Top-down and bottom-up proteomics of sds-containing solutions following mass-based separation

Journal of Proteome Research

Volumn 9, Issue 6, 2010, Pages 2863-2870

  Botelho, Diane ^a   Wall, Mark J ^a   Vieira, Douglas B ^a   Fitzsimmons, Shayla ^a   Liu, Fang ^a   Doucette, Alan ^a  

^a DALHOUSIE UNIVERSITY   (Canada)

Author keywords

Bottom up; Gelc; Gelfree; Mass Spectrometry; Proteins; SDS; SDS PAGE; Sodium Dodecyl Sulfate; Suppression; Top down

Indexed keywords

ACETONE; CHLOROFORM; DODECYL SULFATE SODIUM; METHANOL; PROTEOME; WATER;

ARTICLE; LIQUID CHROMATOGRAPHY; MASS SPECTROMETRY; NONHUMAN; POLYACRYLAMIDE GEL ELECTROPHORESIS; PRECIPITATION; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEOMICS;

CHEMICAL PRECIPITATION; CHROMATOGRAPHY, LIQUID; ELECTROPHORESIS, POLYACRYLAMIDE GEL; MASS SPECTROMETRY; MOLECULAR WEIGHT; PROTEINS; PROTEOME; PROTEOMICS; REPRODUCIBILITY OF RESULTS; SODIUM DODECYL SULFATE;

EID: 77954578929     PISSN: 15353893     EISSN: 15353907     Source Type: Journal    
DOI: 10.1021/pr900949p     Document Type: Article

References (29)

