Application of pressurized solvents for ultrafast trypsin hydrolysis in proteomics: Proteomics on the fly

Journal of Proteome Research

Volumn 7, Issue 8, 2008, Pages 3276-3281

  López Ferrer, Daniel ^a   Petritis, Konstantinos ^a   Hixson, Kim K ^b   Heibeck, Tyler H ^a   Moore, Ronald J ^a   Belov, Mikhail E ^a   Camp II, David G ^a   Smith, Richard D ^a  

^a PACIFIC NORTHWEST NATIONAL LABORATORY   (United States)

^b PACIFIC NORTHWEST NATIONAL LABORATORY   (United States)

Author keywords

Bottom up proteomics; Mass spectrometry; Pressure cycling technology; Trypsin digestion

Indexed keywords

TRYPSIN; BACTERIAL PROTEIN; BUFFER; HEMOGLOBIN; SOLVENT;

ARTICLE; CONTROLLED STUDY; ELECTROSPRAY MASS SPECTROMETRY; FLY; NONHUMAN; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN DEGRADATION; PROTEIN HYDROLYSIS; REVERSED PHASE LIQUID CHROMATOGRAPHY; SHEWANELLA ONEIDENSIS; ANIMAL; CHEMISTRY; HORSE; HYDROLYSIS; LIQUID CHROMATOGRAPHY; METHODOLOGY; PRESSURE; PROTEIN FOLDING; PROTEOMICS; SHEWANELLA; TIME;

SHEWANELLA ONEIDENSIS;

ANIMALS; BACTERIAL PROTEINS; BUFFERS; CHROMATOGRAPHY, LIQUID; HEMOGLOBINS; HORSES; HYDROLYSIS; PRESSURE; PROTEIN FOLDING; PROTEOMICS; SHEWANELLA; SOLVENTS; SPECTROMETRY, MASS, ELECTROSPRAY IONIZATION; TIME FACTORS; TRYPSIN;

EID: 53049107743     PISSN: 15353893     EISSN: None     Source Type: Journal    
DOI: 10.1021/pr7008077     Document Type: Article

References (31)

