Mass spectral compatibility of four proteomics stains

Journal of Proteome Research

Volumn 6, Issue 11, 2007, Pages 4313-4320

  Ball, Malcolm S ^a   Karuso, Peter ^a  

^a MACQUARIE UNIVERSITY   (Australia)

Author keywords

Deep Purple; Epicocconone; Flamingo; Fluorescence; Krypton; LavaPurple; Peptide mass fingerprinting; SYPRO Ruby; Total protein stain

Indexed keywords

CYSTEINE; FLUORESCENT DYE; TRYPTOPHAN;

ARTICLE; CHEMICAL STRUCTURE; GEL ELECTROPHORESIS; IMAGE ANALYSIS; IMAGE QUALITY; MATRIX ASSISTED LASER DESORPTION IONIZATION TIME OF FLIGHT MASS SPECTROMETRY; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEOMICS; STAINING;

BENZOPYRANS; CYSTEINE; FALSE POSITIVE REACTIONS; FURANS; IMAGE PROCESSING, COMPUTER-ASSISTED; KETONES; KRYPTON; MASS SPECTROMETRY; MODELS, CHEMICAL; MODELS, STATISTICAL; PEPTIDES; PROTEINS; PROTEOMICS; REPRODUCIBILITY OF RESULTS; SPECTROMETRY, FLUORESCENCE; TRYPTOPHAN;

EID: 36348982816     PISSN: 15353893     EISSN: None     Source Type: Journal    
DOI: 10.1021/pr070398z     Document Type: Article

References (46)