1. Hillenkamp, F.; Karas, M.; Beavis, R. C.; Chait, B. T. Matrix-assisted laser desorption ionization mass spectrometry of biopolymers. Anal. Chem. 1991, 63, A1193-A1202.
2. Fenn, J. B.; Mann, M.; Meng, C. K.; Wong, S. F.; Whitehouse, C. M. Electrospray ionization for mass spectrometry of large biomolecules. Science 1989, 246, 64-71.
3. Beavis, R. C.; Chait, B. T. Rapid, sensitive analysis of protein mixtures by mass spectrometry. Fresenius' J. Anal. Chem. 1992, 343, 25-25
4. Ikonomou, M. G.; Blades, A. T.; Kebarle, P. Investigations of the electrospray interface for liquid chromatography mass spectrometry. Anal. Chem. 1990, 62, 957-967.
5. Rundlett, K. L.; Armstrong, D. W. Mechanism of signal suppression by anionic surfactants in capillary electrophoresis-electrospray ionization mass spectrometry. Anal. Chem. 1996, 68, 3493-3497.
6. Asanuma, M.; Fukuzawa, S.; Matsuda, T.; Hirota, H. The effect of sodium dodecyl sulfate and anion exchange silica gel on matrix assisted laser desorption/ionization mass spectrometric analysis of proteins. Rapid Commun. Mass Spectrom. 2009, 23, 1647-1653.
7. Breaux, G. A.; Green-Church, K. B.; France, A.; Limbach, P. A. Surfactant-aided matrix assisted laser desorption/ionization mass spectrometry of hydrophobic and hydrophilic peptides. Anal. Chem. 2000, 72, 1169-1174.
8. Tummala, R.; Limbach, P. A. Effect of sodium dodecyl sulfate micelles on peptide mass fingerprinting by matrix assisted laser desorption/ionization mass spectrometry. Rapid Commun Mass Spectrom. 2004, 18, 2031-2035.
9. Chevallet, M.; Santoni, V.; Poinasm, A.; Rouquie, D.; Fuchs, A.; Kieffer, S.; Rossignol, M.; Lunardi, J.; Garin, J.; Rabilloud, T. New zwitterionic detergents improve the analysis of membrane proteins by two-dimensional electrophoresis. Electrophoresis 1998, 19, 1901-1909.
10. Jaeger, D. A.; Jamrozik, J.; Golich, T. G.; Clennan, M. W.; Mohebalian, J. Preparation and characterization of glycerol-based cleavable surfactants and derived vesicles. J. Am. Chem. Soc. 1989, 111, 3001-3006.
11. Anderson, P.; Heron, I. Simultaneous electroelution of whole SDS polyacrylamide gels for the direct cellular analysis of complex protein mixtures. J. Immunol. Methods 1993, 161, 29-39.
12. Hudgin, R. L.; Ashwell, G. Studies on role of glycosyltransferases in hepatic binding of asialoglycoproteins. J. Biol. Chem. 1974, 249, 7369-7372.
13. Wessel, D.; Flügge, U. I. A method for the quantitative recovery of protein in dilute solution in the presence of detergents and lipids. Anal. Biochem. 1984, 138, 141-143.
14. Stearne, P. A.; Vandriel, I. R.; Grego, B.; Simpson, R. J.; Goding, J. W. The murine plasma cell antigen PC-1 purification and partial amino acid sequence. J. Immunol. 1985, 134, 443-448.
15. Puchades, M.; Westman, A.; Blennow, K.; Davidsson, P. Removal of sodium dodecyl sulfate from protein samples prior to matrix assisted laser desorption/ionization mass spectrometry. Rapid Commun. Mass Spectrom. 1999, 13, 344-349.
16. Zhang, N.; Chen, R.; Young, N.; Wishart, D.; Winter, P.; Weiner, J. H.; Li, L. Comparison of SDS-and methanol-assisted protein solubilization and digestion methods for Escherichia coli membrane proteome analysis by 2-D LC-MS/MS. Proteomics 2007, 7, 484-493.
17. Wisniewski, J. R.; Wisniewski, J. R.; Zougman, A.; Nagaraj, N.; Mann, M. Universal sample preparation method for proteome analysis. Nat. Methods 2009, 6, 359-U60.
18. Tran, J. C.; Doucette, A. A. Gel Eluted Liquid Fractionation Entrapment Electrophoresis: An electrophoretic method for broad molecular weight range proteome determination. Anal. Chem. 2008, 80, 1568-1573.
19. Tran, J. C.; Doucette, A. A. Multiplexed size separation of intact proteins in solution phase for mass spectrometry. Anal. Chem., 2009, 81, 6201-6209.
20. Lee, J. E.; Kellie, J. F.; Tran, J. C.; Tipton, J. D.; Catherman, A. D.; Thomas, H. M.; Ahlf, D. R.; Durbin, K. R.; Vellaichamy, A.; Ntai, I.; Marshall, A. G.; Kelleher, N. L. A robust two-dimensional separation for top-down tandem mass spectrometry of the low-mass proteome. J. Am. Soc. Mass Spectrom. 2009, 20 (12), 2183-2191.
21. Shevchenko, A.; Wilm, M.; Vorm, O.; Mann, M. Mass spectrometric sequencing of proteins from silver stained polyacrylamide gels. Anal. Chem. 1996, 68, 850-858.
22. Schirle, M.; Heurtier, M. A.; Kuster, B. Profiling core proteomes of human cell lines by one dimensional PAGE and liquid chromatography-tandem mass spectrometry. Mol. Cell. Proteomics 2003, 2, 1297-1305.
23. de Godoy, L. M. F.; Olsen, J. V.; Cox, J.; Nielsen, M. L.; Hubner, N. C.; Frohlich, F.; Walther, T. C.; Mann, M. Comprehensive mass spectrometry based proteome quantification of haploid versus diploid yeast. Nature 2008, 455, 1251-U60.
24. Lemaire, M.; Deschamps, S.; Moller, J. V.; Lecafer, J. P.; Rossier, J. Electrospray-ionization mass-spectroscopy on hydrophobic peptides electroeluted from sodium dodecyl-sulfate polyacrylamidegel electrophoresis application to the topology of the sarcoplasmicreticulum Ca2+ ATPase. Anal. Biochem. 1993, 214, 50-57.
25. Laemmli, U. K. Cleavage of structural proteins during assembly of the head of bacteriophage T4. Nature 1970, 227, 680-685.
26. Blum, H.; Beier, H.; Gross, H. J. Improved silver staining of plantproteins, RNA and DNA in polyacyrlamide gels. Electrophoresis 1987, 8, 93-99.
27. Shevchenko, A.; Tomas, H.; Havlis, J.; Olsen, J. V.; Mann, M. Ingel digestion for mass spectrometric characterization of proteins. Nat. Protoc. 2006, 1, 2856-2860.
28. Arand, M.; Friedberg, T.; Oesch, F. Colorimetric quantitation of trace amounts of sodium lauryl sulfate in the presence of nucleicacids and proteins. Anal. Biochem. 1992, 207, 73-75.
29. Loo, R. R. O.; Dales, N.; Andrews, P. C. Surfactant effects on protein structure examined by electrospray ionization mass spectrometry. Protein Sci. 1994, 3, 1975-1983.