, a phosphor coating, and a bandpass filter to convert 254 nm light produced to 300-340 nm, uniformity of </=5% CV has been achieved, compared to >80% CV observed in typical UV transilluminators. This system has been used for the quantitative analysis of electrophoretically separated nucleic acids and proteins (CV</=8%) without uniformity correction by software, and continues to outperform typical transilluminators when a uniformity correction is applied.
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Schlautman JD, Rozek W, Stetler R, Mosley RL, Gendelman HE, Ciborowski P. Multidimensional protein fractionation using ProteomeLab PF 2D for profiling amyotrophic lateral sclerosis immunity: A preliminary report. Proteome Sci 2008; 6:26. [PMID: 18789151 PMCID: PMC2543004 DOI: 10.1186/1477-5956-6-26] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2008] [Accepted: 09/12/2008] [Indexed: 11/30/2022] Open
Abstract
Background The ProteomeLab™ PF 2D platform is a relatively new approach to global protein profiling. Herein, it was used for investigation of plasma proteome changes in amyotrophic lateral sclerosis (ALS) patients before and during immunization with glatiramer acetate (GA) in a clinical trial. Results The experimental design included immunoaffinity depletion of 12 most abundant proteins from plasma samples with the ProteomeLab™ IgY-12 LC10 column kit as first dimension separation, also referred to as immuno-partitioning. Second and third dimension separations of the enriched proteome were performed on the PF 2D platform utilizing 2D isoelectric focusing and RP-HPLC with the resulting fractions collected for analysis. 1D gel electrophoresis was added as a fourth dimension when sufficient protein was available. Protein identification from collected fractions was performed using nano-LC-MS/MS approach. Analysis of differences in the resulting two-dimensional maps of fractions obtained from the PF 2D and the ability to identify proteins from these fractions allowed sensitivity threshold measurements. Masked proteins in the PF 2D fractions are discussed. Conclusion We offer some insight into the strengths and limitations of this emerging proteomic platform.
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Affiliation(s)
- Joshua D Schlautman
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, USA.
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125
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Mao L, Dong H, Yang P, Zhou H, Huang X, Lin X, Kijlstra A. MALDI-TOF/TOF-MS reveals elevated serum haptoglobin and amyloid A in Behcet's disease. J Proteome Res 2008; 7:4500-7. [PMID: 18754684 DOI: 10.1021/pr800279m] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Behcet's disease (BD) is a multisystemic autoimmune disease with unclear etiology and pathogenesis. To screen aberrant serum proteins in BD, serum samples were obtained from eight male BD patients with active uveitis and eight male healthy volunteers with informed consent. The serum samples from active BD patients and normal controls were pooled. Highly abundant serum proteins (albumin and IgG) were depleted from these two samples using an affinity capture based kit. The obtained samples were subjected to two-dimensional gel electrophoresis (2-DE). Protein spots were visualized with the "blue silver" staining. Differently expressed proteins were subsequently identified by matrix-assisted laser desorption /ionization tandem time-of-flight mass spectrometry (MALDI-TOF/TOF-MS). Western blot and enzyme-linked immunosorbent assay (ELISA) were performed using the serum samples from 18 patients with active BD, 6 patients with inactive BD, 22 patients with Vogt-Koyanagi-Harada (VKH) syndrome, and 20 healthy volunteers to validate the results of 2-DE and MS. Proteomic profiles of the pooled samples were compared, and approximately 800 protein spots were observed in each of the gels. Expression levels of four of the protein spots in active BD were significantly higher than those in the normal controls. Mass spectrometric protein identification revealed that the four protein spots corresponded to two proteins: haptoglobin (Hp) and serum amyloid A (SAA). Western blot and ELISA showed that Hp was only overexpressed in active BD but not in inactive BD, VKH syndrome, or healthy controls. An obvious band of SAA was detected in 72.2% of the serum samples from BD patients, whereas a vague band of this protein was found in 10.0% of the tested normal samples and 9.1% of VKH samples. Our results revealed a significantly increased expression of Hp and SAA in serum of active BD patients. These two proteins may be involved in the development of BD.