1. Gorg, A.; Weiss, W.; Dunn, M. J. Current two-dimensional electrophoresis technology for proteomics. Proteomics 2004, 4 (12), 3665-3685.
2. Zolotarjova, N.; Martosella, J.; Nicol, G.; Bailey, J.; Boyes, B. E. Differences among techniques for high-abundant protein depletion. Proteomics 2005, 5 (13), 3304-3313.
3. Butt, R. H.; Coorssen, J. R. Pre-extraction sample handling by automated frozen disruption significantly improves subsequent proteomic analyses. J. Proteome Res. 2006, 5 (2), 437-448.
4. Pieper, R.; Gatlin, C. L.; Makusky, A. J.; Russo, P. S.; Schatz, C. R.; Miller, S. S.; Su, Q.; McGrath, A. M.; Estock, M. A.; Parmar, P. P.; Zhao, M.; Huang, S. T.; Zhou, J.; Wang, F.; Esquer-Blasco, R.; Anderson, N. L.; Taylor, J.; Steiner, S. The human serum proteome: Display of nearly 3700 chromatographicaily separated protein spots on two-dimensional electrophoresis gels and identification of 325 distinct proteins. Proteomics 2003, 3 (7), 1345-1364.
5. Wei, H.; Nolkrantz, K.; Powell, D. H.; Woods, J. H.; Ko, M.-C.; Kennedy, R. T. Electrospray sample deposition for matrix-assisted laser desorption/ionization (MALDI) and atmospheric pressure MALDI mass spectrometry with attomole detection limits. Rapid Commun. Mass Spectrom. 2004, 18 (11), 1193-1200.
6. Sommerer, N.; Centeno, D.; Rossignol, M. Peptide mass fingerprinting: Identification of proteins by MALDI-ToF. Methods Mol. Biol. 2007, 355, 219-234.
7. Li, X.; Gong, Y.; Wang, Y.; Wu, S.; Cai, Y.; Ping He, P.; Lu, Z.; Ying, Z.; Zhang, Y.; Jiao, L.; He, H.; Zhang, Z.; He, F.; Zhao, X.; Qian, X. Comparison of alternative analytical techniques for the characterisation of the human serum proteome in HUPO Plasma Proteome Project. Proteomics 2005, 5 (13), 3423-3441.
8. Chen, X.; Murawski, A.; Kuang, G.; Sexton, D. J.; Galbraith, W. Sample preparation for MALDI mass spectrometry using an elastomeric device reversibly sealed on the MALDI target. Anal. Chem. 2006, 78 (17), 6160-6168.
9. de Moreno, M. R.; Smith, J. F.; Smith, R. V. Mechanism studies of Coomassie blue and silver staining of proteins. J. Pharm. Sci. 1986, 75 (9), 907-911.
10. Haebel, S.; Albrecht, T.; Sparbier, K.; Waiden, P.; Körner, R.; Steup, M. Electrophoresis-related protein modification: alkylation of carboxy residues revealed by mass spectrometry. Electrophoresis 1998, 19 (5), 679-686.
11. Patton, W. F. Detection technologies in proteome analysis. J. Chromatogr., B: Analyt. Technol. Biomed. Life Sci. 2002, 771 (1-2), 3-31.
12. Fazekas de St.Groth, S.; Webster, R. G.; Datyner, A. Two new staining procedures for quantitative estimation of proteins on electrophoretic strips. Biochim. Biophys. Acta 1963, 71, 377-391.
13. Neuhoff, V.; Arold, N.; Taube, D.; Ehrhardt, W. Improved staining of proteins in Polyacrylamide gels including isoelectric focusing gels with clear background at nanogram sensitivity using Coomassie Brilliant Blue G-250 and R-250. Electrophoresis 1988, 9 (6), 255-262.
14. Luo, S.; Wehr, N. B.; Levine, R. L. Quantitation of protein on gels and blots by infrared fluorescence of Coomassie blue and Fast Green. Anal. Biochem. 2006, 350 (2), 233-238.
15. Harris, L. R.; Churchward, M. A.; Butt, R. H.; Coorssen J. R. Assessing detection methods for gel-based proteomic J. Proteome Res. 2007, 6 (4), 1418-1425.
16. Switzer, R. C., III; Merril, C. R.; Shifrin, S. A. Highly sensitive silver stain for detecting proteins and peptides in polyacrylamide gels. Anal. Biochem. 1979, 98 (1), 231-237.
17. Jin, L. T.; Hwang, S. Y.; Yoo, G. S.; Choi, J. K. Sensitive silver staining of protein in sodium dodecyl sulfate-polyacrylamide gels using an azo dye, calconcarboxylic acid, as a silver-ion sensitizer. Electrophoresis 2004, 25 (15), 2494-2500.
18. Jin, L. T.; Hwang, S. Y.; Yoo, G. S.; Choi, J. K. A mass spectrometry compatible silver staining method for protein incorporating a new silver sensitizer in sodium dodecyl sulfate-polyacrylamide electrophoresis gels. Proteomics 2006, 6 (8), 2334-2337.
19. White, I. R.; Pickford, R.; Wood, J.; Skehel, J. M.; Gangadharan, B.; Cutler, P. A statistical comparison of silver and SYPRO Ruby staining for proteomic analysis. Electrophoresis 2004, 25 (17), 3048-3054.
20. Mortz, E.; Krogh, T. N.; Vorum, H.; Gorg, A. Improved silver staining protocols for high sensitivity protein identification using matrix-assisted laser desorption/ionization-time of flight analysis. Proteomics 2001, 1 (11), 1359-1363.
21. Chevalier, F.; Rofidal, V.; Vanova, P.; Bergoin, A.; Rossignol, M. Proteomic capacity of recent fluorescent dyes for protein staining. Phytochemistry 2004, 65 (11), 1499-1506.
22. Berggren, K. N.; Schulenberg, B.; Lopez, M. F.; Steinberg, T. H.; Bogdanova, A.; Smejkal, G.; Wang, A.; Patton, W. F. An improved formulation of SYPRO Ruby protein gel stain: comparison with the original formulation and with a ruthenium II tris (bathophenanthroline disulfonate) formulation. Proteomics 2002, 2 (5), 486-498.
