Proteolytic digestion methods for shotgun proteomics

Comprehensive Sampling and Sample Preparation

Volumn 3, Issue , 2012, Pages 261-276

  Fonslow, B R ^a   Yates, J R ^a  

^a SCRIPPS RESEARCH INSTITUTE   (United States)

Author keywords

Digestion; Integral membrane proteins; Liquid chromatography; Mass spectrometry; Peptide; Posttranslational modifications; Protease; Protein abundance; Protein sequence coverage; Sample heterogeneity; Shotgun proteomics; Trypsin

Indexed keywords

EID: 84883930346     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1016/B978-0-12-381373-2.00082-X     Document Type: Chapter

References (46)

1. Link A.J., Eng J., Schieltz D.M., Carmack E., Mize G.J., Morris D.R., Garvik B.M., Yates J.R. Nat. Biotechnol. 1999, 17:676-682.
2. Wolters D.A., Washburn M.P., Yates J.R. Anal. Chem. 2001, 73:5683-5690.
3. Eng J.K., McCormack A.L., Yates J.R. J. Am. Soc. Mass Spectrom. 1994, 5:976-989.
4. Khalsa-Moyers G., McDonald W.H. Brief. Funct. Genomics Proteomics 2006, 5:98-111.
5. Yates J.R., Ruse C.I., Nakorchevsky A. Annu. Rev. Biomed. Eng. 2009, 11:49-79.
6. Bodzon-Kulakowska A., Bierczynska-Krzysik A., Dylag T., Drabik A., Suder P., Noga M., Jarzebinska J., Silberring J. J. Chromatogr. 2007, 849:1-31.
7. Aebersold R., Mann M. Nature 2003, 422:198-207.
8. Cravatt B.F., Simon G.M., Yates J.R. Nature 2007, 450:991-1000.
9. Pariset L., Chillemi G., Bongiorni S., Romano Spica V., Valentini A. New Biotechnol. 2009, 25:272-279.
10. Trevino V., Falciani F., Barrera-Saldana H.A. Mol. Med. 2007, 13:527-541.
11. Mamanova L., Andrews R.M., James K.D., Sheridan,.E.M., Ellis P.D., Langford C.F., Ost T.W., Collins J.E., Turner D.J. Nat. Methods 2010, 7:130-132.
12. Mamanova L., Coffey A.J., Scott C.E., Kozarewa I., Turner E.H., Kumar A., Howard E., Shendure J., Turner D.J. Nat. Methods 2010, 7:111-118.
13. Anderson N.L., Anderson N.G. Mol. Cell. Proteomics 2002, 1:845-867.
14. Science 1998, 282:2012-2018. C. elegans Sequencing Consortium.
15. Adams M.D., Celniker S.E., Holt R.A., Evans C.A., Gocayne J.D., Amanatides P.G., Scherer S.E., Li P.W., Hoskins R.A., Galle R.F., George R.A., Lewis S.E., Richards S., Ashburner M., Henderson S.N., Sutton G.G., Wortman J.R., Yandell M.D., Zhang Q., Chen L.X., Brandon R.C., Rogers Y.H., Blazej R.G., Champe M., Pfeiffer B.D., Wan K.H., Doyle C., Baxter E.G., Helt G., Nelson C.R., Gabor G.L., Abril J.F., Agbayani A., An H.J., Andrews-Pfannkoch C., Baldwin D., Ballew R.M., Basu A., Baxendale J., Bayraktaroglu L., Beasley E.M., Beeson K.Y., Benos P.V., Berman B.P., Bhandari D., Bolshakov S., Borkova D., Botchan M.R., Bouck J., Brokstein P., Brottier P., Burtis K.C., Busam D.A., Butler H., Cadieu E., Center A., Chandra I., Cherry J.M., Cawley S., Dahlke C., Davenport L.B., Davies P., de Pablos B., Delcher A., Deng Z., Mays A.D., Dew I., Dietz S.M., Dodson K., Doup L.E., Downes M., Dugan-Rocha S., Dunkov B.C., Dunn P., Durbin K.J., Evangelista C.C., Ferraz C., Ferriera S., Fleischmann W., Fosler C., Gabrielian A.E., Garg N.S., Gelbart W.M., Glasser K., Glodek A., Gong F., Gorrell J.H., Gu Z., Guan P., Harris M., Harris N.L., Harvey D., Heiman T.J., Hernandez J.R., Houck J., Hostin D., Houston K.A., Howland T.J., Wei M.H., Ibegwam C. Science 2000, 287:2185-2195.
16. Usaite R., Wohlschlegel J., Venable J.D., Park S.K., Nielsen J., Olsson L., Yates Iii J.R. J. Proteome Res. 2008, 7:266-275.
17. Washburn M.P., Wolters D., Yates J.R. Nat. Biotechnol. 2001, 19:242-247.