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Affiliation(s)
- Liming Mao
- Zhongshan Ophthalmic Center, State Key Laboratory of Ophthalmology of Sun Yat-sen University, Guangzhou, P.R. China
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126
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Ebert B, Melle C, Lieckfeldt E, Zöller D, von Eggeling F, Fisahn J. Protein profiling of single epidermal cell types from Arabidopsis thaliana using surface-enhanced laser desorption and ionization technology. JOURNAL OF PLANT PHYSIOLOGY 2008; 165:1227-37. [PMID: 18423788 DOI: 10.1016/j.jplph.2008.01.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2007] [Revised: 01/22/2008] [Accepted: 01/25/2008] [Indexed: 05/24/2023]
Abstract
Here, we describe a novel approach for investigating differential protein expression within three epidermal cell types. In particular, 3000 single pavement, basal, and trichome cells from leaves of Arabidopsis thaliana were harvested by glass micro-capillaries. Subsequently, these single cell samples were joined to form pools of 100 individual cells and analyzed using the ProteinChip technology; SELDI: surface-enhanced laser desorption and ionization. As a result, numerous protein signals that were differentially expressed in the three epidermal cell types could be detected. One of these proteins was characterized by tryptical digestion and subsequent identification via tandem quadrupole-time of flight (Q-TOF) mass spectrometry. Down regulation of this sequenced small subunit precursor of ribulose-1,5 bisphosphate carboxylase(C) oxygenase(O) (RuBisCo) in trichome and basal cells indicates the sink status of these cell types that are located on the surface of A. thaliana source leaves. Based on the obtained protein profiles, we suggest a close functional relationship between basal and trichome cells at the protein level.
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Affiliation(s)
- Berit Ebert
- Max-Planck-Institute of Molecular Plant Physiology, 14776 Potsdam OT Golm, Germany
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127
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Seo J, Suh MS, Thangadurai TD, Kim J, Rhee YH, Yoon HJ, Shin SK. Mass-Balanced 1H/2H Isotope Dipeptide Tag for Simultaneous Protein Quantitation and Identification. Anal Chem 2008; 80:6145-53. [DOI: 10.1021/ac801007y] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jongcheol Seo
- Bio-Nanotechnology Center, Department of Chemistry, Pohang University of Science and Technology, San31 Hyojadong Namgu, Pohang, Korea 790-784
| | - Min-Soo Suh
- Bio-Nanotechnology Center, Department of Chemistry, Pohang University of Science and Technology, San31 Hyojadong Namgu, Pohang, Korea 790-784
| | - T. Daniel Thangadurai
- Bio-Nanotechnology Center, Department of Chemistry, Pohang University of Science and Technology, San31 Hyojadong Namgu, Pohang, Korea 790-784
| | - Jinhee Kim
- Bio-Nanotechnology Center, Department of Chemistry, Pohang University of Science and Technology, San31 Hyojadong Namgu, Pohang, Korea 790-784
| | - Young Ho Rhee
- Bio-Nanotechnology Center, Department of Chemistry, Pohang University of Science and Technology, San31 Hyojadong Namgu, Pohang, Korea 790-784
| | - Hye-Joo Yoon
- Bio-Nanotechnology Center, Department of Chemistry, Pohang University of Science and Technology, San31 Hyojadong Namgu, Pohang, Korea 790-784
| | - Seung Koo Shin
- Bio-Nanotechnology Center, Department of Chemistry, Pohang University of Science and Technology, San31 Hyojadong Namgu, Pohang, Korea 790-784
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128
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Meier RJ, Steiner MS, Duerkop A, Wolfbeis OS. SDS-PAGE of proteins using a chameleon-type of fluorescent prestain. Anal Chem 2008; 80:6274-9. [PMID: 18616346 DOI: 10.1021/ac800581v] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A new prestaining method for protein SDS-PAGE was developed using the fluorogenic amino-reactive label Py-1. This resulted in one of the fastest, most sensitive, and environmentally friendly protocols available. It is mainly due to the unique optical properties of Py-1, which is blue and virtually nonfluorescent but turns to red and becomes much more strongly fluorescent once it is conjugated to the amino group of a protein. Staining times of 30 min are adequate to visualize subnanogram quantities of proteins because pre-electrophoretic labeling Py-1 does not require the time-consuming steps of washing or fixation of gels. LODs as low as 16 pg of protein are found which is better than the best (commercial) poststains and comparable to the best (commercial) prestains. In addition, prestaining requires marginal amounts of staining solution. The change in electrophoretic mobility and band broadening is at a low level because Py-1 causes a mass shift of 288 Da per bound molecule only. By virtue of the small mass shift it causes, this stain is compatible with mass spectrometric protein analysis even though it acts as a covalent label.