23. White, I. R.; Pickford, R.; Wood, J.; Skehel, J. M.; Gangadharan, B.; Cutler, P. A statistical comparison of silver and SYPRO Ruby staining for proteomic analysis. Electrophoresis 2004, 25 (17), 3048-3054.
24. Bell, P. J.; Karuso, P. Epicocconone, a novel fluorescent compound from the fungus Epicoccum nigrum. J. Am. Chem. Soc. 2003, 125 (31), 9304-9305.
25. Mackintosh, J. A.; Choi, H.-Y.; Bae, S. H.; Veal, D. A.; Bell, P. J.; Ferrari, B. C.; Van Dyk, D. D.; Verrills, N. M.; Paik, Y. K.; Karuso, P. A fluorescent natural product for ultra sensitive detection of proteins in one-dimensional and two-dimensional gel electrophoresis. Proteomics 2003, 3 (12), 2273-2288.
26. Coghlan, D. R.; Mackintosh, J. A.; Karuso, P. Mechanism of reversible fluorescent staining of protein with epicocconone. Org. Lett. 2005, 7 (12), 2401-2404.
27. Svensson, E.; Hedberg, J. J.; Malmport, E.; Bjellqvist, B. Fluorescent in-gel protein detection by regulating the pH during staining. Anal. Biochem. 2006, 355 (2), 304-306.
28. Wenzel, M.; Czerney, P.; Schweder, B.; Lehmann, F. Protein identifying and quantifying method. WO2006/079334 Aug. 3 2006, Dyomics GMBH.
29. Wolf, B. D.; Desai, S.; Shiflett, S.; Bell, P. A. Krypton: A sensitive fluorescent protein stain for protein detection in polyacrylamide gels. 20th Annual Symposium of The Protein Society, San Diego, CA, August 5-9, 2006.
30. Berkelman, T. Detection and quantitation of proteins using a novel fluorescent dye. BioRad technical bulletin 5352, http://www.biorad.com/ cmc_upload/Literature/194338/Bulletin_5352.pdf
31. Smejkal, G. B.; Robinson, M. H.; Lazarev, A. Comparison of fluorescent stains: relative photostability and differential staining of proteins in two-dimensional gels. Electrophoresis 2004, 25 (15), 2511-2519.
32. Olson, M. T.; Epstein, J. A.; Yergey, A. L. De novo peptide sequencing using exhaustive enumeration of peptide composition. J. Am. Soc. Mass Spectrom. 2006, 17 (8), 1041-1049.
33. BioRad Instruction Manual 4110064, 2-D SDS-PAGE Standards, Rev A. http://www.bio-rad.com/cmc_upload/Literature/33693/MS4110064A.pdf.
34. Perkins, D. N.; Pappin, D. J.; Creasy, D. M.; Cottrell, J. S. Probability-based protein identification by searching sequence databases using mass spectrometry data. Electrophoresis 1999, 20 (18), 3551-3567.
35. Siepen, J. A.; Keevil, E.-J.; Knight, D.; Hubbard, S. J. Prediction of missed cleavages in tryptic peptides aids protein identification in proteomics. J. Prooteome Res. 2007, 6 (1), 399-408.
36. Lopez, M. F.; Berggren, K.; Chernokalskaya, E.; Lazarev, A.; Robinson, M.; Patton, W. F. A comparison of silver stain and SYPRO Ruby Protein Gel Stain with respect to protein detection in two-dimensional gels and identification by peptide mass profiling. Electrophoresis 2000, 21 (17), 3673-3683.
37. Klenø, T. G.; Andreasen, C. M.; Kjeldal, H. O.; Leonardsen, L. R.; Krogh, T. N.; Nielsen, P. F.; Sorensen, M. V.; Jensen. O. N. MALDI MS peptide mapping performance by in-gel digestion on a probe with prestructured sample supports. Anal. Chem. 2004, 76 (13) 3576-3583.
38. Lanne, B.; Panfilov, O. Protein staining influences the quality of mass spectra obtained by peptide mass fingerprinting after separation on 2-d gels. A comparison of staining with Coomassie brilliant blue and SYPRO ruby. J. Proteome Res. 2005, 4 (1) 175-179.
39. Tannu, N. S.; Sanchez-Brambila, G.; Kirby, P.; Andacht, T. M. Effect of staining reagent on peptide mass fingerprinting from in-gel trypsin digestions: A comparison of SYPRO Ruby and DeepPurple. Electrophoresis 2006, 27 (15) 3136-3143.
40. BioRad product sheet 5346 Flamingo Fluorescent Gel Stain Product Information Sheet, Rev A http://www.bio-rad.com/cmc_upload/Literature/195737/ Bulletin_5346.pdf
41. Pierce product note Prod. No. 46628, 46629, 46630 Doc. No. 1829 Instructions for Krypton Protein Stain http://www.piercenet.com/files/1829as4. pdf
42. Steinberg, T. H.; Jones, L. J.; Haugland, R. P.; Singer, V. L. SYPRO orange and SYPRO red protein gel stains: One-step fluorescent staining of denaturing gels for detection of nanogram levels of protein. Anal. Biochem. 1996, 239 (2), 223-237.
43. Yang, S. H.; Liu, R.; Perez, E. J.; Wen, Y.; Stevens, S. M., Jr.; Valencia, T.; Brun-Zinkernagel, A. M.; Prokai, L.; Will, Y.; Dykens, J.; Koulen, P.; Simpkins, J. W. Mitochondrial localization of estrogen receptor β. Proc. Natl. Acad. Sci. U.S.A. 2004, 101 (12), 4130-4135.
44. Schwend, T.; Gustafsson, J. A. False positives in MALDI-TOF detection of ERβ in mitochondria. Biochem. Biophys. Res. Commun. 2006, 343 (3), 707-711.
45. Povse, V. G.; Olabe, J. A. Kinetics and mechanism of ligand interchange in the [RuIII(edta)L) complexes; L = cysteine and related thiolates. Trans. Metal Chem. 1998, 23 (6), 657-662.
46. Stodt, R.; Gencaslan, S.; Frodl, A.; Schmidt, C.; Sheldrick, W. S. Functional mono- and dinuclear peptide complexes featuring chemospecific κ S- or η 6-coordination of organometallic half-sandwich fragments. Inorg. Chim. Acta 2003, 355, 242-253.