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Reducing Complexity? Cysteine Reduction and S-Alkylation in Proteomic Workflows: Practical Considerations. Methods Mol Biol 2019; 1977:83-97. [PMID: 30980324 DOI: 10.1007/978-1-4939-9232-4_7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Reduction and alkylation are common processing steps in sample preparation for qualitative and quantitative proteomic analyses. In principle, these steps mitigate the limitations resulting from the presence of disulfide bridges. There has been recurring debate in the proteomics community around their use, with concern over negative impacts that result from overalkylation (off-target, non-thiol sites) or incomplete reduction and/or S-alkylation of cysteine. This chapter integrates findings from a number of studies on different reduction and alkylation strategies, to guide users in experimental design for their optimal use in proteomic workflows.
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Swarge BN, Roseboom W, Zheng L, Abhyankar WR, Brul S, de Koster CG, de Koning LJ. "One-Pot" Sample Processing Method for Proteome-Wide Analysis of Microbial Cells and Spores. Proteomics Clin Appl 2018; 12:e1700169. [PMID: 29484825 PMCID: PMC6174930 DOI: 10.1002/prca.201700169] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Revised: 01/22/2018] [Indexed: 11/15/2022]
Abstract
PURPOSE Bacterial endospores, the transmissible forms of pathogenic bacilli and clostridia, are heterogeneous multilayered structures composed of proteins. These proteins protect the spores against a variety of stresses, thus helping spore survival, and assist in germination, by interacting with the environment to form vegetative cells. Owing to the complexity, insolubility, and dynamic nature of spore proteins, it has been difficult to obtain their comprehensive protein profiles. EXPERIMENTAL DESIGN The intact spores of Bacillus subtilis, Bacillus cereus, and Peptoclostridium difficile and their vegetative counterparts were disrupted by bead beating in 6 m urea under reductive conditions. The heterogeneous mixture was then double digested with LysC and trypsin. Next, the peptide mixture was pre-fractionated with zwitterionic hydrophilic interaction liquid chromatography (ZIC-HILIC) followed by reverse-phase LC-FT-MS analysis of the fractions. RESULTS "One-pot" method is a simple, robust method that yields identification of >1000 proteins with high confidence, across all spore layers from B. subtilis, B. cereus, and P. difficile. CONCLUSIONS AND MEDICAL RELEVANCE This method can be employed for proteome-wide analysis of non-spore-forming as well as spore-forming pathogens. Analysis of spore protein profile will help to understand the sporulation and germination processes and to distinguish immunogenic protein markers.
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Affiliation(s)
- Bhagyashree Nandakishor Swarge
- Department of Mass Spectrometry of Bio macromolecules, University of Amsterdam, Amsterdam, The Netherlands
- Department of Molecular Biology and Microbial Food Safety, Swammerdam Institutes of Life Sciences, University of Amsterdam, The Netherlands
| | - Winfried Roseboom
- Department of Mass Spectrometry of Bio macromolecules, University of Amsterdam, Amsterdam, The Netherlands
| | - Linli Zheng
- Department of Mass Spectrometry of Bio macromolecules, University of Amsterdam, Amsterdam, The Netherlands
- Department of Molecular Biology and Microbial Food Safety, Swammerdam Institutes of Life Sciences, University of Amsterdam, The Netherlands
| | - Wishwas R Abhyankar
- Department of Mass Spectrometry of Bio macromolecules, University of Amsterdam, Amsterdam, The Netherlands
- Department of Molecular Biology and Microbial Food Safety, Swammerdam Institutes of Life Sciences, University of Amsterdam, The Netherlands
| | - Stanley Brul
- Department of Molecular Biology and Microbial Food Safety, Swammerdam Institutes of Life Sciences, University of Amsterdam, The Netherlands
| | - Chris G de Koster
- Department of Mass Spectrometry of Bio macromolecules, University of Amsterdam, Amsterdam, The Netherlands
| | - Leo J de Koning
- Department of Mass Spectrometry of Bio macromolecules, University of Amsterdam, Amsterdam, The Netherlands
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Fasoli E, Righetti PG, Moltrasio D, D'Amato A. Extensive heterogeneity of human urokinase, as detected by two-dimensional mapping. Anal Chem 2015; 87:1509-13. [PMID: 25525926 DOI: 10.1021/ac5037796] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Urokinase (uPA, urinary plasminogen activator) is a serine protease belonging to the peptidase S1 family. Specifically, uPA cleaves the zymogen plasminogen into the active form (plasmin), which then degrades the fibrin clots. It is widely used as a fibrinolytic agent in thrombolytic therapy and it is also used clinically as a thrombolytic agent. It can be administered to improve the drainage of complicated pleural effusions and empyemas and it is the most effective drug in myocardial infarction. The enzyme was originally identified in human urine for its ability to catalyze the transformation of plasminogen into its active form (plasmin), which degrades fibrin and extracellular matrix components. The present report deals with the analysis and characterization of this preparation.
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Affiliation(s)
- Elisa Fasoli
- Department of Chemistry, Materials and Chemical Engineering "Giulio Natta", Politecnico di Milano , Via Mancinelli 7, Milano 20131, Italy
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Wu X, Gong F, Wang W. Protein extraction from plant tissues for 2DE and its application in proteomic analysis. Proteomics 2014; 14:645-58. [PMID: 24395710 DOI: 10.1002/pmic.201300239] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2013] [Revised: 12/03/2013] [Accepted: 12/10/2013] [Indexed: 11/09/2022]
Abstract
Plant tissues contain large amounts of secondary compounds that significantly interfere with protein extraction and 2DE analysis. Thus, sample preparation is a crucial step prior to 2DE in plant proteomics. This tutorial highlights the guidelines that need to be followed to perform an adequate total protein extraction before 2DE in plant proteomics. We briefly describe the history, development, and feature of major sample preparation methods for the 2DE analysis of plant tissues, that is, trichloroacetic acid/acetone precipitation and phenol extraction. We introduce the interfering compounds in plant tissues and the general guidelines for tissue disruption, protein precipitation and resolubilization. We describe in details the advantages, limitations, and application of the trichloroacetic acid/acetone precipitation and phenol extraction methods to enable the readers to select the appropriate method for a specific species, tissue, or cell type. The current applications of the sample preparation methods in plant proteomics in the literature are analyzed. A comparative proteomic analysis between male and female plants of Pistacia chinensis is used as an example to represent the sample preparation methodology in 2DE-based proteomics. Finally, the current limitations and future development of these sample preparation methods are discussed. This Tutorial is part of the International Proteomics Tutorial Programme (IPTP17).
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Affiliation(s)
- Xiaolin Wu
- State Key Laboratory of Wheat & Maize Crop Science in Henan Province, Synergetic Innovation Center of Henan Grain Crops, College of Life Science, Henan Agricultural University, Zhengzhou, China
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Abstract
First described nearly 20 years before Marc Wilkins coined the term 'proteomics', two-dimensional electrophoresis (2DGE) is still in adolescence (as is the field of proteomics). It is well recognised that two dimensions are insufficient for deconvoluting the complexity of even the simplest of proteomes, and that 2DGE can only be part of more elaborate 'multidimensional' schemes. As upstream dimensions continue to be developed, the potential of 2DGE may be further realised. Although orthogonal electrophoresis is unrivalled in its ability to resolve the total protein constituency of cells, arraying the 1500 or so most abundant proteins becomes of diminishing importance. Similar to looking into the sun in an effort to see sunspots, candidate biomarkers of extremely low abundance are concealed amid the myriad of proteins of higher abundance. The procedural complexity and inability to automate 2DGE seems to be prohibitive to its use in the clinical laboratory, which is an unfortunate consequence as this is where the promise of proteomics must ultimately be fulfilled.