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Affiliation(s)
- Robert J Meier
- Institute of Analytical Chemistry, Chemo- and Biosensors, University of Regensburg, D-93040 Regensburg, Germany
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129
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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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130
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Gutstein HB, Morris JS, Annangudi SP, Sweedler JV. Microproteomics: analysis of protein diversity in small samples. MASS SPECTROMETRY REVIEWS 2008; 27:316-30. [PMID: 18271009 PMCID: PMC2743962 DOI: 10.1002/mas.20161] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Proteomics, the large-scale study of protein expression in organisms, offers the potential to evaluate global changes in protein expression and their post-translational modifications that take place in response to normal or pathological stimuli. One challenge has been the requirement for substantial amounts of tissue in order to perform comprehensive proteomic characterization. In heterogeneous tissues, such as brain, this has limited the application of proteomic methodologies. Efforts to adapt standard methods of tissue sampling, protein extraction, arraying, and identification are reviewed, with an emphasis on those appropriate to smaller samples ranging in size from several microliters down to single cells. The effects of miniaturization on these analyses are highlighted using neuroscience-related examples, as are statistical issues unique to the high-dimensional datasets generated by proteomic experiments.
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Affiliation(s)
- Howard B Gutstein
- Department of Anesthesiology, University of Texas-MD Anderson Cancer Center, 1515 Holcombe Blvd., Box 110, Houston, TX 77030-4009, USA.
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131
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Chakravarti B, Ratanaprayul W, Dalal N, Chakravarti DN. Comparison of SYPRO Ruby and Deep Purple Using Commonly Available UV Transilluminator: Wide-Scale Application in Proteomic Research. J Proteome Res 2008; 7:2797-802. [DOI: 10.1021/pr7007225] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Bulbul Chakravarti
- Keck Graduate Institute of Applied Life Science, 535 Watson Drive, Claremont, California 91711
| | - Wongrat Ratanaprayul
- Keck Graduate Institute of Applied Life Science, 535 Watson Drive, Claremont, California 91711
| | - Neville Dalal
- Keck Graduate Institute of Applied Life Science, 535 Watson Drive, Claremont, California 91711
| | - Deb N. Chakravarti
- Keck Graduate Institute of Applied Life Science, 535 Watson Drive, Claremont, California 91711
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132
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Schiffer E, Mischak H, Vanholder RC. Biomarkers for Renal Disease and Uremic Toxins. Clin Proteomics 2008. [DOI: 10.1002/9783527622153.ch25] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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133
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134
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Liu J, Liu X, Baeyens WRG, Delanghe JR, Ouyang J. A Novel Probe Au(III) for Chemiluminescent Image Detection of Protein Blots on Nitrocellulose Membranes. J Proteome Res 2008; 7:1884-90. [DOI: 10.1021/pr700616u] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jia Liu
- College of Chemistry, Beijing Normal University, Beijing 100875, P. R. China, Department of Pharmaceutical Analysis, Faculty of Pharmaceutical Sciences, Ghent University, Harelbekestraat 72, B-9000 Ghent, Belgium, and Department of Clinical Chemistry, Microbiology and Immunology, Ghent University Hospital, De Pintelaan 185, B-9000 Ghent, Belgium