1. Fischer, H. P. Towards quantitative biology: integration of biological information to elucidate disease pathways and to guide drug discovery. Biotechnol. Annu. Rev. 2005, 11, 1-68.
2. Hood, L.; Perlmutter, R. M. The impact of systems approaches on biological problems in drug discovery. Nat. Biotechnol. 2004, 22 (10), 1215-7.
3. Bladder, A. R.; Hammer, A. A.; MacCoss, M. J.; Wu, C. C. Quantitative comparison of proteomic data quality between a 2D and 3D quadrupole ion trap. Anal. Chem. 2006, 78 (4), 1337-44.
4. Denison, C.; Rudner, A. D.; Gerber, S. A.; Bakalarski, C. E.; Moazed, D.; Gygi, S. P. A proteomic strategy for gaining insights into protein sumoylation in yeast. Mol. Cell. Proteomics 2005, 4 (3), 246-54.
5. Hu, Q.; Noll, R. J.; Li, H.; Makarov, A.; Hardman, M.; Graham Cooks, R. The Orbitrap: a new mass spectrometer. J. Mass. Spectrom. 2005, 40 (4), 430-43.
6. Washburn, M. P.; Wolters, D.; Yates, J. R. Large-scale analysis of the yeast proteome by multidimensional protein identification technology. Nat. Biotechnol. 2001, 79 (3), 242-7.
7. Hernandez, P.; Muller, M.; Appel, R. D. Automated protein identification by tandem mass spectrometry: issues and strategies. Mass. Spectrom. Rev. 2006, 25 (2), 235-54.
8. López-Ferrer, D.; Cañas, B.; Vázquez, J.; Lodeiro, C; Rial-Otero, R.; Moura, I.; Capelo, J. L. Sample Treatment for Protein Identification by Mass Spectrometry-Based Techniques. Trends Anal. Chem. 2006, 25, 996-1005.
9. Havlis, J.; Thomas, H.; Sebela, M.; Shevchenko, A. Fast-response proteomics by accelerated in-gel digestion of proteins. Anal. Chem. 2003, 75 (6), 1300-6.
10. Stark, G. R.; Stein, W. H.; Moore, S. Reactions of the cyanate present in aqueous urea with amino acids and proteins. J. Biol. Chem. 1960, 235 (11), 3177-81.
11. Hervey, W. J. t.; Strader, M. B.; Hurst, G. B. Comparison of digestion protocols for microgram quantities of enriched protein samples. J. Proteome. Res. 2007, 6 (8), 3054-61.
12. Blonder, J.; Chan, K. C.; Issaq, H. J.; Veenstra, T. D. Identification of membrane proteins from mammalian cell/tissue using methanol-facilitated solubilization and tryptic digestion coupled with 2D-LC-MS/MS. Nat. Protoc. 2006, 1 (6), 2784-90.
13. Chen, E. I.; Cociorva, D.; Norris, J. L.; Yates, J. R., III. Optimization of mass spectrometry-compatible surfactants for shotgun proteomics. J. Proteome. Res. 2007, 6 (7), 2529-38.
14. Russell, W. K.; Park, Z. Y.; Russell, D. H. Proteolysis in mixed organic-aqueous solvent systems: applications for peptide mass mapping using mass spectrometry. Anal. Chem. 2001, 73 (11), 2682-2685.
15. Pramanik, B. N.; Mirza, U. A.; Ing, Y. H.; Liu, Y. H.; Bartner, P. L.; Weber, P. C.; Bose, A. K. Microwave-enhanced enzyme reaction for protein mapping by mass spectrometry: a new approach to protein digestion in minutes. Protein Sci. 2002, 11 (11), 2676-87.
16. Sun, W.; Gao, S.; Wang, L.; Chen, Y.; Wu, S.; Wang, X.; Zheng, D.; Gao, Y. Microwave-assisted protein preparation and enzymatic digestion in proteomics. Mol. Cell. Proteomics 2006, 5 (4), 769-76.
17. Zhong, H.; Zhang, Y.; Wen, Z.; Li, L. Protein sequencing by mass analysis of polypeptide ladders after controlled protein hydrolysis. Nat. Biotechnol. 2004, 22 (10), 1291-6.
18. Lopez-Ferrer, D.; Capelo, J. L.; Vazquez, J. Ultra fast trypsin digestion of proteins by high intensity focused ultrasound. J. Proteome. Res. 2005, 4 (5), 1569-74.
19. Postema, M.; van Wamel, A.; Lancee, C. T.; de Jong, N. Ultrasound induced encapsulated microbubble phenomena. Ultrasound Med. Biol. 2004, 30 (6), 827-40.
20. Cheftel, J. C. Effects of High Hydrostatic Pressure on Food Constituents: An Overview. In High Pressure and Biotechnology, Balny, C., Hayashi, R., Heremans, K., Masson, P. Eds.; John Libbey Eurotext, Ltd.: London, U.K., 1992; pp 195-209.
21. Cano, M. P.; Hernandez, A.; DeAncos, B. High pressure and temperature effects on enzyme inactivation in strawberry and orange products. J. Food Sci. 1997, 62 (1), 85-88.
22. Smejkal, G. B.; Witzmann, F. A.; Ringham, H.; Small, D.; Chase, S. F.; Behnke, J.; Ting, E. Sample preparation for two-dimensional gel electrophoresis using pressure cycling technology. Anal. Biochem. 2007, 363 (2), 309-11.
23. Shen, Y.; Zhao, R.; Belov, M. E.; Conrads, T. P.; Anderson, G. A.; Tang, K.; Pasa-Tolic, L.; Veenstra, T. D.; Lipton, M. S.; Smith, R. D. Packed capillary reversed-phase liquid chromotaography with high-performance electrospray ionization fourier transform ion cyclotron resonance mass spectrometry for proteomics. Anal. Chem. 2001, 73 (8), 1766-75.
24. Wang, H.; Qian, W. J.; Chin, M. H.; Petyuk, V. A.; Barry, R. C.; Liu, T.; Gritsenko, M. A.; Mottaz, H. M.; Moore, R. J.; Camp Ii, D. G.; Khan, A. H.; Smith, D. J.; Smith, R. D. Characterization of the mouse brain proteome using global proteomic analysis complemented with cysteinyl-peptide enrichment. J. Proteome. Res. 2006, 5 (2), 361-9.
25. Elias, D. A.; Monroe, M. E.; Smith, R. D.; Fredrickson, J. K.; Lipton, M. S. Confirmation of the expression of a large set of conserved hypothetical proteins in Shewanella oneidensis MR-1. J. Microbiol. Methods 2006, 66 (2), 223-33.
26. Lopez-Ferrer, D.; Martinez-Bartolome, S.; Villar, M.; Campillos, M.; Martin-Maroto, F.; Vazquez, J. Statistical model for large-scale peptide identification in databases from tandem mass spectra using SEQUEST. Anal. Chem. 2004, 76 (23), 6853-60.
27. Ding, J.; Sorensen, C. M.; Zhang, Q.; Jiang, H.; Jaitly, N.; Livesay, E. A.; Shen, Y.; Smith, R. D.; Metz, T. O. Capillary LC coupled with high-mass measurement accuracy mass spectrometry for metabolic profiling. Anal. Chem. 2007, 79 (16), 6081-93.
28. Adams, M. W.; Kelly, R. M. In Biocatalysis at Extreme Temperatures; Enzyme Systems Near and Above 100°C, ACS Symposium Series 498, American Chemical Society: Washington, DC, 1991; pp 86-107.
29. Gupta, N.; Tanner, S.; Jaitly, N.; Adkins, J. N.; Lipton, M.; Edwards, R.; Romine, M.; Osterman, A.; Bafna, V.; Smith, R. D.; Pevzner, P. A. Whole proteome analysis of post-translational modifications: Applications of mass-spectrometry for proteogenomic annotation. Genome Res. 2007, 17 (9), 1362-77.
30. Olsen, J. V.; Ong, S. E.; Mann, M. Trypsin cleaves exclusively C-terminal to arginine and lysine residues. Mol. Cell. Proteomics 2004, 3 (6), 608-14.
31. Ringham, H.; Bell, R. L.; Smejkal, G. B.; Behnke, J.; Witzmann, F. A. Application of pressure cycling technology to tissue sample preparation for 2-DE. Electrophoresis 2007, 28 (6), 1022-4.