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Thiol redox proteomics seen with fluorescent eyes: The detection of cysteine oxidative modifications by fluorescence derivatization and 2-DE. J Proteomics 2011; 75:329-38. [DOI: 10.1016/j.jprot.2011.09.013] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2011] [Revised: 09/15/2011] [Accepted: 09/19/2011] [Indexed: 12/11/2022]
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Gandhi KS, McKay FC, Diefenbach E, Crossett B, Schibeci SD, Heard RN, Stewart GJ, Booth DR, Arthur JW. Novel approaches to detect serum biomarkers for clinical response to interferon-beta treatment in multiple sclerosis. PLoS One 2010; 5:e10484. [PMID: 20463963 PMCID: PMC2864746 DOI: 10.1371/journal.pone.0010484] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2009] [Accepted: 04/09/2010] [Indexed: 11/28/2022] Open
Abstract
Interferon beta (IFNβ) is the most common immunomodulatory treatment for relapsing-remitting multiple sclerosis (RRMS). However, some patients fail to respond to treatment. In this study, we identified putative clinical response markers in the serum and plasma of people with multiple sclerosis (MS) treated with IFNβ. In a discovery-driven approach, we use 2D-difference gel electrophoresis (DIGE) to identify putative clinical response markers and apply power calculations to identify the sample size required to further validate those markers. In the process we have optimized a DIGE protocol for plasma to obtain cost effective and high resolution gels for effective spot comparison. APOA1, A2M, and FIBB were identified as putative clinical response markers. Power calculations showed that the current DIGE experiment requires a minimum of 10 samples from each group to be confident of 1.5 fold difference at the p<0.05 significance level. In a complementary targeted approach, Cytometric Beadarray (CBA) analysis showed no significant difference in the serum concentration of IL-6, IL-8, MIG, Eotaxin, IP-10, MCP-1, and MIP-1α, between clinical responders and non-responders, despite the association of these proteins with IFNβ treatment in MS.
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Affiliation(s)
- Kaushal S. Gandhi
- Westmead Millennium Institute, University of Sydney, Sydney, Australia
- Discipline of Medicine, Sydney Medical School, University of Sydney, Sydney, Australia
| | - Fiona C. McKay
- Westmead Millennium Institute, University of Sydney, Sydney, Australia
| | - Eve Diefenbach
- Westmead Millennium Institute, University of Sydney, Sydney, Australia
| | - Ben Crossett
- School of Molecular and Microbial Bioscience, University of Sydney, Sydney, Australia
| | | | - Robert N. Heard
- Westmead Millennium Institute, University of Sydney, Sydney, Australia
| | - Graeme J. Stewart
- Westmead Millennium Institute, University of Sydney, Sydney, Australia
| | - David R. Booth
- Westmead Millennium Institute, University of Sydney, Sydney, Australia
| | - Jonathan W. Arthur
- Discipline of Medicine, Sydney Medical School, University of Sydney, Sydney, Australia
- Sydney Bioinformatics, University of Sydney, Sydney, Australia
- * E-mail:
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Hansen RE, Winther JR. An introduction to methods for analyzing thiols and disulfides: Reactions, reagents, and practical considerations. Anal Biochem 2009; 394:147-58. [DOI: 10.1016/j.ab.2009.07.051] [Citation(s) in RCA: 193] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2008] [Revised: 07/31/2009] [Accepted: 07/31/2009] [Indexed: 10/20/2022]
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Wu Y, Zhou J, Zhang X, Zheng X, Jiang X, Shi L, Yin W, Wang J. Optimized sample preparation for two-dimensional gel electrophoresis of soluble proteins from chicken bursa of Fabricius. Proteome Sci 2009; 7:38. [PMID: 19814785 PMCID: PMC2770044 DOI: 10.1186/1477-5956-7-38] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2009] [Accepted: 10/08/2009] [Indexed: 01/10/2024] Open
Abstract
BACKGROUND Two-dimensional gel electrophoresis (2-DE) is a powerful method to study protein expression and function in living organisms and diseases. This technique, however, has not been applied to avian bursa of Fabricius (BF), a central immune organ. Here, optimized 2-DE sample preparation methodologies were constructed for the chicken BF tissue. Using the optimized protocol, we performed further 2-DE analysis on a soluble protein extract from the BF of chickens infected with virulent avibirnavirus. To demonstrate the quality of the extracted proteins, several differentially expressed protein spots selected were cut from 2-DE gels and identified by matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS). RESULTS An extraction buffer containing 7 M urea, 2 M thiourea, 2% (w/v) 3-[(3-cholamidopropyl)-dimethylammonio]-1-propanesulfonate (CHAPS), 50 mM dithiothreitol (DTT), 0.2% Bio-Lyte 3/10, 1 mM phenylmethylsulfonyl fluoride (PMSF), 20 U/ml Deoxyribonuclease I (DNase I), and 0.25 mg/ml Ribonuclease A (RNase A), combined with sonication and vortex, yielded the best 2-DE data. Relative to non-frozen immobilized pH gradient (IPG) strips, frozen IPG strips did not result in significant changes in the 2-DE patterns after isoelectric focusing (IEF). When the optimized protocol was used to analyze the spleen and thymus, as well as avibirnavirus-infected bursa, high quality 2-DE protein expression profiles were obtained. 2-DE maps of BF of chickens infected with virulent avibirnavirus were visibly different and many differentially expressed proteins were found. CONCLUSION These results showed that method C, in concert extraction buffer IV, was the most favorable for preparing samples for IEF and subsequent protein separation and yielded the best quality 2-DE patterns. The optimized protocol is a useful sample preparation method for comparative proteomics analysis of chicken BF tissues.
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Abstract
The degree of protein diversity and dynamic range within organisms means that even the simplest proteome cannot be captured by any single extraction and separation step. New techniques have focused on major protein classes often under-represented in proteome analysis; low abundance, membrane, and alkaline proteins. The last decade has seen considerable technology development in fractionation tools aimed at complexity reduction in many forms. The key outcome of complexity reduction is that each fraction, or sub-proteome, can be studied in more detail, and proteins which would have remained undetected in a total extract are present in sufficient quantities. However, the tools available are fractionations, not amplifications, and like all mining for rare and difficult items, a large amount of starting material is often required. The key shortcomings of many proteome analysis techniques are now well documented. With this knowledge, the best modern proteomics 'platform' involves combining multiple protein extractions, gel and chromatographic separations, and multiple MS analysis methods.
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Affiliation(s)
- Ben Herbert
- Department of Medical and Molecular Biosciences, University of Technology, Sydney, 15 Broadway, Ultimo, Sydney, NSW 2007, Australia
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12
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Two-dimensional gel electrophoresis of wool intermediate filament proteins. J Proteomics 2008; 71:439-47. [DOI: 10.1016/j.jprot.2008.06.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2008] [Revised: 06/06/2008] [Accepted: 06/13/2008] [Indexed: 11/20/2022]
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Abstract
Isotope-coded two-dimensional maps, with either D(0)/D(3)-acrylamide or D(0)/D(4) 2-vinyl pyridine, are described in detail. They have the advantage of running the two samples under investigation within a single slab gel, thus minimizing errors because of spot matching with software packages when samples are run in parallel maps. Labeling with deuterated acrylamide is very simple and inexpensive, because this chemical is commercially available. The experiment has to be carried out at alkaline pH values (pH 8.5-9.0) and with high molarities of alkylating agent (50-100 mM) to ensure good conversion efficiency. On the contrary, labeling with 2-vinyl pyridine (2-VP) can be performed in much lower alkylant molarities (20 mM) and at neutral pH values, thus ensuring essentially 100% conversion efficiency coupled with 100% specificity, because the reaction is sustained by the partial positive and negative charges on the 2-VP and -SH group, respectively. However, deuterated 2-VP is not commercially available and it has to be synthesized ad hoc.