| | - Xia Liu
- College of Chemistry, Beijing Normal University, Beijing 100875, P. R. China, Department of Pharmaceutical Analysis, Faculty of Pharmaceutical Sciences, Ghent University, Harelbekestraat 72, B-9000 Ghent, Belgium, and Department of Clinical Chemistry, Microbiology and Immunology, Ghent University Hospital, De Pintelaan 185, B-9000 Ghent, Belgium
| | - Willy R. G. Baeyens
- College of Chemistry, Beijing Normal University, Beijing 100875, P. R. China, Department of Pharmaceutical Analysis, Faculty of Pharmaceutical Sciences, Ghent University, Harelbekestraat 72, B-9000 Ghent, Belgium, and Department of Clinical Chemistry, Microbiology and Immunology, Ghent University Hospital, De Pintelaan 185, B-9000 Ghent, Belgium
| | - Joris R. Delanghe
- College of Chemistry, Beijing Normal University, Beijing 100875, P. R. China, Department of Pharmaceutical Analysis, Faculty of Pharmaceutical Sciences, Ghent University, Harelbekestraat 72, B-9000 Ghent, Belgium, and Department of Clinical Chemistry, Microbiology and Immunology, Ghent University Hospital, De Pintelaan 185, B-9000 Ghent, Belgium
| | - Jin Ouyang
- College of Chemistry, Beijing Normal University, Beijing 100875, P. R. China, Department of Pharmaceutical Analysis, Faculty of Pharmaceutical Sciences, Ghent University, Harelbekestraat 72, B-9000 Ghent, Belgium, and Department of Clinical Chemistry, Microbiology and Immunology, Ghent University Hospital, De Pintelaan 185, B-9000 Ghent, Belgium
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135
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Smrz D, Lebduska P, Dráberová L, Korb J, Dráber P. Engagement of phospholipid scramblase 1 in activated cells: implication for phosphatidylserine externalization and exocytosis. J Biol Chem 2008; 283:10904-18. [PMID: 18281686 DOI: 10.1074/jbc.m710386200] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Phosphatidylserine (PS) in quiescent cells is predominantly confined to the inner leaflet of the plasma membrane. Externalization of PS is a marker of apoptosis, exocytosis, and some nonapoptotic activation events. It has been proposed that PS externalization is regulated by the activity of PLSCR1 (phospholipid scramblase 1), a Ca(2+)-dependent endofacial plasma membrane protein, which is tyrosine-phosphorylated in activated cells. It is, however, unclear how the phosphorylation of PLSCR1 is related to its membrane topography, PS externalization, and exocytosis. Using rat basophilic leukemia cells as a model, we show that nonapoptotic PS externalization induced through the high affinity IgE receptor (FcepsilonRI) or the glycosylphosphatidylinositol-anchored protein Thy-1 does not correlate with enhanced tyrosine phosphorylation of PLSCR1. In addition, PS externalization in FcepsilonRI- or Thy-1-activated cells is not associated with alterations of PLSCR1 fine topography as detected by electron microscopy on isolated plasma membrane sheets. In contrast, activation by calcium ionophore A23187 induces changes in the cellular distribution of PLSCR1. We also show for the first time that in pervanadate-activated cells, exocytosis occurs even in the absence of PS externalization. Finally, we document here that tyrosine-phosphorylated PLSCR1 is preferentially located in detergent-insoluble membranes, suggesting its involvement in the formation of membrane-bound signaling assemblies. The combined data indicate that changes in the topography of PLSCR1 and its tyrosine phosphorylation, PS externalization, and exocytosis are independent phenomena that could be distinguished by employing specific conditions of activation.