18. Schrimpf S.P., Weiss M., Reiter L., Ahrens C.H., Jovanovic M., Malmstrom J., Brunner E., Mohanty S., Lercher M.J., Hunziker P.E., Aebersold R., von Mering C., Hengartner M.O. PLoS Biol. 2009, 7:e48.
19. Brunner E., Ahrens C.H., Mohanty S., Baetschmann H., Loevenich S., Potthast F., Deutsch E.W., Panse C., de Lichtenberg U., Rinner O., Lee H., Pedrioli P.G., Malmstrom J., Koehler K., Schrimpf S., Krijgsveld J., Kregenow F., Heck A.J., Hafen E., Schlapbach R., Aebersold R. Nat. Biotechnol. 2007, 25:576-583.
20. Taylor C.F., Paton N.W., Lilley K.S., Binz P.A., Julian R.K., Jones A.R., Zhu W., Apweiler R., Aebersold R., Deutsch E.W., Dunn M.J., Heck A.J., Leitner A., Macht M., Mann M., Martens L., Neubert T.A., Patterson S.D., Ping P., Seymour S.L., Souda P., Tsugita A., Vandekerckhove J., Vondriska T.M., Whitelegge J.P., Wilkins M.R., Xenarios I., Yates J.R., Hermjakob H. Nat. Biotechnol. 2007, 25:887-893.
21. Hoogland C., O'Gorman M., Bogard P., Gibson F., Berth M., Cockell S.J., Ekefjard A., Forsstrom-Olsson O., Kapferer A., Nilsson M., Martinez-Bartolome S., Albar J.P., Echevarria-Zomeno S., Martinez-Gomariz M., Joets J., Binz P.A., Taylor C.F., Dowsey A., Jones A.R. Nat. Biotechnol. 2010, 28:655-656.
22. Jones A.R., Carroll K., Knight D., Maclellan K., Domann P.J., Legido-Quigley C., Huang L., Smallshaw L., Mirzaei H., Shofstahl J., Paton N.W. Nat. Biotechnol. 2010, 28:654.
23. Wessel D., Flugge U.I. Anal. Biochem. 1984, 138:141-143.
24. Chen E.I., Cociorva D., Norris J.L., Yates J.R. J. Proteome Res. 2007, 6:2529-2538.
25. Chen E.I., McClatchy D., Park S.K., Yates J.R. Anal. Chem. 2008, 80:8694-8701.
26. Keil B. Specificity of Proteolysis 1992, Springer-Verlag, Berlin; New York.
27. Siepen J.A., Keevil E.J., Knight D., Hubbard S.J. J. Proteome Res. 2007, 6:399-408.
28. Thiede B., Lamer S., Mattow J., Siejak F., Dimmler C., Rudel T., Jungblut P.R. Rapid Commun. Mass Spectrom. 2000, 14:496-502.
29. Cagney G., Amiri S., Premawaradena T., Lindo M., Emili A. Proteome Sci. 2003, 1:5.
30. Swaney D.L., Wenger C.D., Coon J.J. J. Proteome Res. 2010, 9:1323-1329.
31. Liu H., Sadygov R.G., Yates J.R. Anal. Chem. 2004, 76:4193-4201.
32. Klammer A.A., MacCoss M.J. J. Proteome Res. 2006, 5:695-700.
33. Choudhary G., Wu S.L., Shieh P., Hancock W.S. J. Proteome Res. 2003, 2:59-67.
34. MacCoss M.J., McDonald W.H., Saraf A., Sadygov R., Clark J.M., Tasto J.J., Gould K.L., Wolters D., Washburn M., Weiss A., Clark J.I., Yates J.R. Proc. Natl. Acad. Sci. USA 2002, 99:7900-7905.
35. Cantin G.T., Yates J.R. J. Chromatogr. A 2004, 1053:7-14.
36. Farley A.R., Link A.J. Methods Enzymol. 2009, 463:725-763.
37. Young, N. L.; Plazas-Mayorca, M. D.; Garcia, B. A. Expert Rev. Proteomics2010,7, 79-92.
38. McCarthy J., Hopwood F., Oxley D., Laver M., Castagna A., Righetti P.G., Williams K., Herbert B. J. Proteome Res. 2003, 2:239-242.
39. Nielsen M.L., Vermeulen M., Bonaldi T., Cox J., Moroder L., Mann M. Nat. Methods 2008, 5:459-460.
40. Schuchard M.D., Mehigh R.J., Cockrill S.L., Lipscomb G.T., Stephan J.D., Wildsmith J., Valdes-Camin R., Kappel W.K., Rai A.J., Scott G.B. Biotechniques 2005, 39:239-247.
41. Conrads T.P., Veenstra T.D. Nat. Biotechnol. 2005, 23:36-37.
42. Xu T., Wong C.C., Kashina A., Yates J.R. Nat. Protoc. 2009, 4:325-332.
43. Alberts B. Molecular Biology of the Cell 2008, Garland Science, New York. 5th ed.
44. Speers A.E., Blackler A.R., Wu C.C. Anal. Chem. 2007, 79:4613-4620.
45. Wu C.C., MacCoss M.J., Howell K.E., Yates J.R. Nat. Biotechnol. 2003, 21:532-538.
46. Blackler A.R., Speers A.E., Ladinsky M.S., Wu C.C. J. Proteome Res. 2008, 7:3028-3034.