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Simó C, Bachi A, Cattaneo A, Guerrier L, Fortis F, Boschetti E, Podtelejnikov A, Righetti PG. Performance of Combinatorial Peptide Libraries in Capturing the Low-Abundance Proteome of Red Blood Cells. 1. Behavior of Mono- to Hexapeptides. Anal Chem 2008; 80:3547-56. [DOI: 10.1021/ac702635v] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Carolina Simó
- Department of Chemistry, Materials and Chemical Engineering “Giulio Natta”, Polytechnic of Milano, 20131 Milano, Italy, San Raffaele Scientific Institute, 20132 Milano, Italy, Bio-Rad Laboratories, C/o CEA-Saclay 91181 Gif-sur-Yvette, France, and Proxeon A/S, DK-5230 Odense, Denmark
| | - Angela Bachi
- Department of Chemistry, Materials and Chemical Engineering “Giulio Natta”, Polytechnic of Milano, 20131 Milano, Italy, San Raffaele Scientific Institute, 20132 Milano, Italy, Bio-Rad Laboratories, C/o CEA-Saclay 91181 Gif-sur-Yvette, France, and Proxeon A/S, DK-5230 Odense, Denmark
| | - Angela Cattaneo
- Department of Chemistry, Materials and Chemical Engineering “Giulio Natta”, Polytechnic of Milano, 20131 Milano, Italy, San Raffaele Scientific Institute, 20132 Milano, Italy, Bio-Rad Laboratories, C/o CEA-Saclay 91181 Gif-sur-Yvette, France, and Proxeon A/S, DK-5230 Odense, Denmark
| | - Luc Guerrier
- Department of Chemistry, Materials and Chemical Engineering “Giulio Natta”, Polytechnic of Milano, 20131 Milano, Italy, San Raffaele Scientific Institute, 20132 Milano, Italy, Bio-Rad Laboratories, C/o CEA-Saclay 91181 Gif-sur-Yvette, France, and Proxeon A/S, DK-5230 Odense, Denmark
| | - Frederic Fortis
- Department of Chemistry, Materials and Chemical Engineering “Giulio Natta”, Polytechnic of Milano, 20131 Milano, Italy, San Raffaele Scientific Institute, 20132 Milano, Italy, Bio-Rad Laboratories, C/o CEA-Saclay 91181 Gif-sur-Yvette, France, and Proxeon A/S, DK-5230 Odense, Denmark
| | - Egisto Boschetti
- Department of Chemistry, Materials and Chemical Engineering “Giulio Natta”, Polytechnic of Milano, 20131 Milano, Italy, San Raffaele Scientific Institute, 20132 Milano, Italy, Bio-Rad Laboratories, C/o CEA-Saclay 91181 Gif-sur-Yvette, France, and Proxeon A/S, DK-5230 Odense, Denmark
| | - Alexander Podtelejnikov
- Department of Chemistry, Materials and Chemical Engineering “Giulio Natta”, Polytechnic of Milano, 20131 Milano, Italy, San Raffaele Scientific Institute, 20132 Milano, Italy, Bio-Rad Laboratories, C/o CEA-Saclay 91181 Gif-sur-Yvette, France, and Proxeon A/S, DK-5230 Odense, Denmark
| | - Pier Giorgio Righetti
- Department of Chemistry, Materials and Chemical Engineering “Giulio Natta”, Polytechnic of Milano, 20131 Milano, Italy, San Raffaele Scientific Institute, 20132 Milano, Italy, Bio-Rad Laboratories, C/o CEA-Saclay 91181 Gif-sur-Yvette, France, and Proxeon A/S, DK-5230 Odense, Denmark
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Pretzer E, Wiktorowicz JE. Saturation fluorescence labeling of proteins for proteomic analyses. Anal Biochem 2008; 374:250-62. [PMID: 18191033 PMCID: PMC2268766 DOI: 10.1016/j.ab.2007.12.014] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2007] [Revised: 12/07/2007] [Accepted: 12/10/2007] [Indexed: 11/25/2022]
Abstract
We present here an optimized and cost-effective approach to saturation fluorescence labeling of protein thiols for proteomic analysis. We investigated a number of conditions and reagent concentrations, including the disulfide reducing agent tris(2-carboxyethyl)phosphine (TCEP), pH, incubation time, linearity of labeling, and saturating dye/protein thiol ratio with protein standards to gauge specific and nonspecific labeling. Efficacy of labeling under these conditions was quantified using specific fluorescence estimation, defined as the ratio of fluorescence pixel intensities and Coomassie-stained pixel intensities of bands after digital imaging. Factors leading to specific versus nonspecific labeling in the presence of thiourea are also discussed. We found that reproducible saturation of available Cys residues of the proteins used as labeling standards (human carbonic anhydrase I, enolase, and alpha-lactalbumin) is achieved at 50- to 100-fold excess of the uncharged maleimide-functionalized BODIPY dyes over Cys. We confirmed our previous findings, and those of others, that the maleimide dyes are not affected by the presence of 2 M thiourea. Moreover, we established that 2 mM TCEP used as reductant is optimal. We also established that labeling is optimal at pH 7.5 and complete after 30 min. Low nonspecific labeling was gauged by the inclusion of non-Cys-containing proteins (horse myoglobin and bovine carbonic anhydrase) to the labeling mixture. We also showed that the dye exhibits little to no effect on the two-dimensional mobilities of labeled proteins derived from cells.
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Park SC, Pham BP, Van Duyet L, Jia B, Lee S, Yu R, Han SW, Yang JK, Hahm KS, Cheong GW. Structural and functional characterization of osmotically inducible protein C (OsmC) from Thermococcus kodakaraensis KOD1. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2008; 1784:783-8. [PMID: 18319068 DOI: 10.1016/j.bbapap.2008.02.002] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2007] [Revised: 01/14/2008] [Accepted: 02/04/2008] [Indexed: 11/26/2022]
Abstract
Osmotically inducible protein C (OsmC) is involved in the cellular defense mechanism against oxidative stress caused by exposure to hyperoxides or elevated osmolarity. OsmC was identified by two-dimensional electrophoresis (2DE) analysis as a protein that is overexpressed in response to osmotic stress, but not under heat and oxidative stress. Here, an OsmC gene from T. kodakaraensis KOD1 was cloned and expressed in Escherichia coli. TkOsmC showed a homotetrameric structure based on gel filtration and electron microscopic analyses. TkOsmC has a significant peroxidase activity toward both organic and inorganic peroxides in high, but not in low temperature.
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Affiliation(s)
- Seong-Cheol Park
- Division of Applied Life Sciences (BK21 Program), Gyeongsang National University, Jinju, 660-701, Republic of Korea
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Bile duct ligation in the rat causes upregulation of ZO-2 and decreased colocalization of claudins with ZO-1 and occludin. Histochem Cell Biol 2008; 129:289-99. [PMID: 18197414 DOI: 10.1007/s00418-007-0374-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/18/2007] [Indexed: 12/22/2022]
Abstract
As the only barrier between blood and bile compartments hepatocellular tight junctions play a crucial role in cholestasis-induced increase of biliary permeability. The molecular basis of this reversible defect is not known. We, therefore, examined expression, phosphorylation, distribution and colocalization of the junctional proteins occludin, claudin-1-3, ZO-1 and ZO-2 in rats after bile duct ligation and release of ligation. In control rats, claudin-1 and ZO-2 displayed a lobular gradient with highest expression levels in periportal cells, whereas claudin-2 showed a reciprocal distribution. Other proteins were evenly expressed in the liver lobule. Ligation resulted in upregulation of ZO-2 (2.7-fold), ZO-1 (1.4-fold) and occludin (1.2-fold) but not of claudins. Only ZO-2 showed increased phosphorylation. Distribution patterns were unchanged except for a strong accumulation of ZO-2 in perivenous hepatocytes. Colocalization analysis demonstrated that perivenous ZO-2 was the only protein examined revealing strongly increased overlap with occludin and ZO-1, whereas claudins and other proteins displayed a decrease. All changes were partially reversed by release of ligation. We conclude that differential expression of claudin-1-2 and ZO-2 has functional implications for bile formation. The moderately increased ZO-1 and occludin levels account for the known elongation of tight junction strands. The highly increased expression and changed distribution of ZO-2 suggests that ZO-1 is partly substituted by ZO-2, an alteration possibly causing impaired barrier function.