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Affiliation(s)
- Daniel Smrz
- Department of Signal Transduction, Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, CZ 14220 Prague 4, Czech Republic
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136
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Liu J, Ouyang J, Baeyens WRG, Delanghe JR, Wang Z, Liu J, Zhang H. A novel probe for chemiluminescent image detection of proteins in two-dimensional gel electrophoresis. Electrophoresis 2008; 29:716-25. [DOI: 10.1002/elps.200700424] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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137
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Schröder S, Zhang H, Yeung ES, Jänsch L, Zabel C, Wätzig H. Quantitative Gel Electrophoresis: Sources of Variation. J Proteome Res 2008; 7:1226-34. [DOI: 10.1021/pr700589s] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Simone Schröder
- Institute of Pharmaceutical Chemistry, TU Braunschweig, Beethovenstrasse 55, 38106 Braunschweig, Germany, Iowa State University, Ames, Iowa, 50011, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, 38124 Braunschweig, Germany, and Institute for Human Genetics, Charité−University Medicine Berlin, Augustenburger Platz 1, 13353 Berlin, Germany
| | - Hui Zhang
- Institute of Pharmaceutical Chemistry, TU Braunschweig, Beethovenstrasse 55, 38106 Braunschweig, Germany, Iowa State University, Ames, Iowa, 50011, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, 38124 Braunschweig, Germany, and Institute for Human Genetics, Charité−University Medicine Berlin, Augustenburger Platz 1, 13353 Berlin, Germany
| | - Edward S. Yeung
- Institute of Pharmaceutical Chemistry, TU Braunschweig, Beethovenstrasse 55, 38106 Braunschweig, Germany, Iowa State University, Ames, Iowa, 50011, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, 38124 Braunschweig, Germany, and Institute for Human Genetics, Charité−University Medicine Berlin, Augustenburger Platz 1, 13353 Berlin, Germany
| | - Lothar Jänsch
- Institute of Pharmaceutical Chemistry, TU Braunschweig, Beethovenstrasse 55, 38106 Braunschweig, Germany, Iowa State University, Ames, Iowa, 50011, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, 38124 Braunschweig, Germany, and Institute for Human Genetics, Charité−University Medicine Berlin, Augustenburger Platz 1, 13353 Berlin, Germany
| | - Claus Zabel
- Institute of Pharmaceutical Chemistry, TU Braunschweig, Beethovenstrasse 55, 38106 Braunschweig, Germany, Iowa State University, Ames, Iowa, 50011, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, 38124 Braunschweig, Germany, and Institute for Human Genetics, Charité−University Medicine Berlin, Augustenburger Platz 1, 13353 Berlin, Germany
| | - Hermann Wätzig
- Institute of Pharmaceutical Chemistry, TU Braunschweig, Beethovenstrasse 55, 38106 Braunschweig, Germany, Iowa State University, Ames, Iowa, 50011, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, 38124 Braunschweig, Germany, and Institute for Human Genetics, Charité−University Medicine Berlin, Augustenburger Platz 1, 13353 Berlin, Germany
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138
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139
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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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140
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Loethen YL, Knudsen GM, Davis B, Gudihal R, Davisson VJ, Ben-Amotz D. Protein Quantitation in 2-D Gels Using Fluorescence with Water Raman as an Internal Standard. J Proteome Res 2007; 7:1341-5. [PMID: 18088088 DOI: 10.1021/pr0704579] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Yvette L. Loethen
- Department of Chemistry and Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana
| | - Giselle M. Knudsen
- Department of Chemistry and Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana
| | - Brandon Davis
- Department of Chemistry and Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana
| | - Ravindra Gudihal
- Department of Chemistry and Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana
| | - V. Jo Davisson
- Department of Chemistry and Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana
| | - Dor Ben-Amotz
- Department of Chemistry and Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana
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141
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Roger E, Mitta G, Moné Y, Bouchut A, Rognon A, Grunau C, Boissier J, Théron A, Gourbal BEF. Molecular determinants of compatibility polymorphism in the Biomphalaria glabrata/Schistosoma mansoni model: new candidates identified by a global comparative proteomics approach. Mol Biochem Parasitol 2007; 157:205-16. [PMID: 18083248 DOI: 10.1016/j.molbiopara.2007.11.003] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2007] [Revised: 10/23/2007] [Accepted: 11/02/2007] [Indexed: 10/22/2022]
Abstract
The co-evolutionary dynamics that exist in host-parasite interactions sometimes lead to compatibility polymorphisms, the molecular bases of which are rarely investigated. To identify key molecules that are involved in this phenomenon in the Schistosoma mansoni/Biomphalaria glabrata model, we developed a comparative proteomics approach using the larval stages that interact with the invertebrate host. We used qualitative and quantitative analyses to compare the total proteomes of primary sporocysts from compatible and incompatible parasite strains. The differentially expressed proteins thus detected belong to three main functional groups: (i) scavengers of reactive oxygen species, (ii) components of primary metabolism, and (iii) mucin-like proteins. We discuss the putative roles played by these protein families as determinants of compatibility polymorphism. Since mucins are known to play key roles in the host-parasite interplay, we consider the newly discovered S. mansoni mucin-like proteins (SmMucin-like) as the most promising candidates for influencing the fate of host-parasite interactions. An analysis of their expression is presented in a paper published in the same journal issue.
