Overview on modern approaches to speed up protein identification workflows relying on enzymatic cleavage and mass spectrometry-based techniques

Analytica Chimica Acta

Volumn 650, Issue 2, 2009, Pages 151-159

  Capelo, J L ^a   Carreira, R ^b   Diniz, M ^b   Fernandes, L ^b   Galesio, M ^b   Lodeiro, C ^a   Santos, H M ^b   Vale, G ^b  

^a UNIVERSITY OF VIGO   (Spain)

^b UNIVERSIDADE NOVA DE LISBOA   (Portugal)

Author keywords

Fast methods; Mass spectrometry; Protein identification; Proteomics

Indexed keywords

ALTERNATING ELECTRIC FIELD; ENZYMATIC CLEAVAGE; FAST METHODS; FUTURE PROSPECTS; HIGH PRESSURE; INFRARED ENERGY; MICRO REACTOR; MICROWAVE ENERGIES; PROTEIN DIGESTION; PROTEIN IDENTIFICATION; PROTEOMICS; SAMPLE TREATMENT; SPEED-UPS; ULTRASONIC ENERGY; WORK-FLOWS;

CHEMICAL REACTORS; ELECTRIC FIELDS; GELATION; HYDROCARBONS; MASS SPECTROMETERS; MASS SPECTROMETRY; MOLECULAR BIOLOGY; PROTEINS;

ELECTRIC TOOLS;

ALKYLATION; HIGH PERFORMANCE LIQUID CHROMATOGRAPHY; MASS SPECTROMETRY; MICROWAVE RADIATION; PRIORITY JOURNAL; PROCESS OPTIMIZATION; PROTEIN ANALYSIS; PROTEIN CLEAVAGE; PROTEIN DENATURATION; PROTEOMICS; REACTOR DESIGN; REVIEW; TWO DIMENSIONAL GEL ELECTROPHORESIS; ULTRASOUND;

ENZYMES; MASS SPECTROMETRY; PROTEIN DENATURATION; PROTEIN PROCESSING, POST-TRANSLATIONAL; PROTEINS; PROTEOMICS;

EID: 69249125736     PISSN: 00032670     EISSN: 18734324     Source Type: Journal    
DOI: 10.1016/j.aca.2009.07.034     Document Type: Review

References (47)