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18
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Chapter 17 Mass Spectrometry-Driven Approaches to Quantitative Proteomics and Beyond. ACTA ACUST UNITED AC 2008. [DOI: 10.1016/s0166-526x(08)00217-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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Yang Z, Attygalle AB. LC/MS characterization of undesired products formed during iodoacetamide derivatization of sulfhydryl groups of peptides. JOURNAL OF MASS SPECTROMETRY : JMS 2007; 42:233-43. [PMID: 17206739 DOI: 10.1002/jms.1157] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Many undesired by-products have been noticed during alkylation with iodoacetamide, a widely used derivatization reaction in proteomics for the determination of sulfhydryl groups in peptides and proteins. We report here that iodoacetamide reacts with the N-terminal NH2 and the C-terminal carboxylic acid groups, in addition to the peripheral residues bearing protic functional groups. If sufficient reaction time is given, the N-terminal NH2 group is readily dialkylated by iodoacetamide. In fact, the N-terminal NH2 group reacts even faster than the reactive sites present in residues, such as tyrosine or histidine. LC/MS investigations with certain reactive peptides show that by-products are formed in a relatively short reaction time, even at room temperature. Interestingly, derivatives formed in this way are useful for sequence determination of peptides by MS since the intensities of y'' ions are highly suppressed in the spectra of N-terminus mono- and dialkylated peptides, whereas those of b-ions are significantly enhanced. For example, in the spectrum of N,N-dicarboxamidomethyl derivative of Val-Ala-Ala-Phe (VAAF), the y-series ions are virtually absent. On the other hand, when the derivatization takes place at the carboxylic group, the y-series ions are markedly observed in the spectra of these undesired O-carboxamidomethyl derivatives.
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Affiliation(s)
- Zhihua Yang
- Center for Mass Spectrometry, Department of Chemistry and Chemical Biology, Stevens Institute of Technology, NJ 07030, USA
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Richards DP, Sojo LE, Keller BO. Quantitative analysis with modern bioanalytical mass spectrometry and stable isotope labeling. J Labelled Comp Radiopharm 2007. [DOI: 10.1002/jlcr.1392] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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The study of three extraction methods for pre-separation and enrichment: Application to the complex proteome separation in rat liver. Sep Purif Technol 2006. [DOI: 10.1016/j.seppur.2006.04.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Righetti PG. Real and imaginary artefacts in proteome analysis via two-dimensional maps. J Chromatogr B Analyt Technol Biomed Life Sci 2006; 841:14-22. [PMID: 16517224 DOI: 10.1016/j.jchromb.2006.02.022] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2005] [Revised: 01/20/2006] [Accepted: 02/11/2006] [Indexed: 11/27/2022]
Abstract
The present review touches on a long-lasting debate on possible artefacts (i.e. generation of spurious spots, not belonging to the biological sample under analysis) induced by the separation technique (in this case, two-dimensional mapping) per se. It is shown here that some of the biggest offenders, always blamed in the past (at least since 1970, i.e. since the inception of gel-base isoelectric focusing protocols), namely deamidation (of Asn and Gln residues) and carbamylation (due to cyanate produced in urea solution), simply do not occur in properly handled samples and have never indeed been demonstrated in real samples, except when forced in purpose. Conversely, two unexpected major artefacts have been recently shown to plague 2D mapping. One is formation of homo- and hetero-oligomers in samples that have been reduced but not alkylated prior to entering the electric field. The phenomenon is highly aggravated in alkaline pH regions and can lead to an impressive number of spurious spots not existing in the original sample. Thus, alkylation (best if performed with acrylamide or vinylpyridines) is a must for avoiding such spurious spots, as well as sample streaking and smearing in the alkaline gel region, and for maintaining sample integrity. In fact, the other unexpected artefact is desulfuration (beta-elimination) by which, upon prolonged electrophoresis, the sample looses an -SH group fro Cys residues. This loss, in the long run, is accompanied by massive protein degradation due to lysis of a C-N bond along the polypeptide chain. Here too, alkylation of -SH groups of Cys almost completely prevents this noxious degradation phenomenon.
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Affiliation(s)
- Pier Giorgio Righetti
- Polytechnic of Milano, Department of Chemistry, Giulio Natta, Materials and Engineering Chemistry, Via Mancinelli 7, Milano 20131, Italy.
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Vâlcu CM, Schlink K. Efficient extraction of proteins from woody plant samples for two-dimensional electrophoresis. Proteomics 2006; 6:4166-75. [PMID: 16791823 DOI: 10.1002/pmic.200500660] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Protein extraction from plant samples is usually challenging due to the low protein content and high level of contaminants. Therefore, the 2-DE pattern resolution is strongly influenced by the procedure of sample preparation. Efficient solubilization of proteins strictly depends on the chaotrope and detergent in the extraction buffer. Despite the large number of detergents that have been developed for the use in protein extraction and IEF, there is no single compound able to efficiently extract proteins from any source. Hence, optimization has to be performed for each type of sample. We tested several chaotrope/detergent combinations to achieve optimal solubilization and separation of proteins from Norway spruce [Picea abies (L.) H. Karst.] needles and European beech (Fagus sylvatica L.) leaves and roots. The same chaotrope mixture (7 M urea, 2 M thiourea) was found to be suitable for the extraction and separation of proteins from all samples. Nonetheless, the efficiency of the surfactants tested varied between samples so that optimal extraction and separation was achieved with different detergents or combination of detergents for each sample. The 2-DE separation of spruce needle proteins was optimal in a mixture of two zwitterionic detergents (2% CHAPS and 2% decyl dimethylammonio propanesulfonate). Beech proteins were best separated in buffers containing sugar-based detergents (2% n-octyl beta-D-glucopiranoside in the case of leaf samples and 2% dodecyl maltoside for the root samples). IEF was performed in buffers with the same composition as the extraction buffer except for the root proteins that were better focused in a buffer containing 2% CHAPS.
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Affiliation(s)
- Cristina-Maria Vâlcu
- Section of Forest Genetics, Technische Universität München, Freising-Weihenstephan, Germany.
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Vâlcu CM, Schlink K. Reduction of proteins during sample preparation and two-dimensional gel electrophoresis of woody plant samples. Proteomics 2006; 6:1599-605. [PMID: 16456882 DOI: 10.1002/pmic.200500314] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Protein extraction procedure and the reducing agent content (DTT, dithioerythritol, tributyl phosphine and tris (2-carboxyethyl) phosphine (TCEP)) of the sample and rehydration buffers were optimised for European beech leaves and roots and Norway spruce needles. Optimal extraction was achieved with 100 mM DTT for leaves and needles and a mixture of 2 mM TCEP and 50 mM DTT for roots. Performing IEF in buffers containing hydroxyethyldisulphide significantly enhanced the quality of separation for all proteins except for acidic root proteins, which were optimally focused in the same buffer as extracted.
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Affiliation(s)
- Cristina-Maria Vâlcu
- Section of Forest Genetics, Technische Universität München, Freising-Weihenstephan, Germany.