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Affiliation(s)
- Emmanuel Roger
- Parasitologie Fonctionnelle et Evolutive, UMR 5244, CNRS, EPHE, UPVD, Biologie & Ecologie Tropicale et Méditerranéenne, Université de Perpignan, Perpignan Cedex, France
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142
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New technologies around biomarkers and their interplay with drug development. Anal Bioanal Chem 2007; 390:141-54. [PMID: 17987283 DOI: 10.1007/s00216-007-1688-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2007] [Revised: 10/07/2007] [Accepted: 10/08/2007] [Indexed: 12/25/2022]
Abstract
What conductors are to their orchestras, biomarkers are to their associated technologies. Building fundamental science, supporting early diagnosis of diseases and following their progression, improving efficacy and safety of treatments, optimizing patient selection and adapting dosing of drugs, helping decide which therapy is most appropriate; these are examples of a few contexts in which biomarkers are key players. Technology development can definitely not escape being associated with these steps. In other words, today's biomarkers are the thermometers of tomorrow's therapies. This review provides an overview of recently established platforms as well as new and upcoming technologies for biomarker development in the context of drug development. The roles as well as the pros and cons of different disciplines such as genetics, genomics, proteomics, metabonomics, and assay development will be discussed.
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143
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Assiddiq BF, Williamson JC, Snijders APL, Cook K, Dickman MJ. Multidimensional liquid phase protein separations in conjunction with stable isotope labelling for quantitative proteomics. Proteomics 2007; 7:3826-34. [DOI: 10.1002/pmic.200700367] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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144
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Smith JR, Olivier M, Greene AS. Relative quantification of peptide phosphorylation in a complex mixture using 18O labeling. Physiol Genomics 2007; 31:357-63. [PMID: 17684036 PMCID: PMC2771636 DOI: 10.1152/physiolgenomics.00096.2007] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
We have developed a method to determine the degree of phosphorylation of a peptide in a complex mixture without enrichment or operation of the mass spectrometer in negative ion mode. Yeast lysate containing known amounts of synthetic peptides (VPQLEIVPNSAEERLHSMK and VPQLEIVPN[pS]AEERLHSMK) was labeled with (16)O and (18)O during hydrolysis. After treatment of one sample with a cocktail of phosphatases, the two samples were pooled. The intensity of the dephosphorylated peptide peaks was used to infer the degree of phosphorylation present before treatment. The linear dynamic range of this method is >10-fold before either of the peptide envelopes becomes indistinguishable from the surrounding noise. Since both the site of posttranslational modification and the proportion of the protein population that is modified are vital in protein function, the employment of this technique will provide a valuable tool for the analysis of the functional implications of protein phosphorylation.
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Affiliation(s)
- Julia R Smith
- Biotechnology and Bioengineering Center, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
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145
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Nesatyy VJ, Suter MJF. Proteomics for the analysis of environmental stress responses in organisms. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2007; 41:6891-6900. [PMID: 17993125 DOI: 10.1021/es070561r] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Thousands of man-made chemicals are constantly released into the environment by agricultural and industrial production processes, traffic, and countless other human activities. Hence, very complex mixtures of anthropogenic chemicals and the transformation products of non-persistent compounds can be found in the aquatic environment. They reflect regional input but are also influenced by long-range transport. Thus, predicting effects on organisms and assessing the quality of a specific ecosystem based on chemical analysis is a challenge. This is not only because of the wide variety of chemicals, with far ranging physicochemical properties, but also because of the sometimes very low effect levels and concerted effects caused by concentration additivity or even synergism. The situation is further complicated by the temporal variability of the exposure concentrations caused, for example, by rain events or regular daily fluctuations as seen in wastewater treatment plant effluents. The analysis of an organism's proteome allows the detection of subtle changes in the level of individual proteins in response to environmental stressors. This potentially leads to the discovery of biomarkers of exposure and helps to gain insights into underlying mechanisms of toxicity. Today, studies using environmental proteomics have investigated many organisms, ranging from microorganisms and plants to invertebrates and vertebrates. Nevertheless, proteomics is a field of environmental research still in its infancy, due to a number of caveats, such as the limited number of organisms fully covered in the sequence databases, the high genetic variability, and the dependence on environmental factors. However, it is gradually becoming an established technology. This review article highlights recent advances in the field of proteomics, mainly focusing on experimental techniques that have the potential to help us understand toxic modes of action and identify novel ecotoxicological biomarkers.
