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Chatterjee S, Karuso P, Boulangé A, Franck X, Datta A. Excited State Dynamics of Brightly Fluorescent Second Generation Epicocconone Analogues. J Phys Chem B 2015; 119:6295-303. [DOI: 10.1021/acs.jpcb.5b02190] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Soumit Chatterjee
- Department of Chemistry & Biomolecular Sciences, Macquarie University, Sydney 2109, Australia
| | - Peter Karuso
- Department of Chemistry & Biomolecular Sciences, Macquarie University, Sydney 2109, Australia
| | - Agathe Boulangé
- Normandie Univ,
COBRA, UMR 6014 et FR 3038, CNRS, Univ Rouen, INSA Rouen, 1 rue Tesnières, 76821 Mont-Saint-Aignan, Cedex, France
| | - Xavier Franck
- Normandie Univ,
COBRA, UMR 6014 et FR 3038, CNRS, Univ Rouen, INSA Rouen, 1 rue Tesnières, 76821 Mont-Saint-Aignan, Cedex, France
| | - Anindya Datta
- Department
of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India
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Butt RH, Coorssen JR. Coomassie blue as a near-infrared fluorescent stain: a systematic comparison with Sypro Ruby for in-gel protein detection. Mol Cell Proteomics 2013; 12:3834-50. [PMID: 24043422 DOI: 10.1074/mcp.m112.021881] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Quantitative proteome analyses suggest that the well-established stain colloidal Coomassie Blue, when used as an infrared dye, may provide sensitive, post-electrophoretic in-gel protein detection that can rival even Sypro Ruby. Considering the central role of two-dimensional gel electrophoresis in top-down proteomic analyses, a more cost effective alternative such as Coomassie Blue could prove an important tool in ongoing refinements of this important analytical technique. To date, no systematic characterization of Coomassie Blue infrared fluorescence detection relative to detection with SR has been reported. Here, seven commercial Coomassie stain reagents and seven stain formulations described in the literature were systematically compared. The selectivity, threshold sensitivity, inter-protein variability, and linear-dynamic range of Coomassie Blue infrared fluorescence detection were assessed in parallel with Sypro Ruby. Notably, several of the Coomassie stain formulations provided infrared fluorescence detection sensitivity to <1 ng of protein in-gel, slightly exceeding the performance of Sypro Ruby. The linear dynamic range of Coomassie Blue infrared fluorescence detection was found to significantly exceed that of Sypro Ruby. However, in two-dimensional gel analyses, because of a blunted fluorescence response, Sypro Ruby was able to detect a few additional protein spots, amounting to 0.6% of the detected proteome. Thus, although both detection methods have their advantages and disadvantages, differences between the two appear to be small. Coomassie Blue infrared fluorescence detection is thus a viable alternative for gel-based proteomics, offering detection comparable to Sypro Ruby, and more reliable quantitative assessments, but at a fraction of the cost.
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Gauci VJ, Wright EP, Coorssen JR. Quantitative proteomics: assessing the spectrum of in-gel protein detection methods. J Chem Biol 2011; 4:3-29. [PMID: 21686332 PMCID: PMC3022124 DOI: 10.1007/s12154-010-0043-5] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2010] [Accepted: 06/02/2010] [Indexed: 11/28/2022] Open
Abstract
Proteomics research relies heavily on visualization methods for detection of proteins separated by polyacrylamide gel electrophoresis. Commonly used staining approaches involve colorimetric dyes such as Coomassie Brilliant Blue, fluorescent dyes including Sypro Ruby, newly developed reactive fluorophores, as well as a plethora of others. The most desired characteristic in selecting one stain over another is sensitivity, but this is far from the only important parameter. This review evaluates protein detection methods in terms of their quantitative attributes, including limit of detection (i.e., sensitivity), linear dynamic range, inter-protein variability, capacity for spot detection after 2D gel electrophoresis, and compatibility with subsequent mass spectrometric analyses. Unfortunately, many of these quantitative criteria are not routinely or consistently addressed by most of the studies published to date. We would urge more rigorous routine characterization of stains and detection methodologies as a critical approach to systematically improving these critically important tools for quantitative proteomics. In addition, substantial improvements in detection technology, particularly over the last decade or so, emphasize the need to consider renewed characterization of existing stains; the quantitative stains we need, or at least the chemistries required for their future development, may well already exist.