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25
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Bi X, Lin Q, Foo TW, Joshi S, You T, Shen HM, Ong CN, Cheah PY, Eu KW, Hew CL. Proteomic Analysis of Colorectal Cancer Reveals Alterations in Metabolic Pathways. Mol Cell Proteomics 2006; 5:1119-30. [PMID: 16554294 DOI: 10.1074/mcp.m500432-mcp200] [Citation(s) in RCA: 125] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Colorectal cancer is the second leading killer cancer worldwide and presently the most common cancer among males in Singapore. The study aimed to detect changes of protein profiles associated with the process of colorectal tumorigenesis to identify specific protein markers for early colorectal cancer detection and diagnosis or as potential therapeutic targets. Seven pairs of colorectal cancer tissues and adjacent normal mucosa were examined by two-dimensional gel electrophoresis at basic pH range (pH 7-10). Intensity changes of 34 spots were detected with statistical significance. 16 of the 34 spots were identified by MALDI-TOF/TOF tandem mass spectrometry. Changes in protein expression levels revealed a significantly enhanced glycolytic pathway (Warburg effect), a decreased gluconeogenesis, a suppressed glucuronic acid pathway, and an impaired tricarboxylic acid cycle. Observed changes in protein abundance were verified by two-dimensional DIGE. These changes reveal an underlying mechanism of colorectal tumorigenesis in which the roles of impaired tricarboxylic acid cycle and the Warburg effect may be critical.
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Affiliation(s)
- Xuezhi Bi
- Department of Biological Sciences, National University of Singapore, Singapore 117543
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26
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Herbert BR, Grinyer J, McCarthy JT, Isaacs M, Harry EJ, Nevalainen H, Traini MD, Hunt S, Schulz B, Laver M, Goodall AR, Packer J, Harry JL, Williams KL. Improved 2-DE of microorganisms after acidic extraction. Electrophoresis 2006; 27:1630-40. [PMID: 16609937 DOI: 10.1002/elps.200500753] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
2-DE separations of protein extracts sometimes have problems with poor resolution and streaking. This problem is particularly apparent with microorganisms, most notably those with a large cell wall. Here we describe a novel, rapid protocol for the extraction of microorganisms in acidic conditions, leading to increased resolution and 2-D gel quality. The efficiency of the protocol is demonstrated with extracts of bacteria, Escherichia coli and Bacillus subtilis; fungus, Trichoderma harzianum and yeast, Saccharomyces cerevisiae. We also demonstrate using a membrane centrifugal filtration, that large acidic molecules in excess of 100 kDa, probably including cell wall material, are responsible for the separation difficulties. A range of acidic extraction conditions were investigated, and it was found that optimal extraction is achieved using an extraction solution acidified to pH 3 by 80 mM citric acid. These findings have significant implications for the proteomic study of many medically, agriculturally and environmentally significant microorganisms, as the cell walls of these organisms are often considerably more complex than many commonly studied laboratory strains.
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Affiliation(s)
- Ben R Herbert
- Proteome Systems, North Ryde, Sydney, NSW, Australia.
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27
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Dhingra V, Gupta M, Andacht T, Fu ZF. New frontiers in proteomics research: A perspective. Int J Pharm 2005; 299:1-18. [PMID: 15979831 DOI: 10.1016/j.ijpharm.2005.04.010] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2004] [Revised: 03/01/2005] [Accepted: 04/04/2005] [Indexed: 12/12/2022]
Abstract
Substantial advances have been made in the fundamental understanding of human biology, ranging from DNA structure to identification of diseases associated with genetic abnormalities. Genome sequence information is becoming available in unprecedented amounts. The absence of a direct functional correlation between gene transcripts and their corresponding proteins, however, represents a significant roadblock for improving the efficiency of biological discoveries. The success of proteomics depends on the ability to identify and analyze protein products in a cell or tissue and, this is reliant on the application of several key technologies. Proteomics is in its exponential growth phase. Two-dimensional electrophoresis complemented with mass spectrometry provides a global view of the state of the proteins from the sample. Proteins identification is a requirement to understand their functional diversity. Subtle difference in protein structure and function can contribute to complexity and diversity of life. This review focuses on the progress and the applications of proteomics science with special reference to integration of the evolving technologies involved to address biological questions.
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Affiliation(s)
- Vikas Dhingra
- Department of Pathology, University of Georgia, Athens, GA 30602, USA.
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Chan HL, Gharbi S, Gaffney PR, Cramer R, Waterfield MD, Timms JF. Proteomic analysis of redox- and ErbB2-dependent changes in mammary luminal epithelial cells using cysteine- and lysine-labelling two-dimensional difference gel electrophoresis. Proteomics 2005; 5:2908-26. [PMID: 15954156 DOI: 10.1002/pmic.200401300] [Citation(s) in RCA: 85] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Differential protein expression analysis based on modification of selected amino acids with labelling reagents has become the major method of choice for quantitative proteomics. One such methodology, two-dimensional difference gel electrophoresis (2-D DIGE), uses a matched set of fluorescent N-hydroxysuccinimidyl (NHS) ester cyanine dyes to label lysine residues in different samples which can be run simultaneously on the same gels. Here we report the use of iodoacetylated cyanine (ICy) dyes (for labelling of cysteine thiols, for 2-D DIGE-based redox proteomics. Characterisation of ICy dye labelling in relation to its stoichiometry, sensitivity and specificity is described, as well as comparison of ICy dye with NHS-Cy dye labelling and several protein staining methods. We have optimised conditions for labelling of nonreduced, denatured samples and report increased sensitivity for a subset of thiol-containing proteins, allowing accurate monitoring of redox-dependent thiol modifications and expression changes. Cysteine labelling was then combined with lysine labelling in a multiplex 2-D DIGE proteomic study of redox-dependent and ErbB2-dependent changes in epithelial cells exposed to oxidative stress. This study identifies differentially modified proteins involved in cellular redox regulation, protein folding, proliferative suppression, glycolysis and cytoskeletal organisation, revealing the complexity of the response to oxidative stress and the impact that overexpression of ErbB2 has on this response.
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Affiliation(s)
- Hong-Lin Chan
- Ludwig Institute for Cancer Research, Department of Biochemistry and Molecular Biology, University College London, London, UK
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Hopkinson A, McIntosh RS, Layfield R, Keyte J, Dua HS, Tighe PJ. Optimised two-dimensional electrophoresis procedures for the protein characterisation of structural tissues. Proteomics 2005; 5:1967-79. [PMID: 15816006 DOI: 10.1002/pmic.200401073] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The protein analysis of structural tissues is typically highly problematic. Amniotic membrane displays unique wound healing and anti-scarring properties; however, little is known concerning its active protein content. The structural nature of amniotic membrane necessitated development and extensive optimisation of the entire two-dimensional (2-D) workflow. Proteins were extracted using powerful solubilisation buffers and analysis carried out using 2-D electrophoresis followed by mass spectrometry (MS) identification. Preservation and processing resulted in prefractionation of soluble from structural and membrane-associated proteins. Enhanced protein solubility was achieved by cysteine blocking using both N,N-dimethylacrylamide (DMA) alkylation and bis(2-hydroxyethyl) disulphide (HED); an alternative procedure for the effective application of HED is demonstrated. The benefits of precipitation and cup-loading versus in-gel rehydration were also assessed, with procedures for the employment of HED with the latter described. Following optimisation, a representative sample 21 proteins were identified from amniotic membrane using MS verify procedures were MS-compatible. Our results demonstrate that techniques for the reproducible separation of proteins from a proteinaceous structural tissue have been optimised. Briefly, proteins are extracted using a thiourea/urea extraction buffer containing carrier ampholytes, dithiothreitol (DTT), and 3-(cyclohexylamino)-1-propanesulfonic acid (CHAPS). After DMA alkylation, proteins were precipitated (using the 2-D clean-up kit from Amersham Biosciences) and resolubilised in extraction buffer containing a lower concentration of DTT. Samples were either cup-loaded onto rehydrated HED-containing strips or rebuffered into HED-containing buffer followed by in-gel rehydration.
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Affiliation(s)
- Andrew Hopkinson
- University of Nottingham Division of Ophthalmology and Visual Sciences, EENT Centre, UK.