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Affiliation(s)
- Victor J Nesatyy
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Ueberlandstrasse 133, PO Box 611, 8600 Duebendorf, Switzerland
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146
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Abstract
Proteomics holds the promise of evaluating global changes in protein expression and post-translational modification in response to environmental stimuli. However, difficulties in achieving cellular anatomic resolution and extracting specific types of proteins from cells have limited the efficacy of these techniques. Laser capture microdissection has provided a solution to the problem of anatomical resolution in tissues. New extraction methodologies have expanded the range of proteins identified in subsequent analyses. This review will examine the application of laser capture microdissection to proteomic tissue sampling, and subsequent extraction of these samples for differential expression analysis. Statistical and other quantitative issues important for the analysis of the highly complex datasets generated are also reviewed.
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Affiliation(s)
- Howard B Gutstein
- MD Anderson Cancer Center, 1515 Holcombe Blvd, Box 110, Houston, TX 77030-4009, USA.
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147
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Aspinall-O'Dea M, Costello E. The pancreatic cancer proteome - recent advances and future promise. Proteomics Clin Appl 2007; 1:1066-79. [DOI: 10.1002/prca.200700144] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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148
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Nebrich G, Herrmann M, Sagi D, Klose J, Giavalisco P. High MS-compatibility of silver nitrate-stained protein spots from 2-DE gels using ZipPlates and AnchorChips for successful protein identification. Electrophoresis 2007; 28:1607-14. [PMID: 17447244 DOI: 10.1002/elps.200600656] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The availability of easy-to-handle, sensitive, and cost-effective protein staining protocols for 2-DE, in conjunction with a high compatibility for subsequent MS analysis, is still a prerequisite for successful proteome research. In this article we describe a quick and easy-to-use methodological protocol based on sensitive, homogeneous, and MS-compatible silver nitrate protein staining, in combination with an in-gel digestion, employing the Millipore 96-well ZipPlate system for peptide preparation. The improved quality and MS compatibility of the generated protein digests, as compared to the otherwise weakly MS-compatible silver nitrate staining, were evaluated on real tissue samples by analyzing 192 Coomassie-stained protein spots against their counterparts from a silver-stained 2-DE gel. Furthermore, the applicability of the experimental setup was evaluated and demonstrated by the analysis of a large-scale MALDI-TOF MS experiment, in which we analyzed an additional ~1000 protein spots from 2-DE gels from mouse liver and mouse brain tissue.
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Affiliation(s)
- Grit Nebrich
- Institute for Human Genetics Humboldt-University Berlin, Charité, Berlin, Germany
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149
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Abstract
Viruses have long been studied not only for their pathology and associated disease but also as model systems for molecular processes and as tools for identifying important cellular regulatory proteins and pathways. Recent advances in mass spectrometry methods coupled with the development of proteomic approaches have greatly facilitated the detection of virion components, protein interactions in infected cells, and virally induced changes in the cellular proteome, resulting in a more comprehensive understanding of viral infection. In addition, a rapidly increasing number of high-resolution structures for viral proteins have provided valuable information on the mechanism of action of these proteins as well as aided in the design and understanding of specific inhibitors that could be used in antiviral therapies. In this paper, we discuss proteomic studies conducted on all eukaryotic viruses and bacteriophages, covering virion composition, viral protein structures, virus-virus and virus-host protein interactions, and changes in the cellular proteome upon viral infection.
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Affiliation(s)
- Karen L Maxwell
- Department of Medical Genetics and Microbiology, University of Toronto, Toronto, Ontario M5S 1A8, Canada
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150
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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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