1. Blow N. Nat. Methods 5 (2008) 741-748
2. Dieguez-Acuna F.J. Mol. Cell. Proteomics 4 (2005) 1459-1470
3. Park S.K., Venable J.D., Xu T., and Yates III J.R. Nat. Methods 5 (2008) 319-322
4. López-Ferrer D., Cañas B., Vázquez J., Lodeiro C., Rial-Otero R., Moura I., and Capelo J.L. Trends Anal. Chem. 25 (2006) 996-1005
5. Craft D., and Li L. Anal. Chem. 77 (2005) 2649-2655
6. Duncan M.W., Yergay A.L., and Patterson S.D. Proteomics 9 (2009) 1124-1127
7. Sherman J., McKay M.J., Ashman K., and Molloy M.P. Proteomics 9 (2009) 1120-1123
8. Sandra K., Moshir M., D'hondt F., Tuytten R., Verleysen K., Kasa K., Francois I., and Sandra P. J. Chromatogr. B 877 (2009) 1019-1039
9. Chang J., Ruiz V., and Vancura A. Methods Mol. Biol. 457 (2008) 141-149
10. Roche S., Tiers L., Provansal M., Seveno M., Piva M.-T., Jouin P., and Lehmann S. J. Proteome Res. (2009) 10.1016/j.jprot.2009.03.008
11. Cañas B., Piñeiro C., Calvo E., López-Ferrer D., and Gallardo J.M. J. Chromatogr. A 1153 (2007) 235-258
12. Ruth M.C., Old W.M., Emrick M.A., Meyer-Arendt K., Aveline-Wolf L.D., Pierce K.G., Mendoza A.M., Sevinsky J.R., Hamady M., Knight R.D., Resing K.A., and Ahn N.G. J. Proteome Res. 5 (2006) 709-719
13. Bennion B.J., and Daggett V. Proc. Natl. Acad. Sci. U.S.A. 29 (2003) 5142-5147
14. http://www.millipore.com/catalogue/module.do;jsessionid=5BA346CF5894935347F0EF3DB2A3208 4?id=C5737, last accessed May 25, 2009.
15. Santos H.M., Mota C., Lodeiro C., Moura I., Isaac I., and Capelo J.L. Talanta 15 (2008) 870-875
16. Sun W., Gao S., Wang L., Chen Y., Wu S., Wang X., Zheng D., and Gao Y. Mol. Cell. Proteomics 5 (2006) 769-776
17. Huan H.F., Chang S.C., Huang H.C., and Chen S.T. Proteomics 5 (2005) 840-842
18. Starder M.B., Tabb D.L., Hervey W.J., Pan C., and Hurst G.B. Anal. Chem. 78 (2006) 125-134
19. López-Ferrer D., Capelo J.L., and Vázquez J. J. Proteome Res. 4 (2005) 1569-1574
20. Lozzia I., Puccia A., Pantania O.L., D'Acquib L.P., and Calamaia L. Anal. Biochem. 1 (2008) 108-114
21. Lowry O.H., Rosebrough N.J., Farr A.L., and Randall R.J. J. Biol. Chem. 193 (1951) 265-275
22. Ibáñez A.J., Muck A., Halim V., and Svatos A. J. Proteome Res. 6 (2007) 1183-1189
23. A. Monzo, E. Sperling, A. Guttman, Trac Trends Anal. Chem., 2009, doi:10.1016/j.trac.2009.03.002.
24. Galesio M., Vieira D.V., Rial-Otero R., Lodeiro C., Moura I., and Capelo J.L. J. Proteome Res. 7 (2008) 2097-2106
25. Havlis J., Thomas H., Sebela M., and Shevchenko A. Anal. Chem. 75 (2003) 1300-1306
26. Turapov O.A., Mukamolova G.V., Bottrill A.R., and Pangburn M.K. Anal. Chem. 80 (2008) 6093-6099
27. http://www.sigmaaldrich.com/etc/medialib/docs/Sigma/Bulletin/tt0010bul.Par.0001.File.tmp/tt0010bul.pdf, last accessed 27 May 2009.
28. http://www.sigmaaldrich.com/etc/medialib/docs/Sigma/General_Information/immobtrypsinspin.Par.0001.File.tmp/immobtrypsinspin.pdf, last accessed 27 May 2009.
29. Rial-Otero R., Carreira R.J., Cordeiro F.M., Moro A.J., Fernandes L., Moura I., and Capelo J.L. J. Proteome Res. 6 (2007) 909-912
30. Rial-Otero R., Carreira R.J., Cordeiro F.M., Moro A.J., Santos H.M., Moura I., and Capelo J.L. J. Chromatogr. A 1153 (2007) 291-299
31. Santos H.M., and Capelo J.L. Talanta 73 (2007) 795-802
32. Santos H.M., Rial-Otero R., Fernandes L., Vale G., Rivas M.G., Moura I., and Capelo J.L. J. Proteome Res. 6 (2007) 3393-3399
33. Klimek J., Eddes J.S., Hohmann L., Jackson J., Peterson A., Letarte S., Gafken P.R., Katz J.E., Mallick P., Lee H., Schmidt A., Ossola R., Eng J.K., Aebersold R., and Martin D.B. J. Proteome Res. 7 (2008) 96-103
34. Lopez-Ferrer D., Petritis K., Hixson K.K., Heibeck T.H., Moore R.J., Belov M.E., Camp D.G., and Smith R.D. J. Proteome Res. 7 (2008) 32766-33281
35. Lopez-Ferrer D., Petritis K., Lourette N.M., Clowers B., Hixson K.K., Heibeck T., Prior D.C., Pasa-Tolic L., Camp II D.G., Belov M.E., and Smith R.D. Anal. Chem. 80 (2008) 8930-8936
36. Wang S., Zhang L., Yang P., and Chen G. Proteomics 8 (2008) 2579-2582
37. Wang S., Liu T., Zhang L., and Chen G. J. Proteome Res. 7 (2008) 5049-5054
38. Bao H., Liu T., Chen X., and Chen G. J. Proteome Res. 7 (2008) 5339-5344
39. Bao H., Lui T., Zhang L., and Chen G. Proteomics 9 (2009) 1114-1117
40. Pramanik B.N., Mirza U.A., Ing Y.H., Liu Y.-H., Bartner P.L., Weber P.C., and Bose A.K. Protein Sci. 11 (2002) 2676-2687
41. Lin S., Yun D., Qi D., Deng C., Li Y., and Zhang X. J. Proteome Res. 7 (2008) 1297-1307
42. Wang S., Bao H., Liu T., Zhang L., Yang P., and Chen G. Rapid Commun. Mass Spectrom. 22 (2008) 3225-3232
43. Wang S., Wei B., Yang P., and Chen G. Proteomics 8 (2008) 4637-4641
44. Shuang J.L., Lin S., Qi D., Deng C., Yang P., and Zhang X. J. Chromatogr. A 1176 (2007) 169-177
45. Bonneil E., Mercier M., and Waldrom K.C. Anal. Chim. Acta 404 (2000) 29-45
46. Slysz G.W., and Schriemer D.C. Anal. Chem. 77 (2005) 1572
47. http://www.genomicsolutions.com/news/pr/release/20070605-2.aspx, last accessed 29 May 2009.