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Righetti PG, Castagna A, Antonucci F, Piubelli C, Cecconi D, Campostrini N, Antonioli P, Astner H, Hamdan M. Critical survey of quantitative proteomics in two-dimensional electrophoretic approaches. J Chromatogr A 2004; 1051:3-17. [PMID: 15532550 DOI: 10.1016/j.chroma.2004.05.106] [Citation(s) in RCA: 86] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The present review attempts to cover a number of methods that appeared in the last few years for performing quantitative proteome analysis. However, due to the large number of methods described for both electrophoretic and chromatographic approaches, we have limited this excursus only to conventional two-dimensional (2D) map analysis, coupling orthogonally a charge-based step (isoelectric focusing) to a size-based separation (sodium dodecyl sulfate (SDS)-electrophoresis). The first and oldest method applied in 2D mapping is based on statistical analysis performed on sets of gels via powerful software packages, such as the Melanie, PDQuest, Z3 and Z4000, Phoretix and Progenesis. This method calls for separately-running a number of replicas for control and treated samples, the merging and comparing between these two sets of data being accomplished via the softwares just mentioned. Recent developments permit analyses on a single gel containing mixed samples differentially labelled and resolved by either fluorescence or isotopic means. In one approach, a set of fluorophors, called Cy3 and Cy5, are selected for differentially tagging Lys residues, via a "minimal labelling" protocol. A variant of this, adopts a newer set of fluorophors, also of the Cy3 and Cy5 type, reacting on Cys residues, via a strategy of "saturation labelling". There are at present two methods for quantitative proteomics in a 2D gel format exploiting stable isotopes: one utilizes tagging Cys residues with [2H0]/[2H3]-acrylamide; the other one, also based on a Cys reactive compound, exploits [2H0]/[2H4] 2-vinylpyridine. The latter reagent achieves 100% efficiency coupled to 100% specificity. The advantages and limitations of the various protocols are discussed.
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Affiliation(s)
- Pier Giorgio Righetti
- Department of Agricultural and Industrial Biotechnologies, University of Verona, Verona, Italy.
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Khoudoli GA, Porter IM, Blow JJ, Swedlow JR. Optimisation of the two-dimensional gel electrophoresis protocol using the Taguchi approach. Proteome Sci 2004. [PMID: 15357868 DOI: 10.1186/1477–5956–2–6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023] Open
Abstract
BACKGROUND: Quantitative proteomic analyses have traditionally used two-dimensional gel electrophoresis (2DE) for separation and characterisation of complex protein mixtures. Among the difficulties associated with this approach is the solubilisation of protein mixtures for isoelectric focusing (IEF). To find the optimal formulation of the multi-component IEF rehydration buffer (RB) we applied the Taguchi method, a widely used approach for the robust optimisation of complex industrial processes, to determine optimal concentrations for the detergents, carrier ampholytes and reducing agents in RB for 2DE using commercially supplied immobilised pH gradient (IPG) gel strips. RESULTS: Our optimisation resulted in increased protein solubility, improved resolution and reproducibility of 2D gels, using a wide variety of samples. With the updated protocol we routinely detected approximately 4-fold more polypeptides on samples containing complex protein mixtures resolved on small format 2D gels. In addition the pI and size ranges over which proteins could be resolved was substantially improved. Moreover, with improved sample loading and resolution, analysis of individual spots by immunoblotting and mass spectrometry revealed previously uncharacterised posttranscriptional modifications in a variety of chromatin proteins. CONCLUSIONS: While the optimised RB (oRB) is specific to the gels and analysis approach we use, our use of the Taguchi method should be generally applicable to a broad range of electrophoresis and analysis systems.
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Affiliation(s)
- Guennadi A Khoudoli
- Division of Gene Regulation and Expression, School of Life Sciences, Wellcome Trust Biocentre, University of Dundee, Dow Street, Dundee DD1 5EH, UK.
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Khoudoli GA, Porter IM, Blow JJ, Swedlow JR. Optimisation of the two-dimensional gel electrophoresis protocol using the Taguchi approach. Proteome Sci 2004; 2:6. [PMID: 15357868 PMCID: PMC517948 DOI: 10.1186/1477-5956-2-6] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2004] [Accepted: 09/09/2004] [Indexed: 02/04/2023] Open
Abstract
Background Quantitative proteomic analyses have traditionally used two-dimensional gel electrophoresis (2DE) for separation and characterisation of complex protein mixtures. Among the difficulties associated with this approach is the solubilisation of protein mixtures for isoelectric focusing (IEF). To find the optimal formulation of the multi-component IEF rehydration buffer (RB) we applied the Taguchi method, a widely used approach for the robust optimisation of complex industrial processes, to determine optimal concentrations for the detergents, carrier ampholytes and reducing agents in RB for 2DE using commercially supplied immobilised pH gradient (IPG) gel strips. Results Our optimisation resulted in increased protein solubility, improved resolution and reproducibility of 2D gels, using a wide variety of samples. With the updated protocol we routinely detected approximately 4-fold more polypeptides on samples containing complex protein mixtures resolved on small format 2D gels. In addition the pI and size ranges over which proteins could be resolved was substantially improved. Moreover, with improved sample loading and resolution, analysis of individual spots by immunoblotting and mass spectrometry revealed previously uncharacterised posttranscriptional modifications in a variety of chromatin proteins. Conclusions While the optimised RB (oRB) is specific to the gels and analysis approach we use, our use of the Taguchi method should be generally applicable to a broad range of electrophoresis and analysis systems.
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Affiliation(s)
- Guennadi A Khoudoli
- Division of Gene Regulation and Expression, School of Life Sciences, Wellcome Trust Biocentre, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Iain M Porter
- Division of Gene Regulation and Expression, School of Life Sciences, Wellcome Trust Biocentre, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - J Julian Blow
- Division of Gene Regulation and Expression, School of Life Sciences, Wellcome Trust Biocentre, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Jason R Swedlow
- Division of Gene Regulation and Expression, School of Life Sciences, Wellcome Trust Biocentre, University of Dundee, Dow Street, Dundee DD1 5EH, UK
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Chapter 15 Electrophoresis of proteins and peptides. ACTA ACUST UNITED AC 2004. [DOI: 10.1016/s0301-4770(04)80028-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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Righetti PG, Campostrini N, Pascali J, Hamdan M, Astner H. Quantitative proteomics: a review of different methodologies. EUROPEAN JOURNAL OF MASS SPECTROMETRY (CHICHESTER, ENGLAND) 2004; 10:335-348. [PMID: 15187293 DOI: 10.1255/ejms.600] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
The present review attempts to cover the vast array of methods which have appeared in the last few years for performing quantitative proteome analysis. These methods are divided into two classes: those applicable to conventional two-dimensional map analysis, coupling orthogonally a charge-based step (isoelectric focusing) to a size-based separation [sodium dodecylsulfate (SDS)-electrophoresis] and those applicable to two-dimensional chromatographic protocols. The first method, although being by and large the most popular approach, can offer differential display of paired samples with relatively few methods, the oldest one being based on statistical analysis performed on sets of gels via powerful software packages, such as the MELANIE, PDQuest, Z3 and Z4000, Phoretix and Progenesis. Recent developments comprise analysis performed on a single gel containing mixed samples differentially labeled, either with fluorophors (Cy3 and Cy5) or with d(0)/d(3) acrylamide. Conversely, chromatographic approaches, which mostly rely on analysis not of intact proteins but of their tryptic digests, offer a panoply of differential labeling protocols, most of which rely on stable isotope tagging. Essentially, all possible reactions have been described, such as those involving Lys, Asp, Glu, Cys residues, as well as a number of methods exploiting differential derivatization of amine and carboxyl groups generated during proteolysis. All such methods are described and evaluated.