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Affiliation(s)
- Victoria J. Gauci
- Molecular Physiology, School of Medicine, and Molecular Medicine Research Group, University of Western Sydney, Campbelltown, NSW 1797 Australia
| | - Elise P. Wright
- Molecular Physiology, School of Medicine, and Molecular Medicine Research Group, University of Western Sydney, Campbelltown, NSW 1797 Australia
| | - Jens R. Coorssen
- Molecular Physiology, School of Medicine, and Molecular Medicine Research Group, University of Western Sydney, Campbelltown, NSW 1797 Australia
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Schröder S, Brandmüller A, Deng X, Ahmed A, Wätzig H. Improving precision in gel electrophoresis by stepwisely decreasing variance components. J Pharm Biomed Anal 2009; 50:320-7. [DOI: 10.1016/j.jpba.2009.04.034] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2009] [Revised: 04/27/2009] [Accepted: 04/29/2009] [Indexed: 11/30/2022]
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5
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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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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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Tannu NS, Hemby SE. Two-dimensional fluorescence difference gel electrophoresis for comparative proteomics profiling. Nat Protoc 2007; 1:1732-42. [PMID: 17487156 PMCID: PMC2001252 DOI: 10.1038/nprot.2006.256] [Citation(s) in RCA: 137] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Quantitative proteomics is the workhorse of the modern proteomics initiative. The gel-based and MuDPIT approaches have facilitated vital advances in the measurement of protein expression alterations in normal and disease phenotypic states. The methodological advance in two-dimensional gel electrophoresis (2DGE) has been the multiplexing fluorescent two-dimensional fluorescence difference gel electrophoresis (2D-DIGE). 2D-DIGE is based on direct labeling of lysine groups on proteins with cyanine CyDye DIGE Fluor minimal dyes before isoelectric focusing, enabling the labeling of 2-3 samples with different dyes and electrophoresis of all the samples on the same 2D gel. This capability minimizes spot pattern variability and the number of gels in an experiment while providing simple, accurate and reproducible spot matching. This protocol can be completed in 3-5 weeks depending on the sample size of the experiment and the level of expertise of the investigator.
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Affiliation(s)
- Nilesh S Tannu
- Department of Physiology and Pharmacology, Wake Forest University School of Medicine, Winston-Salem, North Carolina 27157, USA
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Ball MS, Karuso P. Mass Spectral Compatibility of Four Proteomics Stains. J Proteome Res 2007; 6:4313-20. [DOI: 10.1021/pr070398z] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Malcolm S. Ball
- FLUOROtechnics Pty Limited, Macquarie University, Sydney, NSW, 2109, Australia, and Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW, 2109, Australia
| | - Peter Karuso
- FLUOROtechnics Pty Limited, Macquarie University, Sydney, NSW, 2109, Australia, and Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW, 2109, Australia
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Tannu N, Mash DC, Hemby SE. Cytosolic proteomic alterations in the nucleus accumbens of cocaine overdose victims. Mol Psychiatry 2007; 12:55-73. [PMID: 17075605 PMCID: PMC2442480 DOI: 10.1038/sj.mp.4001914] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/26/2006] [Revised: 08/01/2006] [Accepted: 08/21/2006] [Indexed: 11/08/2022]
Abstract
Chronic cocaine use in humans and animal models is known to lead to pronounced alterations in neuronal function in the nucleus accumbens (NAc), a brain region associated with drug reinforcement. Two-dimensional gel electrophoresis was used to compare protein alterations in the NAc between cocaine overdose (COD) victims (n=10) and controls (n=10). Following image normalization, spots with significantly differential image intensities (P<0.05) were identified, excised, trypsin digested and analyzed by matrix-assisted laser desorption ionization-time of flight-time of flight. A total of 1407 spots were found to be present in a minimum of five subjects per group and the intensity of 18 spots was found to be differentially abundant between the groups, leading to positive identification of 15 proteins by peptide mass fingerprinting (PMF). Of an additional 37 protein spots that were constitutively expressed, 32 proteins were positively identified by PMF. Increased proteins in COD included beta-tubulin, liprin-alpha3 and neuronal enolase, whereas decreased proteins included parvalbumin, ATP synthase beta-chain and peroxiredoxin 2. The present data provide a preliminary protein profile of COD, suggesting the involvement of novel proteins and pathways in the expression of this complex disease. Additional studies are warranted to further characterize alterations in the differentially regulated proteins. Understanding the coordinated involvement of multiple proteins in cocaine abuse provides insight into the molecular basis of the disease and offers new targets for pharmacotherapeutic intervention for drug abuse-related disorders.
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Affiliation(s)
- N Tannu
- Department of Physiology and Pharmacology, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - DC Mash
- Department of Neurology, University of Miami School of Medicine, Miami, FL, USA
| | - SE Hemby
- Department of Physiology and Pharmacology, Wake Forest University School of Medicine, Winston-Salem, NC, USA
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