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Affiliation(s)
- Pier Giorgio Righetti
- Department of Agricultural and Industrial Biotechnologies, University of Verona, Strada Le Grazie No. 15, 37134 Verona, Italy.
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Hamdan M, Righetti PG. Assessment of protein expression by means of 2-D gel electrophoresis with and without mass spectrometry. MASS SPECTROMETRY REVIEWS 2003; 22:272-284. [PMID: 12884390 DOI: 10.1002/mas.10056] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Careful examination of current literature, particularly over the last 5 years, reveals a wide range of approaches for the relative quantification of protein expression in cells, tissues, and body fluids. In view of such an observation, it is reasonable to ask whether researchers need new methods, or whether it is more productive to optimize and tune already existing ones. It is generally agreed that none of the existing methodologies on its own can give a full account of protein expression in a complex medium; this limitation, however, has not prevented the use of existing methods to provide valuable information on a wide range of proteins, where their expression has been correlated to certain pathologies and/or to pharmacological, genetic, or environmental factors. In the present work, an attempt is made to review the application of one of these methodologies, namely two-dimensional polyacrylamide gel electrophoresis on its own or in conjunction with mass spectrometry, to assess protein expression, particularly when such expression can be correlated to certain pathologies.
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Affiliation(s)
- Mahmoud Hamdan
- Computational, Analytical & Structural Sciences, GlaxoSmithKline, Verona, Italy.
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36
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Righetti PG, Castagna A, Antonucci F, Piubelli C, Cecconi D, Campostrini N, Zanusso G, Monaco S. The proteome: anno Domini 2002. Clin Chem Lab Med 2003; 41:425-38. [PMID: 12747583 DOI: 10.1515/cclm.2003.065] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
We present some current definitions related to functional and structural proteomics and the human proteome, and we review the following aspects of proteome analysis: Classical 2-D map analysis (isoelectric focusing (IEF) followed by SDS-PAGE); Quantitative proteomics (isotope-coded affinity tag (ICAT), fluorescent stains) and their use in e.g., tumor analysis and identification of new target proteins for drug development; Electrophoretic pre-fractionation (how to see the hidden proteome!); Multidimensional separations, such as: (a) coupled size-exclusion and reverse-phase (RP)-HPLC; (b) coupled ion-exchange and RP-HPLC; (c) coupled RP-HPLC and RP-HPLC at 25/60 degrees C; (d) coupled RP-HPLC and capillary electrophoresis (CE); (e) metal affinity chromatography coupled with CE; Protein chips. Some general conclusions are drawn on proteome analysis and we end this review by trying to decode the glass ball of the aruspex and answer the question: "Quo vadis, proteome"?
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Affiliation(s)
- Pier Giorgio Righetti
- Department of Agricultural and Industrial Biotechnologies, Faculty of Sciences, University of Verona, Verona, Italy.
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Sebastiano R, Citterio A, Lapadula M, Righetti PG. A new deuterated alkylating agent for quantitative proteomics. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2003; 17:2380-2386. [PMID: 14587083 DOI: 10.1002/rcm.1206] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Weakly basic molecules containing a double bond, such as 2- and 4-vinylpyridine, are able to react and selectively alkylate -SH groups in proteins, thus preventing their re-oxidation to disulphide bridges. In contrast to conventional alkylating agents such as iodoacetamide and non-charged acrylamide derivatives, such molecules achieve 100% alkylation of all -SH residues, even in complex proteins, without reacting with other functional groups. Their use is particularly effective in proteome analysis and more generally for analyzing proteins in which the -SH groups should be blocked. Additionally, the use of vinylpyridines, partially or totally deuterated and thus with a mass difference compared with their non-deuterated counterparts of 4-7 Da, allows studies of induction/repression of protein synthesis (quantitative proteomics).
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Affiliation(s)
- Roberto Sebastiano
- Department of Chemistry, Material and Engineering Chemistry, Politecnico of Milano, Via Mancinelli 7, Milano 20131, Italy
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38
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Hamdan M, Righetti PG. Modern strategies for protein quantification in proteome analysis: advantages and limitations. MASS SPECTROMETRY REVIEWS 2002; 21:287-302. [PMID: 12533801 DOI: 10.1002/mas.10032] [Citation(s) in RCA: 79] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Over the last 3 years, a number of mass spectrometry-based methods for the simultaneous identification and quantification of individual proteins within complex mixtures have been reported. Most, if not all, of such strategies apply a two-step approach: the first for the separation of proteins or peptides, and the second uses mass spectrometry to identify and quantify the individual components. To simplify the outcome of both steps, certain chemicals and heavy-isotope-labeling are commonly used in the early stages of sample preparation (except in differential fluorescence labeling protocols). The ultimate goal of these strategies is to be able to identify every protein expressed in a cell or tissue, and to determine each protein's abundance, state of modification, and possible involvement in multi-protein complexes. In this review, an attempt is made to highlight the salient characteristics of the existing strategies with particular attention to their strengths and weaknesses.
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Affiliation(s)
- Mahmoud Hamdan
- Computational, Analytical, and Structural Sciences, GlaxoSmithKline, Verona, Italy.
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Affiliation(s)
- John J Kopchick
- Edison Biotechnology Institute, Molecular and Cellular Biology Program, Department of Biomedical Sciences, College of Osteopathic Medicine, Ohio University, Athens, Ohio 45701, USA.
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40
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Gianazza E, Eberini I, Villa P, Fratelli M, Pinna C, Wait R, Gemeiner M, Miller I. Monitoring the effects of drug treatment in rat models of disease by serum protein analysis. J Chromatogr B Analyt Technol Biomed Life Sci 2002; 771:107-30. [PMID: 12015995 DOI: 10.1016/s0378-4347(01)00562-x] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
In this review we list from literature investigations on rat serum proteins using electrophoretic techniques in connection with drug testing. From our own research work, we provide annotated two-dimensional maps of rat serum proteins under control and experimental conditions. Emphasis is on species-specific components and on the effects of acute and chronic inflammation. We discuss our project of structural proteomics on rat serum as a minimally invasive approach to pharmacological investigation, and we outline a typical experimental plan for drug testing according to the above guidelines. We then report in detail on the results of our trials of anti-inflammatory drugs on adjuvant arthritis, an animal model of disease resembling in many aspects human rheumatoid arthritis. We demonstrate a correlation between biochemical parameters and therapeutic findings and outline the advantages of the chosen methodological approach, which proved also sensitive in revealing "side effects" of the test drugs. In an appendix we describe our experimental protocol when performing two-dimensional electrophoresis of rat serum.
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Affiliation(s)
- Elisabetta Gianazza
- Dipartimento di Scienze Farmacologiche, Università degli Studi di Milano via Balzaretti 9, I-20133 Milan, Italy.
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41
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Piubelli C, Galvani M, Hamdan M, Domenici E, Righetti PG. Proteome analysis of rat polymorphonuclear leukocytes: a two-dimensional electrophoresis/mass spectrometry approach. Electrophoresis 2002; 23:298-310. [PMID: 11840539 DOI: 10.1002/1522-2683(200202)23:2<298::aid-elps298>3.0.co;2-i] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The development of a two-dimensional (2-D) map of rat polymorphonuclear (PMN) leukocytes is here reported for the first time. The map is built up by utilizing a wide immobilized pH gradient (IPG), pH 3-10, in the first dimension and also a narrower IPG pH 4.5-8.5 gradient. In addition, the map is constructed by adopting the most recent protocols in 2-D mapping, which call for reduction and alkylation of the sample prior to the start of any electrophoretic step, including the IPG dimension. Fifty-two major protein spots have been so far identified by utilizing both matrix assisted laser desorption/ionization-time of flight (MALDI-TOF) and electrospray quadrupole (Q)-TOF mass spectrometry. A large number of house-keeping and cytoskeleton proteins were detected, together with proteins which are specific to PMN organelles or related to PMN functions such as phagocytosis and chemotaxis. The results obtained demonstrate the possibility of obtaining a single 2-D gel based proteomic map of PMN with representative proteins from different cellular compartments, also including membrane components, allowing the study of PMN protein expression on a proteome-wide scale. The aim of this project is to build an extensive database of such proteins, to be utilized for future studies where the expression of PMN proteins is used as a disease- or drug treatment marker.
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Affiliation(s)
- Chiara Piubelli
- Department of Agricultural and Industrial Biotechnologies, University of Verona, Italy
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42
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Antonucci F, Chilosi M, Santacatterina M, Herbert B, Righetti PG. Proteomics and immunomapping of reactive lymph-node and lymphoma. Electrophoresis 2002; 23:356-62. [PMID: 11840544 DOI: 10.1002/1522-2683(200202)23:2<356::aid-elps356>3.0.co;2-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
In the present study we show that two-dimensional (2-D) maps together with immuno-detection allow the precise identification of important leukocyte differentiation and tumor markers (e.g., CD3 and CD5), and important cell cycle regulatory molecules such as cyclin dependent kinases, notably CDK6. In addition, the comparative evaluation of molecular expression (e.g., CD5) in maps developed with normal and lymphoma samples can provide reproducible and precise information regarding the molecular expression in different cell populations. Accordingly, we could detect a much increased level of expression of CD5 in mantle cell lymphoma, up to ten times higher than in the control. In addition, CD5 in tumor tissues seems to be microheterogeneous as compared to normal samples.
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Affiliation(s)
- Francesca Antonucci
- Department of Agricultural and Industrial Biotechnologies, University of Verona, Italy
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43
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Gehanne S, Cecconi D, Carboni L, Righetti PG, Domenici E, Hamdan M. Quantitative analysis of two-dimensional gel-separated proteins using isotopically marked alkylating agents and matrix-assisted laser desorption/ionization mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2002; 16:1692-1698. [PMID: 12203238 DOI: 10.1002/rcm.773] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
We describe a simple approach for the relative quantification of individual proteins within a mixture. The method is based on the differential labelling of the mixtures by use of a commercially available acrylamide and deuterium-labelled [2,3,3'-d(3)]-acrylamide to alkylate proteins prior to two-dimensional (2-D) gel electrophoresis. The tryptic digests of the separated proteins were subjected to reflector matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) analysis and the relative peak heights of cysteine-containing peptides were used to quantify their precursor proteins. This approach was tested for the relative quantification of proteins within an artificial mixture of standard proteins and for proteins observed in a 2-D map of rat serum. A good correlation was found between the measured ratios derived from MALDI-TOF data and those theoretically calculated prior to 2-D analysis via known mixing ratios of the two alkylating reagents. The described procedure has proved to be effective for comparative measurements of protein abundances within the investigated mixtures.
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Affiliation(s)
- Sylvie Gehanne
- Computational, Analytical and Structural Sciences, Discovery Research, GlaxoSmithKline, Verona, Italy
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44
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Castagna A, Campostrini N, Farinazzo A, Zanusso G, Monaco S, Righetti PG. Comparative two-dimensional mapping of prion protein isoforms in human cerebrospinal fluid and central nervous system. Electrophoresis 2002; 23:339-46. [PMID: 11840542 DOI: 10.1002/1522-2683(200202)23:2<339::aid-elps339>3.0.co;2-y] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The cellular prion protein (PrP(C)) is a glycosylphosphatidylinositol (GPI)-anchored glycoprotein abundant in neurons. Although its precise function is unknown, PrP(C) represents the substrate for the generation of a conformational pathogenic isoform (PrP(Sc)) in human and animal transmissible spongiform encephalopathies, or prion diseases. By applying novel solubilization cocktails, we analyzed normal human brain and cerebrospinal fluid (CSF) PrP(C) by immunoblot of two-dimensional (2-D) gel electrophoresis preparations, using specific antibodies. Here, we show that PrP(C) from brain and CSF is composed of several charge isomers of differently glycosylated isoforms of the full-length PrP(C) and two N-terminally truncated fragments of 20 and 18 kDa. In the CSF, substantial amounts of the highly glycosylated PrP(C) isoforms and of the unglycosylated 18 kDa fragment are detected. Our study, for the first time, provides a detailed 2-D map of human PrP(C) both in brain and CSF, and establishes an innovative and sensitive method that might help in detecting the CSF pathological PrP(Sc) isoform in vivo. It also shows the incredible microheterogeneity of such isoforms (ca. 60 spots!), as revealed in 2-D mapping, as opposed to 3-4 main zones by mono-dimensional sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE).
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Affiliation(s)
- Annalisa Castagna
- Department of Agricultural and Industrial Biotechnologies, University of Verona, Italy
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45
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Candiano G, Musante L, Bruschi M, Ghiggeri GM, Herbert B, Antonucci F, Righetti PG. Two-dimensional maps in soft immobilized pH gradient gels: a new approach to the proteome of the Third Millennium. Electrophoresis 2002; 23:292-7. [PMID: 11840538 DOI: 10.1002/1522-2683(200202)23:2<292::aid-elps292>3.0.co;2-5] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Same major improvements in proteome analysis of cytosolic and membrane proteins by two-dimensional mapping are here reported. A much improved transfer of proteins from the first to the second dimensional sodium dodecyl sulfate (SDS)-gel is obtained by simply diluting the gel matrix, normally composed of 4%T polyacrylamide in all commercially available Immobiline strips down to as low as 3%T. In the analysis of total lysates of platelets, this augmented transfer has been evaluated as being 2-3 times higher than in standard 4%T gels. A second major improvement, in the case of analysis of membrane protein preparations, has been demonstrated to consist in a delipidation step in a tertiary solvent mixture composed of tri-n-butyl phosphate:acetone:methanol in a 1:12:1 ratio. By adopting this protocol, large amounts of spectrins (240-220 kDa, filamentous proteins of the red blood cell membranes) could be transferred vs. essentially none when delipidation was omitted. The present report also confirms the importance of a reduction and alkylation step of the protein sample prior to all electrophoretic steps, including focusing in the Immobiline gel, as recently reported by Herbert et al.
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46
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Current literature in mass spectrometry. JOURNAL OF MASS SPECTROMETRY : JMS 2001; 36:1324-1333. [PMID: 11754125 DOI: 10.1002/jms.99] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
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47
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Hamdan M, Galvani M, Righetti PG. Monitoring 2-D gel-induced modifications of proteins by MALDI-TOF mass spectrometry. MASS SPECTROMETRY REVIEWS 2001; 20:121-141. [PMID: 11746345 DOI: 10.1002/mas.10000] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
In addition to more than 200 endogenously produced post-translational modifications, a detailed analysis of 2-D gel-separated proteins must also consider other modifications that a protein can experience during various steps of its separation. This review describes the use of matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry to investigate some of these modifications, which can originate during sample preparation and/or during the separation phase. The analyses described were mostly conducted at pH 9-9.5, and yielded reliable information on stable adduct formation that involved protein-bound amino acids and a number of gel components, including acrylamide derivatives, gel cross-linkers, and Immobiline chemicals. The -SH group of Cys was found to be the prime target of such adducts; however, longer reaction times revealed the involvement of the epsilon-NH2 of Lys. The same analysis revealed that the failure to achieve full reduction/alkylation prior to any electrophoretic step could result in protein-protein interaction, which could lead to a number of spurious spots in the final 2-D map. The implications of these modifications on the MS analysis in particular and on proteome research in general are discussed.
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Affiliation(s)
- M Hamdan
- GlaxoSmithKline Group, Medicines Research Center, via Fleming 4, Verona, Italy.
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48
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Current Awareness on Comparative and Functional Genomics. Comp Funct Genomics 2001. [PMCID: PMC2447222 DOI: 10.1002/cfg.60] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
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